U.S. patent application number 15/801830 was filed with the patent office on 2018-05-03 for therapeutic microbiota for the treatment and/or prevention of food allergy.
This patent application is currently assigned to THE BRIGHAM AND WOMEN'S HOSPITAL, INC.. The applicant listed for this patent is THE BRIGHAM AND WOMEN'S HOSPITAL, INC., CHILDREN'S MEDICAL CENTER CORPORATION. Invention is credited to Azza Abdel-Gadir, Lynn Bry, Talal A. Chatila, Georg Gerber, Rima Rachid.
Application Number | 20180117099 15/801830 |
Document ID | / |
Family ID | 58662738 |
Filed Date | 2018-05-03 |
United States Patent
Application |
20180117099 |
Kind Code |
A1 |
Chatila; Talal A. ; et
al. |
May 3, 2018 |
THERAPEUTIC MICROBIOTA FOR THE TREATMENT AND/OR PREVENTION OF FOOD
ALLERGY
Abstract
Disclosed are methods and compositions for the prevention and
treatment of food allergy. In particular, described herein are
microbial consortia, including minimal microbial consortia, that
can prevent and/or cure food allergy. In certain embodiments, the
consortia comprise certain members of the taxa Clostridiales and/or
Bacteroidetes.
Inventors: |
Chatila; Talal A.; (Belmont,
MA) ; Bry; Lynn; (Jamaica Plain, MA) ; Gerber;
Georg; (Boston, MA) ; Abdel-Gadir; Azza;
(Boston, MA) ; Rachid; Rima; (Belmont,
MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE BRIGHAM AND WOMEN'S HOSPITAL, INC.
CHILDREN'S MEDICAL CENTER CORPORATION |
Boston
Boston |
MA
MA |
US
US |
|
|
Assignee: |
THE BRIGHAM AND WOMEN'S HOSPITAL,
INC.
Boston
MA
CHILDREN'S MEDICAL CENTER CORPORATION
Boston
MA
|
Family ID: |
58662738 |
Appl. No.: |
15/801830 |
Filed: |
November 2, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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PCT/US2016/060353 |
Nov 3, 2016 |
|
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15801830 |
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62250277 |
Nov 3, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 9/0053 20130101;
A61K 35/745 20130101; Y02A 50/473 20180101; A61K 9/19 20130101;
A61P 37/00 20180101; A61K 45/06 20130101; A61K 35/742 20130101;
A61K 35/744 20130101; A61K 35/74 20130101; A61K 35/741 20130101;
A61P 37/08 20180101; Y02A 50/30 20180101 |
International
Class: |
A61K 35/742 20060101
A61K035/742; A61K 9/00 20060101 A61K009/00; A61K 35/74 20060101
A61K035/74; A61P 37/08 20060101 A61P037/08 |
Goverment Interests
GOVERNMENT SUPPORT
[0002] This invention was made with Government Support under Grant
Nos. 1R56A111798-01 and P30 DK056338 awarded by the National
Institutes of Health. The Government has certain rights in the
invention.
Claims
1. A pharmaceutical composition comprising: (i) a preparation
comprising a minimal microbial consortium consisting essentially of
four to eleven strains of viable gut bacteria, in an amount
sufficient to increase immune system tolerance when administered to
an individual in need thereof, and (ii) a pharmaceutically
acceptable carrier.
2. The pharmaceutical composition of claim 1, wherein the
pharmaceutical composition is formulated for oral delivery.
3. The pharmaceutical composition of claim 2, wherein the
pharmaceutical composition is in the oral dosage form of a capsule,
a reconstituted lyophilisate, a food item, or is formulated as a
liquid, gel, or fluid-gel.
4. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria consisting essentially of
strains of Clostridium or Bacteroides.
5. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria consisting essentially of
strains of Clostridium.
6. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria consisting essentially of
strains of Bacteroides.
7. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria comprise Clostridium ramosum,
Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, or Prevotella tannerae.
8. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria comprise Clostridium ramosum,
Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, or Clostridium sardiniensis.
9. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria comprise Bacteroides
fragilis, Bacteroides thetaiotaomicron, Bacteroides ovatus,
Parabacteroides goldsteinii, or Prevotella tannerae.
10. The pharmaceutical composition of claim 1, wherein the four to
eleven strains of viable gut bacteria are in an amount are
sufficient to treat or prevent a food allergy.
11. The pharmaceutical composition of claim 1, wherein four to
eleven strains of viable gut bacteria are present in substantially
equal biomass.
12. The pharmaceutical composition of claim 1, wherein four to
eleven strains of viable gut bacteria are each present in an amount
of at least about 1.times.108 CFUs/ml.
13. The pharmaceutical composition of claim 1, wherein the
pharmaceutical composition does not comprise any of the Species
Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis,
Enterobacter cloacae, Bilophila wadsworthia, Alistipes onderdonkii,
Desulfovibrio species, Lactobacillus johnsonii, or Parasutterella
excrementihominis.
14. The pharmaceutical composition of claim 1, wherein minimal
microbial consortium consisting essentially of four to eleven
strains of viable gut bacteria is present in an amount sufficient
to increase the proportion of T regulatory cells in a subject.
15. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that expresses exopolysaccharide, lipoteichoic
acid (LTA), lipopolysaccharide (LPS) or other microbial adjuvant
molecules that promote the development of regulatory T cells
(Treg).
16. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that produces butyrate and/or propionate
fermentation products via fermentation of carbohydrates and other
carbon sources in the gut lumen.
17. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium performs the full complement of bile acid
transformations.
18. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that produces compounds capable of stimulating the
aryl hydrocarbon receptor (AhR) receptor pathway in gut epithelial
cells, antigen presenting cells and/or T cells to stimulate
development of regulatory T cell responses.
19. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that produces compounds capable of stimulating the
pregnane X receptor with beneficial effects upon gut barrier
function and/or development of regulatory T cell responses.
20. The pharmaceutical composition of claim 19, wherein the viable,
culturable, anaerobic gut bacterial strain expresses desmolase or
hydroxysteroid dehydrogenase.
21. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that produces compounds capable of stimulating the
RORgamma (RAR-related orphan receptor gamma) pathways to stimulate
development of regulatory T cell responses via direct stimulation
or RORgamma-activated pathways in gut antigen presenting cells
and/or epithelial cells that then stimulate regulatory T cell
responses.
22. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that stimulates host production of mucins and
complex glycoconjugates that improve gut barrier function and
colonization by protective commensal species.
23. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that alters the gut luminal environment to reduce
the deleterious activities of dysbiotic species promoting
development of unhealthy allergic T cell responses to food
antigens
24. The pharmaceutical composition of claim 1, wherein the minimal
microbial consortium comprises a viable, culturable, anaerobic gut
bacterial strain that alters the gut luminal environment to promote
improved colonization by other members of the administered
consortium for any of the above stated effects, and/or colonization
by existing beneficial species in the patients underlying
microbiota.
25. A method for increasing immune system tolerance, comprising
administering the pharmaceutical composition of claim 1 to a
subject in need thereof.
26. The method of claim 25, wherein the pharmaceutical composition
is formulated for oral delivery.
27. The method of claim 25, administration of the pharmaceutical
composition is in an amount sufficient to treat or prevent a food
allergy.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This Application is a Continuation Application of
International Application No. PCT/US2016/060353 filed Nov. 3, 2016,
which designates the U.S. and which claims benefit under 35 U.S.C.
.sctn. 119(e) of the U.S. Provisional Application No. 62/250,277
filed Nov. 3, 2015, the contents of each of which are incorporated
herein by reference in their entireties.
FIELD OF THE DISCLOSURE
[0003] The present disclosure relates to the treatment and/or
prevention of food allergy.
BACKGROUND
[0004] Food allergies are a growing public health problem in both
developed and rapidly developing countries and affects large
numbers of children and adults. The incidence of food allergy has
increased dramatically in the last few decades. This increase can
be associated with sensitization to multiple foods in up to 50% of
subjects. Growing evidence indicates that the microbial flora is a
key environmental influence in programming oral tolerance.
SUMMARY
[0005] Provided herein are methods and compositions for the
treatment and/or prevention of food allergy, based in part, on the
discovery that altered intestinal microbiota (e.g., from antibiotic
treatments, C-section births, diet etc.) can promote food allergy
while some combinations of microbes can prevent and/or cure food
allergies.
[0006] Accordingly, provided herein in one aspect is a
pharmaceutical composition comprising: (i) a preparation comprising
a minimal microbial consortium consisting essentially of four to
eleven strains of viable gut bacteria, in an amount sufficient to
treat or prevent a food allergy when administered to an individual
in need thereof, and (ii) a pharmaceutically acceptable
carrier.
[0007] Another aspect provided herein relates to a pharmaceutical
composition comprising a minimal microbial consortium of culturable
species, and a pharmaceutically acceptable carrier, wherein the
consortium is comprised in at least four of the preparations
selected from the group consisting of: (i) a preparation of a
viable, culturable, anaerobic gut bacterial strain(s) that
expresses exopolysaccharide, lipoteichoic acid (LTA),
lipopolysaccharide (LPS) or other microbial adjuvant molecules that
promote the development of regulatory T cells (Treg); (ii) a
preparation of a viable, culturable, anaerobic gut bacterial
strain(s) that produces butyrate and/or propionate fermentation
products via fermentation of carbohydrates and other carbon sources
in the gut lumen; (iii) a preparation of one or more viable,
culturable, anaerobic gut bacterial strains that alone or in
combination performs the full complement of bile acid
transformations; (iv) a preparation of a viable, culturable,
anaerobic gut bacterial strain that produces compounds capable of
stimulating the aryl hydrocarbon receptor (AhR) receptor pathway in
gut epithelial cells, antigen presenting cells and/or T cells to
stimulate development of regulatory T cell responses; (v) a
preparation of a viable, culturable, anaerobic gut bacterial
strain(s) that produces compounds capable of stimulating the
pregnane X receptor with beneficial effects upon gut barrier
function and/or development of regulatory T cell responses; (vi) a
preparation of a viable, culturable, anaerobic gut bacterial
strain(s) that produces compounds capable of stimulating the
RORgamma (RAR-related orphan receptor gamma) pathways to stimulate
development of regulatory T cell responses via direct stimulation
or RORgamma-activated pathways in gut antigen presenting cells
and/or epithelial cells that then stimulate regulatory T cell
responses; (vii) a preparation of viable, culturable, anaerobic gut
bacterial strain(s) that stimulates host production of mucins and
complex glycoconjugates that improve gut barrier function and
colonization by protective commensal species; (viii) a preparation
of a viable, culturable, anaerobic gut bacterial strain(s) that
alters the gut luminal environment to reduce the deleterious
activities of dysbiotic species promoting development of unhealthy
allergic T cell responses to food antigens; (ix) a preparation of a
viable, culturable, anaerobic gut bacterial strain(s) that alters
the gut luminal environment to promote improved colonization by
other members of the administered consortium for any of the above
stated effects, and/or colonization by existing beneficial species
in the patients underlying microbiota; (x) a preparation of a
viable, culturable, anaerobic gut bacterial strain(s) that promotes
the colonization or growth of a bacterial strain in a preparation
of (i)-(ix) above, in vivo.
[0008] In one embodiment of this aspect and all other aspects
described herein, the viable, culturable, anaerobic gut bacterial
strain(s) that expresses exopolysaccharide that promotes the
development of regulatory T cells (Treg) is selected from the group
consisting of: Eubacterium rectale, Clostridium ramosum,
Butyrovibrio crossatus, Roseburia intestinalis, Clostridium
scindens, Clostridium hylemonae, Hungatella hathawayi, Clostridium
symbiosum, Faecalibacterium prausnitzii, Subdoligranulum variabile,
Bacteroides thetaiotaomicron, Bacteroides fragilis, Bacteroides
ovatus, Parabacetroides goldsteinii, Parabacteroides merdae,
Parabacteroides distasonis, and Prevotella tannerae.
[0009] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that produces butyrate, propionate and/or succinate
fermentation products via fermentation of carbohydrates in the gut
lumen is selected from the group consisting of: Bacteroides
fragilis, Bacteroides thetaiotaomicron, Bacteroides ovatus,
Clostridium sardiniensis, Clostridium hiranonsis, Facealibacterium
prausnitzii, Butyrovibrio spp., Eubacterium rectale and Roseburia
intestinalis
[0010] In another embodiment of this aspect and all other aspects
provided herein, the one or more viable, culturable, anaerobic gut
bacterial strains that alone or in combination performs the full
complement of bile acid transformations is Clostridium scindens,
Clostridium hiranonsis, Clostridium sardiniensis and/or Bacteroides
spp.
[0011] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that produces aryl hydrocarbon receptor agonists
sufficient to stimulate host aryl hydrocarbon receptor pathways
comprises at least one gene associated with the synthesis of
tryptophan, tyrosine or the synthesis of quinone molecules.
[0012] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that promotes the colonization or growth of a bacterial
strain in a preparation is Bacteroides thetaiotaomicron, or
Bacteroides fragilis.
[0013] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that produces compounds endogenously or by metabolizing
exogenous precursors, that is capable of stimulating the pregnane X
receptor with beneficial effects upon gut barrier function and/or
development of regulatory T cell responses is a strain that
expresses desmolase and/or hydroxysteroid dehydrogenase. In this
context, exogenous precursors include not just dietary compounds or
factors, but also factors produced by the host and excreted into
the gut which are then acted upon by one or more members of a
microbial consortium as described herein.
[0014] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that produces compounds endogenously or by metabolizing
exogenous precursors, that is capable of stimulating the RORgamma
(RAR-related orphan receptor gamma) pathways to stimulate
development of regulatory T cell responses is a strain that
expresses at least one cholesterol reductase or another enzyme
capable of metabolizing sterol compounds.
[0015] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that is capable of stimulating host mucins and complex
glycoconjugates that improve gut barrier function and colonization
by protective commensal species is Bacteroides thetaiotaomicron or
Bacteroides fragilis.
[0016] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) that alter the gut luminal environment to reduce the
deleterious activities of dysbiotic species that contribute to
development of pathogenic allergic T cell responses to food
antigens is Bacteroides thetaiotaomicron, Bacteroides fragilis or
another Bacteroides spp. An examples includes alterations of the
gut environment from Bacteroides species that reduces the biomass
of dysbiotic species in the Enterobacteriaceae or
Desulfonovibriaceae and/or prevent full expression of dysbiotic
biochemical or microbiologic activities expressed by these
species.
[0017] In another embodiment of this aspect and all other aspects
provided herein, the viable, culturable, anaerobic gut bacterial
strain(s) alter the gut luminal environment to promote improved
colonization by other members of the administered consortium for
any of the above stated effects, and/or colonization by existing
beneficial species in the patients underlying microbiota is
Bacteroides thetaiotaomicron, Bacteroides fragilis, or Bacteroides
spp. In another embodiment of this aspect and all other aspects
provided herein, the beneficial species comprises Clostridium spp
(e.g., Clostridium ramosum, Clostridium scindens, Clostridium
hiranonsis, Clostridium bifermentans, Clostridium leptum,
Clostridium sardiniensis, Clostridium hathewayi, Clostridium
nexile, Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium lavalense, Clostridium fimetarium, Clostridium
symbiosum, Clostridium sporosphaeroides etc.) or another
non-pathogenic commensal strain.
[0018] In another embodiment of this aspect and all other aspects
provided herein, the pharmaceutically acceptable carrier comprises
an enteric coating composition that encapsulates the minimal
microbial consortium.
[0019] In another embodiment of this aspect and all other aspects
provided herein, the pharmaceutical composition is formulated to
deliver the viable bacteria to the small intestine.
[0020] In another embodiment of this aspect and all other aspects
provided herein, the enteric-coating composition is in the form of
a capsule, gel, pastille, tablet or pill.
[0021] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, culturable, anaerobic gut
bacteria are human gut bacteria.
[0022] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, culturable, anaerobic gut
bacteria are selected from the group consisting of: Clostridium
ramosum, Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, Prevotella tannerae,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum fimetarium, Clostridium symbiosum,
Clostridium sporosphaeroides, Dialister proprionicfaceins,
Dialister succinatiphilus, Parabacteroides distasonis,
Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0023] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, culturable, anaerobic gut
bacteria are selected from the group consisting of: Clostridium
ramosum, C. scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0024] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, culturable, anaerobic gut
bacteria are selected from the group consisting of: (i) Clostridium
ramosum, C. scindens, C. hiranonsis, C. bifermentans, C. leptum,
and C. sardiniensis, or (ii) Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0025] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, culturable, anaerobic gut
bacteria are present in substantially equal biomass.
[0026] In another embodiment of this aspect and all other aspects
provided herein, the composition is formulated to deliver a dose of
at least 1.times.10.sup.9 colony forming units (CFUs).
[0027] In another embodiment of this aspect and all other aspects
provided herein, the composition is formulated to deliver at least
1.times.10.sup.9 CFUs in less than 30 capsules per one time
dose.
[0028] In another embodiment of this aspect and all other aspects
provided herein, the composition is frozen for storage.
[0029] In another embodiment of this aspect and all other aspects
provided herein, the strain(s) of viable culturable, anaerobic gut
bacteria are encapsulated under anaerobic conditions.
[0030] In another embodiment of this aspect and all other aspects
provided herein, the strain(s) of viable culturable, anaerobic gut
bacteria are lyophilized under anaerobic conditions.
[0031] In another embodiment of this aspect and all other aspects
provided herein, anaerobic conditions comprise one or more of the
following: (i) oxygen impermeable capsules, (ii) addition of
reducing agents including N-acetylcysteine, cysteine, or methylene
blue to the composition, and (iii) use of spores for organisms that
sporulate.
[0032] In another embodiment of this aspect and all other aspects
provided herein, the consortium comprises at least one bacterial
strain comprising a 16S rDNA sequence at least 97% identical to a
16S rDNA sequence present in a reference strain operational
taxonomic unit, the reference strain selected from the group
consisting of: Clostridium ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum, and C. sardiniensis, or wherein the
consortium comprises at least one bacterial strain comprising a 16S
rDNA sequence at least 97% identical to a 16S rDNA sequence present
in a reference strain operational taxonomic unit, the reference
strain selected from the group consisting of: Bacteroides fragilis,
B. thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0033] In another embodiment of this aspect and all other aspects
provided herein, the consortium does not comprise any of the
Species Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis,
Enterobacter cloacae, Bilophila wadsworthia, Alistipes onderdonkii,
Desulfovibrio species, Lactobacillus johnsoni, Parasutterella
excrementihominis.
[0034] In another embodiment of this aspect and all other aspects
provided herein, the consortium does not comprise bacteria of the
Genera Bilophila, Enterobacter, Escherichia, Klebsiella, Proteus,
Alistipes, Blautia, Desulfovibrio, or Parasutterella.
[0035] In another embodiment of this aspect and all other aspects
provided herein, the consortium does not comprise bacteria of the
Families Desulfovibrionaceae, Enterobacteriaceae, Rikenellaceae,
and Sutterellaceae.
[0036] In another embodiment of this aspect and all other aspects
provided herein, the consortium does not comprise bacteria of the
Families Lactobacillaceae, or Enterbacteriaceae.
[0037] In another embodiment of this aspect and all other aspects
provided herein, the consortium does not comprise bacteria of the
Order Burkholdales, Desulfovibrionales, or Enterobacteriales.
[0038] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least five strains of
viable non-pathogenic gut bacteria.
[0039] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises up to eleven strains of
viable non-pathogenic gut bacteria.
[0040] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, and C.
sardiniensis.
[0041] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0042] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises: Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0043] In another embodiment of this aspect and all other aspects
provided herein, the bacterial strains in the composition consists
essentially of Clostridium ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum, and C. sardiniensis.
[0044] In another embodiment of this aspect and all other aspects
provided herein, the microbial consortium consists essentially of
Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0045] In another embodiment of this aspect and all other aspects
provided herein, the microbial consortium consists essentially of:
Clostridium ramosum, C. scindens, C. hiranonsis, C. bifermentans,
C. leptum, C. sardiniensis, Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0046] In another embodiment of this aspect and all other aspects
provided herein, the enteric-coating comprises a polymer,
nanoparticle, fatty acid, shellac, or a plant fiber.
[0047] In another embodiment of this aspect and all other aspects
provided herein, the composition further comprises a pre-biotic
composition.
[0048] In another embodiment of this aspect and all other aspects
provided herein, the composition is encapsulated, a reconstituted
lyophilisate, a food item, or is formulated as a liquid, gel,
fluid-gel, or nanoparticles in a liquid.
[0049] Another aspect provided herein relates to a pharmaceutical
composition comprising: (i) a preparation comprising at least four
strains of viable, anaerobic, culturable gut bacteria selected from
the group consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti, in an amount sufficient to treat or prevent a
food allergy when administered to an individual in need thereof,
and (ii) a pharmaceutically acceptable carrier.
[0050] In one embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than forty
strains of viable, anaerobic, culturable gut bacteria.
[0051] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than thirty
strains of viable, anaerobic, culturable gut bacteria.
[0052] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than twenty
strains of viable, anaerobic, culturable gut bacteria.
[0053] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than fifteen
strains of viable, anaerobic, culturable gut bacteria.
[0054] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than eleven
strains of viable, anaerobic, culturable gut bacteria.
[0055] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least five strains of
viable, anaerobic, culturable gut bacteria selected from the group
consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0056] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least six strains of
viable, anaerobic, culturable gut bacteria selected from the group
consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0057] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least seven strains
of viable, anaerobic, culturable gut bacteria selected from the
group consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0058] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least eight strains
of viable, anaerobic, culturable gut bacteria selected from the
group consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0059] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least nine strains of
viable, anaerobic, culturable gut bacteria selected from the group
consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0060] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least ten strains of
viable, anaerobic, culturable gut bacteria selected from the group
consisting of: Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Bacteroides fragilis, Bacteroides
thetaiotaomicron, Bacteroides ovatus, Parabacteroides goldsteinii,
Prevotella tannerae, Clostridum hathewayi, Clostridum nexile,
Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0061] In other embodiments of this aspect and all other aspects
provided herein, the composition comprises a range of 4-28, 4-35,
4-30, 4-25, 4-20, 4-15, 4-12, 4-11, 4-10, 4-9, 4-8, 4-6, 35-40,
30-40, 25-40, 20-40, 15-40, 12-40, 11-40, 10-40, 6-40, 5-40, 10-20,
10-30, 10-25, 15-40, 15-35, 15-30, 15-25, 15-20, 20-35, 20-30,
20-25, 30-35 strains of viable, anaerobic, culturable gut
bacteria.
[0062] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, anaerobic, culturable gut
bacteria are selected from the group consisting of: (i) Clostridium
ramosum, C. scindens, C. hiranonsis, C. bifermentans, C. leptum,
and C. sardiniensis, or (ii) Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0063] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises viable, anaerobic,
culturable gut bacteria including each of Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum and C.
sardiniensis.
[0064] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises viable, anaerobic,
culturable gut bacteria including each of, Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae.
[0065] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises viable, anaerobic,
culturable gut bacteria including each of Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0066] Another aspect described herein relates to a pharmaceutical
composition comprising: at least four strains of viable, anaerobic,
culturable gut bacteria comprising: at least one bacterial strain
comprising a 16S rDNA sequence at least 97% identical to a 16S rDNA
sequence present in a reference strain operational taxonomic unit,
the reference strain selected from the group consisting of:
Clostridium ramosum, C. scindens, C. hiranonsis, C. bifermentans,
C. leptum, and C. sardiniensis; or at least one bacterial strain
comprising a 16S rDNA sequence at least 97% identical to a 16S rDNA
sequence present in a reference strain operational taxonomic unit,
the reference strain selected from the group consisting of:
Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae; wherein the
at least four strains of viable, anaerobic, culturable gut bacteria
are present in an amount sufficient to treat or prevent a food
allergy when administered to an individual in need thereof; and a
pharmaceutically acceptable carrier.
[0067] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than forty
strains of viable, anaerobic, culturable gut bacteria.
[0068] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than thirty
strains of viable, anaerobic, culturable gut bacteria.
[0069] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than twenty
strains of viable, anaerobic, culturable gut bacteria.
[0070] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than fifteen
strains of viable, anaerobic, culturable gut bacteria.
[0071] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises not more than eleven
strains of viable, anaerobic, culturable gut bacteria.
[0072] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least five strains of
viable, anaerobic, culturable gut bacteria.
[0073] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least six strains of
viable, anaerobic, culturable gut bacteria.
[0074] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least seven strains
of viable, anaerobic, culturable gut bacteria.
[0075] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least eight strains
of viable, anaerobic, culturable gut bacteria.
[0076] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least nine strains of
viable, anaerobic, culturable gut bacteria.
[0077] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least ten strains of
viable, anaerobic, culturable gut bacteria.
[0078] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises eleven strains of
viable, anaerobic, culturable gut bacteria.
[0079] In another embodiment of this aspect and all other aspects
provided herein, the microbial strains do not comprise any of the
Species Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis,
Enterobacter cloacae, Bilophila wadsworthia, Alistipes onderdonkii,
Desulfovibrio species, Lactobacillus johnsoni, and Parasutterella
excrementihominis.
[0080] In another embodiment of this aspect and all other aspects
provided herein, the microbial strains do not comprise bacteria of
the Genera Bilophila, Enterobacter, Escherichia, Klebsiella,
Proteus, Alistipes, Blautia, Desulfovibrio, or Parasutterella.
[0081] In another embodiment of this aspect and all other aspects
provided herein, the microbial strains do not comprise bacteria of
the Families Desulfovibrionaceae, Enterobacteriaceae,
Rikenellaceae, and Sutterellaceae.
[0082] In another embodiment of this aspect and all other aspects
provided herein, the microbial strains do not comprise bacteria of
the Families Lactobacillaceae, or Enterbacteriaceae
[0083] In another embodiment of this aspect and all other aspects
provided herein, the microbial strains do not comprise bacteria of
the Order Burkholdales, Desulfovibrionales, or
Enterobacteriales.
[0084] Another aspect provided herein relates to a pharmaceutical
composition comprising a microbial consortium of culturable
species, and a pharmaceutically acceptable carrier, wherein the
composition comprises at least four preparations selected from the
group consisting of: (i) a preparation of a viable, culturable,
anaerobic gut bacterial strain (or strains) that expresses
exopolysaccharide, lipoteichoic acid (LTA), lipopolysaccharide
(LPS) or other microbial adjuvant molecules that promote the
development of regulatory T cells (Treg); (ii) a preparation of a
viable, culturable, anaerobic gut bacterial strain (or strains)
that produces butyrate and/or propionate fermentation products via
fermentation of carbohydrates and other carbon sources in the gut
lumen; (iii) a preparation of one or more viable, culturable,
anaerobic gut bacterial strains that alone or in combination
performs the full complement of bile acid transformations; (iv) a
preparation of a viable, culturable, anaerobic gut bacterial strain
(or strains) that produces compounds capable of stimulating the
aryl hydrocarbon receptor (AhR) receptor pathway in gut epithelial
cells, antigen presenting cells and/or T cells to stimulate
development of regulatory T cell responses; (v) a preparation of a
viable, culturable, anaerobic gut bacterial strain (or strains)
that produces compounds capable of stimulating the pregnane X
receptor with beneficial effects upon gut barrier function and/or
development of regulatory T cell responses; (vi) a preparation of a
viable, culturable, anaerobic gut bacterial strain (or strains)
that produces compounds capable of stimulating the RORgamma
(RAR-related orphan receptor gamma) pathways to stimulate
development of regulatory T cell responses via direct stimulation
or RORgamma-activated pathways in gut antigen presenting cells
and/or epithelial cells that then stimulate regulatory T cell
responses; (vii) a preparation of a viable, culturable, anaerobic
gut bacterial strain (or strains) that stimulates host production
of mucins and complex glycoconjugates that improve gut barrier
function and colonization by protective commensal species; (viii) a
preparation of a viable, culturable, anaerobic gut bacterial strain
(or strains) that alters the gut luminal environment to reduce the
deleterious activities of dysbiotic species promoting development
of unhealthy allergic T cell responses to food antigens; (ix) a
preparation of a viable, culturable, anaerobic gut bacterial strain
(or strains) that alters the gut luminal environment to promote
improved colonization by other members of the administered
consortium for any of the above stated effects, and/or colonization
by existing beneficial species in the patients underlying
microbiota; and (x) a preparation of a viable, culturable,
anaerobic gut bacterial strain (or strains) that promotes the
colonization or growth of a bacterial strain in a preparation of
(i)-(ix) above, in vivo; and wherein the composition comprises no
more than forty microbial species.
[0085] In one embodiment of this aspect and all other aspects
provided herein, the composition comprises no more than thirty
microbial species.
[0086] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises no more than twenty
microbial species.
[0087] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises no more than fifteen
microbial species.
[0088] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises no more than eleven
microbial species.
[0089] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least five of the
preparations (i)-(x).
[0090] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least six of the
preparations (i)-(x).
[0091] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least seven of the
preparations (i)-(x).
[0092] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least eight of the
preparations (i)-(x).
[0093] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises at least nine of the
preparations (i)-(x).
[0094] In another embodiment of this aspect and all other aspects
provided herein, the composition comprises each of the preparations
(i)-(x).
[0095] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that expresses
exopolysaccharide that promotes the development of regulatory T
cells (Treg) is selected from the group consisting of: Eubacterium
rectale, Clostridium ramosum, Butyrovibrio crossatus, Roseburia
intestinalis, Clostridium scindens, Clostridium hylemonae,
Hungatella hathawayi, Clostridium symbiosum, Faecalibacterium
prausnitzii, Subdoligranulum variabile, Bacteroides
thetaiotaomicron, Bacteroides fragilis, Bacteroides ovatus,
Parabacetroides goldsteinii, Parabacteroides merdae,
Parabacteroides distasonis, and Prevotella tannerae.
[0096] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that strain
that produces butyrate, propionate and/or succinate fermentation
products via fermentation of carbohydrates in the gut lumen is
selected from the group consisting of: Bacteroides fragilis,
Bacteroides thetaiotaomicron, Bacteroides ovatus, Clostridium
sardiniensis, Clostridium hiranonsis, Facealibacterium prausnitzii,
Butyrovibrio spp., Eubacterium rectale, and Roseburia
intestinalis.
[0097] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that alone or
in combination performs the full complement of bile acid
transformations lumen is selected from the group consisting of:
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Clostridium sardiniensis, Clostridium hiranonsis,
Facealibacterium prausnitzii, Butyrovibrio spp., Eubacterium
rectale, and Roseburia intestinalis.
[0098] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that produces
aryl hydrocarbon receptor agonists sufficient to stimulate host
aryl hydrocarbon receptor pathways comprises at least one gene
associated with the synthesis of tryptophan, tyrosine or the
synthesis of quinone molecules
[0099] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that promotes
the colonization or growth of a bacterial strain in a preparation
recited in claim 2 is Bacteroides thetaiotaomicron, or Bacteroides
fragilis.
[0100] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that produces
compounds endogenously or by metabolizing ingested precursors, that
is capable of stimulating the pregnane X receptor with beneficial
effects upon gut barrier function and/or development of regulatory
T cell responses is a strain that expresses desmolase and/or
hydroxysteroid dehydrogenase.
[0101] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that produces
compounds endogenously or by metabolizing ingested precursors, that
is capable of stimulating the RORgamma (RAR-related orphan receptor
gamma) pathways to stimulate development of regulatory T cell
responses is a strain that expresses at least one cholesterol
reductase or another enzyme(s) capable of metabolizing sterol
compounds.
[0102] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strain that is capable
of stimulating host mucins and complex glycoconjugates that improve
gut barrier function and colonization by protective commensal
species is Bacteroides thetaiotaomicron or Bacteroides
fragilis.
[0103] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strains that alter the
gut luminal environment to reduce the deleterious activities of
dysbiotic species that contribute to development of pathogenic
allergic T cell responses to food antigens is Bacteroides
thetaiotaomicron, Bacteroides fragilis, or Bacteroides spp. In
another embodiment of this aspect and all other aspects provided
herein, the dysbiotic species comprises a species in the Families
Enterobacteriaceae or Desulfonovibriacaea.
[0104] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic gut bacterial strains alter the gut
luminal environment to promote improved colonization by other
members of the administered consortium for any of the above stated
effects, and/or colonization by existing beneficial species in the
patients underlying microbiota is Bacteroides thetaiotaomicron,
Bacteroides fragilis, or Bacteroides spp. In another embodiment of
this aspect and all other aspects provided herein, the beneficial
species comprises non-pathogenic Clostridia spp. and other
non-pathogenic commensal strains.
[0105] In another embodiment of this aspect and all other aspects
provided herein, the pharmaceutically acceptable carrier comprises
an enteric coating composition that encapsulates the anaerobic gut
bacterial strains.
[0106] In another embodiment of this aspect and all other aspects
provided herein, the composition is formulated to deliver the
viable bacteria to the small intestine.
[0107] In another embodiment of this aspect and all other aspects
provided herein, wherein the enteric-coating composition is in the
form of a capsule, gel, pastille, tablet or pill.
[0108] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable, anaerobic gut bacteria are
human anaerobic gut bacteria.
[0109] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria are
selected from the group consisting of: Clostridium ramosum,
Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, Prevotella tannerae,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum fimetarium, Clostridium symbiosum,
Clostridium sporosphaeroides, Dialister proprionicfaceins,
Dialister succinatiphilus, Parabacteroides distasonis,
Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0110] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria are
selected from the group consisting of: Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0111] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria are
selected from the group consisting of: (i) Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, and C.
sardiniensis, or (ii) Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae.
[0112] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria
consist essentially of Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum, and C. sardiniensis.
[0113] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria
consist essentially of Bacteroides fragilis, B. thetaiotaomicron,
B. ovatus, Parabacteroides goldsteinii, and Prevotella
tannerae.
[0114] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria
consist essentially of Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum, C. sardiniensis,
Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0115] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria are
present in substantially equal biomass.
[0116] In another embodiment of this aspect and all other aspects
provided herein, the composition is formulated to deliver a dose of
at least 1.times.10.sup.9 colony forming units (CFUs).
[0117] In another embodiment of this aspect and all other aspects
provided herein, the composition is formulated to deliver at least
1.times.10.sup.9 CFUs in less than 30 capsules per one time
dose.
[0118] In another embodiment of this aspect and all other aspects
provided herein, the composition is frozen for storage.
[0119] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable anaerobic gut bacteria are
encapsulated under anaerobic conditions. In another embodiment of
this aspect and all other aspects provided herein, the strains of
viable anaerobic gut bacteria are lyophilized under anaerobic
conditions.
[0120] In another embodiment of this aspect and all other aspects
provided herein, wherein anaerobic conditions comprise one or more
of the following: (i) oxygen impermeable capsules, (ii) addition of
N-acetylcysteine, cysteine or methylene blue to the composition,
(iii) use of spores for organisms that sporulate, and (iv) addition
of a reducing factor to the composition.
[0121] In another embodiment of this aspect and all other aspects
provided herein, the enteric-coating comprises a polymer,
nanoparticle, fatty acid, shellac, or a plant fiber.
[0122] In another embodiment of this aspect and all other aspects
provided herein, the composition further comprises a pre-biotic
composition.
[0123] In another embodiment of this aspect and all other aspects
provided herein, the composition is encapsulated, a reconstituted
lyophilisate, a food item, or is formulated as a liquid, gel,
fluid-gel, or nanoparticles in a liquid.
[0124] Another aspect described herein relates to a method for
preventing the onset of a food allergy in a subject, the method
comprising: administering to a subject a composition as described
herein, thereby preventing the onset of a food allergy in the
subject.
[0125] In one embodiment of this aspect and all other aspects
provided herein, the at least 4 strains of gut bacteria
administered are selected from the group consisting of: Clostridium
ramosum, Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, Prevotella tannerae,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum fimetarium, Clostridium symbiosum,
Clostridium sporosphaeroides, Dialister proprionicfaceins,
Dialister succinatiphilus, Parabacteroides distasonis,
Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0126] In another embodiment of this aspect and all other aspects
provided herein, the strains of gut bacteria administered are
selected from the group consisting of: Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0127] In another embodiment of this aspect and all other aspects
provided herein, the strains of gut bacteria administered are
selected from the group consisting of: (i) Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, and C.
sardiniensis, or (ii) Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae.
[0128] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered by oral
administration, enema, suppository, or orogastric tube.
[0129] In another embodiment of this aspect and all other aspects
provided herein, the minimal microbial consortium or viable,
culturable, anaerobic gut bacterial strain(s) is/are isolated
and/or purified from a subject known to be tolerant to a selected
food allergen.
[0130] In another embodiment of this aspect and all other aspects
provided herein, the strains of gut bacteria are cultured under
anaerobic conditions.
[0131] In another embodiment of this aspect and all other aspects
provided herein, the anaerobic conditions comprise one or more of
the following: (i) oxygen impermeable capsules, (ii) addition of
N-acetylcysteine, cysteine, methylene blue, or a reducing factor to
the composition, or (iii) use of spores for organisms that
sporulate.
[0132] In another embodiment of this aspect and all other aspects
provided herein, the composition administered further comprises a
pre-biotic composition.
[0133] In another embodiment of this aspect and all other aspects
provided herein, the composition is enteric-coated.
[0134] In another embodiment of this aspect and all other aspects
provided herein, the treatment administered prevents and/or
reverses TH2 programming of Tregs and other mucosal T cell
populations.
[0135] In another embodiment of this aspect and all other aspects
provided herein, the subject is a human subject.
[0136] In another embodiment of this aspect and all other aspects
provided herein, the method further comprises a step of diagnosing
the subject as likely to develop a food allergy.
[0137] In another embodiment of this aspect and all other aspects
provided herein, the method further comprising a step of testing a
fecal sample from the subject for the presence and/or levels of the
bacteria in the minimal microbial consortium or the viable,
culturable, anaerobic gut bacterial strain(s).
[0138] In another embodiment of this aspect and all other aspects
provided herein, the food allergy comprises allergy to soy, wheat,
eggs, dairy, peanuts, tree nuts, shellfish, fish, mushrooms, stone
fruits and other fruits.
[0139] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered before the first
exposure to a potential food allergen.
[0140] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered upon clinical
signs of atopic symptoms.
[0141] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered to individuals
with diagnosed food allergy
[0142] In another embodiment of this aspect and all other aspects
provided herein, the subject is pretreated with an antibiotic.
[0143] In another embodiment of this aspect and all other aspects
provided herein, the subject is not pretreated with an
antibiotic.
[0144] Another aspect described herein relates to a method for
reducing or eliminating a subject's immune reaction to a food
antigen, the method comprising: administering to a subject a
composition as described herein, thereby reducing or eliminating a
subject's immune reaction to a food allergen.
[0145] In one embodiment of this aspect and all other aspects
provided herein, the strains of bacteria administered are selected
from the group consisting of: Clostridium ramosum, Clostridium
scindens, Clostridium hiranonsis, Clostridium bifermentans,
Clostridium leptum, Clostridium sardiniensis, Bacteroides fragilis,
Bacteroides thetaiotaomicron, Bacteroides ovatus, Parabacteroides
goldsteinii, Prevotella tannerae, Clostridum hathewayi, Clostridum
nexile, Clostridium hylemonae, Clostridium glycyrrhizinilyticum,
Clostridium scindens, Clostridium lavalense, Clostridum fimetarium,
Clostridium symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0146] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable gut bacteria are selected
from the group consisting of: Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum, C. sardiniensis,
Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0147] In another embodiment of this aspect and all other aspects
provided herein, the strains of viable gut bacteria are selected
from the group consisting of: (i) Clostridium ramosum, C. scindens,
C. hiranonsis, C. bifermentans, C. leptum, and C. sardiniensis, or
(ii) Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0148] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered by oral
administration, enema, suppository, or orogastric tube.
[0149] In another embodiment of this aspect and all other aspects
provided herein, the minimal microbial consortium or the viable,
culturable, anaerobic gut bacterial strain(s) is/are isolated
and/or purified from a subject known to be tolerant to a selected
food allergen.
[0150] In another embodiment of this aspect and all other aspects
provided herein, the strains of bacteria or minimal microbial
consortium is cultured and/or maintained under anaerobic
conditions.
[0151] In another embodiment of this aspect and all other aspects
provided herein, anaerobic conditions comprise one or more of the
following: (i) oxygen impermeable capsules, (ii) addition of
N-acetylcysteine, cysteine, methylene blue or a reducing factor to
the composition, or (iii) use of spores for organisms that
sporulate.
[0152] In another embodiment of this aspect and all other aspects
provided herein, the composition administered further comprises a
pre-biotic composition.
[0153] In another embodiment of this aspect and all other aspects
provided herein, the composition is enteric-coated.
[0154] In another embodiment of this aspect and all other aspects
provided herein, the treatment prevents and/or reverses TH2
programming of Tregs.
[0155] In another embodiment of this aspect and all other aspects
provided herein, the subject is a human subject.
[0156] In another embodiment of this aspect and all other aspects
provided herein, the method further comprises a step of diagnosing
the subject as having an IgE-mediated food allergy.
[0157] In another embodiment of this aspect and all other aspects
provided herein, the method further comprises a step of testing a
fecal sample from the subject for the presence and/or levels of the
bacteria in the minimal microbial consortium or viable, culturable,
anaerobic gut bacterial strain(s).
[0158] In another embodiment of this aspect and all other aspects
provided herein, the food allergy comprises allergy to soy, wheat,
eggs, dairy, peanuts, tree nuts, shellfish, fish, mushrooms, stone
fruits or other fruits.
[0159] In another embodiment of this aspect and all other aspects
provided herein, the composition is administered after an initial
exposure and/or reaction to a potential food allergen.
[0160] In another embodiment of this aspect and all other aspects
provided herein, the biomass of each of the microbes in the
administered compositions is greater than the biomass of each of
the microbes relative to a reference.
[0161] In another embodiment of this aspect and all other aspects
provided herein, the subject is pretreated with an antibiotic.
[0162] In another embodiment of this aspect and all other aspects
provided herein, the subject is not pretreated with an
antibiotic.
[0163] In another embodiment of this aspect and all other aspects
provided herein, the subject is pretreated with a fasting period
not longer than 24 hours.
[0164] Another aspect provided herein relates to a method of
monitoring a subject's microbiome, the method comprising:
determining the presence and/or biomass of at least one member of a
minimal microbial consortium in a biological sample obtained from a
subject, and wherein if the at least one member is absent or the
biomass of the at least one member is low relative to a reference,
the subject is treated with the composition as described
herein.
[0165] In another embodiment of this aspect and all other aspects
provided herein, the method further comprises predicting that a
subject will have an immune response to a food allergen when the at
least one member is absent, the biomass of the at least one member
is low relative to a reference, or at least one member of a
dysbiotic species is present, or is elevated relative to a
reference.
[0166] In another embodiment of this aspect and all other aspects
provided herein, the method is repeated at least one additional
time.
[0167] In another embodiment of this aspect and all other aspects
provided herein, the biological sample is a fecal sample.
[0168] Another aspect described herein relates to a synergistic
microbial composition comprising: (a) a first microbial consortium
consisting essentially of four to six strains of viable,
non-pathogenic gut bacteria, wherein the strains of viable
non-pathogenic gut bacteria are selected from the group consisting
of: Clostridium ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum, and C. sardiniensis, and (b) a second
microbial consortium consisting essentially of four to five strains
of viable, non-pathogenic gut bacteria, wherein the strains of
viable non-pathogenic gut bacteria are selected from the group
consisting of: Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae,
wherein one or more members of the second microbial consortium
increases the colonization and/or persistence of one or more
members of the first microbial consortium in a mammalian host.
BRIEF DESCRIPTION OF THE FIGURES
[0169] FIG. 1. Tolerance failure in food allergy. Food allergy is a
failure of oral tolerance to food antigens associated with Th2
immunity and allergen-specific IgE responses.
[0170] FIG. 2. Experimental model: Il4raF709 mutant mice.
[0171] FIG. 3. An exemplary ovalbumin sensitization protocol.
[0172] FIG. 4. Ovalbumin (OVA)-induced food allergic reaction in
Il4raF709 mice.
[0173] FIG. 5. Allergen-specific TR cell deficiency in allergic
Il4raF709 mice.
[0174] FIG. 6. Oral allergic sensitization in F709 mutant mice is
associated with dysbiosis.
[0175] FIG. 7. An exemplary protocol to test if microbiota of
sensitized Il4raF709 mice transmit susceptibility to food
allergy.
[0176] FIG. 8. The microbiota of Il4raF709 mice promotes allergic
sensitization and anaphylaxis in germ free mice.
[0177] FIG. 9. The microbiota of Il4raF709 mice promotes allergic
sensitization and anaphylaxis.
[0178] FIG. 10. An exemplary protocol to determine if microbiota of
food tolerant mice transmits protection against food allergy.
[0179] FIG. 11A-FIG. 11D. The microbiota of food tolerant mice
protect against allergic sensitization and anaphylaxis in a
genetically susceptible host.
[0180] FIG. 12A-FIG. 12D. The microbiota of food tolerant mice
promotes the formation of allergen-specific Treg cells.
[0181] FIG. 13. A graphical visualization of relative abundances of
phyla: 8 weeks ovalbumin (OVA) treatment.
[0182] FIG. 14. Selected OTUs showing differences between WT and
F709 mice: OVA, duodenum, jejunum, ileum.
[0183] FIG. 15. An exemplary protocol for testing whether treatment
with defined bacterial mixes will protect against food allergy.
[0184] FIG. 16A-FIG. 16D. Clostridia and Bacteriodetes protect
against development of allergen-specific responses and
anaphylaxis.
[0185] FIG. 17. Oral allergic sensitization is associated with TR
cell TH2 reprogramming.
[0186] FIG. 18A-FIG. 18F. Deletion of Il4/Il13 in TR cells protects
against food allergy.
[0187] FIG. 19. Reduced TH2-skewed Treg phenotype indicating that
Clostridia and Bacteriodetes have two different molecular
mechanisms of action.
[0188] FIG. 20A-FIG. 20C. Short chain fatty acid (SCFA) therapy
does not rescue food allergy in Il4raF709 mice.
[0189] FIG. 21A-FIG. 21I. Gut protect (GP)-I and GP-II are
effective in treat-to-prevent food allergy in conventional
wild-type and IL4RA F709 mice. FIG. 21A, Conventional IL4raF709
mice are pre-treated with oral broad-spectrum antibiotics 1 week
prior to initiating OVA sensitization. Mice receive weekly doses of
5.times.10.sup.8 CFU of the aggregate consortia of either GP-1,
GP-II or NCC before oral OVA challenge. Mice receive the final OVA
challenge at 8 weeks, after which temperature drop (FIG. 21B), from
anaphylaxis, impact to IgE titers (FIG. 21C), mast cell protease-1
(FIG. 21D), mast cell recruitment to the small bowel (FIG. 21E),
development of Foxp3+ regulatory T cells (FIG. 21F), and total
numbers (FIG. 21G), and interferon gamma vs. IL-4 producing T cells
(FIGS. 21H & 21I), are measured.
[0190] FIG. 22A-FIG. 22H. GP-1 (Clostridiales) and GP-II
(Bacteroidetes) consortia protect germ-free mice in
treat-to-prevent regimens. Gnotobiotic mice inoculated with either
the GP-I or GP-II consortia (one time) prior to OVA sensitization
(left arrow, FIG. 22A) and final challenge (right arrow, FIG.
22A).
[0191] FIG. 23A-FIG. 23H. GP-I and GP-II consortia cure food
allergy in conventional IL4raF709 mice while negative control
consortia (NCC) does not. FIG. 23A, Conventional IL4raF709 mice are
sensitized to OVA for 8 weeks and then given oral antibiotics prior
to challenge over 4 weeks with the GP-I (Clostridiales), GP-II
(Bacteroidetes) or NCC (Proteobacteria) consortia. Afterward, mice
receive a final OVA challenge and the following analyses: FIG. 23B,
temperature changes after OVA challenge as a clinical marker of
anaphylaxis. FIG. 23C, Changes to total and OVA-specific IgE
titers. FIG. 23D, MMCP-1 production (indicative of mast cell
degranulation). FIGS. 23E & 23F, Effect of consortia on
development of mucosal Foxp3+ CD4+ T cells. FIGS. 23G & 23H,
Effects on IL-4 and interferon gamma (IFN.gamma.) production in
mucosal CD4+ T cells.
[0192] FIG. 24A-FIG. 24L. GP-II consortia (Bacteriodetes) protects
against food allergy without prior antibiotic knockdown of the
flora.
[0193] FIG. 25A-FIG. 25I. GP-I consortia (Clostridiales) can cure
food allergy without the use of antibiotics in conventional mice.
FIG. 25A, Conventional wild-type or IL4raF709 mice were challenged
weekly with OVA for 8 weeks, after which they received
5.times.10.sup.8 CFU of the GP-I consortium 8 times over 4 weeks
prior to final OVA challenge. Mice received no prior antibiotic
knockdown of the underlying microbiota prior to GP-I
administration. FIG. 25B, Temperature changes with final OVA
challenge. FIG. 25C, Changes in total and OVA-specific IgE titers.
FIG. 25D, Changes in percentages of mucosal T cells, Foxp3
regulatory T cells. FIG. 25E, IL4+ mucosal cells and regulatory T
cells. FIGS. 25F & 25G, Changes in CD4+ IL-17 production in
wild-type and IL4raF709 mice receiving PBS or GP-I consortia. FIGS.
25H & 25I, Changes in IL-17 production of Foxp3+ regulatory
cells.
DETAILED DESCRIPTION
Definitions
[0194] As used herein, the term "food allergy" refers to a failure
of oral tolerance to food antigens associated with Th2 immunity and
allergen-specific IgE responses. That is, an immune response is
generated in response to particular food antigens and can lead to
hives, gastrointestinal symptoms, abdominal pain, anaphylaxis and
even death.
[0195] As used herein, the term "microbiota" can refer to the human
microbiome, the human microbiota, or the human gut microbiota. The
human microbiome (or human microbiota) may be understood as the
aggregate of microorganisms that reside on the surface and in deep
layers of skin, in the saliva and oral mucosa, in the conjunctiva,
and in the genitourinary and gastrointestinal tracts of humans. The
human microbiome is comprised of bacteria, fungi, viruses, and
archaea. At least some of these organisms perform tasks that are
useful for the human host. Under normal circumstances, these
microorganisms do not cause acute disease to the human host, but
instead cause no harm or participate in maintaining health. Hence,
this population of organisms is frequently referred to as the
"normal flora." The population of microorganisms living in the
human gastrointestinal tract is commonly referred to as "microbial
flora", "gut flora", and/or "gut microbiota". The microbial flora
of the human gut encompasses a wide variety of microorganisms that
aid in digestion, the synthesis of vitamins and other metabolites,
and creating enzymes not produced by the human body.
[0196] As used herein, the term "minimal microbial consortium"
refers to a mixed population of cells comprising at least two
species of gut bacteria that do not promote acute disease in a
subject. The microbial consortium is "minimal" when an additional
bacterial species is added and there is no additional benefit
(e.g., less than 5%) in avoiding or mitigating an allergic
response. In some embodiments, the minimal microbial consortium
comprises at least 3, at least 4, at least 5, at least 6, at least
7, at least 8, at least 9, at least 10, at least 11, or more
different species of bacteria. In some embodiments, the minimal
microbial consortium comprises at least one species of bacteria
from the phyla Clostridia and/or Bacteroidetes.
[0197] "Operational taxonomic unit (OTU, plural OTUs)" refers to a
terminal leaf in a phylogenetic tree and is defined by a specific
genetic sequence and all sequences that share a specified degree of
sequence identity to this sequence at the level of species. A
"type" or a plurality of "types" of bacteria includes an OTU or a
plurality of different OTUs, and also encompasses a strain,
species, genus, family or order of bacteria. The specific genetic
sequence may be the 16S rRNA sequence or a portion of the 16S rRNA
sequence, or it may be a functionally conserved housekeeping gene
found broadly across the eubacterial kingdom. OTUs generally share
at least 95%, 96%, 97%, 98%, or 99% sequence identity. OTUs are
frequently defined by comparing sequences between organisms.
Sequences with less than the specified sequence identity (e.g.,
less than 97%) are not considered to form part of the same OTU.
[0198] "Clade" refers to the set of OTUs or members of a
phylogenetic tree downstream of a statistically valid node in a
phylogenetic tree. The clade comprises a set of terminal leaves in
the phylogenetic tree that is a distinct monophyletic evolutionary
unit.
[0199] In microbiology, "16S sequencing" or "16S rRNA" or
"16S-rRNA" or "16S" refers to sequence derived by characterizing
the nucleotides that comprise the 16S ribosomal RNA gene(s). The
bacterial 16S rDNA is approximately 1500 nucleotides in length and
is used in reconstructing the evolutionary relationships and
sequence similarity of one bacterial isolate to a second isolate
using phylogenetic approaches. 16S sequences are used for
phylogenetic reconstruction as they are in general highly
conserved, but contain specific hypervariable regions that harbor
sufficient nucleotide diversity to differentiate genera and species
of most bacteria, as well as fungi.
[0200] The "V1-V9 regions" of the 16S rRNA refers to the first
through ninth hypervariable regions of the 16S rRNA gene that are
used for genetic typing of bacterial samples. These regions in
bacteria are defined by nucleotides 69-99, 137-242, 433-497,
576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465
respectively using numbering based on the E. coli system of
nomenclature. Brosius et al., Complete nucleotide sequence of a 16S
ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805
(1978). In some embodiments, at least one of the V1, V2, V3, V4,
V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In
one embodiment, the V1, V2, and V3 regions are used to characterize
an OTU. In another embodiment, the V3, V4, and V5 regions are used
to characterize an OTU. In another embodiment, the V4 region is
used to characterize an OTU. A person of ordinary skill in the art
can identify the specific hypervariable regions of a candidate 16S
rRNA by comparing the candidate sequence in question to the
reference sequence and identifying the hypervariable regions based
on similarity to the reference hypervariable regions.
[0201] "Dysbiosis" refers to a state of the microbiota or
microbiome of the gut or other body area, including mucosal or skin
surfaces in which the normal diversity and/or function of the
ecological network is disrupted. Any disruption from the preferred
(e.g., ideal) state of the microbiota can be considered a
dysbiosis, even if such dysbiosis does not result in a detectable
decrease in health. This state of dysbiosis may be unhealthy, it
may be unhealthy under only certain conditions, or it may prevent a
subject from becoming healthier. Dysbiosis may be due to a decrease
in diversity, the overgrowth of one or more pathogens or
pathobionts, symbiotic organisms able to cause disease only when
certain genetic and/or environmental conditions are present in a
patient, or the shift to an ecological network that no longer
provides a beneficial function to the host and therefore no longer
promotes health.
[0202] The terms "patient", "subject" and "individual" are used
interchangeably herein, and refer to an animal, particularly a
human, to whom treatment, including prophylactic treatment is
provided. The term "subject" as used herein refers to human and
non-human animals. The term "non-human animals" and "non-human
mammals" are used interchangeably herein includes all vertebrates,
e.g., mammals, such as non-human primates, (particularly higher
primates), sheep, dog, rodent (e.g. mouse or rat), guinea pig,
goat, pig, cat, rabbits, cows, and non-mammals such as chickens,
amphibians, reptiles etc. In one embodiment, the subject is human.
In another embodiment, the subject is an experimental animal or
animal substitute as a disease model. In another embodiment, the
subject is a domesticated animal including companion animals (e.g.,
dogs, cats, rats, guinea pigs, hamsters etc.).
[0203] As used herein, the term "enteric coated drug delivery
device" or "enteric coated composition" refers to any drug delivery
method that can be administered orally but is not degraded or
activated until the device enters the intestines. Such methods can
utilize a coating or encapsulation that is degraded using e.g., pH
dependent means, permitting protection of the delivery device and
the microbial consortium to be administered or transplanted
throughout the upper gastrointestinal tract until the device
reaches the alkaline pH of the intestines. In one embodiment, the
enteric coated drug delivery device comprises a capsule or a pill.
Such drug delivery devices are known to those of skill in the
art.
[0204] As used herein, a "prebiotic" refers to an ingredient that
allows or promotes specific changes, both in the composition and/or
activity in the gastrointestinal microbiota that may (or may not)
confer benefits upon the host. In some embodiments, a prebiotic can
include one or more of the following: fructooligosaccharide,
galactooligosaccharides, hemicelluloses (e.g., arabinoxylan, xylan,
xyloglucan, and glucomannan), inulin, chitin, lactulose, mannan
oligosaccharides, oligofructose-enriched inulin, gums (e.g., guar
gum, gum arabic and carrageenan), oligofructose, oligodextrose,
tagatose, resistant maltodextrins (e.g., resistant starch),
trans-galactooligosaccharide, pectins (e.g., xylogalactouronan,
citrus pectin, apple pectin, and rhamnogalacturonan-I), dietary
fibers (e.g., soy fiber, sugarbeet fiber, pea fiber, corn bran, and
oat fiber) and xylooligosaccharides.
[0205] As used herein, the terms "administering," "introducing" and
"transplanting" are used interchangeably in the context of the
placement of cells, e.g. a microbial consortium, as described
herein into a subject, by a method or route which results in at
least partial localization of the introduced cells at a desired
site, such as the intestines or a region thereof, such that a
desired effect(s) is produced (e.g., tolerance to a food allergen).
The cells can be administered by any appropriate route which
results in delivery to a desired location in the subject where at
least a portion of the delivered cells or components of the cells
remain viable. The period of viability of the cells after
administration to a subject can be as short as a few hours, e.g.,
twenty-four hours, to a few days, to as long as several years,
i.e., long-term engraftment.
[0206] As used herein "preventing" or "prevention" refers to any
methodology where the disease state does not occur due to the
actions of the methodology (such as, for example, administration of
a composition comprising a microbial consortium as described
herein). In one aspect, it is understood that prevention can also
mean that the disease is not established to the extent that occurs
in untreated controls. For example, there can be a 5, 10, 15, 20,
25, 30, 35, 40, 50, 60, 70, 80, 90, or 100% reduction in the
establishment of disease frequency relative to untreated controls.
Accordingly, prevention of a disease encompasses a reduction in the
likelihood that a subject will develop the disease, relative to an
untreated subject (e.g. a subject who is not treated with a
composition comprising a microbial consortium as described
herein).
[0207] As used herein, the term "full complement of bile acid
transformations" refers to the metabolism of primary bile acids to
secondary bile acids. Bile acid transformations performed by gut
microbes include deconjugation, deglucuronidation, oxidation of
hydroxyl groups, reduction of oxo groups to yield epimeric hydroxyl
bile acids, esterification and dehydroxylation. These reactions on
bile acids are the full complement of bile acid transformations as
the term is used herein.
[0208] "Synergy" or "synergistic interactions" refers to the
interaction or cooperation of two or more microbes to produce a
combined effect greater than the sum of their separate effects. For
example, in one embodiment, "synergy" between two or more microbes
can result from a first microbe secreting a waste product or
metabolite that the second microbe uses to fuel growth or other
processes.
[0209] As used herein, the term "persistence" refers to the
maintenance of one or more members of the microbial consortium in
the gastrointestinal tract at a number, biomass or activity that is
at or above the threshold for treating and/or preventing food
allergy. Persistence can be measured by obtaining a stool sample to
determine the number, biomass, and/or activity of one or more
members of the microbial consortium. In some embodiments,
persistence can be measured by obtaining a ratio of the measured
biomass of at least two members of the microbial consortium in the
stool sample.
[0210] The terms "decrease", "reduced", "reduction", or "inhibit"
are all used herein to mean a decrease or lessening of a property,
level, or other parameter by a statistically significant amount. In
some embodiments, "reduce," "reduction" or "decrease" or "inhibit"
typically means a decrease by at least 10% as compared to a
reference level (e.g., the absence of a given treatment) and can
include, for example, a decrease by at least about 10%, at least
about 20%, at least about 25%, at least about 30%, at least about
35%, at least about 40%, at least about 45%, at least about 50%, at
least about 55%, at least about 60%, at least about 65%, at least
about 70%, at least about 75%, at least about 80%, at least about
85%, at least about 90%, at least about 95%, at least about 98%, at
least about 99%, or more. As used herein, "reduction" or
"inhibition" does not encompass a complete inhibition or reduction
as compared to a reference level. "Complete inhibition" is a 100%
inhibition as compared to a reference level. A decrease can be
preferably down to a level accepted as within the range of normal
for an individual without a given disorder.
[0211] The terms "increased", "increase" or "enhance" or "activate"
are all used herein to generally mean an increase of a property,
level, or other parameter by a statically significant amount; for
the avoidance of any doubt, the terms "increased", "increase" or
"enhance" or "activate" means an increase of at least 10% as
compared to a reference level, for example an increase of at least
about 20%, or at least about 30%, or at least about 40%, or at
least about 50%, or at least about 60%, or at least about 70%, or
at least about 80%, or at least about 90% or up to and including a
100% increase or any increase between 10-100% as compared to a
reference level, or at least about a 2-fold, or at least about a
3-fold, or at least about a 4-fold, or at least about a 5-fold or
at least about a 10-fold increase, at least about a 20-fold
increase, at least about a 50-fold increase, at least about a
100-fold increase, at least about a 1000-fold increase or more as
compared to a reference level.
[0212] The term "pharmaceutically acceptable" can refer to
compounds and compositions which can be administered to a subject
(e.g., a mammal or a human) without undue toxicity.
[0213] As used herein, the term "pharmaceutically acceptable
carrier" can include any material or substance that, when combined
with an active ingredient, allows the ingredient to retain
biological activity and is non-reactive with the subject's immune
system. Examples include, but are not limited to, any of the
standard pharmaceutical carriers such as a phosphate buffered
saline solution, emulsions such as oil/water emulsion, and various
types of wetting agents. The term "pharmaceutically acceptable
carriers" excludes tissue culture media.
[0214] As used herein, the term "comprising" means that other
elements can also be present in addition to the defined elements
presented. The use of "comprising" indicates inclusion rather than
limitation.
[0215] As used herein the term "consisting essentially of" refers
to those elements required for a given embodiment. The term permits
the presence of additional elements that do not materially affect
the basic and novel or functional characteristic(s) of that
embodiment of the invention.
[0216] The term "consisting of" refers to compositions, methods,
and respective components thereof as described herein, which are
exclusive of any element not recited in that description of the
embodiment.
[0217] Further, unless otherwise required by context, singular
terms shall include pluralities and plural terms shall include the
singular.
[0218] It should be understood that this invention is not limited
to the particular methodologies, protocols, and reagents, etc.,
described herein and as such can vary therefrom. The terminology
used herein is for the purpose of describing particular embodiments
only, and is not intended to limit the scope of the present
invention, which is defined solely by the claims.
Microbial Flora
[0219] Each individual has a personalized gut microbiota including
an estimated 500 to 5000 or more species of bacteria, fungi,
viruses, archaea and other microorganisms, up to 100 trillion
individual organisms, that reside in the digestive tract, providing
a host of useful symbiotic functions, for example, including aiding
in digestion, providing nutrition for the colon, producing
vitamins, regulating the immune system, assisting in defense
against exogenous bacteria, modulating energy metabolism, and the
production of short chain fatty acids (SCFAs), e.g., via dietary
carbohydrates, including resistant starches and dietary fiber,
which are substrates for fermentation that produce SCFAs, primarily
acetate, propionate, succinate, butyrate, 1,2 propanediol or 1,3
propanediol as end products.
[0220] An imbalance in the microbial flora found in and on the
human body is known to be associated with a variety of disease
states. For example, obesity in both humans and experimental mouse
models is associated with alterations in the intestinal microbiota
that appear to be pathogenic. In settings of `dysbiosis` or
disrupted symbiosis, microbiota functions that can be lost or
deranged, resulting in increased susceptibility to pathogens,
include altered metabolic profiles, or induction of proinflammatory
signals that can result in local or systemic inflammation or
autoimmunity. In addition, in asthmatic subjects, both the
bacterial burden and bacterial diversity were significantly higher
as compared to control subjects, which were also correlated with
bronchial hyper-responsiveness. Thus, the intestinal microbiota
plays a significant role in the pathogenesis of many diseases and
disorders, including a variety of pathogenic infections of the gut.
For instance, patients become more susceptible to pathogenic
infections when the normal intestinal microbiota has been disturbed
due to use of broad-spectrum antibiotics. Many of these diseases
and disorders are chronic conditions that significantly decrease a
patient's quality of life and can be ultimately fatal.
Microbial Consortia
[0221] In some embodiments, a microbial consortium comprises at
least 4, at least 5, at least 6, at least 7, at least 8, at least
9, at least 10, at least 11, at least 12 or more different viable,
bacterial species, e.g., 15 or more, 20 or more, 25 or more, 30 or
more, or even 40 or more. In one embodiment, a microbial consortium
comprises fewer than 40 species, e.g., 30 or fewer species, 25 or
fewer species, 20 or fewer species, or 15 or fewer species. In
another embodiment, a minimal microbial consortium comprises 12 or
less, 11 or less, 10 or less, 9 or less, 8 or less, 7 or less, 6 or
less, 5 or less, or 4 or less different viable bacterial species.
In one embodiment, at least one (e.g., at least 2, at least 3, at
least 4, at least 5, at least 6, at least 7, at least 8, 8 or
fewer, 7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer,
2 or fewer) of the bacterial constituents is a non-pathogenic
bacterial strain. Also contemplated are consortia of 4 to 40
species, 4 to 30 species, 4 to 25 species, 4 to 20 species, 4 to 15
species, 4 to 11 species, 5 to 40 species, 5 to 30 species, 5 to 25
species, 5 to 20 species, 5 to 15 species, 5 to 11 species, 6 to 40
species, 6 to 30 species, 6 to 25 species, 6 to 20 species, 6 to 15
species, 6 to 11 species, 7 to 40 species, 7 to 30 species, 7 to 25
species, 7 to 20 species, 7 to 15 species, 7 to 11 species, 8 to 40
species, 8 to 30 species, 8 to 25 species, 8 to 20 species, 8 to 15
species, 8 to 11 species, 9 to 40 species, 9 to 30 species, 9 to 25
species, 9 to 20 species, 9 to 15 species, 9 to 11 species, 10 to
40 species, 10 to 30 species, 10 to 25 species, 10 to 20 species,
10 to 15 species, or 10 to 11 species.
[0222] In one embodiment, the at least 1 bacterial constituent of a
microbial consortium is a bacterial strain(s) of viable gut
bacteria selected from the group consisting of: Clostridium
ramosum, Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, Prevotella tannerae,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum limetarium, Clostridium symbiosum,
Clostridium sporosphaeroides, Dialister proprionicfaceins,
Dialister succinatiphilus, Parabacteroides distasonis,
Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti.
[0223] In another embodiment, the strains of viable gut bacteria
are selected from the group consisting of: Clostridium ramosum, C.
scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
[0224] In another embodiment, the strains of viable gut bacteria
are selected from the group consisting of: (i) Clostridium ramosum,
C. scindens, C. hiranonsis, C. bifermentans, C. leptum, and C.
sardiniensis, or (ii) Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae.
[0225] In one embodiment, the strains of viable gut bacteria do not
include Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis,
Enterobacter cloacae, Bilophila wadsworthia, Alistipes onderdonkii,
Desulfovibrio species, Lactobacillus johnsoni, and Parasutterella
excrementihominis.
[0226] In another embodiment, the consortium does not comprise
bacteria of the Genera Bilophila, Enterobacter, Escherichia,
Klebsiella, Proteus, Alistipes, Desulfovibrio, Blautia, or
Parasutterella.
[0227] In another embodiment, the consortium does not comprise
bacteria of the Families Desulfovibrionaceae, Enterobacteriaceae,
Rikenellaceae, and Sutterellaceae.
[0228] In another embodiment, the consortium does not comprise
bacteria of the Families Lactobacillaceae or Enterbacteriaceae.
[0229] In another embodiment, the consortium does not comprise
bacteria of the Order Burkholdales, Desulfovibrionates, or
Enterobacteriales.
[0230] Metabolic Features:
[0231] Various features of gut microbes are beneficial for
protection from or therapy for allergy, including food allergy. In
the following, features and corresponding functions contemplated to
render particular species or taxa of gut microbes well-suited for a
protective or therapeutic microbial consortium as described herein
are described. In practice, a consortium comprising four or more,
e.g., five or more, six or more, seven or more, eight or more, nine
or more or ten or more of these features and corresponding
functions is considered a likely candidate for protection or
therapy for food allergy.
[0232] In some embodiments, the microbial consortium comprises one
or more types of microbes capable of producing butyrate in a
mammalian subject. Butyrate-producing microbes can be identified
experimentally, e.g., by NMR or gas chromatography analyses of
microbial products or colorimetric assays (Rose I A. 1955. Methods
Enzymol. 1: 591-5). Butyrate-producing microbes can also be
identified computationally, e.g., by the identification of one or
more enzymes involved in butyrate synthesis. Non-limiting examples
of enzymes found in butyrate-producing microbes include butyrate
kinase, phosphotransbutyrylase, and butyryl CoA:acetate CoA
transferase (Louis P., et al. 2004. J Bact. 186(7): 2099-2106).
Butyrate-producing strains include, but are not limited to,
Clostridium sardiniensis, Clostridium hiranonsis, Facealibacterium
prausnitzii, Butyrovibrio spp., Eubacterium rectale, and Roseburia
intestinalis.
[0233] In some embodiments, a pharmaceutical composition comprises
two or more types of microbes or bacterial strains, wherein the at
least two types of microbes are capable of producing butyrate in a
mammalian subject. In other embodiments, the composition comprises
two or more types of microbes, wherein two or more types of microbe
cooperate (i.e., cross-feed) to produce an immunomodulatory short
chain fatty acid (SCFA) (e.g., butyrate) in a mammalian subject. In
one embodiment, the composition comprises at least one type of
microbe (e.g., Bifidobacterium spp., Bacteroides thetaiotaomicron,
Bacteroides fragilis or Clostridium ramosum) is capable of
metabolizing a prebiotic, including but not limited to, inulin,
inulin-type fructans, fucose-containing glycoconjugates including
the H1, H2, Lewis A, B, X, or Y antigens, or oligofructose, such
that the resulting metabolic product can be converted by a second
type of microbe (e.g., a butyrate-producing microbe such as
Roseburia spp.) to an immunomodulatory SCFA such as butyrate
(Falony G., E T al. 2006 Appl. Environ. Microbiol. 72(12):
7835-7841). In other aspects, the composition comprises at least
one acetate-consuming, butyrate-producing microbe (e.g.,
Faecalibacterium prausnitzii or Roseburia intestinalis).
[0234] In some embodiments, the composition comprises one or more
types of microbe capable of producing propionate and/or succinate
in a mammalian subject, optionally further comprising a prebiotic
or substrate appropriate for propionate and/or succinate
biosynthesis. Examples of prebiotics or substrates used for the
production of propionate include, but are not limited to,
L-rhamnose, D-tagalose, resistant starch, inulin, polydextrose,
arabinoxylans, arabinoxylan oligosaccharides,
mannooligosaccharides, and laminarans (Hosseini E., et al. 2011.
Nutrition Reviews. 69(5): 245-258). Propionate-producing microbes
can be identified experimentally, such as by NMR or gas
chromatography analyses of microbial products or colorimetric
assays (Rose I A. 1955. Methods Enzymol. 1: 591-5).
Propionate-producing microbes can also be identified
computationally, such as by the identification of one or more
enzymes involved in propionate synthesis. Non-limiting examples of
enzymes found in propionate-producing microbes include enzymes of
the succinate pathway, including but not limited to
phosphoenylpyruvate carboxykinase, pyruvate kinase, pyruvate
carboxylase, malate dehydrogenase, fumarate hydratase, succinate
dehydrogenase, succinyl CoA synthetase, methylmalonyl Coa
decarboxylase, and propionate CoA transferase, as well as enzymes
of the acrylate pathway, including but not limited to L-lactate
dehydrogenase, propionate CoA transferase, lactoyl CoA dehydratase,
acyl CoA dehydrogenase, phosphate acetyltransferase, and propionate
kinase. For example, microbes that utilize the succinate pathway
include certain species of the Bacteroides genus, such as
Bacteroides fragilis, Clostridium sardiniensis and Clostridum
hiranonsis. In one embodiment, the propionate-producing species is
Bacteroides fragilis, Bacteroides thetaiotaomicron, or Bacteroides
ovatus. In one embodiment, the succinate-producing species is
Bacteroides fragilis, Bacteroides thetaiotaomicron, or Bacteroides
ovatus.
[0235] Functional methods to define species that produce butyrate,
propionate and/or succinate includes analysis of short-chain fatty
acid (SCFA) production using gas-chromatography/liquid
chromatography (GC/LC) to identify propionate, butyrate, and/or
succinate or mass spectroscopy based methods to detect these SCFA,
as well as 1,2-propanediol, and 1,3-propanediol. Studies can be
performed in cultured supernatants from colonized gnotobiotic mice
and from conventional patients and/or animal samples.
[0236] Additional methods for identifying species that produce
butyrate comprise those species expressing butyryl-CoA:acetate CoA
transferases (But genes) or butyrate kinases (Buk genes) for
production of butyrate from anaerobic fermentation of sugars. In
another embodiment, organisms producing butyrate (from amino acids
such as lysine, glutarate or 4-aminobutyrate pathways) express
enzymes including e.g., L2Hgdh, 2-hydroxyglutarate dehydrogenase;
Gct, glutaconate CoA transferase (.alpha., .beta. subunits);
HgCoAd, 2-hydroxy-glutaryl-CoA dehydrogenase (.alpha., .beta.,
.gamma. subunits); Gcd, glutaconyl-CoA decarboxylase (.alpha.,
.beta. subunits); Th1, thiolase; hbd, .beta.-hydroxybutyryl-CoA
dehydrogenase; Cro, crotonase; Bcd, butyryl-CoA dehydrogenase
(including electron transfer protein .alpha., .beta. subunits);
KamA, lysine-2,3-aminomutase; KamD,E, .beta.-lysine-5,6-aminomutase
(.alpha., .beta. subunits); Kdd, 3,5-diaminohexanoate
dehydrogenase; Kce, 3-keto-5-aminohexanoate cleavage enzyme; Kal,
3-aminobutyryl-CoA ammonia lyase; AbfH, 4-hydroxybutyrate
dehydrogenase; AbfD, 4-hydroxybutyryl-CoA dehydratase; Isom,
vinylacetyl-CoA 3,2-isomerase (same protein as AbfD): 4Hbt,
butyryl-CoA:4-hydroxybutyrate CoA transferase; But,
butyryl-CoA:acetate CoA transferase; Ato, butyryl-CoA:acetoacetate
CoA transferase (.alpha., .beta. subunits); Ptb, phosphate
butyryltransferase; Buk, and butyrate kinase (see e.g., Vital et
al. mBIO 5(2):e00889-14).
[0237] In some embodiments, a microbial consortium comprises at
least one bacterial species that produces compounds capable of
stimulating the aryl hydrocarbon (AhR) receptor in gut epithelial
cells, antigen-presenting cells and/or T cells. Without wishing to
be bound by theory, stimulation of the AhR receptor can aid in the
development of regulatory T cell processes that can prevent and/or
treat food allergy. Some non-limiting examples of compounds that
stimulate host aryl hydrocarbon receptor pathways include (i)
indole, (ii) intermediates from microbial synthesis of indole,
tryptophan, tyrosine and histidine, (iii) microbial synthesis of
flavonoids, phenazines and/or quinones or (iv) compounds or
intermediates of metabolism of host ingested flavonoids, phenazines
and/or quinones. In one example, a viable, culturable, anaerobic
gut bacterial strain produces aryl hydrocarbon receptor agonists
sufficient to stimulate host aryl hydrocarbon receptor pathways
comprises at least one gene associated with the synthesis of
tryptophan or the synthesis of quinone molecules. In an additional
example, a viable, culturable, anaerobic gut bacterial strain that
produces aryl hydrocarbon receptor agonists sufficient to stimulate
host aryl hydrocarbon receptor pathways by microbial synthesis of
flavonoids, phenazines, and/or quinones. Thus microbes that express
or encode biosynthetic enzymes that participate in the synthesis of
flavonoids, phenazines and/or quinones are identified as microbes
that produce host aryl hydrocarbon receptor agonists. In one
embodiment, the biosynthetic enzymes include the last enzyme in the
pathway that catalyzes the final biosynthetic reaction producing
e.g., flavonoids, phenazine or quinone compounds.
[0238] In some embodiments, a microbial consortium comprises at
least one bacterial species that produces compounds capable of
stimulating the pregnane X receptor that e.g., has beneficial
effects on gut barrier function and/or the development of
regulatory T cell processes. Non-limiting examples of compounds
that stimulate the pregnane X receptor include (i) desmolase, (ii)
compounds or intermediates of hydroxysteroid dehydrogenase
activity, or (iii) compounds or intermediates derived from
flavonoid metabolism enzymes. Thus, bacteria that encode and
express steroid desmolase and/or hydroxysteroid dehydrogenase
enzymes are expected to produce compounds that stimulate the
pregnane X receptor. Clostridium sardiniensis and Clostridium
scindens are non-limiting examples of bacterial species that
produce compounds capable of stimulating the pregnane X
receptor.
[0239] In some embodiments, the microbial consortium comprises at
least one bacterial species that produces compounds capable of
stimulating the RAR-related orphan receptor gamma (RORgamma)
pathways, for example, to stimulate development of regulatory T
cell responses via direct stimulation of RORgamma-activated
pathways in gut antigen presenting cells and/or epithelial cells
that then stimulate regulatory T cell responses. In one embodiment,
the viable, culturable, anaerobic gut bacterial strain that
produces compounds endogenously or by metabolizing ingested
precursors, that is capable of stimulating the RORgamma
(RAR-related orphan receptor gamma) pathways to stimulate
development of regulatory T cell responses is a strain that
expresses at least one cholesterol reductase and other enzymes
capable of metabolizing sterol compounds. Non-limiting examples of
microbes that produce compounds that stimulate the RORgamma pathway
include Clostridium scindens, Clostridia hiranonsis, and
Clostridium sardiniensis. In one instance, those species express
bile acid transforming enzymes that can also produce RORgamma
pathway agonists.
[0240] In some embodiments, a microbial consortium described herein
improves gut function, for example, by stimulating host mucins and
complex glycoconjugates and improving colonization by protective
commensal strains. In one embodiment, the microbial consortium
comprises at least one bacterial strain, such as Bacteroides
thetaiotaomicron, that stimulates production of mucins and complex
glycoconjugates by the host.
[0241] Immunomodulation:
[0242] Other exemplary compositions useful for treatment of food
allergy contain bacterial strains capable of altering the
proportion of immune subpopulations, e.g., T cell subpopulations,
e.g., Tregs in the subject.
[0243] For example, immunomodulatory bacteria can increase or
decrease the proportion of Treg cells, Th17 cells, Th1 cells, or
Th2 cells in a subject. The increase or decrease in the proportion
of immune cell subpopulations can be systemic, or it can be
localized to a site of action of the colonized consortium, e.g., in
the gastrointestinal tract or at the site of a distal dysbiosis. In
some embodiments, a microbial consortium comprising
immunomodulatory bacteria is used for treatment of food allergy
based on the desired effect of the probiotic composition on the
differentiation and/or expansion of subpopulations of immune cells
in the subject.
[0244] In one embodiment, the microbial consortium contains
immunomodulatory bacteria that increase the proportion of Treg
cells in a subject or in a particular location in a subject, e.g.,
the gut tissues. In one embodiment, a microbial consortium contains
immunomodulatory bacteria that increase the proportion of Th17
cells in a subject. In another embodiment, a microbial consortium
contains immunomodulatory bacteria that decrease the proportion of
Th17 cells in a subject. In one embodiment, a microbial consortium
contains immunomodulatory bacteria that increase the proportion of
Th1 cells in a subject. In another embodiment, a microbial
consortium contains immunomodulatory bacteria that decrease the
proportion of Th1 cells in a subject. In one embodiment, a
microbial consortium contains immunomodulatory bacteria that
increase the proportion of Th2 cells in a subject. In another
embodiment, a microbial consortium contains immunomodulatory
bacteria that decrease the proportion of Th2 cells in a
subject.
[0245] In one embodiment, a microbial consortium contains
immunomodulatory bacteria capable of modulating the proportion of
one or more of Treg cells, Th17 cells, Th1 cells, Th2 cells, and
combinations thereof in a subject. Certain immune cell profiles can
be particularly desirable to treat or prevent inflammatory
disorders, such as food allergies. For example, in some
embodiments, treatment or prevention of e.g., food allergy can be
promoted by increasing numbers of Treg cells and Th2 cells, and
decreasing numbers of Th17 cells and Th1 cells. Accordingly, a
microbial consortium for the treatment or prevention of food
allergy can contain a microbial consortium capable of promoting
Treg cells and Th2 cells, and reducing Th17 and Th1 cells.
[0246] In one embodiment, the anaerobic gut bacterial strain in the
methods and compositions described herein express agonists capable
of binding to and modulating responses mediated by Toll-like
receptors (TLR), CD14 and/or lipid binding proteins in antigen
presenting cells, gut epithelial cells and/or T cells to promote
the development of regulatory T cells. Non-limiting examples of TLR
agonists include lipopolysaccharide (LPS), exopolysaccharides
(PSA), peptidoglycan or CpG motifs produced by commensal members of
Bacteroides, or lipoteichoic acids (LTA) produced by members of
Clostridium. In one embodiment, an anaerobic gut bacterial strain
that acts as a TLR agonist is selected from the following
Table.
TABLE-US-00001 Family Genus Species Clostridieaceae Clostridium,
Hungatella Hungatella hathawayi Eubacteriaceae Eubacterium
Eubacterium rectale Erysipelotrichaceae Erysipelatoclostridium
Erysipelatoclostridium (formerly species in ramosum (Clostridium
genus Clostridium) ramosum) Lachnospiraceae Blautia, Butyrovibrio,
Butyrovibrio crossatus, Cellulosyliticum, Roseburia intestinalis,
Clostridium cluster Clostridium scindens, XIVa species, Clostridium
hylemonae, Coprococcus, Dorea, Clostridium symbiosum Lachnospira,
Robinsonella, Roseburia, Ruminococcaceae Faecalobacterium,
Faecalibacterium Ruminococcus, prausnitzii, Subdoligranulum,
Subdoligranulum Clostridium cluster variabile XIVa species
Bacteroidaceae Bacteroides Bacteroides thetaiotaomicron,
Bacteroides fragilis, Bacteroides ovatus Prophyromonadaceae
Parabacteroides, Parabacteroides Porphyromonas, goldsteinii,
Tannerella Parabacteroides merdae, Parabacteroides distasonis
Prevotellaceae Prevotella Prevotella tannerae
[0247] Bile Acid Transformation:
[0248] Primary bile acids (e.g., cholic and chenodeoxycholic acids
in humans) are generated in the liver of mammals, including humans,
mainly by conjugation with the amino acids taurine or glycine, and
are secreted in bile. In the intestinal tract, primary bile acids
are metabolized by microbes that transform the primary bile acids
to secondary bile acids. Intestinal microbial transformation of
primary bile acids can include deconjugation, deglucuronidation,
oxidation of hydroxyl groups, reduction of oxo groups to yield
epimeric hydroxyl bile acids, esterification, and dehydroxylation.
Non-limiting examples of bacteria that perform deconjugation of
primary bile acids include Bacteroides, Bifidobacterium,
Clostridium, and Lactobacillus. Non-limiting examples of bacteria
that perform oxidation and epimerization of primary bile acids
include Bacteroides, Clostridium, Egghertella, Eubacterium,
Peptostreptococcus, and Ruminococcus. Non-limiting examples of
bacteria that perform 7-dehydroxylation of primary bile acids
include Clostridium, and Eubacterium. Non-limiting examples of
bacteria that perform esterification of primary bile acids include
Bacteroides, Eubacterium, and Lactobacillus.
[0249] In one embodiment, a microbial consortium as described
herein comprises at least one bacterial constituent that transforms
bile acids by deconjugation. In another embodiment, a microbial
consortium as described herein comprises at least one bacterial
constituent that transforms bile acids by 7-dehydroxylation. In
another embodiment, a microbial consortium as described herein
comprises at least one bacterial constituent that transforms bile
acids by esterification.
[0250] In one embodiment, a microbial consortium as described
herein comprises at least 2, at least 3, at least 4, at least 5, at
least 6, at least 7, at least 8, at least 9, at least 10, at least
11 or more bacterial constituents that perform bile acid
transformation.
[0251] In one embodiment, a microbial consortium as described
herein comprises 11 or fewer, 10 or fewer, 9 or fewer, 8 or fewer,
7 or fewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, 2 or
fewer 1 or fewer or zero bacterial constituents that perform bile
acid transformation, such as deconjugation, esterification or
7-dehydroxylation.
[0252] In one embodiment, a microbial consortium comprises at least
one anaerobic gut bacterial strain that alone, or in combination,
performs the full complement of bile acid transformations.
[0253] Engineered Microbes:
[0254] In some embodiments, one or more members of the microbial
consortium comprises an engineered microbe(s). For example,
engineered microbes include microbes harboring i) one or more
introduced genetic changes, such change being an insertion,
deletion, translocation, or substitution, or any combination
thereof, of one or more nucleotides contained on the bacterial
chromosome or on an endogenous plasmid, wherein the genetic change
can result in the alteration, disruption, removal, or addition of
one or more protein coding genes, non-protein-coding genes, gene
regulatory regions, or any combination thereof, and wherein such
change can be a fusion of two or more separate genomic regions or
can be synthetically derived; ii) one or more foreign plasmids
containing a mutant copy of an endogenous gene, such mutation being
an insertion, deletion, or substitution, or any combination
thereof, of one or more nucleotides; and iii) one or more foreign
plasmids containing a mutant or non-mutant exogenous gene or a
fusion of two or more endogenous, exogenous, or mixed genes. The
engineered microbe(s) can be produced using techniques including
but not limited to site-directed mutagenesis, transposon
mutagenesis, knock-outs, knock-ins, polymerase chain reaction
mutagenesis, chemical mutagenesis, ultraviolet light mutagenesis,
transformation (chemically or by electroporation), phage
transduction, or any combination thereof.
[0255] Excluded Bacteria:
[0256] In one embodiment, a microbial consortium does not include
an organism conventionally classified as a pathogenic or
opportunistic organism. It is possible that a function shared by
all members of a given taxonomic group could be beneficial, e.g.,
for providing particular metabolites, yet for other reasons the
overall effect of one or more particular members of the group is
not beneficial and is, for example, pathogenic. Clearly, members of
a given taxonomic group that cause pathogenesis, e.g., acute
gastrointestinal pathologies, are to be excluded from the
therapeutic or preventive methods and compositions described
herein.
[0257] In one embodiment, the bacterial composition does not
comprise at least one of: Acidaminococcus intestinalis, Escherichia
coli, Lactobacillus casei, Lactobacillus paracasei, Raoultella sp.,
and Streptococcus mitis.
[0258] In another embodiment, the bacterial composition does not
comprise at least one of Bamesiella intestinihominis; Lactobacillus
reuteri; Enterococcus hirae, Enterococus faecium, or Enterococcus
durans; Anaerostipes caccae or Clostridium indolis; Staphylococcus
wameri or Staphylococcus pasteuri; and Adlercreutzia
equolifaciens.
[0259] In another embodiment, the bacterial composition does not
comprise at least one of Clostridium botulinum, Clostridium
cadaveric, Clostridium chauvoei, Clostridium clostridioforme,
Clostridium cochlearium, Clostridium difficile, Clostridium
haemolyticum, Clostridium hastiforme, Clostridium histolyticum,
Clostridium indolis, Clostridium irregulare, Clostridium limosum,
Clostridium malenominatum, Clostridium novyi, Clostridium oroticum,
Clostridium paraputrificum, Clostridium perfringens, Clostridium
piliforme, Clostridium putrefaciens, Clostridium putrificum,
Clostridium septicum, Clostridium sordellii, Clostridium
sphenoides, and Clostridium tetani.
[0260] In another embodiment, the bacterial composition does not
comprise at least one of Escherichia coli, and Lactobacillus
johnsonii.
[0261] In another embodiment, the bacterial composition does not
comprise at least one of Clostridium innocuum, Clostridium
butyricum, Escherichia coli, and Blautia producta (previously known
as Peptostreptococcus productus).
[0262] In another embodiment, the bacterial composition does not
comprise at least one of Eubacteria, Fusobacteria,
Propionibacteria, Escherichia coli, and Gemmiger.
[0263] In another embodiment, the compositions described herein do
not comprise pathogenic bacteria such as e.g., Yersinia, Vibrio,
Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella,
Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma,
Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella,
Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia,
Enterococcus, Coxiella, Corynebacterium, Chlamydia, Chlamydophila,
Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella,
Bacillus, multi-drug resistant bacteria, extended spectrum
beta-lactam resistant Enterococci (ESBL), Carbapenem-resistant
Enterobacteriaceae (CRE), and vancomycin-resistant Enterococci
(VRE).
[0264] In other embodiments, the compositions described herein do
not comprise pathogenic species or strains, such as Aeromonas
hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus
cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium
difficile, Clostridium perfringens, enteroaggregative Escherichia
coli, enterohemorrhagic Escherichia coli, enteroinvasive
Escherichia coli, enterotoxigenic Escherichia coli (such as, but
not limited to, LT and/or ST), Escherichia coli 0157:H7,
Helicobacter pylori, Klebsiellia pneumonia, Lysteria monocytogenes,
Plesiomonas shigelloides, Salmonella spp., Salmonella typhi,
Salmonella paratyphi, Shigella spp., Staphylococcus spp.,
Staphylococcus aureus, vancomycin-resistant enterococcus spp.,
Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio
vulnificus, and Yersinia enterocolitica.
[0265] In one embodiment, the microbial consortia and compositions
thereof do not comprise Escherichia coli, Klebsiella pneumoniae,
Proteus mirabilis, Enterobacter cloacae, and/or Bilophila
wadsworthia.
[0266] Reduction of Pathogenic Organisms:
[0267] In some embodiments, compositions comprising a microbial
consortium as described herein offer a protective or therapeutic
effect against dysbiosis or against infection by one or more GI
pathogens of interest. In one embodiment, a microbial consortium as
described herein reduces the biomass of one or more dysbiotic or
pathogenic bacterial strains.
[0268] In one embodiment, a microbial consortium as described
herein decreases the biomass of one or more dysbiotic or pathogenic
bacterial strains by at least 10% compared to the biomass of the
one or more dysbiotic or pathogenic bacterial strains in the
absence of treatment with such microbial consortium. In other
embodiments the biomass of one or more pathogenic bacterial strains
is decreased by at least 20%, at least 30%, at least 40%, at least
50%, at least 60%, at least 70%, at least 80%, at least 90%, at
least 95%, at least 99%, or even 100% (i.e., below detectable
limits of the assay) as compared to the biomass of the dysbiotic or
pathogenic bacterial strains in the gut of the subject prior to
treatment with the microbial consortium or compositions
thereof.
[0269] In some embodiments, a microbial consortium as described
herein alters the gut environment such that the number, biomass, or
activity of one or more dysbiotic or pathogenic organisms is
decreased by at least 10% (e.g., at least 20%, at least 30%, at
least 40%, at least 50%, at least 60%, at least 70%, at least 80%,
at least 90%, at least 95%, at least 99%, or even 100% (i.e., below
detectable limits of the assay)). As but one example, colonization
of Bacteroides reduces the biomass of dysbiotic species in the
Enterobacteriaceae or Desulfonovibriacaea Families.
[0270] In some embodiments, the pathogenic bacterium is selected
from the group consisting of Yersinia, Vibrio, Treponema,
Streptococcus, Staphylococcus, Escherichia/Shigella, Salmonella,
Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma,
Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella,
Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia,
Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia,
Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia,
Bordetella, Bifidobacterium, Bacillus, Bilophila, Desulfovibrio,
multi-drug resistant bacteria, extended spectrum beta-lactam
resistant Enterococci (ESBL), Carbapenem-resistant
Enterobacteriaceae (CRE), and vancomycin-resistant Enterococci
(VRE).
[0271] In some embodiments, these pathogens include, but are not
limited to, Aeromonas hydrophila, Campylobacter fetus, Plesiomonas
shigelloides, Bacillus cereus, Campylobacter jejuni, Clostridium
botulinum, Clostridium difficile, Clostridium perfringens,
enteroaggregative Escherichia coli, entero hemorrhagic Escherichia
coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia
coli (such as, but not limited to, LT and/or ST), Escherichia coli
0157:H7, Helicobacter pylori, Klebsiellia pneumonia, Lysteria
monocytogenes, Plesiomonas shigelloides, Salmonella spp.,
Salmonella typhi, Salmonella paratyphi, Shigella spp.,
Staphylococcus spp., Staphylococcus aureus, vancomycin-resistant
enterococcus spp., Vibrio spp., Vibrio cholerae, Vibrio
parahaemolyticus, Vibrio vulnificus, and Yersinia
enterocolitica.
[0272] In one embodiment, the pathogen of interest is at least one
pathogen chosen from Clostridium difficile, Salmonella spp.,
pathogenic Escherichia coli, vancomycin-resistant Enterococcus
spp., and extended spectrum beta-lactam resistant Enterococci
(ESBL).
[0273] Methods for testing the efficacy of the compositions
comprising a microbial composition to reduce the number, biomass,
or activity of one or more dysbiotic or pathogenic organisms are
discussed in the following. While certain of the methods are
described in the following in terms of assaying reduced number,
biomass or activity of C. difficile, one of skill in the art can
readily adapt the methods to measure the number, biomass or
activity of one or more further microbial strains.
[0274] In one embodiment, provided is an In Vitro Assay utilizing
competition between the bacterial compositions or subsets thereof
and C. difficile or other dysbiotic or pathogenic strain. This test
in known in the art and as such is not described in detail
herein.
[0275] In another embodiment, provided is an In Vitro Assay
utilizing 10% (wt/vol) Sterile-Filtered Feces. This assay tests for
the protective effect of the bacterial compositions and screens in
vitro for combinations of microbes that inhibit the growth of a
given pathogenic or dysbiotic microbe. The assay can operate in
automated high-throughput or manual modes. Under either system,
human or animal feces can be re-suspended in an anaerobic buffer
solution, such as pre-reduced PBS or other suitable buffer, the
particulate removed by centrifugation, and filter sterilized. This
10% sterile-filtered feces material serves as the base media for
the in vitro assay. To test a bacterial composition, an
investigator can add it to the sterile-filtered feces material for
a first incubation period and then can inoculate the incubated
microbial solution with a pathogenic or dysbiotic microbe of
interest for a second incubation period. The resulting titer of the
pathogenic or dysbiotic microbe is quantified by any number of
methods such as those described below, and the change in the amount
of pathogen is compared to standard controls including the
pathogenic or dysbiotic microbe cultivated in the absence of the
bacterial composition. The assay is conducted using at least one
control. Feces from a healthy subject can be used as a positive
control. As a negative control, antibiotic-treated feces or
heat-treated feces can be used. Various bacterial compositions can
be tested in this material and the bacterial compositions
optionally compared to the positive and/or negative controls. The
ability to inhibit the growth of a pathogenic or dysbiotic microbe
can be measured by plating the incubated material on selective
media and counting colonies. After competition between the
bacterial composition and the pathogenic or dysbiotic microbe, each
well of the in vitro assay plate is serially diluted ten-fold six
times, and plated on selective media. For Clostridium difficile
this would include, for example, cycloserine cefoxitin mannitol
agar (CCMA) or cycloserine cefoxitin fructose agar (CCFA), and
incubated. Colonies of the pathogenic or dysbiotic microbes are
then counted to calculate the concentration of viable cells in each
well at the end of the competition.
[0276] Alternatively, the ability to inhibit the growth of a
pathogenic or dysbiotic species can be measured by quantitative PCR
(qPCR). Standard techniques can be followed to generate a standard
curve for the pathogenic or dysbiotic strain of interest. Genomic
DNA can be extracted from samples using commercially-available
kits, such as the Mo Bio Powersoil.RTM.-htp 96 Well Soil DNA
Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), the Mo Bio
Powersoil.RTM. DNA Isolation Kit (Mo Bio Laboratories, Carlsbad,
Calif.), or the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia,
Calif.) according to the manufacturer's instructions. The qPCR can
be conducted using HotMasterMix (5PRIME, Gaithersburg, Md.) and
primers specific for the pathogenic or dysbiotic microbe of
interest, and can be conducted on a MicroAmp.RTM. Fast Optical
96-well Reaction Plate with Barcode (0.1 mL) (Life Technologies,
Grand Island, N.Y.) and performed on a BioRad C1000.TM. Thermal
Cycler equipped with a CFX96.TM. Real-Time System (BioRad,
Hercules, Calif.), with fluorescent readings of the FAM and ROX
channels. The Cq value for each well on the FAM channel is
determined by the CFX Manager.TM. software version 2.1. The
log.sub.10 (cfu/ml) of each experimental sample is calculated by
inputting a given sample's Cq value into linear regression model
generated from the standard curve comparing the Cq values of the
standard curve wells to the known log.sub.10 (cfu/ml) of those
samples. The skilled artisan can employ alternative qPCR modes.
[0277] Also provided are In Vivo Assays establishing the protective
effect of bacterial compositions. The assay is described in terms
of protective effect against Clostridium difficile, but can be
adapted by one of skill in the art for other pathogens or dysbiotic
species. Provided is an in vivo mouse model to test for the
protective effect of the bacterial compositions against C.
difficile. In this model (based on Chen, et al., Gastroenterology
135(6):1984-1992 (2008)), mice are made susceptible to C. difficile
by a 7 day treatment (days -12 to -5 of experiment) with 5 to 7
antibiotics (including kanamycin, colistin, gentamycin,
metronidazole and vancomycin and optionally including ampicillin
and ciprofloxacin) delivered via their drinking water, followed by
a single dose with Clindamycin on day -3, then challenged three
days later on day 0 with 10.sup.4 spores of C. difficile via oral
gavage (i.e., oro-gastric lavage). Bacterial compositions can be
given either before (prophylactic treatment) or after (therapeutic
treatment) C. difficile gavage. Further, bacterial compositions can
be given after (optional) vancomycin treatment to assess their
ability to prevent recurrence and thus suppress the pathogen in
vivo. The outcomes assessed each day from day -1 to day 6 (or
beyond, for prevention of recurrence) are weight, clinical signs,
mortality and shedding of C. difficile in the feces. Weight loss,
clinical signs of disease and C. difficile shedding are typically
observed without treatment. Vancomycin provided by oral gavage on
days -1 to 4 protects against these outcomes and serves as a
positive control. Clinical signs are subjective, and scored each
day by the same experienced observer. Animals that lose greater
than or equal to 25% of their body weight are euthanized and
counted as infection-related mortalities. Feces are gathered from
mouse cages (5 mice per cage) each day, and the shedding of C.
difficile spores is detected in the feces using a selective plating
assay as described for the in vitro assay above, or via qPCR for
the toxin gene. The effects of test materials including 10%
suspension of human feces (as a positive control), bacterial
compositions, or PBS (as a negative vehicle control), are
determined by introducing the test article in a 0.2 mL volume into
the mice via oral gavage on day -1, one day prior to C. difficile
challenge, on day 1, 2 and 3 as treatment or post-vancomycin
treatment on days 5, 6, 7 and 8. Vancomycin, as discussed above, is
given on days 1 to 4 as another positive control. Alternative
dosing schedules and routes of administration (e.g. rectal) may be
employed, including multiple doses of test article, and 10.sup.3 to
10.sup.13 of a given organism or composition may be delivered.
[0278] Enhancement of Beneficial Organisms:
[0279] In some embodiments, compositions comprising a microbial
consortium offer a therapeutic effect of enhancing beneficial
organisms in the GI tract. In one embodiment, a microbial
consortium as described herein increases the biomass of one or more
beneficial bacterial strains by at least 10%. In other embodiments
the biomass of one or more beneficial bacterial strains is
increased by at least 20%, at least 30%, at least 40%, at least
50%, at least 60%, at least 70%, at least 80%, at least 90%, at
least 1-fold, at least 2-fold, at least 5-fold, at least 10-fold,
at least 50-fold, at least 100-fold, at least 500-fold, at least
1000-fold, at least 5000-fold, at least 10,000-fold, at least
15,000-fold or at least 20,000-fold over the biomass of the
beneficial bacterial strains in the gut of the subject prior to
treatment with the microbial consortium or compositions thereof. In
one embodiment, the beneficial organisms are commensal bacterial
strains that currently reside or exist in the gut. In another
embodiment, the beneficial organisms are one or more of the
bacterial strains in the microbial consortium itself.
[0280] In some embodiments, a microbial consortium as described
herein alters the gut environment such that the number, biomass, or
activity of one or more beneficial organisms is increased by at
least 10% (e.g., by at least 20%, at least 30%, at least 40%, at
least 50%, at least 60%, at least 70%, at least 80%, at least 90%,
at least 1-fold, at least 2-fold, at least 5-fold, at least
10-fold, at least 50-fold, at least 100-fold, at least 500-fold, at
least 1000-fold, at least 5000-fold, at least 10,000-fold, at least
15,000-fold or at least 20,000-fold). For example, the microbial
consortium stimulates the host's production of mucins and complex
glycoconjugates to improve gut barrier function and colonization of
beneficial organisms, additional probiotic compositions, or the
microbial consortium itself. In some embodiments, the microbial
composition for enhancing the biomass and/or activity of beneficial
organisms comprises e.g., Bacteroides thetaiotaomicron, which
enhances colonization by other Bacteroidetes and Clostridiales. In
some embodiments, the microbial consortium influences gut pH,
reduction of oxygen tension, secretion of glycosidases, and
improving the reduction potential of the gut lumen to improve the
colonization of beneficial organisms.
[0281] In another embodiment, the beneficial species comprises a
Clostridium spp, such as Clostridium ramosum, Clostridium scindens,
Clostridium hiranonsis, Clostridium bifermentans, Clostridium
leptum, Clostridium sardiniensis, Clostridium hathewayi,
Clostridium nexile, Clostridium hylemonae, Clostridium
glycyrrhizinilyticum, Clostridium lavalense, Clostridium
fimetarium, Clostridium symbiosum, or Clostridium
sporosphaeroides.
Characterization of Bacteria and Bacterial Consortia
[0282] In certain embodiments, methods are provided for testing
certain characteristics of compositions comprising a microbial
consortium. For example, the sensitivity of bacterial compositions
to certain environmental variables is determined, e.g., in order to
select for particular desirable characteristics in a given
composition, formulation and/or use. For example, the bacterial
constituents of the composition can be tested for pH resistance,
bile acid resistance, and/or antibiotic sensitivity, either
individually on a constituent-by-constituent basis or collectively
as a bacterial composition comprised of multiple bacterial
constituents (collectively referred to in this section as a
microbial consortium).
[0283] pH Sensitivity Testing:
[0284] If a pharmaceutical composition will be administered other
than to the colon or rectum (i.e., for example, an oral route),
optionally testing for pH resistance enhances the selection of
microbes or therapeutic compositions that will survive at the
highest yield possible through the varying pH environments of the
distinct regions of the GI tract or genitourinary tracts.
Understanding how the bacterial compositions react to the pH of the
GI or genitourinary tracts also assists in formulation, so that the
number of microbes in a dosage form can be increased if beneficial
and/or so that the composition can be administered in an
enteric-coated capsule or tablet or with a buffering or protective
composition.
[0285] As the pH of the stomach can drop to a pH of 1 to 2 after a
high-protein meal for a short time before physiological mechanisms
adjust it to a pH of 3 to 4 and often resides at a resting pH of 4
to 5, and as the pH of the small intestine can range from a pH of 6
to 7.4, bacterial compositions can be prepared that survive these
varying pH ranges (specifically wherein at least 1%, 5%, 10%, 15%,
20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or as much as 100% of
the bacteria can survive gut transit times through various pH
ranges). This can be tested by exposing the bacterial composition
to varying pH ranges for the expected gut transit times through
those pH ranges. Therefore, as a non-limiting example only, 18-hour
cultures of compositions comprising one or more bacterial species
or strains can be grown in standard media, such as gut microbiota
medium ("GMM", see Goodman et al., PNAS 108(15):6252-6257 (2011))
or another animal-products-free medium, with the addition of pH
adjusting agents for a pH of 1 to 2 for 30 minutes, a pH of 3 to 4
for 1 hour, a pH of 4 to 5 for 1 to 2 hours, and a pH of 6 to 7.4
for 2.5 to 3 hours. An alternative method for testing stability to
acid is described in e.g., U.S. Pat. No. 4,839,281. Survival of
bacteria can be determined by culturing the bacteria and counting
colonies on appropriate selective or non-selective media.
[0286] Bile Acid Sensitivity Testing:
[0287] Additionally, in some embodiments, testing for bile-acid
resistance enhances the selection of microbes or therapeutic
compositions that will survive exposures to bile acid during
transit through the GI tract. Bile acids are secreted into the
small intestine and can, like pH, affect the survival of bacterial
compositions. This can be tested by exposing the compositions to
bile acids for the expected gut exposure time to bile acids. For
example, bile acid solutions can be prepared at desired
concentrations using 0.05 mM Tris at pH 9 as the solvent. After the
bile acid is dissolved, the pH of the solution can be adjusted to
7.2 with 10% HCl. Bacterial components of the therapeutic
compositions can be cultured in 2.2 ml of a bile acid composition
mimicking the concentration and type of bile acids in the patient,
1.0 ml of 10% sterile-filtered feces media and 0.1 ml of an 18-hour
culture of the given strain of bacteria. Incubations can be
conducted for from 2.5 to 3 hours or longer. An alternative method
for testing stability to bile acid is described in e.g., U.S. Pat.
No. 4,839,281. Survival of bacteria can be determined by culturing
the bacteria and counting colonies on appropriate selective or
non-selective media.
[0288] Antibiotic Sensitivity Testing:
[0289] As a further optional sensitivity test, the bacterial
components of the microbial compositions can be tested for
sensitivity to antibiotics. In one embodiment, the bacterial
components can be chosen so that they are sensitive to antibiotics
such that if necessary they can be eliminated or substantially
reduced from the patient's gastrointestinal tract by at least one
antibiotic targeting the bacterial composition.
[0290] Adherence to Gastrointestinal Cells:
[0291] The compositions can optionally be tested for the ability to
adhere to gastrointestinal cells. A method for testing adherence to
gastrointestinal cells is described in e.g., U.S. Pat. No.
4,839,281.
[0292] Identification of Immunomodulatory Bacteria:
[0293] In some embodiments, immunomodulatory bacteria are
identified by the presence of nucleic acid sequences that modulate
sporulation. In particular, signature sporulation genes are highly
conserved across members of distantly related genera including
Clostridium and Bacillus. Traditional approaches of forward
genetics have identified many, if not all, genes that are essential
for sporulation (spo). The developmental program of sporulation is
governed in part by the successive action of four
compartment-specific sigma factors (appearing in the order
.sigma.F, .sigma.E, .sigma.G and .sigma.K), whose activities are
confined to the forespore (.sigma.F and .sigma.G) or the mother
cell (.sigma.E and .sigma.K). In other embodiments,
immunomodulatory bacteria are identified by the biochemical
activity of DPA producing enzymes or by analyzing DPA content of
cultures. As part of the bacterial sporulation, large amounts of
DPA are produced, and comprise 5-15% of the mass of a spore.
Because not all viable spores germinate and grow under known media
conditions, it is difficult to assess a total spore count in a
population of bacteria. As such, a measurement of DPA content
highly correlates with spore content and is an appropriate measure
for characterizing total spore content in a bacterial
population.
[0294] In other embodiments, immunomodulatory bacteria are
identified by screening bacteria to determine whether the bacteria
induce secretion of pro-inflammatory or anti-inflammatory cytokines
by host cells. For example, human or mammalian cells capable of
cytokine secretion, such as immune cells (e.g., PBMCs, macrophages,
T cells, etc.) can be exposed to candidate immunomodulatory
bacteria, or supernatants obtained from cultures of candidate
immunomodulatory bacteria, and changes in cytokine expression or
secretion can be measured using standard techniques, such as ELISA,
immunoblot, Luminex.TM., antibody array, quantitative PCR,
microarray, etc. Bacteria can be selected for inclusion in a
microbial consortium based on the ability to induce a desired
cytokine profile in human or mammalian cells. For example,
anti-inflammatory bacteria can be selected for inclusion (or
alternatively exclusion) in a microbial consortium or composition
thereof, based on the ability to induce secretion of one or more
anti-inflammatory cytokines, and/or the ability to reduce secretion
of one or more pro-inflammatory cytokines. Anti-inflammatory
cytokines include, for example, IL-10, IL-13, IL-9, IL-4, IL-5, and
combinations thereof. Other inflammatory cytokines include, for
example, TGF.beta.. Pro-inflammatory cytokines include, for
example, IFN.gamma., IL-12p70, IL-1.alpha., IL-6, IL-8, MCP1,
MIP1.alpha., MIP1.beta., TNF.alpha., and combinations thereof. In
some embodiments, anti-inflammatory bacteria can be selected for
inclusion in a microbial consortium based on the ability to
modulate secretion of one or more anti-inflammatory cytokines
and/or the ability to reduce secretion of one or more
pro-inflammatory cytokines by a host cell induced by a bacteria of
a different type (e.g., a bacteria from a different species or from
a different strain of the same species).
[0295] In other embodiments, immunomodulatory bacteria are
identified by screening bacteria to determine whether the bacteria
impact the differentiation and/or expansion of particular
subpopulations of immune cells. For example, candidate bacteria can
be screened for the ability to promote differentiation and/or
expansion of Treg cells, Th17 cells, Th1 cells and/or Th2 cells
from precursor cells, e.g. naive T cells. By way of example, naive
T cells can be cultured in the presence of candidate bacteria or
supernatants obtained from cultures of candidate bacteria, and
numbers of Treg cells, Th17 cells, Th1 cells and/or Th2 cells can
be determined using standard techniques, such as FACS analysis.
Markers indicative of Treg cells include, for example,
CD25.sup.+CD127.sup.lo. Markers indicative of Th17 cells include,
for example, CXCR3.sup.- CCR6.sup.+. Markers indicative of Th1
cells include, for example, CD4.sup.+, CXCR3.sup.+, and CCR6.sup.-.
Markers indicative of Th2 cells include, for example, CD4.sup.+,
CCR4.sup.+, and CXCR3.sup.-, CCR6.sup.-. Other markers indicative
of particular T cells subpopulations are known in the art, and may
be used in the assays described herein, e.g., to identify
populations of immune cells impacted by candidate immunomodulatory
bacteria. Bacteria can be selected for inclusion (or exclusion) in
a microbial consortium based on the ability to promote
differentiation and/or expansion of a desired immune cell
subpopulation.
[0296] In other embodiments, immunomodulatory bacteria are
identified by screening bacteria to determine whether the bacteria
secrete short chain fatty acids (SCFA), such as, for example,
butyrate, acetate, propionate, or valerate, or combinations
thereof. For example, secretion of short chain fatty acids into
bacterial supernatants can be measured using standard techniques.
In one embodiment, bacterial supernatants can be screened to
measure the level of one or more short chain fatty acids using NMR,
mass spectrometry (e.g., GC-MS, tandem mass spectrometry,
matrix-assisted laser desorption/ionization, etc.), ELISA, or
immunoblot. Expression of bacterial genes responsible for
production of short chain fatty acids can also be determined by
standard techniques, such as Northern blot, microarray, or
quantitative PCR.
[0297] Exemplary Minimal Microbial Consortia:
[0298] Minimal microbial consortia are shown herein in the Examples
section and can prevent and/or treat existing symptoms of a food
allergy. These exemplary minimal microbial consortia should not be
construed as limiting and are intended only for the better
understanding of the methods and compositions described herein.
[0299] In one embodiment, a minimal microbial consortium consists
essentially of: Clostridum ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum and C. sardiniensis.
[0300] In one embodiment, a minimal microbial consortium consisting
essentially of: Clostridum ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum and C. sardiniensis is used in the
prevention and/or treatment of existing allergic reactions to
food.
[0301] In one embodiment, a minimal microbial consortium consists
essentially of: Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae.
[0302] In one embodiment, a minimal microbial consortium consisting
essentially of: Bacteroides fragilis, B. thetaiotaomicron, B.
ovatus, Parabacteroides goldsteinii, and Prevotella tannerae is
used to treat existing allergic reactions to food.
[0303] By "consists essentially of" in this context is meant that
if the addition of another microbe does not improve the treatment
or prevention of allergy as described and defined herein, that
microbe is not essential to the protective or therapeutic
effect.
Prebiotics
[0304] A prebiotic is a selectively fermented ingredient that
allows specific changes, both in the composition and/or activity in
the gastrointestinal microbiota, that confers neutral or positive
benefits upon host well-being and health. Prebiotics can include
complex carbohydrates, amino acids, peptides, or other nutritional
components useful for the survival, colonization and persistence of
the bacterial composition. Prebiotics include, but are not limited
to, amino acids, biotin, fructooligosaccharide,
galactooligosaccharides, inulin, lactulose, mannan
oligosaccharides, oligofructose-enriched inulin, oligofructose,
oligodextrose, tagatose, trans-galactooligosaccharide, and
xylooligosaccharides.
[0305] Suitable prebiotics are usually plant-derived complex
carbohydrates, oligosaccharides or polysaccharides. Generally,
prebiotics are indigestible or poorly digested by humans and serve
as a food source for bacteria. Prebiotics, which can be used in the
pharmaceutical dosage forms, and pharmaceutical compositions
provided herein include, without limitation,
galactooligosaccharides (GOS), trans-galactooligosaccharides,
fructooligosaccharides or oligofructose (FOS), inulin,
oligofructose-enriched inulin, lactulose, arabinoxylan,
xylooligosaccharides (XOS), mannooligosaccharides, gum guar, gum
Arabic, tagatose, amylose, amylopectin, xylan, pectin, and the like
and combinations of thereof. Prebiotics can be found in certain
foods, e.g., chicory root, Jerusalem artichoke, Dandelion greens,
garlic, leek, onion, asparagus, wheat bran, wheat flour, banana,
milk, yogurt, sorghum, burdock, broccoli, Brussels sprouts,
cabbage, cauliflower, collard greens, kale, radish and rutabaga,
and miso. Alternatively, prebiotics can be purified or chemically
or enzymatically synthesized.
[0306] In some embodiments, the composition comprises at least one
prebiotic. In one embodiment, the prebiotic is a carbohydrate. In
some embodiments, the composition comprises a prebiotic mixture,
which comprises at least one carbohydrate. A "carbohydrate" refers
to a sugar or polymer of sugars. The terms "saccharide,"
"polysaccharide," "carbohydrate," and "oligosaccharide" can be used
interchangeably. Most carbohydrates are aldehydes or ketones with
many hydroxyl groups, usually one on each carbon atom of the
molecule. Carbohydrates generally have the molecular formula
(CH.sub.2O)n. A carbohydrate can be a monosaccharide, a
disaccharide, trisaccharide, oligosaccharide, or polysaccharide.
The most basic carbohydrate is a monosaccharide, such as glucose,
sucrose, galactose, mannose, ribose, arabinose, xylose, and
fructose. Disaccharides are two joined monosaccharides. Exemplary
disaccharides include sucrose, maltose, cellobiose, and lactose.
Typically, an oligosaccharide includes between three and six
monosaccharide units (e.g., raffinose, stachyose), and
polysaccharides include six or more monosaccharide units. Exemplary
polysaccharides include starch, glycogen, and cellulose.
Carbohydrates can contain modified saccharide units, such as
2'-deoxyribose wherein a hydroxyl group is removed, 2'-fluororibose
wherein a hydroxyl group is replace with a fluorine, or
N-acetylglucosamine, a nitrogen-containing form of glucose (e.g.,
2'-fluororibose, deoxyribose, and hexose). Carbohydrates can exist
in many different forms, for example, conformers, cyclic forms,
acyclic forms, stereoisomers, tautomers, anomers, and isomers.
Carbohydrates can be purified from natural (e.g., plant or
microbial) sources (i.e., they are enzymatically synthesized), or
they can be chemically synthesized or modified.
[0307] Suitable prebiotic carbohydrates can include one or more of
a carbohydrate, carbohydrate monomer, carbohydrate oligomer, or
carbohydrate polymer. In certain embodiments, the pharmaceutical
composition or dosage form comprises at least one type of microbe
and at least one type of non-digestible saccharide, which includes
non-digestible monosaccharides, non-digestible oligosaccharides, or
non-digestible polysaccharides. In one embodiment, the sugar units
of an oligosaccharide or polysaccharide can be linked in a single
straight chain or can be a chain with one or more side branches.
The length of the oligosaccharide or polysaccharide can vary from
source to source. In one embodiment, small amounts of glucose can
also be contained in the chain. In another embodiment, the
prebiotic composition can be partially hydrolyzed or contain
individual sugar moieties that are components of the primary
oligosaccharide (see e.g., U.S. Pat. No. 8,486,668).
[0308] Prebiotic carbohydrates can include, but are not limited to
monosaccharides (e.g., trioses, tetroses, pentoses, aldopentoses,
ketopentoses, hexoses, cyclic hemiacetals, ketohexoses, heptoses)
and multimers thereof, as well as epimers, cyclic isomers,
stereoisomers, and anomers thereof. Non-limiting examples of
monosaccharides include (in either the L- or D-conformation)
glyceraldehyde, threose, ribose, altrose, glucose, mannose, talose,
galactose, gulose, idose, lyxose, arabanose, xylose, allose,
erythrose, erythrulose, tagalose, sorbose, ribulose, psicose,
xylulose, fructose, dihydroxyacetone, and cyclic (alpha or beta)
forms thereof. Multimers (disaccharides, trisaccharides,
oligosaccharides, polysaccharides) thereof include, but are not
limited to, sucrose, lactose, maltose, lactulose, trehalose,
cellobiose, kojibiose, nigerose, isomaltose, sophorose,
laminaribiose, gentioboise, turanose, maltulose, palatinose,
gentiobiulose, mannobiose, melibiulose, rutinose, rutinulose,
xylobiose, primeverose, amylose, amylopectin, starch (including
resistant starch), chitin, cellulose, agar, agarose, xylan,
glycogen, bacterial polysaccharides such as capsular
polysaccharides, LPS, and peptidoglycan, and biofilm
exopolysaccharide (e.g., alginate, EPS), N-linked glycans, and
O-linked glycans. Prebiotic sugars can be modified and carbohydrate
derivatives include amino sugars (e.g., sialic acid,
N-acetylglucosamine, galactosamine), deoxy sugars (e.g., rhamnose,
fucose, deoxyribose), sugar phosphates, glycosylamines, sugar
alcohols, and acidic sugars (e.g., glucuronic acid, ascorbic
acid).
[0309] In one embodiment, the prebiotic carbohydrate component of
the pharmaceutical composition consists essentially of one or more
non-digestible saccharides.
[0310] In one embodiment, the prebiotic carbohydrate component of
the pharmaceutical composition allows the commensal colonic
microbiota, comprising microorganisms associated with a
healthy-state microbiome or presenting a low risk of a patient
developing an autoimmune or inflammatory condition, to be regularly
maintained. In one embodiment, the prebiotic carbohydrate allows
the co-administered or co-formulated microbe or microbes to
engraft, grow, and/or be regularly maintained in a mammalian
subject. In some embodiments, the mammalian subject is a human
subject, for example, a human subject having or suspected of having
a food allergy.
[0311] In some embodiments, the prebiotic favors the growth of an
administered microbe, wherein the growth of the administered
microbe and/or the fermentation of the administered prebiotic by
the administered microbe slows or reduces the growth of a pathogen
or pathobiont. For example, FOS, neosugar, or inulin promotes the
growth of acid-forming bacteria in the colon such as bacteria
belonging to the genus Lactobacillus or Bifidobacterium and
Lactobacillus acidophilus and Bifidobacterium bifidus can play a
role in reducing the number of pathogenic bacteria in the colon
(see e.g., U.S. Pat. No. 8,486,668). Other polymers, such as
various galactans, lactulose, and carbohydrate based gums, such as
psyllium, guar, carrageen, gellan, and konjac, are also known to
improve gastrointestinal (GI) health.
[0312] In some embodiments, the prebiotic comprises one or more of
GOS, lactulose, raffinose, stachyose, lactosucrose, FOS (i.e.,
oligofructose or oligofructan), inulin, isomalto-oligosaccharide,
xylo-oligosaccharide, paratinose oligosaccharide,
transgalactosylated oligosaccharides (i.e.,
transgalacto-oligosaccharides), transgalactosylate disaccharides,
soybean oligosaccharides (i.e., soyoligosaccharides),
gentiooligosaccharides, glucooligosaccharides,
pecticoligosaccharides, palatinose polycondensates, difructose
anhydride III, sorbitol, maltitol, lactitol, polyols, polydextrose,
reduced paratinose, cellulose, .beta.-glucose, .beta.-galactose,
.beta.-fructose, verbascose, galactinol, and .beta.-glucan, guar
gum, pectin, high, sodium alginate, and lambda carrageenan, or
mixtures thereof. The GOS may be a short-chain GOS, a long-chain
GOS, or any combination thereof. The FOS can be a short-chain FOS,
a long-chain FOS, or any combination thereof.
[0313] In some embodiments, the prebiotic composition comprises two
carbohydrate species (non-limiting examples being a GOS and FOS) in
a mixture of at least 1:1, at least 2:1, at least 5:1, at least
9:1, at least 10:1, about 20:1, or at least 20:1.
[0314] In some embodiments, the prebiotic comprises a mixture of
one or more non-digestible oligosaccharides, non-digestible
polysaccharides, free monosaccharides, non-digestible saccharides,
starch, or non-starch polysaccharides.
[0315] Oligosaccharides are generally considered to have a reducing
end and a non-reducing end, whether or not the saccharide at the
reducing end is in fact a reducing sugar. Most oligosaccharides
described herein are described with the name or abbreviation for
the non-reducing saccharide (e.g., Gal or D-Gal), preceded or
followed by the configuration of the glycosidic bond (a or (3), the
ring bond, the ring position of the reducing saccharide involved in
the bond, and then the name or abbreviation of the reducing
saccharide (e.g., Glc or D-Glc). The linkage (e.g., glycosidic
linkage, galactosidic linkage, glucosidic linkage) between two
sugar units can be expressed, for example, as 1,4, 1->4, or
(1-4).
[0316] Both FOS and GOS are non-digestible saccharides. .beta.
glycosidic linkages of saccharides, such as those found in, but not
limited to, FOS and GOS, make these prebiotics mainly
non-digestible and unabsorbable in the stomach and small intestine
.alpha.-linked GOS (.alpha.-GOS) is also not hydrolyzed by human
salivary amylase, but can be used by Bifidobacterium bifidum and
Clostridium butyricum (Yamashita A. et al., 2004. J. Appl.
Glycosci. 51:115-122). FOS and GOS can pass through the small
intestine and into the large intestine (colon) mostly intact,
except where commensal microbes and microbes administered as part
of a pharmaceutical composition are able to metabolize the
oligosaccharides.
[0317] GOS (also known as galacto-oligosaccharides,
galactooligosaccharides, trans-oligosaccharide (TOS),
trans-galacto-oligosaccharide (TGOS), and
trans-galactooligosaccharide) are oligomers or polymers of
galactose molecules ending mainly with a glucose or sometimes
ending with a galactose molecule and have varying degree of
polymerization (generally the DP is between 2-20) and type of
linkages. In one embodiment, GOS comprises galactose and glucose
molecules. In another embodiment, GOS comprises only galactose
molecules. In a further embodiment, GOS are galactose-containing
oligosaccharides of the form of
[.beta.-D-Gal-(1-6)].sub.n-.beta.-D-Gal-(1-4)-D-Glc wherein n is
2-20. In another embodiment, GOS are galactose-containing
oligosaccharides of the form Glc .alpha.1-4-[.beta. Gal 1-6)].sub.n
where n=2-20. In another embodiment, GOS are in the form of
.alpha.-D-Glc (1-4)-[.beta.-D-Gal-(1-6)].sub.n where n=2-20. Gal is
a galactopyranose unit and Glc (or Glu) is a glucopyranose
unit.
[0318] In one embodiment, a prebiotic composition comprises a
GOS-related compound. A GOS-related compound can have the following
properties: a) a "lactose" moiety; e.g., GOS with a gal-glu moiety
and any polymerization value or type of linkage; or b) be
stimulatory to "lactose fermenting" microbes in the human GI tract;
for example, raffinose (gal-fru-glu) is a "related" GOS compound
that is stimulatory to both lactobacilli and bifidobacteria.
[0319] Linkages between the individual sugar units found in GOS and
other oligosaccharides include .beta.-(1-6), .beta.-(1-4),
.beta.-(1-3) and .beta.-(1-2) linkages. In one embodiment, the
administered oligosaccharides (e.g., GOS) are branched saccharides.
In another embodiment, the administered oligosaccharides (e.g.,
GOS) are linear saccharides.
[0320] Alpha-GOS (also called alpha-bond GOS or alpha-linked GOS)
are oligosaccharides having an alpha-galactopyranosyl group.
Alpha-GOS comprises at least one alpha glycosidic linkage between
the saccharide units. Alpha-GOS are generally represented by
.alpha.-(Gal).sub.n (n usually represents an integer of 2 to 10) or
.alpha.-(Gal).sub.n Glc (n usually represents an integer of 1 to
9). Examples include a mixture of .alpha.-galactosylglucose,
.alpha.-galactobiose, .alpha.-galactotriose,
.alpha.-galactotetraose, and higher oligosaccharides. Additional
non-limiting examples include melibiose, manninootriose, raffinose,
stachyose, and the like, which can be produced from beat, soybean
oligosaccharide, and the like.
[0321] Commercially available and enzyme synthesized alpha-GOS
products are also useful for the compositions described herein.
Synthesis of alpha-GOS with an enzyme is conducted utilizing the
dehydration condensation reaction of .alpha.-galactosidase with the
use of galactose, galactose-containing substance, or glucose as a
substrate. The galactose-containing substance includes hydrolysates
of galactose-containing substances, for example, a mixture of
galactose and glucose obtained by allowing beta-galactosidase to
act on lactose, and the like. Glucose can be mixed separately with
galactose and be used as a substrate with .alpha.-galactosidase
(see e.g., WO 02/18614). Methods of preparing alpha-GOS have been
described (see e.g., EP 514551 and EP2027863).
[0322] In one embodiment, a GOS composition comprises a mixture of
saccharides that are alpha-GOS and saccharides that are produced by
transgalactosylation using .beta.-galactosidase. In another
embodiment, GOS comprises alpha-GOS. In another embodiment,
alpha-GOS comprises .alpha.-(Gal).sub.2 from 10% to 100% by weight.
In one embodiment, GOS comprises only saccharides that are produced
by transgalactosylation using .beta.-galactosidase.
[0323] In one embodiment, the pharmaceutical composition comprises,
in addition to one or more microbes, an oligosaccharide composition
that is a mixture of oligosaccharides comprising 1-20% by weight of
di-saccharides, 1-20% by weight tri-saccharides, 1-20% by weight
tetra-saccharides, and 1-20% by weight penta-saccharides. In
another embodiment, an oligosaccharide composition is a mixture of
oligosaccharides consisting essentially of 1-20% by weight of
di-saccharides, 1-20% by weight tri-saccharides, 1-20% by weight
tetra-saccharides, and 1-20% by weight penta-saccharides.
[0324] In one embodiment, a prebiotic composition is a mixture of
oligosaccharides comprising 1-20% by weight of saccharides with a
degree of polymerization (DP) of 1-3, 1-20% by weight of
saccharides with DP of 4-6, 1-20% by weight of saccharides with DP
of 7-9, and 1-20% by weight of saccharides with DP of 10-12, 1-20%
by weight of saccharides with DP of 13-15.
[0325] In another embodiment, a prebiotic composition comprises a
mixture of oligosaccharides comprising 50-55% by weight of
di-saccharides, 20-30% by weight tri-saccharides, 10-20% by weight
tetra-saccharide, and 1-10% by weight penta-saccharides. In one
embodiment, a GOS composition is a mixture of oligosaccharides
comprising 52% by weight of di-saccharides, 26% by weight
tri-saccharides, 14% by weight tetra-saccharide, and 5% by weight
penta-saccharides. In another embodiment, a prebiotic composition
comprises a mixture of oligosaccharides comprising 45-55% by weight
tri-saccharides, 15-25% by weight tetra-saccharides, 1-10% by
weight penta-saccharides.
[0326] In certain embodiments, the composition comprises a mixture
of neutral and acid oligosaccharides as disclosed in e.g., WO
2005/039597 (N.V. Nutricia) and US Patent Application 20150004130.
In one embodiment, the acid oligosaccharide has a degree of
polymerization (DP) between 1 and 5000. In another embodiment, the
DP is between 1 and 1000. In another embodiment, the DP is between
2 and 250. If a mixture of acid oligosaccharides with different
degrees of polymerization is used, the average DP of the acid
oligosaccharide mixture is preferably between 2 and 1000. The acid
oligosaccharide can be a homogeneous or heterogeneous carbohydrate.
The acid oligosaccharides can be prepared from pectin, pectate,
alginate, chondroitine, hyaluronic acids, heparin, heparane,
bacterial carbohydrates, sialoglycans, fucoidan,
fucooligosaccharides or carrageenan, and are preferably prepared
from pectin or alginate. The acid oligosaccharides can be prepared
by the methods described in e.g., WO 01/60378, which is hereby
incorporated by reference. The acid oligosaccharide is preferably
prepared from high methoxylated pectin, which is characterized by a
degree of methoxylation above 50%. As used herein, "degree of
methoxylation" (also referred to as DE or "degree of
esterification") is intended to mean the extent to which free
carboxylic acid groups contained in the polygalacturonic acid chain
have been esterified (e.g. by methylation). In some embodiments,
the acid oligosaccharides have a degree of methoxylation above
about 10%, above about 20%, above about 50%, above about 70%. In
some embodiments, the acid oligosaccharides have a degree of
methylation above about 10%, above about 20%, above about 50%,
above about 70%.
[0327] The term neutral oligosaccharides as used in the present
invention refers to saccharides which have a degree of
polymerization of monose units exceeding 2, exceeding 3, exceeding
4, or exceeding 10, which are not or only partially digested in the
intestine by the action of acids or digestive enzymes present in
the human upper digestive tract (small intestine and stomach) but
which are fermented by the human intestinal flora and preferably
lack acidic groups. The neutral oligosaccharide is structurally
(chemically) different from the acid oligosaccharide. The term
"neutral oligosaccharides", as used herein, refers to saccharides
which have a degree of polymerization of the oligosaccharide below
60 monose units. The term "monose units" refers to units having a
closed ring structure e.g., the pyranose or furanose forms. In some
embodiments, the neutral oligosaccharide comprises at least 90% or
at least 95% monose units selected from the group consisting of
mannose, arabinose, fructose, fucose, rhamnose, galactose,
-D-galactopyranose, ribose, glucose, xylose and derivatives
thereof, calculated on the total number of monose units contained
therein. Suitable neutral oligosaccharides are preferably fermented
by the gut flora. Non-limiting examples of suitable neutral
oligosaccharides are cellobiose
(4-O-.beta.-D-glucopyranosyl-D-glucose), cellodextrins
((4-O-.beta.-D-glucopyranosyl)n-D-glucose), .beta.-cyclo-dextrins
(Cyclic molecules of .alpha.-1-4-linked D-glucose;
.alpha.-cyclodextrin-hexamer, .beta.-cyclodextrin-heptamer and
.gamma.-cyclodextrin-octamer), indigestible dextrin,
gentiooligosaccharides (mixture of .beta.-1-6 linked glucose
residues, some 1-4 linkages), glucooligosaccharides (mixture of
.alpha.-D-glucose), isomaltooligosaccharides (linear .alpha.-1-6
linked glucose residues with some 1-4 linkages), isomaltose
(6-O-.alpha.-D-glucopyranosyl-D-glucose); isomaltriose
(6-O-.alpha.-D-glucopyranosyl-(1-6)-.alpha.-D-glucopyranosyl-D-glucose),
panose
(6-O-.alpha.-D-glucopyranosyl-(1-6)-.alpha.-D-glucopyranosyl-(1-4)-
-D-glucose), leucrose
(5-O-.alpha.-D-glucopyranosyl-D-fructopyranoside), palatinose or
isomaltulose (6-O-.alpha.-D-glucopyranosyl-D-fructose), theanderose
(O-.alpha.-D-glucopyranosyl-(1-6)-O-.alpha.-D-glucopyranosyl-(1-2)-.beta.-
-D-fructofuranoside), D-agatose, D-lyxo-hexylose, lactosucrose
(O-.beta.-D-galactopyranosyl-(1-4)-O-.alpha.-D-glucopyranosyl-(1-2)-.beta-
.-D-fructofuranoside), .alpha.-galactooligosaccharides including
raffinose, stachyose and other soy oligosaccharides
(O-.alpha.-D-galactopyranosyl-(1-6)-.alpha.-D-glucopyranosyl-.beta.-D-fru-
ctofuranoside), .beta.-galactooligosaccharides or
transgalacto-oligosaccharides
(.beta.-D-galactopyranosyl-(1-6)-[.beta.-D-glucopyranosyl]n-(1-4)
.alpha.-D glucose), lactulose
(4-O-.beta.-D-galactopyranosyl-D-fructose), 4'-galatosyllactose
(.beta.-D-galactopyranosyl-(1-4)-O-.beta.-D-glucopyranosyl-(1-4)-D-glucop-
yranose), synthetic galactooligosaccharide (neogalactobiose,
isogalactobiose, galsucrose, isolactose I, II and III),
fructans-Levan-type (.beta.-D-(2.fwdarw.6)-fructofuranosyl)n
.alpha.-D-glucopyranoside), fructans-Inulin-type
(.beta.-D-((2.fwdarw.1)-fructofuranosyl)n
.alpha.-D-glucopyranoside), 1 f-.beta.-fructofuranosylnystose
(.beta.-D-((2.fwdarw.1)-fructofuranosyl)n B-D-fructofuranoside),
xylooligo-saccharides (B-D-((1.fwdarw.4)-xylose)n, lafinose,
lactosucrose and arabinooligosaccharides.
[0328] In some embodiments, the neutral oligosaccharide is selected
from the group consisting of fructans, fructooligosaccharides,
indigestible dextrins galactooligo-saccharides (including
transgalactooligosaccharides), xylooligosaccharides,
arabinooligo-saccharides, glucooligosaccharides,
mannooligosaccharides, fucooligosaccharides and mixtures
thereof.
[0329] Suitable oligosaccharides and their production methods are
further described in Laere K. J. M. (Laere, K. J. M., Degradation
of structurally different non-digestible oligosaccharides by
intestinal bacteria: glycosylhydrolases of Bi, adolescentis.
PhD-thesis (2000), Wageningen Agricultural University, Wageningen,
The Netherlands), the entire content of which is hereby
incorporated by reference. Transgalactooligosaccharides (TOS) are
for example sold under the trademark Vivinal.TM. (Borculo Domo
Ingredients, Netherlands). Indigestible dextrin, which can be
produced by pyrolysis of corn starch, comprises .alpha.(1.fwdarw.4)
and .alpha.(1.fwdarw.6) glucosidic bonds, as are present in the
native starch, and contains 1.fwdarw.2 and 1.fwdarw.3 linkages and
levoglucosan. Due to these structural characteristics, indigestible
dextrin contains well-developed, branched particles that are
partially hydrolyzed by human digestive enzymes. Numerous other
commercial sources of indigestible oligosaccharides are readily
available and known to skilled persons in the art. For example,
transgalactooligosaccharide is available from Yakult Honsha Co.,
Tokyo, Japan. Soybean oligosaccharide is available from Calpis
Corporation distributed by Ajinomoto U.S.A. Inc., Teaneck, N.J.
[0330] In a further embodiment, the prebiotic mixture of the
pharmaceutical composition described herein comprises an acid
oligosaccharide with a DP between 1 and 5000, prepared from pectin,
alginate, and mixtures thereof; and a neutral oligosaccharide,
selected from the group of fructans, fructooligosaccharides,
indigestible dextrins, galactooligosaccharides including
transgalacto-oligosaccharides, xylooligosaccharides,
arabinooligosaccharides, glucooligosaccharides,
mannooligosaccharides, fucooligosaccharides, and mixtures
thereof.
[0331] In certain embodiments, the prebiotic mixture comprises
xylose. In other embodiments, the prebiotic mixture comprises a
xylose polymer (i.e. xylan). In some embodiments, the prebiotic
comprises xylose derivatives, such as xylitol, a sugar alcohol
generated by reduction of xylose by catalytic hydrogenation of
xylose, and also xylose oligomers (e.g., xylooligosaccharide).
While xylose can be digested by humans, via xylosyltransferase
activity, most xylose ingested by humans is excreted in urine. In
contrast, some microorganisms are efficient at xylose metabolism or
can be selected for enhanced xylose metabolism. Microbial xylose
metabolism can occur by at least four pathways, including the
isomerase pathway, the Weimburg pathway, the Dahms pathway, and,
for eukaryotic microorganisms, the oxido-reductase pathway.
[0332] The xylose isomerase pathway involves the direct conversion
of D-xylose into D-xylulose by xylose isomerase, after which
D-xylulose is phosphorylated by xylulose kinase to yield
D-xylolose-5-phosphate, an intermediate of the pentose phosphate
pathway.
[0333] In the Weimberg pathway, D-xylose is oxidized to
D-xylono-lactone by a D-xylose dehydrogenase. Then D-xylose
dehydrogenase is hydrolyzed by a lactonase to yield D-xylonic acid,
and xylonate dehydratase activity then yields
2-keto-3-deoxy-xylonate. The final steps of the Weimberg pathway
are a dehydratase reaction to form 2-keto glutarate semialdehyde
and an oxidizing reaction to form 2-ketoglutarate, an intermediate
of the Krebs cycle.
[0334] The Dahms pathway follows the same mechanism as the Weimberg
pathway but diverges once it has yielded 2-keto-3-deoxy-xylonate.
In the Dahms pathway, an aldolase splits 2-keto-3-deoxy-xylonate
into pyruvate and glycolaldehyde.
[0335] The xylose oxido-reductase pathway, also known as the xylose
reductase-xylitol dehydrogenase pathway, begins by the reduction of
D-xylose to xylitol by xylose reductase followed by the oxidation
of xylitol to D-xylulose by xylitol dehydrogenase. As in the
isomerase pathway, the next step in the oxido-reductase pathway is
the phosphorylation of D-xylulose by xylulose kinase to yield
D-xylolose-5-phosphate.
[0336] Xylose is present in foods like fruits and vegetables and
other plants such as trees for wood and pulp production. Thus,
xylose can be obtained in the extracts of such plants. Xylose can
be obtained from various plant sources using known processes
including acid hydrolysis followed by various types of
chromatography. Examples of such methods to produce xylose include
those described in Maurelli, L. et al. (2013), Appl. Biochem.
Biotechnol. 170:1104-1118; Hooi H. T et al. (2013), Appl. Biochem.
Biotechnol. 170:1602-1613; Zhang H-J. et al. (2014), Bioprocess
Biosyst. Eng. 37:2425-2436.
Culture and Storage of Consortium Constituents
[0337] For banking, the strains included in the bacterial
composition can be (1) isolated directly from a specimen or taken
from a banked stock, (2) optionally cultured on a nutrient agar or
broth that supports growth to generate viable biomass, and (3) the
biomass optionally preserved in multiple aliquots in long-term
storage.
[0338] In embodiments using a culturing step, the agar or broth
contains nutrients that provide essential elements and specific
factors that enable growth. An example would be a medium composed
of 20 g/L glucose, 10 g/L yeast extract, 10 g/L soy peptone, 2 g/L
citric acid, 1.5 g/L sodium phosphate monobasic, 100 mg/L ferric
ammonium citrate, 80 mg/L magnesium sulfate, 10 mg/L hemin
chloride, 2 mg/L calcium chloride, and 1 mg/L menadione. A variety
of microbiological media and variations are well known in the art
(e.g. R. M. Atlas, Handbook of Microbiological Media (2010) CRC
Press). Medium can be added to the culture at the start, can be
added during the culture, or can be intermittently/continuously
flowed through the culture. The strains in the bacterial
composition can be cultivated alone, as a subset of the bacterial
composition, or as an entire collection comprising the bacterial
composition. As an example, a first strain can be cultivated
together with a second strain in a mixed continuous culture, at a
dilution rate lower than the maximum growth rate of either cell to
prevent the culture from washing out of the cultivation.
[0339] The inoculated culture is incubated under favorable
conditions for a time sufficient to build biomass. For bacterial
compositions for human use this is often at normal body temperature
(37.degree. C.), pH, and other parameter with values similar to the
normal human niche. The environment can be actively controlled,
passively controlled (e.g., via buffers), or allowed to drift. For
example, for anaerobic bacterial compositions (e.g., gut
microbiota), an anoxic/reducing environment can be employed. This
can be accomplished by addition of reducing agents/factors such as
cysteine to the broth, and/or stripping it of oxygen. As an
example, a culture of a bacterial composition can be grown at
37.degree. C., pH 7, in the medium above, pre-reduced with 1 g/L
cysteine.HCl.
[0340] When the culture has generated sufficient biomass, it can be
preserved for banking or storage. The organisms can be placed into
a chemical milieu that protects from freezing (adding
`cryoprotectants`), drying (`lyoprotectants`), and/or osmotic shock
(`osmoprotectants`), dispensing into multiple (optionally
identical) containers to create a uniform bank, and then treating
the culture for preservation. Containers are generally impermeable
and have closures that assure isolation from the environment.
Cryopreservation treatment is accomplished by freezing a liquid at
ultra-low temperatures (e.g., at or below -80.degree. C.). Dried
preservation removes water from the culture by evaporation (in the
case of spray drying or `cool drying`) or by sublimation (e.g., for
freeze drying, spray freeze drying). Removal of water improves
long-term bacterial composition storage stability at temperatures
elevated above cryogenic. If the bacterial composition comprises
spore forming species and results in the production of spores, the
final composition can be purified by additional means such as
density gradient centrifugation preserved using the techniques
described above. Bacterial composition banking can be done by
culturing and preserving the strains individually, or by mixing the
strains together to create a combined bank. As an example of
cryopreservation, a bacterial composition culture can be harvested
by centrifugation to pellet the cells from the culture medium, the
supernate decanted and replaced with fresh culture broth containing
15% glycerol. The culture can then be aliquoted into 1 mL
cryotubes, sealed, and placed at -80.degree. C. for long-term
viability retention. This procedure achieves acceptable viability
upon recovery from frozen storage.
[0341] Organism production can be conducted using similar culture
steps to banking, including medium composition and culture
conditions. It can be conducted at larger scales of operation,
especially for clinical development or commercial production. At
larger scales, there can be several subcultivations of the
bacterial composition prior to the final cultivation. At the end of
cultivation, the culture is harvested to enable further formulation
into a dosage form for administration. This can involve
concentration, removal of undesirable medium components, and/or
introduction into a chemical milieu that preserves the bacterial
composition and renders it acceptable for administration via the
chosen route. For example, a bacterial composition can be
cultivated to a concentration of 10.sup.10 CFU/mL, then
concentrated 20-fold by tangential flow microfiltration; the spent
medium may be exchanged by diafiltering with a preservative medium
consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium
phosphate buffer. The suspension can then be freeze-dried to a
powder and titrated.
[0342] After drying, the powder can be blended to an appropriate
potency, and mixed with other cultures and/or a filler such as
microcrystalline cellulose for consistency and ease of handling,
and the bacterial composition formulated as provided herein.
[0343] In one embodiment, a composition comprising a microbial
consortium as described herein, is not a fecal transplant. In some
embodiments all or essentially all of the bacterial entities
present in a purified population are originally obtained from a
fecal material and subsequently, e.g., for production of
pharmaceutical compositions, are grown in culture as described
herein or otherwise known in the art. In one embodiment, the
bacterial cells are cultured from a bacterial stock and purified as
described herein. In one embodiment, each of the populations of
bacterial cells are independently cultured and purified, e.g., each
population is cultured separately and subsequently mixed together.
In one embodiment, one or more of the populations of bacterial
cells in the composition are co-cultured.
Dosage, Administration and Formulations
[0344] In some embodiments, cells over a range of, for example,
2-5.times.10.sup.5, or more, e.g., 1.times.10.sup.6,
1.times.10.sup.7, 1.times.10.sup.8, 5.times.10.sup.8,
1.times.10.sup.9, 5.times.10.sup.9, 1.times.10.sup.10,
5.times.10.sup.10 or more can be administered in a composition
comprising a microbial consortium. The dosage range for the
bacteria depends upon the potency, and include amounts large enough
to produce the desired effect, e.g., reduction in at least one
symptom of a food allergy in a treated subject. The dosage should
not be so large as to cause unacceptable adverse side effects.
Generally, the dosage will vary with the type of illness, and with
the age, condition, and sex of the patient. The dosage can be
determined by one of skill in the art and can also be adjusted by
the individual physician in the event of any complication.
[0345] For use in the various aspects described herein, an
effective amount of cells in a composition as described herein
comprises at least 10.sup.2 bacterial cells, at least
1.times.10.sup.3 bacterial cells, at least 1.times.10.sup.4
bacterial cells, at least 1.times.10.sup.5 bacterial cells, at
least 1.times.10.sup.6 bacterial cells, at least 1.times.10.sup.7
bacterial cells, at least 1.times.10.sup.8 bacterial cells, at
least 1.times.10.sup.9 bacterial cells, at least 1.times.10.sup.10
bacterial cells, at least 1.times.10.sup.11 bacterial cells, at
least 1.times.10.sup.12 bacterial cells or more. Where a microbial
consortium is isolated and/or purified from a subject that is
tolerant to a selected food allergen, the bacterial cells can be
derived from one or more donors, or can be obtained from an
autologous source. In some embodiments of the aspects described
herein, the cells of the microbial consortium are expanded or
maintained in culture prior to administration to a subject in need
thereof. In one embodiment, the microbial consortium is obtained
from a microbe bank. Members of a therapeutic or
preventive/prophylactic consortium are generally administered
together, e.g., in a single admixture. However, it is specifically
contemplated herein that members of a given consortium can be
administered as separate dosage forms or sub-mixtures or
sub-combinations of the consortium members. Thus, for a consortium
of e.g., six members, the consortium can be administered, for
example, as a single preparation including all six members (in one
or more dosage units, e.g., one or more capsules) or as two or more
separate preparations that, in sum, include all members of the
given consortium. While administration as a single admixture is
preferred, a potential advantage of the use of e.g., individual
units for each member of a consortium, is that the actual strains
administered to any given subject can be tailored, if necessary, by
selecting the appropriate combination of, for example, single
species dosage units that together comprise the desired
consortium.
[0346] Biomass of Administered Species, Per Dose, Vs. Known In Vivo
Biomass:
[0347] It is contemplated herein that the consortium composition is
formulated to deliver a larger biomass than the normal biomass of
the commensal organisms in a "healthy" individual. For example, the
range of biomasses contemplated for delivery and colonization can
be found in Table 1, column 2, as compared to the normal biomass in
a healthy individual as shown in Table 1, columns 3 & 4. The
table below shows the range of administered biomasses of organisms
relative to published data at specific locations. Note, in many
cases the bacterial quantitation in Gustafsson, 1982 was to general
categories of organisms, such as Clostridia, and incorporated
multiple species under those headers. Individual species in the
consortia would thus likely be less than the actual highest
reported biomass at the specific locations; the small and large
intestinal biomass data should thus be considered an upper-bound
for what might occur in vivo in normal individuals.
TABLE-US-00002 Small Large Consortia Intestinal Intestinal Species
Biomass Biomass Biomass Reference Bacteroides 1 .times. 10.sup.7-
<10.sup.3 CFU/g in 10.sup.8-10.sup.11 Gustafsson, fragilis 5
.times. 10.sup.8 duodenum- CFU/g 1982. [1] CFU/mL jejunum
10.sup.3-10.sup.8 CFU/g in ileum B. 1 .times. 10.sup.7-
<10.sup.3 CFU/g in 10.sup.8-10.sup.11 Gustafsson,
thetaiotaomicron 5 .times. 10.sup.8 duodenum- CFU/g 1982. CFU/mL
jejunum Bry, 1996. [2] 10.sup.3-10.sup.8 CFU/g in ileum B. ovatus 1
.times. 10.sup.7- <10.sup.3 CFU/g in 10.sup.8-10.sup.11
Gustafsson, 5 .times. 10.sup.8 duodenum- CFU/g 1982. CFU/mL jejunum
10.sup.3-10.sup.8 CFU/g in ileum C. bifermentans 1 .times.
10.sup.7- <10.sup.3 CFU/g in 0-10.sup.6 Gustafsson, 5 .times.
10.sup.8 duodenum- CFU/g 1982. CFU/mL jejunum 10.sup.2-10.sup.4
CFU/g in ileum C. hiranonsis 1 .times. 10.sup.7- <10.sup.3 CFU/g
in 0-10.sup.6 Gustafsson, 5 .times. 10.sup.8 duodenum- CFU/g 1982.
CFU/mL jejunum 10.sup.2-10.sup.4 CFU/g in ileum C. leptum 1 .times.
10.sup.7- <10.sup.3 CFU/g in 0-10.sup.6 Gustafsson, 5 .times.
10.sup.8 duodenum- CFU/g 1982. CFU/mL jejunum 10.sup.2-10.sup.4
CFU/g in ileum Clostridium 1 .times. 10.sup.7- <10.sup.3 CFU/g
in 0-10.sup.6 Gustafsson, ramosum 5 .times. 10.sup.8 duodenum-
CFU/g 1982. CFU/mL jejunum 10.sup.2-10.sup.4 CFU/g in ileum C.
sardiniensis 1 .times. 10.sup.7- <10.sup.3 CFU/g in 0-10.sup.6
Gustafsson, 5 .times. 10.sup.8 duodenum- CFU/g 1982. CFU/mL jejunum
10.sup.2-10.sup.4 CFU/g in ileum C. scindens 1 .times. 10.sup.7-
<10.sup.3 CFU/g in 0-10.sup.6 Gustafsson, 5 .times. 10.sup.8
duodenum- CFU/g 1982. CFU/mL jejunum 10.sup.2-10.sup.4 CFU/g in
ileum Parabacteroides 1 .times. 10.sup.7- <10.sup.3 CFU/g in
0-10.sup.6 Gustafsson, goldsteinii 5 .times. 10.sup.8 duodenum-
CFU/g 1982. CFU/mL jejunum 10.sup.3-10.sup.8 CFU/g in ileum
Prevotella 1 .times. 10.sup.7- <10.sup.3 CFU/g in 0-10.sup.6
Gustafsson, tannerae 5 .times. 10.sup.8 duodenum- CFU/g 1982.
CFU/mL jejunum <10.sup.4 CFU/g in ileum References: 1.
Gustafsson, B E. The physiological importance of the colonic
microflora. Scand J. Gastroenterol Suppl. 1982, 77: 117-31. 2. Bry
L, et al. A model of host-microbial interactions in an open
mammalian ecosystem. Science. 1996, 273(5280): 1380-3.
[0348] A pharmaceutical composition comprising a microbial
consortium can be administered by any method suitable for
depositing in the gastrointestinal tract, preferably the colon, of
a subject (e.g., human, mammal, animal, etc.). Examples of routes
of administration include rectal administration by colonoscopy,
suppository, enema, upper endoscopy, or upper push enteroscopy.
Additionally, intubation through the nose or the mouth by
nasogastric tube, nasoenteric tube, or nasal jejunal tube can be
utilized. Oral administration by a solid such as a pill, tablet, a
suspension, a gel, a geltab, a semisolid, a tablet, a sachet, a
lozenge or a capsule or microcapsule, or as an enteral formulation,
or re-formulated for final delivery as a liquid, a suspension, a
gel, a geltab, a semisolid, a tablet, a sachet, a lozenge or a
capsule, or as an enteral formulation can be utilized as well. Also
contemplated herein are food items that are inoculated with a
microbial consortium as described herein. Compositions can also be
treated or untreated fecal flora, entire (or substantially entire)
microbiota, or partially, substantially or completely isolated or
purified fecal flora, and can be lyophilized, freeze-dried or
frozen, or processed into a powder.
[0349] In some embodiments, the compositions described herein can
be administered in a form containing one or more pharmaceutically
acceptable carriers. Suitable carriers are well known in the art
and vary with the desired form and mode of administration of the
composition. For example, pharmaceutically acceptable carriers can
include diluents or excipients such as fillers, binders, wetting
agents, disintegrators, surface-active agents, glidants,
lubricants, and the like. Typically, the carrier may be a solid
(including powder), liquid, or combinations thereof. Each carrier
is preferably "acceptable" in the sense of being compatible with
the other ingredients in the composition and not injurious to the
subject. The carrier may be biologically acceptable and inert
(e.g., it permits the composition to maintain viability of the
biological material until delivered to the appropriate site).
[0350] Oral compositions can include an inert diluent or an edible
carrier. For the purpose of oral therapeutic administration, the
active compound can be incorporated with excipients and used in the
form of tablets, lozenges, pastilles, troches, or capsules, e.g.,
gelatin capsules. Oral compositions can also be prepared by
combining a composition of the present disclosure with a food. In
one embodiment a food used for administration is chilled, for
instance, iced flavored water. In certain embodiments, the food
item is not a potentially allergenic food item (e.g., not soy,
wheat, peanut, tree nuts, dairy, eggs, shellfish or fish).
Pharmaceutically compatible binding agents, and/or adjuvant
materials can be included as part of the composition. The tablets,
pills, capsules, troches and the like can contain any of the
following ingredients, or compounds of a similar nature: a binder
such as microcrystalline cellulose, gum tragacanth or gelatin; an
excipient such as starch or lactose, a disintegrating agent such as
alginic acid, primogel, or corn starch; a lubricant such as
magnesium stearate or sterotes; a glidant such as colloidal silicon
dioxide; a sweetening agent such as sucrose or saccharin; or a
flavoring agent such as peppermint, methyl salicylate, orange
flavoring, or other suitable flavorings. These are for purposes of
example only and are not intended to be limiting.
[0351] The compositions comprising a microbial consortium can also
be prepared in the form of suppositories (e.g., with conventional
suppository bases such as cocoa butter and other glycerides) or
retention enemas for rectal delivery. The compositions can be
prepared with carriers that will protect the consortium against
rapid elimination from the body, such as a controlled release
formulation, including implants. Biodegradable, biocompatible
polymers can be used, such as ethylene vinyl acetate,
polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and
polylactic acid. Such formulations can be prepared using standard
techniques. The materials can also be obtained commercially from,
for instance, Alza Corporation and Nova Pharmaceuticals, Inc.
Liposomal suspensions can also be used as pharmaceutically
acceptable carriers. These can be prepared according to methods
known to those skilled in the art.
[0352] In some embodiments, a composition can be encapsulated
(e.g., enteric-coated formulations). For instance, when the
composition is to be administered orally, the dosage form is
formulated so the composition is not exposed to conditions
prevalent in the gastrointestinal tract before the small intestine,
e.g., high acidity and digestive enzymes present in the stomach.
The encapsulation of compositions for therapeutic use is routine in
the art. Encapsulation can include hard-shelled capsules, which can
be used for dry, powdered ingredients soft-shelled capsules.
Capsules can be made from aqueous solutions of gelling agents such
as animal protein (e.g., gelatin), plant polysaccharides or
derivatives like carrageenans and modified forms of starch and
cellulose. Other ingredients can be added to a gelling agent
solution such as plasticizers (e.g., glycerin and or sorbitol),
coloring agents, preservatives, disintegrants, lubricants and
surface treatment.
[0353] In one embodiment, a microbial consortium as described
herein is formulated with an enteric coating. An enteric coating
can control the location of where a microbial consortium is
released in the digestive system. Thus, an enteric coating can be
used such that a microbial consortium-containing composition does
not dissolve and release the microbes in the stomach, which can be
a toxic environment for many microbes, but rather travels to the
small intestine, where it dissolves and releases the microbes in an
environment where they can survive. An enteric coating can be
stable at low pH (such as in the stomach) and can dissolve at
higher pH (for example, in the small intestine). Material that can
be used in enteric coatings includes, for example, alginic acid,
cellulose acetate phthalate, plastics, waxes, shellac, and fatty
acids (e.g., stearic acid, palmitic acid). Enteric coatings are
described, for example, in U.S. Pat. Nos. 5,225,202, 5,733,575,
6,139,875, 6,420,473, 6,455,052, and 6,569,457, all of which are
herein incorporated by reference in their entirety. The enteric
coating can be an aqueous enteric coating. Examples of polymers
that can be used in enteric coatings include, for example, shellac
(trade name EmCoat 120 N, Marcoat 125); cellulose acetate phthalate
(trade names AQUACOAT.TM., AQUACOAT ECD.TM., SEPIFILM.TM.,
KLUCEL.TM., and METOLOSE.TM.); polyvinylacetate phthalate (trade
name SURETERIC.TM.); and methacrylic acid (trade name
EUDRAGIT.TM.).
In one embodiment, an enteric coated probiotic composition
comprising members of a microbial consortium as described herein is
administered to a subject. In another embodiment, an enteric coated
probiotic and prebiotic composition is administered to a
subject.
[0354] Formulations suitable for rectal administration include
gels, creams, lotions, aqueous or oily suspensions, dispersible
powders or granules, emulsions, dissolvable solid materials,
douches, and the like. The formulations are preferably provided as
unit-dose suppositories comprising the active ingredient in one or
more solid carriers forming the suppository base, for example,
cocoa butter. Suitable carriers for such formulations include
petroleum jelly, lanolin, polyethyleneglycols, alcohols, and
combinations thereof. Alternatively, colonic washes with the rapid
recolonization deployment agent of the present disclosure can be
formulated for colonic or rectal administration.
[0355] Formulations suitable for oral administration may be
provided as discrete units, such as tablets, capsules, cachets,
syrups, elixirs, prepared food items, microemulsions, solutions,
suspensions, lozenges, or gel-coated ampules, each containing a
predetermined amount of the active compound; as powders or
granules; as solutions or suspensions in aqueous or non-aqueous
liquids; or as oil-in-water or water-in-oil emulsions.
[0356] In some embodiments, the microbial consortium can be
formulated in a food item. Some non-limiting examples of food items
to be used with the methods and compositions described herein
include: popsicles, cheeses, creams, chocolates, milk, meat,
drinks, yogurt, pickled vegetables, kefir, miso, sauerkraut, etc.
In other embodiments, the food items can be juices, refreshing
beverages, tea beverages, drink preparations, jelly beverages, and
functional beverages; alcoholic beverages such as beers;
carbohydrate-containing foods such as rice food products, noodles,
breads, and pastas; paste products such as fish, hams, sausages,
paste products of seafood; retort pouch products such as curries,
food dressed with a thick starchy sauce, and Chinese soups; soups;
dairy products such as milk, dairy beverages, ice creams, cheeses,
and yogurts; fermented products such as fermented soybean pastes,
fermented beverages, and pickles; bean products; various
confectionery products including biscuits, cookies, and the like,
candies, chewing gums, gummies, cold desserts including jellies,
cream caramels, and frozen desserts; instant foods such as instant
soups and instant soy-bean soups; and the like. It is preferred
that food preparations not require cooking after admixture with the
microbial consortium to avoid killing the microbes.
[0357] Formulations of a microbial consortium can be prepared by
any suitable method, typically by uniformly and intimately admixing
the consortium with liquids or finely divided solid carriers or
both, in the required proportions and then, if necessary, shaping
the resulting in mixture into the desired shape. In addition, the
microbial consortium can be treated to prolong shelf-life,
preferably the shelf-life of the pre-determined gut flora will be
extended via freeze drying.
[0358] In some embodiments, the microbial consortium as described
herein is combined with one or more additional probiotic organisms
prior to treatment of a subject. As used herein, the term
"probiotic" refers to microorganisms that form at least a part of
the transient or endogenous flora or microbial consortium and
thereby exhibit a beneficial prophylactic and/or therapeutic effect
on the host organism. Probiotics are generally known to be
clinically safe (i.e., non-pathogenic) by those individuals skilled
in the art. Typical lactic acid-producing bacteria useful as a
probiotic of this invention are efficient lactic acid producers
which include non-pathogenic members of the Bacillus genus which
produce bacteriocins or other compounds which inhibit the growth of
pathogenic organisms.
[0359] Exemplary lactic acid-producing, non-pathogenic Bacillus
species include, but are not limited to: Bacillus coagulans;
Bacillus coagulans Hammer; and Bacillus brevis subspecies
coagulans.
[0360] Exemplary lactic acid-producing Lactobacillus species
include, but are not limited to: Lactobacillus acidophilus,
Lactobacillus casei, Lactobacillus DDS-1, Lactobacillus GG,
Lactobacillus rhamnosus, Lactobacillus plantarum, Lactobacillus
reuteri, Lactobacillus gasserii, Lactobacillus jensenii,
Lactobacillus delbruekii, Lactobacillus, bulgaricus, Lactobacillus
salivarius and Lactobacillus sporogenes (also designated as
Bacillus coagulans). Exemplary lactic acid-producing
Sporolactobacillus species include all Sporolactobacillus species,
for example, Sporolactobacillus P44.
[0361] Exemplary lactic acid-producing Bifidiobacterium species
include, but are not limited to: Bifidiobacterium adolescentis,
Bifidiobacterium animalis, Bifidiobacterium bifidum,
Bifidiobacterium bifidus, Bifidiobacterium breve, Bifidiobacterium
infantis, Bifidiobacterium infantus, Bifidiobacterium longum, and
any genetic variants thereof.
[0362] Examples of suitable non-lactic acid-producing Bacillus
include, but are not limited to: Bacillus subtilis, Bacillus
uniflagellatus, Bacillus lateropsorus, Bacillus laterosporus BOD,
Bacillus megaterium, Bacillus polymyxa, Bacillus licheniformis,
Bacillus pumilus, and Bacillus sterothermophilus. Other strains
that could be employed due to probiotic activity include members of
the Streptococcus (Enterococcus) genus. For example, Enterococcus
faecium, is commonly used as a livestock probiotic and, thus, could
be utilized as a co-administration agent. Furthermore, it is also
intended that any of the acid-producing species of probiotic or
nutritional bacteria known in the art can be used in the
compositions comprising a microbial consortium as described
herein.
[0363] A nutrient supplement comprising the microbial consortium as
described herein can include any of a variety of nutritional
agents, including vitamins, minerals, essential and nonessential
amino acids, carbohydrates, lipids, foodstuffs, dietary
supplements, short chain fatty acids and the like. Preferred
compositions comprise vitamins and/or minerals in any combination.
Vitamins for use in a composition as described herein can include
vitamins B, C, D, E, folic acid, K, niacin, and like vitamins. The
composition can contain any or a variety of vitamins as may be
deemed useful for a particularly application, and therefore, the
vitamin content is not to be construed as limiting. Typical
vitamins are those, for example, recommended for daily consumption
and in the recommended daily amount (RDA), although precise amounts
can vary. The composition can preferably include a complex of the
RDA vitamins, minerals and trace minerals as well as those
nutrients that have no established RDA, but have a beneficial role
in healthy human or mammal physiology. The preferred mineral format
would include those that are in either the gluconate or citrate
form because these forms are more readily metabolized by lactic
acid bacteria. In a related embodiment, the compositions described
herein are contemplated to comprise a microbial consortium in
combination with a viable lactic acid bacteria in combination with
any material to be adsorbed, including but not limited to nutrient
supplements, foodstuffs, vitamins, minerals, medicines, therapeutic
compositions, antibiotics, hormones, steroids, and the like
compounds where it is desirable to insure efficient and healthy
absorption of materials from the gastrointestinal tract into the
blood. The amount of material included in the composition can vary
widely depending upon the material and the intended purpose for its
absorption, such that the composition is not to be considered as
limiting.
[0364] In some embodiments, the compositions described herein can
further include a prebiotic and/or a fiber. Many forms of "fiber"
exhibit some level of prebiotic effect. Thus, there is considerable
overlap between substances that can be classified as "prebiotics"
and those that can be classified as "fibers". Non-limiting examples
of prebiotics suitable for use in the compositions and methods
include psyllium, fructo-oligosaccharides, inulin, oligofructose,
galacto-oligosaccharides, isomalto-oligosaccharides
xylo-oligosaccharides, soy-oligosaccharides,
gluco-oligosaccharides, mannan-oligosaccharides, arabinogalactan,
arabinxylan, lacto sucrose, gluconannan, lactulose, polydextrose,
oligodextran, gentioligosaccharide, pectic oligosaccharide, xanthan
gum, gum arabic, hemicellulose, resistant starch and its
derivatives, and mixtures and/or combinations thereof. The
compositions can comprise from about 100 mg to about 100 g,
alternatively from about 500 mg to about 50 g, and alternatively
from about 1 g to about 40 g, of prebiotic, per day or on a less
than daily schedule.
[0365] Aspects of the technology described herein also include
short chain fatty acids (SCFAs) and medium chain triglycerides
(MCTs). Short chain fatty acids can have immunomodulatory (i.e.,
immunosuppressive) effects and therefore their production (i.e.,
biosynthesis or conversion by fermentation) is advantageous for the
prevention, control, mitigation, and treatment of autoimmune and/or
inflammatory disorders (Lara-Villoslada F. et al., 2006. Eur J
Nutr. 45(7): 418-425). In germ-free mice and vancomycin-treated
conventional mice, administration of SCFA (acetate, propionate, or
butyrate) restored normal numbers of Tregs in the large intestine
(Smith P M, et al. Science. 2013; 569-573). Short-chain fatty acids
(SCFA) are produced by some bacteria as a byproduct of xylose
fermentation. SCFA are one of the most abundant metabolites
produced by the gut microbiome, particularly the family
Clostridiaceae, including members of the genus Clostridium,
Ruminococcus, or Blautia. In some aspects, the pharmaceutical
composition, dosage form, or kit comprises at least one type of
microbe (e.g., one or more microbial species, such as a bacterial
species, or more than one strain of a particular microbial species)
and at least one type of prebiotic such that the composition,
dosage form, or kit is capable of increasing the level of one or
more immunomodulatory SCFA (e.g., acetate, propionate, butyrate, or
valerate) in a mammalian subject. Optionally, the pharmaceutical
composition, dosage form, or kit further comprises one or more
substrates of one or more SCFA-producing fermentation and/or
biosynthesis pathways. In certain embodiments, the administration
of the composition, dosage form, or kit to a mammalian subject
results in the increase of one or more SCFAs in the mammalian
subject by approximately 1.5-fold, 2-fold, 5-fold, 10-fold,
20-fold, 50-fold, 100-fold, or greater than 100-fold. In some
embodiments, the dysbiosis is caused by a deficiency in microbes
that produce short chain fatty acids. Accordingly, in some
embodiments, the probiotic composition can contain a species of
bacteria that produce short chain fatty acids.
[0366] MCTs passively diffuse from the GI tract to the portal
system (longer fatty acids are absorbed into the lymphatic system)
without requirement for modification like long-chain fatty acids or
very-long-chain fatty acids. In addition, MCTs do not require bile
salts for digestion. Patients who have malnutrition or
malabsorption syndromes are treated with MCTs because they do not
require energy for absorption, use, or storage. Medium-chain
triglycerides are generally considered a good biologically inert
source of energy that the human body finds reasonably easy to
metabolize. They have potentially beneficial attributes in protein
metabolism, but may be contraindicated in some situations due to
their tendency to induce ketogenesis and metabolic acidosis. Due to
their ability to be absorbed rapidly by the body, medium-chain
triglycerides have found use in the treatment of a variety of
malabsorption ailments. MCT supplementation with a low-fat diet has
been described as the cornerstone of treatment for primary
intestinal lymphangiectasia (Waldmann's disease). MCTs are an
ingredient in parenteral nutritional emulsions.
[0367] Also contemplated herein are kits comprising, at a minimum,
a microbial consortium prep or formulations comprising all of the
members of the consortium in an admixture or comprising all of the
members of the consortium in sub-combinations or sub-mixtures. In
some embodiments, the kit further comprises empty capsules to be
filled by the practitioner and/or one or more reagents for enteric
coating such capsules. It is also contemplated herein that the
microbe preparation is provided in a dried, lyophilized or powdered
form. In one embodiment, the kits comprise at least 4 strains
selected from the group consisting of: Clostridium ramosum,
Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides
ovatus, Parabacteroides goldsteinii, Prevotella tannerae,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum fimetarium, Clostridium symbiosum,
Clostridium sporosphaeroides, Dialister proprionicfaceins,
Dialister succinatiphilus, Parabacteroides distasonis,
Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti. In another embodiment, the kits comprise at least
four strains selected from the group consisting of: Clostridium
ramosum, C. scindens, C. hiranonsis, C. bifermentans, C. leptum, C.
sardiniensis, Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae. In another
embodiment, the kits comprise at least four strains selected from
the group consisting of: Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum, and C. sardiniensis. In
another embodiment, the kits comprise at least four strains
selected from the group consisting of: Bacteroides fragilis, B.
thetaiotaomicron, B. ovatus, Parabacteroides goldsteinii, and
Prevotella tannerae. In one embodiment, the kits comprise
Bacteroides thetaiotaomicron or Bacteroides fragilis and at least
one of a strain selected from the group consisting of: Clostridium
ramosum, Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Bacteroides ovatus, Parabacteroides goldsteinii, Prevotella
tannerae, Clostridum hathewayi, Clostridum nexile, Clostridium
hylemonae, Clostridium glycyrrhizinilyticum, Clostridium scindens,
Clostridium lavalense, Clostridum fimetarium, Clostridium
symbiosum, Clostridium sporosphaeroides, Dialister
proprionicfaceins, Dialister succinatiphilus, Parabacteroides
distasonis, Parabacteroides goldsteinii, Parabacteroides merdae,
Peptostreptococcus anaerobius, Subdoligranulum variabile, and
Veilonella ratti. In one embodiment, the kits comprise Bacteroides
thetaiotaomicron or Bacteroides fragilis and at least one of a
strain selected from the group consisting of: Clostridium ramosum,
Clostridium scindens, Clostridium hiranonsis, Clostridium
bifermentans, Clostridium leptum, Clostridium sardiniensis,
Clostridum hathewayi, Clostridum nexile, Clostridium hylemonae,
Clostridium glycyrrhizinilyticum, Clostridium scindens, Clostridium
lavalense, Clostridum fimetarium, Clostridium symbiosum, and
Clostridium sporosphaeroides. In another embodiment, the kit
comprises at least one reducing agent such as N-acetylcysteine,
cysteine, or methylene blue for growing, maintaining and/or
encapsulating the microbes under anaerobic conditions. The kits
described herein are also contemplated to include cell growth media
and supplements necessary for expanding the microbial preparation.
The kits described herein are also contemplated to include one or
more prebiotics as described herein.
[0368] Prior to administration of the bacterial composition, the
patient may optionally have a pretreatment protocol to prepare the
gastrointestinal tract to receive the bacterial composition. In
certain embodiments, the pretreatment protocol is advisable, such
as when a patient has an acute infection with a highly resilient
pathogen. In other embodiments, the pretreatment protocol is
entirely optional, such as when the pathogen causing the infection
is not resilient, or the patient has had an acute infection that
has been successfully treated but where the physician is concerned
that the infection may recur. In these instances, the pretreatment
protocol can enhance the ability of the bacterial composition to
affect the patient's microbiome. In an alternative embodiment, the
subject is not pre-treated with an antibiotic.
[0369] As one way of preparing the patient for administration of
the microbial ecosystem, at least one antibiotic can be
administered to alter the bacteria in the patient. As another way
of preparing the patient for administration of the microbial
ecosystem, a standard colon-cleansing preparation can be
administered to the patient to substantially empty the contents of
the colon, such as used to prepare a patient for a colonoscopy. By
"substantially emptying the contents of the colon," this
application means removing at least 75%, at least 80%, at least
90%, at least 95%, or about 100% of the contents of the ordinary
volume of colon contents. Antibiotic treatment can precede the
colon-cleansing protocol.
[0370] If a patient has received an antibiotic for treatment of an
infection, or if a patient has received an antibiotic as part of a
specific pretreatment protocol, in one embodiment the antibiotic
should be stopped in sufficient time to allow the antibiotic to be
substantially reduced in concentration in the gut before the
bacterial composition is administered. In one embodiment, the
antibiotic may be discontinued 1, 2, or 3 days before the
administration of the bacterial composition. In one embodiment, the
antibiotic can be discontinued 3, 4, 5, 6, or 7 antibiotic
half-lives before administration of the bacterial composition. If
the pretreatment protocol is part of treatment of an acute
infection, the antibiotic may be chosen so that the infection is
sensitive to the antibiotic, but the constituents in the bacterial
composition are not sensitive to the antibiotic.
[0371] Any of the preparations described herein can be administered
once on a single occasion or on multiple occasions, such as once a
day for several days or more than once a day on the day of
administration (including twice daily, three times daily, or up to
five times daily). Or the preparation can be administered
intermittently according to a set schedule, e.g., once weekly, once
monthly, or when the patient relapses from the primary illness. In
another embodiment, the preparation can be administered on a
long-term basis to assure the maintenance of a protective or
therapeutic effect.
[0372] In one embodiment, a first microbial consortium comprising
at least one bacterial species known to enhance colonization of
beneficial organisms (e.g., Bacteroides thetaiotaomicron) is
administered to a subject prior to administration of a second
microbial consortium.
[0373] Another aspect described herein relates to a method for
enhancing the colonization and/or persistence of a microbial
consortium, the method comprising administering a first microbial
consortium comprising at least 4 bacterial strains selected from
the group consisting of: Bacteroides fragilis, B. thetaiotaomicron,
B. ovatus, Parabacteroides goldsteinii, and Prevotella tannerae, to
a subject prior to administering a second microbial consortium
comprising at least 4 bacterial strains selected from the group
consisting of: Clostridium ramosum, C. scindens, C. hiranonsis, C.
bifermentans, C. leptum and C. sardiniensis, wherein the first
microbial consortium enhances the colonization and/or persistence
of the second microbial consortium.
[0374] It is also contemplated herein that a first microbial
consortium comprising at least 4 bacterial strains selected from
the group consisting of: Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum and C. sardiniensis, is
administered to a subject prior to administering a second microbial
consortium comprising at least 4 bacterial strains selected from
the group consisting of: Bacteroides fragilis, B. thetaiotaomicron,
B. ovatus, Parabacteroides goldsteinii, and Prevotella
tannerae.
[0375] It is also contemplated herein that a first microbial
consortium comprising at least 4 bacterial strains selected from
the group consisting of: Clostridium ramosum, C. scindens, C.
hiranonsis, C. bifermentans, C. leptum and C. sardiniensis, is
administered to a subject in combination with (e.g.,
simultaneously) a second microbial consortium comprising at least 4
bacterial strains selected from the group consisting of:
Bacteroides fragilis, B. thetaiotaomicron, B. ovatus,
Parabacteroides goldsteinii, and Prevotella tannerae.
Efficacy
[0376] Typically, a food allergy response can manifest with one of
more of the following symptoms or indicators: (i) a marked drop in
core body temperature, (ii) an increase in total IgE, (iii) an
increase in allergen-specific IgE, (iv) mast cell expansion, (v)
release of mast cell granule protease 1 (MMCP-1) and (vi) increase
in Th2 cell skewing. Thus, efficacious treatment and/or prevention
of food allergy using the methods and compositions described herein
can reduce or eliminate at least one of the symptoms or indicators
associated with food allergy, as described above. "Reduced"
symptoms or indicators mean at least 20% reduced, at least 30%
reduced, at least 40% reduced, at least 50% reduced, at least 60%
reduced, at least 70% reduced, at least 80% reduced, at least 90%
reduced, at least 95% reduced, at least 98% reduced or even at
least 99% or further reduction. Methods for the measurement of each
of these parameters are known to those of ordinary skill in the
art.
[0377] The methods and compositions described herein provide
treatment or prevention of food allergy involving or provoking
anaphylaxis--i.e., IgE-mediated histamine release or direct
allergen-mediated degranulation of mast cells and basophils and
resulting pathology. Non-limiting examples include allergy or
anaphylactic reaction to peanut, tree nuts, and shellfish, among
others noted elsewhere herein. Food sensitivity, e.g., lactose
intolerance or gluten intolerance involves different mechanisms.
While it is contemplated that a microbial consortium as described
herein can benefit those with food sensitivities (e.g., by reducing
or eliminating a dysbiotic state and thereby reducing gut
inflammation), the distinction between food sensitivities and food
allergies should be specifically noted. First and foremost,
sensitivities do not provoke an anaphylactic response.
[0378] Effective prevention of food allergy can be assessed using
an accepted animal model, such as that described herein or others
known to those of ordinary skill in the art, wherein a regimen that
sensitizes the animals to a given food allergen in the absence of
microbial consortium treatment fails to provoke a substantial
allergic response in animals administered a protective microbial
consortium as described herein. As used herein, the term "fails to
provoke a substantial allergic response" means that there is less
than 20% of the allergic response (as measured by one or more of
the criteria (i)-(vi) described above) seen in animals sensitized
to the allergen but without administration of a protective or
therapeutic microbial consortium as described herein. In human
clinical practice, prevention or cure can be evaluated by
administration of the given microbial consortium followed by
administration of an allergen under controlled circumstances in a
doctor's office or hospital setting. For prevention, the microbial
consortium can be administered prior to a patient's initial
exposure to or consumption of a given food allergen. For therapy
for established food allergy, the microbial consortium can be
administered as described herein, followed by consumption of the
food allergen in a controlled clinical setting. A lack of allergic
reaction, or even a reduced allergic reaction relative to the
patient's previous allergic responses to the allergen (i.e., at
least 20% reduced, at least 30% reduced, at least 40% reduced, at
least 50% reduced, at least 60% reduced, at least 70% reduced, at
least 80% reduced, at least 90% reduced, at least 95% reduced, at
least 98% reduced or even at least 99% or further reduction) is
evidence of effective treatment.
[0379] Repeated administration of the microbial consortium may be
beneficial to maintain a protective or curative effect.
[0380] In addition, efficacy of a particular formulation can be
determined in vitro or in an in vivo or in situ mouse model as
described in herein or as known in the art (e.g., Noval Rivas et
al. J Allergy Clin Immunol (2013) 131(1):201-212 or Noval Rivas et
al., Immunity (2015) 42:512-523, the contents of which are each
incorporated herein in their entirety).
[0381] The singular terms "a," "an," and "the" include plural
referents unless context clearly indicates otherwise. Similarly,
the word "or" is intended to include "and" unless the context
clearly indicates otherwise. Although methods and materials similar
or equivalent to those described herein can be used in the practice
or testing of this disclosure, suitable methods and materials are
described below. The abbreviation, "e.g." is derived from the Latin
exempli gratia, and is used herein to indicate a non-limiting
example. Thus, the abbreviation "e.g." is synonymous with the term
"for example."
[0382] Definitions of common terms in cell biology and molecular
biology can be found in "The Merck Manual of Diagnosis and
Therapy", 19th Edition, published by Merck Research Laboratories,
2006 (ISBN 0-911910-19-0); Robert S. Porter et al. (eds.), The
Encyclopedia of Molecular Biology, published by Blackwell Science
Ltd., 1994 (ISBN 0-632-02182-9); Benjamin Lewin, Genes X, published
by Jones & Bartlett Publishing, 2009 (ISBN-10: 0763766321);
Kendrew et al. (eds.), Molecular Biology and Biotechnology: a
Comprehensive Desk Reference, published by VCH Publishers, Inc.,
1995 (ISBN 1-56081-569-8) and Current Protocols in Protein Sciences
2009, Wiley Intersciences, Coligan et al., eds.
[0383] Unless otherwise stated, the present invention was performed
using standard procedures, as described, for example in Sambrook et
al., Molecular Cloning: A Laboratory Manual (4 ed.), Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012);
Davis et al., Basic Methods in Molecular Biology, Elsevier Science
Publishing, Inc., New York, USA (1995); or Methods in Enzymology:
Guide to Molecular Cloning Techniques Vol. 152, S. L. Berger and A.
R. Kimmel Eds., Academic Press Inc., San Diego, USA (1987); Current
Protocols in Protein Science (CPPS) (John E. Coligan, et. al., ed.,
John Wiley and Sons, Inc.), Current Protocols in Cell Biology
(CPCB) (Juan S. Bonifacino et. al. ed., John Wiley and Sons, Inc.),
and Culture of Animal Cells: A Manual of Basic Technique by R. Ian
Freshney, Publisher: Wiley-Liss; 5th edition (2005), Animal Cell
Culture Methods (Methods in Cell Biology, Vol. 57, Jennie P. Mather
and David Barnes editors, Academic Press, 1st edition, 1998) which
are all incorporated by reference herein in their entireties.
[0384] Other terms are defined herein within the description of the
various aspects of the invention.
[0385] All patents and other publications; including literature
references, issued patents, published patent applications, and
co-pending patent applications; cited throughout this application
are expressly incorporated herein by reference for the purpose of
describing and disclosing, for example, the methodologies described
in such publications that might be used in connection with the
technology described herein. These publications are provided solely
for their disclosure prior to the filing date of the present
application. Nothing in this regard should be construed as an
admission that the inventors are not entitled to antedate such
disclosure by virtue of prior invention or for any other reason.
All statements as to the date or representation as to the contents
of these documents is based on the information available to the
applicants and does not constitute any admission as to the
correctness of the dates or contents of these documents.
[0386] The description of embodiments of the disclosure is not
intended to be exhaustive or to limit the disclosure to the precise
form disclosed. While specific embodiments of, and examples for,
the disclosure are described herein for illustrative purposes,
various equivalent modifications are possible within the scope of
the disclosure, as those skilled in the relevant art will
recognize. For example, while method steps or functions are
presented in a given order, alternative embodiments may perform
functions in a different order, or functions may be performed
substantially concurrently. The teachings of the disclosure
provided herein can be applied to other procedures or methods as
appropriate. The various embodiments described herein can be
combined to provide further embodiments. Aspects of the disclosure
can be modified, if necessary, to employ the compositions,
functions and concepts of the above references and application to
provide yet further embodiments of the disclosure. Moreover, due to
biological functional equivalency considerations, some changes can
be made in protein structure without affecting the biological or
chemical action in kind or amount. These and other changes can be
made to the disclosure in light of the detailed description. All
such modifications are intended to be included within the scope of
the appended claims.
[0387] Specific elements of any of the foregoing embodiments can be
combined or substituted for elements in other embodiments.
Furthermore, while advantages associated with certain embodiments
of the disclosure have been described in the context of these
embodiments, other embodiments may also exhibit such advantages,
and not all embodiments need necessarily exhibit such advantages to
fall within the scope of the disclosure.
[0388] The technology described herein is further illustrated by
the following examples which in no way should be construed as being
further limiting.
EXAMPLES
[0389] The data provided herein, e.g., in the figures and
elsewhere, show that a microbial consortium of several species
(i.e., 2, 3, 4, 5, or 6 species, for example) can protect against
developing food allergy in a mouse model. Treatment with such a
consortium of bacteria can reverse TH2 programming of Tregs.
Treatment and/or prevention of food allergy using a similar
microbial consortium of microbes in humans is specifically
indicated.
[0390] Further methods for testing or measuring the efficacy of a
microbial consortium in a mouse model of food allergy are known in
the art and/or can be found in e.g., Noval Rivas et al. J Allergy
Clin Immunol (2013) 131(1):201-212 or Noval Rivas et al., Immunity
(2015) 42:512-523, the contents of which are each incorporated
herein in their entirety.
Example 1: Therapeutic Microbiota to Treat Food Allergy
Summary
[0391] Food allergy is a growing national problem, affecting 6% of
children, and 3% of US teens and adults. Unfortunately for these
children and their families, the standard of care remains to avoid
offending foods and manage symptoms as they occur. Therapies using
oral desensitization, alone or with anti-IgE (Omalizumab.TM.),
remain experimental with limited success. Needed are therapies that
target the aberrant immune responses. As such, this study shows the
use of gut microbiota as a therapeutic intervention to promote
tolerizing responses that can prevent or mitigate effects of
Th2/allergic responses.
[0392] Food allergies occur with development of Th2-allergic
responses to foodstuffs, in contrast to tolerizing T-regulatory
responses that mitigate such responses mucosally. The Th2 responses
promote food antigen-specific IgE antibody and recruitment of
mucosal mast cells, in contrast to regulatory responses, which
inhibit these effects. Once sensitized to one or more food
antigens, re-exposure can induce life-threatening anaphylactic
responses. Capacity to promote tolerizing responses supports a
broad-based therapeutic approach that can act at the earliest
stages of exposure as well as in the already-sensitized patient to
prevent aberrant allergic responses across a spectrum of
foodstuffs.
[0393] Leveraging the genetically susceptible IL4RA F709 mouse
model [1,2] of food allergy defined human commensal communities
that can both prevent and cure food allergies in preclinical models
have been developed. These communities leverage a new therapeutic
pathway for patients--immunomodulation from the luminal side of the
gut, the space in which the gut microbiota resides. Human gut
microbiota consists of many hundreds of species that provide
critical functions in normal human development and health, from
maturing of the immune system, providing essential nutrients such
as B vitamins and vitamin K, and assisting in digestion and
metabolism of dietary and exogenous compounds, including drugs and
ingested foodstuffs.
Background
[0394] The therapeutic consortia consist of defined and culturable
human commensal strains that stimulate protective regulatory T cell
responses in the gut. Two protective communities have been
developed, Gut-Protect I (GP-I) and Gut-Protect II (GP-II). All
have complete or contig-level genomic sequences, and select members
from each group can be genetically manipulated. In addition, a
third community has been developed that demonstrates worsened
effects (Negative Control Consortium, Neg-CC), which is providing
further information on dysbiotic effects in vivo and potential
biomarkers to assist in diagnosis and selection of therapy.
[0395] (1) Gut-protect I: Community of culturable gut commensals
that has demonstrated treat-to-protect and treat-to-cure efficacy
in food antigen sensitization of IL4RA F709 mice.
[0396] (2) Gut-protect II: Community of culturable gut commensals
that has demonstrated robust treat-to-prevent efficacy in animal
models and less robust treat-to-cure efficacy than Gut-protect I.
However, in standard solutions administered to the host, this
community tolerates greater ambient air exposure than the
Gut-protect I community.
[0397] (3) Negative Control Community: Community of culturable gut
commensals that promote food antigen sensitization in
treat-to-prevent and treat-to-cure regimens. This community is
defining the nature of dysbiosis in food allergy and supporting
development of biomarkers that could predict microbiota-derived
factors that enhance susceptibility to development of food
allergies.
[0398] In pre-clinical models of food allergy to egg, leveraging a
susceptible mouse model that does not require the use of adjuvants,
GP-I and GP-II each demonstrated treat-to-prevent efficacy, when
used in a period of sensitization to the allergy-inducing
foodstuff. GP-I was also effective in treat-to-cure regimens when
used in animals that had already been sensitized to egg protein, to
the point that re-exposure would induce life-threatening
anaphylactic responses. In contrast, the negative control community
worsened effects, and provides further insights as to the
underlying dysbiosis that may contribute to development of food
allergies, while also providing potential biomarkers to identify
individuals at risk, or for whom microbial therapy may be
efficacious.
Consortia Development
[0399] For pre-clinical studies in mice the component members are
grown individually in nutrient-rich media under appropriate
anaerobic conditions, quantitated for biomass, and then the
consortium is mixed under anaerobic conditions with approximately
equal biomass of each component organism to a final concentration
.about.5.0.times.10.sup.8 colony forming units (CFU)/mL. Input
culture volumes for each species have been in the range of 100 mL-1
L. As needed, cultures with a stationary phase biomass
<5.times.10.sup.8 CFU/mL are concentrated by centrifugation with
re-suspension handled under anaerobic conditions.
[0400] When mixed, the total biomass remains approximately
5.times.10.sup.8 CFU/mL. 2 mL aliquots are placed in cryovials with
an anaerobic/pre-reduced atmosphere, snap frozen on liquid nitrogen
and stored at -80.degree. C. until use. Rapid freezing has shown to
have <1/2 log effects on the biomass of the component organisms
and no effect on efficacy in animal models. For studies, tubes are
thawed and mice administered 200 uL of this solution weekly to
twice weekly by oral gavage, resulting in a total introduced
biomass of 1.times.10.sup.8 CFU/mouse. The measurements of gut
contents in adult mice (stomach through anus) range from 4-8 mL of
material. The gavaged consortium is thus 2.5-5% of the total volume
of contents in the mouse gut and >10% of the volume of contents
in the small bowel.
[0401] In terms of pre-existing microbial biomass from the
conventional microbiota--the mouse small intestine on average has
.about.10.sup.4 CFU/mL in proximal duodenum with increase to
10.sup.8 CFU/mL in the ileum. Biomass increases to
10.sup.9-10.sup.10 CFU/mL in the cecum and colon. From the
standpoint of microbial biomass at locations in the mouse small
bowel, the primary site of action of the consortia to promote
regulatory T cell responses, the consortium is 10,000.times. the
biomass of the duodenal microbiota, and 1-2.times. the biomass of
the jejunal and ileal microbiota.
[0402] In comparison, the adult human gut may contain 4.5 L of
material, of which 1 L relates to ingested foodstuffs with 3.5 L of
secretions including saliva, bile, and other fluids from the
pancreas and intestines [3]. These fluids and electrolytes are
largely resorbed in the right colon, subsequent to fecal compaction
and passage. Within the intestines, the biomass of organisms also
varies, with the highest concentration in the cecum and right side
of the colon (10.sup.10-10.sup.12 CFU/mL). In contrast, in the
small intestine--the believed site of action, the biomass also
ranges from 10.sup.4 CFU/mL in the duodenum to 10.sup.8 CFU/mL in
the ileum [4, 5].
Human Dosing
[0403] The CFU/dose for humans is based on the following
parameters:
[0404] (1) Treatment of C. difficile with oral capsule formulations
of human stool: Data from OpenBiome and other groups have shown
successful treatment of C. difficile colitis with capsule
formulation that administers 3-5.times.10.sup.9 CFU in a range of
12-30 capsules taken per one-time dose [6]. A standard 12-capsule
regimen is expected to deliver approximately 4.2.times.10.sup.9 CFU
per dose.
[0405] (2) Alter the small intestinal microbiota to promote
immunomodulation. An encapsulated formulation releasing contents in
the proximal small bowel will deliver a dose of 3-5.times.10.sup.9
CFU, exceeding the duodenal biomass by a factor of 10,000, and
approaching a 1:1 ratio with communities in the jejunum and
ileum.
[0406] Other formulations including nanoparticles in liquid, with
optional pre-biotic compounds to enhance colonization and
viability, or a reconstituted lyophilisate are contemplated,
however given the need to prevent exposure to oxygen and for ease
of storage and administration, the first formulation uses
encapsulated material.
Administration
[0407] Given the obligately anaerobic nature of the component
species, phase I studies will use encapsulated formulations with
the following properties:
Stage I:
[0408] Can be swallowed by an adult or child >8 years of age.
[0409] Excludes oxygen [0410] Holds a volume so that a person needs
to take 15 or less capsules per dose [0411] Can be stored frozen
(-20.degree. C. or -80.degree. C.) and thawed prior to
administration [0412] Releases contents after passage through the
stomach
[0413] In one embodiment, the capsules used by OpenBiome.TM. for
oral FMT therapy are used to encapsulate the GP-I and GP-II
mixtures [i]. Other options are also available commercially and
contemplated herein. In some embodiments, the capsules consist of
frozen material (in order to ensure an adequate product) that is
thawed prior to administration and is encapsulated, free of oxygen,
with material that survives intact into the small intestine.
Scale of Culture
[0414] The animal studies used pilot cultures in the range of
100-1000 mL. To generate human doses, the culture is scaled by at
least a factor of 10. The following steps are contemplated herein.
[0415] (1) Perform growth curves in different media conditions--to
optimize growth conditions and correlate an OD600 with plated
biomass. [0416] (2) Grow the component members anaerobically in
liquid media. Media is pre-reduced and incubated at 37.degree. C.
with some level of agitation (e.g., 150 rpm or with
stirring/fermenter baffles) to insure a maximal culture density.
Depending upon the fermenter system, nitrogen or anaerobic gas
mixtures can be sparged to maintain anaerobic conditions. However,
none of the component species require H.sub.2 or CO.sub.2 for
growth, beyond maintaining appropriate acid/base balance. [0417]
(3) Concentrate select members as needed to obtain desired input
density: commonly done by centrifugation at 5-10K RPM with pull-off
of supernatant under anaerobic conditions and resuspension in a
lesser volume of new culture media or appropriate suspension
buffer. The new culture density is confirmed by OD600 reading and
viability by plating to solid media. [0418] (4) Aggregate the
cultured into the combined consortium: Estimated biomass from the
OD600 readings are used to estimate the volume and prepare the
aggregate. [0419] (5) Prepare capsules: done under anaerobic
conditions to preserve viability. [0420] (6) Store capsules:
optimal to store at conditions available clinically, e.g.
-20.degree. C. [0421] (7) Quality Control: In addition to QC for
prior steps and media, the final community will be evaluated to
insure the appropriate species are present and in desired viable
biomass. Analyses on materials for pre-clinical studies used 16S
rRNA gene phylotyping with culture a qPCR-based methods.
Metagenomic approaches may also be used to rule-out contamination
with nonbacterial species or viruses.
[0422] It is further contemplated herein that growth conditions are
optimized for the scaled cultures.
[0423] In some embodiments, media formulations are developed such
that they lack animal products and/or substrates that might be
associated with sensitizing antigens in foodstuffs. In addition,
one of skill in the art can assess if additives to the inoculum
enhance viability in capsules and once released in vivo. Materials
can include preservatives and prebiotic compounds.
[0424] Stage II:
[0425] It is further contemplated herein that the consortia
described herein are formulated as a liquid formulation that can be
administered to infants and young children. It is contemplated
herein that such formulations comprise mixtures of spores from
sporulating species, leveraging non-sporulating obligate anaerobes
with limited aerotolerance, and including reducing factors in a
liquid formula to buffer against short-term exposure to oxygen in
ambient air and upon entry into the digestive tract. Compounds such
as the amino acid cysteine or n-acetylcysteine, which have been
used therapeutically in infants and have a robust safety profile
are contemplated [7,8].
[0426] Additional pre-clinical animal models for use in testing
formulations include e.g., neonatal swine models of food allergy,
including ones for foodstuffs common in the diet of both humans and
pigs [9].
REFERENCES
[0427] 1. Mathias C B, Hobson S A, Garcia-Lloret M, Lawson G,
Poddighe D, Freyschmidt E J, Xing W, Gurish M F, Chatila T A,
Oettgen H C. IgE-mediated systemic anaphylaxis and impaired
tolerance to food antigens in mice with enhanced IL-4 receptor
signaling. J Allergy Clin Immunol. 2011 March; 127(3):795-805.e
1-6. [0428] 2. Noval Rivas M, Burton O T, Wise P, Zhang Y Q, Hobson
S A, Garcia Lloret M, Chehoud C, Kuczynski J, DeSantis T,
Warrington J, Hyde E R, Petrosino J F, Gerber G K, Bry L, Oettgen H
C, Mazmanian S K, Chatila T A. A microbiota signature associated
with experimental food allergy promotes allergic sensitization and
anaphylaxis. J Allergy Clin Immunol. 2013 January; 131(1):201-12.
[0429] 3. Secretions in the GI tract--available on the world wide
web at:
en.wikibooks.org/wiki/Medical_Physiology/Gastrointestinal_Physiology/Secr-
etions [0430] 4. Genes Nutr. 2011 August; 6(3): 209-240 [0431] 5.
Stool substitute transplant therapy for the eradication of
Clostridium difficile infection: `RePOOPulating` the gut.
Microbiome Journal Open Access (2013) DOI: 10.1186/2049-2618-1-3.
[0432] 6. Open Biome FMTcapsules F30 and G3: available on the world
wide web at openbiome.org/fmtcapsules/ [0433] 7. Zlotkin, S H, et
al. Cysteine supplementation to cysteine-free intravenous feeding
regimens in newborn infants. Am J Clin Nutr. 1981, 34(5): 914-923.
[0434] 8. Marzullo, L. An update of N-acetylcysteine treatment for
acute acetaminophen toxicity in children. Curr Op Peds. 2005,
17(2): 239-245. [0435] 9. Helm, R H et al. A neonatal swine model
for peanut allergy. JACI. 2002, 109(1): 136-142.
Example 2: OTU Clustering Method for Data from Human and Animal
Studies
[0436] DNA Extraction and Sequencing for 16S rRNA Gene
Phylotyping.
[0437] A multiplexed amplicon library covering the V4 region of the
16S rDNA gene was generated from DNA extracted from human stool,
mouse fecal pellets or segments of snap-frozen gut tissues using MO
BIO.TM. Power-Fecal.TM. DNA Isolation Kits (MO BIO.TM.
Laboratories) with custom modification to enhance lysis of Gram
positive commensals with thick cell walls. The rest of library
preparation followed the protocol of [1] with dual-index barcodes.
Aggregated libraries are sequenced with paired-end 250 bp reads on
the Illumina.TM. MiSeq platform. The aggregate library pool was
size selected from 300-500 bp on a Pippin.TM. prep 1.5% agarose
cassette (Sage Sciences.TM.) according to the manufacturer's
instructions. Concentration of the pool is measured by qPCR (Kapa
Biosystems.TM.) and loaded onto the MiSeg.TM. (Illumina.TM.) at 6-9
pM with 20% phiX spike-in to compensate for low base diversity
according to Illumina.TM.'s standard loading protocol.
[0438] 16S rRNA Data Preprocessing.
[0439] Sequencing aims to obtain 10-50K usable reads per sample
after quality filtering. Raw sequencing reads were processed using
the mothur software package (v.1.35.1)[2] and custom Python and R
scripts [3], which perform de-noising, quality filtering, alignment
against the ARB Silva reference database of 16S rDNA gene
sequences, and clustering into Operational Taxonomic Units (OTUs)
at 97% identity.
[0440] 16S rRNA Data Analysis.
[0441] To statistically test for differences between control and
food allergic subjects in abundances of microbial taxa (OTUs), the
DESeq2 software package was employed to support of analyses
relative to host co-variates such as age, food allergy status, diet
and antibiotic use in human cohort, OTUs showing significant
differences were defined by: (1) adjusted p-value <=0.1; (2)
relative abundance >=0.01 in either control or food allergic
groups; (3) absolute value of log 2 fold changes >=2.
[0442] To improve the resolution of taxonomic calls and show
phylogenetic relationships, a separate method used the pplacer
software package to perform phylogenetic placement of individual
OTU [4]. Pplacer uses a likelihood-based methodology to place short
sequencing reads of 16S rRNA amplicons on a reference tree, and
also generates taxonomic classifications of the short sequencing
reads using a least common ancestor-based algorithm. The reference
tree required for phylogenetic placement is generated using
full-length or near full-length (>1,200 nt) 16S rDNA sequences
of type strains from the Ribosomal Database Project (RDP)[5].
[0443] For all statistical testing for 16S rDNA data analysis,
p-values were adjusted for multiple hypothesis testing using the
method of Benjamini and Hochberg (BH) [6]. Heat map plots are
generated using custom R scripts [3].
[0444] Alpha diversity values (richness of a sample in terms of the
diversity of the OTUs observed in it) were calculated using Shannon
entropy to measure diversity in each sample. Beta-diversity values
(distance between samples based on differences in OTUs present in
each sample) were calculated using the unweighted/weighted Unifrac
dissimilarity measure, to assess differences in overall microbial
community structure.
[0445] (3) OTU Mappings of the Defined Species
[0446] The following operational taxonomic units map to the defined
species, as identified in gnotobiotic mice colonized with these
consortia. Fecal pellets were subjected to the above described 16S
rRNA gene phylotyping over the V4 variable region.
TABLE-US-00003 TABLE 2 Mapping of the defined therapeutic species
to OTU based on the 16S rRNA V4 region. Species OTU taxonomic
mappings, V4 region- Bacteroides Bacteria: Bacteroidetes:
Bacteroidia: Bacteroidales fragilis Bacteria: Bacteroidetes:
Bacteroidia: Bacteroidales: Bacteroidaceae Bacteria: Bacteroidetes:
Bacteroidia: Bacteroidales: Bacteroidaceae: Bacteroides Bacteroides
Bacteria: Bacteroidetes: Bacteroidia: Bacteroidales
thetaiotaomicron Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Bacteroidaceae Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Bacteroidaceae: Bacteroides Bacteroides Bacteria:
Bacteroidetes: Bacteroidia: Bacteroidales ovatus Bacteria:
Bacteroidetes: Bacteroidia: Bacteroidales: Bacteroidaceae Bacteria:
Bacteroidetes: Bacteroidia: Bacteroidales: Bacteroidaceae:
Bacteroides Clostridium Bacteria: Firmicutes: Clostridia:
Clostridiales: Peptostreptococcaceae bifermentans Bacteria:
Firmicutes: Clostridia: Clostridiales: Peptostreptococcaceae:
Clostridium cluster XI Clostridium Bacteria: Firmicutes:
Clostridia: Clostridiales: Peptostreptococcaceae hiranonsis
Bacteria: Firmicutes: Clostridia: Clostridiales:
Peptostreptococcaceae: Clostridium cluster XI Clostridium Bacteria:
Firmicutes: Clostridia: Clostridiales: Ruminococcaceae leptum
Bacteria: Firmicutes: Clostridia: Clostridiales: Ruminococcaceae:
Clostridium cluster IV Clostridium Bacteria: Firmicutes:
Erysipelotrichia: Erysipelotrichales: Erysipelotrichaceae ramosum
Erysipelotrichales: Erysipelotrichaceae: Clostridium cluster XVIII
Clostridium Bacteria: Firmicutes: Clostridia: Clostridiales:
sardiniensis Bacteria: Firmicutes: Clostridia: Clostridiales:
Clostridiaceae I (absonum) Clostridium Bacteria: Firmicutes:
Clostridia: Clostridiales: Lachnospiraceae scindens Bacteria:
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae: Clostridium
cluster XIVa Parabacteroides Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Porphyoromondaceae goldsteinii Bacteria:
Bacteroidetes: Bacteroidia: Bacteroidales: Porphyoromondaceae:
Parabacteroides Prevotella Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: tannerae Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Prevotellaceae Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Prevotellaceae: Prevotella
TABLE-US-00004 TABLE 3 Mapping of the dysbiotic consortium species
to OTU based on the 16S rRNA V4 region Species OTU mapping
Bilophila Bacteria: Proteobacteria: Deltaproteobacteria:
Desulfovibrionales wadsworthia Bacteria: Proteobacteria:
Deltaproteobacteria: Desulfovibrionales: Desolfovibrionaceae
Bacteria: Proteobacteria: Deltaproteobacteria: Desulfovibrionales:
Desolfovibrionaceae: Bilophila Enterobacter Bacteria:
Proteobacteria: Gammaproteobacteria: Enterobacteriales cloacae
Bacteria: Proteobacteria: Gammaproteobacteria: Enterobacteriales:
Enterobacteriaceae Bacteria: Proteobacteria: Gammaproteobacteria:
Enterobacteriales: Enterobacteriaceae: Enterbacter Escherichia
Bacteria: Proteobacteria: Gammaproteobacteria: Enterobacteriales
coli Bacteria: Proteobacteria: Gammaproteobacteria:
Enterobacteriales: Enterobacteriaceae Bacteria: Proteobacteria:
Gammaproteobacteria: Enterobacteriales: Enterobacteriaceae:
Escherichia Klebsiella Bacteria: Proteobacteria:
Gammaproteobacteria: Enterobacteriales pneumonia Bacteria:
Proteobacteria: Gammaproteobacteria: Enterobacteriales:
Enterobacteriaceae Bacteria: Proteobacteria: Gammaproteobacteria:
Enterobacteriales: Enterobacteriaceae: Klebsiella Proteus Bacteria:
Proteobacteria: Gammaproteobacteria: Enterobacteriales mirabilis
Bacteria: Proteobacteria: Gammaproteobacteria: Enterobacteriales:
Enterobacteriaceae Bacteria: Proteobacteria: Gammaproteobacteria:
Enterobacteriales: Enterobacteriaceae: Proteus
TABLE-US-00005 TABLE 4 Additional "beneficial" OTU identified in
the longitudinal pediatric human cohort as associated with
protection from development of food allergy. Nearest species
mapping(s) with OTU taxonomic mappings with sequencing of the V4
region- pplacer Bacteria: Firmicutes: Clostridia: Clostridiales:
Lachnospiraceae Clostridium hathewayi Bacteria: Firmicutes:
Clostridia: Clostridiales: Lachnospiraceae: Clostridium cluster
XIVa Bacteria: Firmicutes: Clostridia: Clostridiales:
Lachnospiraceae: Hungatella Bacteria: Firmicutes: Clostridia:
Clostridiales: Lachnospiraceae Clostridium nexile, Bacteria:
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae: Clostridium
cluster Clostridium XIVa hylemonae, Clostridium
glycyrrhizinilyticum, Clostridium scindens, Clostridium lavalense,
Clostridium fimetarium, Clostridium symbiosum Bacteria: Firmicutes:
Clostridia: Clostridiales: Ruminococcaceae Clostridium Bacteria:
Firmicutes: Clostridia: Clostridiales: Ruminococcaceae: Clostridium
sporosphaeroides cluster IV Bacteria: Firmicutes: Negativicutes:
Selenomonadales: Veillonellaceae Dialister Bacteria: Firmicutes:
Negativicutes: Selenomonadales: Veillonellaceae: Dialister
proprionicifaciens, Dialister succinatiphilus Bacteria:
Bacteroidetes: Bacteroidia: Bacteroidales: Porphyoromondaceae
Parabacteroides Bacteria: Bacteroidetes: Bacteroidia:
Bacteroidales: Porphyoromondaceae: distasonis, Parabacteroides
Parabacteroides goldsteinii, Parabacteroides merdae Bacteria:
Firmicutes: Clostridia: Clostridiales: Peptostreptococcaceae
Peptostreptococcus Bacteria: Firmicutes: Clostridia: Clostridiales:
Peptostreptococcaceae: anaerobius Peptostreptococcus Bacteria:
Firmicutes: Clostridia: Clostridiales: Ruminococcaceae
Subdoligranulum Bacteria: Firmicutes: Clostridia: Clostridiales:
Ruminococcaceae: Subdoligranulum variabile Bacteria: Firmicutes:
Negativicutes: Selenomonadales: Veillonellaceae Veilonella ratti
Bacteria: Firmicutes: Negativicutes: Selenomonadales:
Veillonellaceae: Veillonella
TABLE-US-00006 TABLE 5 Additional "dysbiotic" OTU identified in the
longitudinal pediatric human cohort as associated with development
of food allergy. Nearest species mapping OTU taxonomic mappings
with sequencing of the V4 region with pplacer Bacteroidetes:
Bacteroidia: Bacteroidales: Rikenellaceae: Alistipes Bacteroidetes:
Bacteroidia: Bacteroidales: Rikenellaceae: Alistipes onderdonkii
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae Blautia
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae: Blautia
wexlerae, Blautia henselae Bacteria: Proteobacteria:
Deltaproteobacteria: Desulfovibrionales Bilophila Bacteria:
Proteobacteria: Deltaproteobacteria: Desulfovibrionales:
Desolfovibrionaceae wadsworthia, Bacteria: Proteobacteria:
Deltaproteobacteria: Desulfovibrionales: Desolfovibrionaceae:
Desulfovibrio Bilophila species Bacteria: Proteobacteria:
Deltaproteobacteria: Desulfovibrionales: Desolfovibrionaceae:
Bilophila: Desulfovibrio Firmicutes: Bacilli: Lactobacillales:
Lactobacillaceae: Lactobacillus Lactobacillus johnsoni Bacteria:
Proteobacteria: Betaproteobacteria: Burkholderales: Parasutterella
Bacteria: Proteobacteria: Betaproteobacteria: Burkholderales:
Sutterellaceae excrementihominis Bacteria: Proteobacteria:
Betaproteobacteria: Burkholderales: Sutterellaceae: Parasutterella
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae Roseburia
Firmicutes: Clostridia: Clostridiales: Lachnospiraceae: Roseburia
inulinivorans
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Example 3: Microbiology-Level Activities Used in Selection of
Defined Species
[0453] The species in the defined consortia were selected per known
biochemical, immunologic and microbiologic functions with capacity
to affect beneficial immunomodulatory responses in the host.
Without wishing to be bound by theory, microbiologic mechanisms of
action can include the following.
[0454] Adjuvant effects of microbial products to stimulate the
development of regulatory T cells through TLR->MyD88 and other
immune cell pathways. The production of key microbial antigens from
commensal anaerobes, including their lipoteichoic acid (LTA),
exo-polysaccharides (PSA), LPS, bacterial flagellin, and bacterial
DNA can act through stimulating toll-like-receptor pathways to skew
mucosal T cells to a regulatory vs. allergic phenotype. In
contrast, published data have shown that bacterial cell wall
fractions from members of the negative control consortium can
promote aberrant stimulation of both allergic (Th2) and
pro-inflammatory (Th1) responses. The distinct portions of these
molecules that skew towards tolerance vs. allergy or inflammation
highlight the interplay between mammalian hosts and colonizing
microbiota, including the microbial products that signal the host
to maintain a healthy homeostasis versus elicit pathogenic immune
responses.
[0455] Mucosal and Immunoprotective Functions of Microbial
End-Products of Metabolism:
[0456] Short chain fatty acids (SCFA) are natural end-products of
microbial anaerobic fermentation as are additional small molecule
metabolites from anaerobic fermentation of different carbon
sources. End-products such as butyrate have been shown to provide a
primary energy source to the gut epithelium and to contribute to
the development of tolerizing responses in mucosal locations. The
consortia selected produce a dominance of butyrate and propionate
from the fermentation of simple and complex carbohydrates that may
be in the gut lumen, per the diet and secretion of host factors.
These factors would likely act in combination with other microbial
activities to mediate the desired immunomodulatory effects.
[0457] Biochemical Activities:
[0458] The species selected perform the full complement of bile
acid transformations and also transform a variety of other
molecules including other cholesterol-derivatives, biogenic amines,
lipids and production of aryl hydrocarbons which may serve as
microbial siderophores, quorum sensing molecules and other
metabolic intermediates within the microbial cell. Such metabolites
are potentially capable of stimulating host aryl-hydrocarbon
receptor (AHR) pathways which have also been demonstrated to
promote tolerizing responses in the gut mucosa.
[0459] Gut Conditioning:
[0460] Microbiologically, select members of the consortia are known
to aid the subsequent colonization, biochemical and further
immunoprotective roles of other species. Both Bacteroides fragilis
and Bacteroides thetaiotaomicron, when included in defined flora,
assist the growth of more fastidious members of the Bacteroidetes,
Firmicutes and Actinobacteria. Clostridium ramosum has demonstrated
comparable effects in defined colonizations of germ-free mice with
other commensals. Effects are multi-factorial, and include maturing
of gut epithelial responses, altered host secretion of
glycoconjugates which can serve as carbon sources for the commensal
flora, enhancing gut peristalsis and digestion, reducing lumen gut
oxygen tension so more obligately anaerobic species can flourish,
and releasing metabolites, and/or extracellular products of
microbial digestion which support the growth of additional species
by providing carbon and/or nitrogen sources, vitamins, and other
essential micronutrients.
[0461] Reducing the Biomass of Dysbiotic or Pathogenic Species:
[0462] Animal models conducted by our group have also shown that
the species in the gut protect communities can reduce the biomass
of the Proteobacterial species in the negative control consortium.
Without wishing to be bound by theory, mechanistically these
biomass reductions also reduce the antigen burden of products from
these species that preferentially skew towards allergic
responses.
Example 4. GP-I and GP-II Consortia are Effective in
Treat-to-Prevent Food Allergy in Conventional Wild-Type and IL4RA
F709 Mice
[0463] The protective effects of consortia GP-I (Clostridial
species) and GP-II (Bacteroidetes species) were examined in
conventional and food allergy-prone IL4RA F709 mice. In this series
of experiments, the animals were conventional, i.e., not germ-free.
Animals were treated with a course of oral broad-spectrum
antibiotics one week prior to initiating sensitization with egg
ovalbumin (OVA) and staphylococcal enterotoxin B (SEB). After
antibiotic treatment, the mice received weekly doses of the GP-I,
GP-II or negative control consortia (NCC), and weekly doses of
OVA-SEB before challenge at week 8 with oral ovalbumin. See FIG.
21A. Following challenge, animals were examined for temperature
drop (FIG. 21B), total and OVA-specific IgE titers (FIG. 21C), mast
cell protease-1 levels (FIG. 21D), mast cell recruitment to the
small bowel (FIG. 2E) and the development of FoxP3+ regulatory T
cells (FIGS. 21F and G) versus IL-4 producing T cells (FIGS. 21H
and I). The data clearly show that the Clostridiales and
Bacteroidetes consortia (GP-I and GP-II, respectively) protected
against allergy as measured by these criteria, while animals
treated with the negative control consortium (denoted
"Proteobacteria") or no bacteria showed a clear allergic response.
Thus, GP-1I and GP-II are effective to prevent the development of
food allergy.
Example 5. GP-I and GP-II Consortia Protect Germ-Free Mice in
Treat-to-Prevent Regimens
[0464] The protective effects of the GP-I and GP-II consortia were
examined in germ-free mice treated with saline (PBS) or with
OVA-SEB. The germ-free mice received either no bacteria or
consortia GP-I or GP-II prior to 7 weekly sensitizing doses of
OVA-SEB (see FIG. 22A). Challenged on the 8.sup.th week with OVA,
the mice were examined for evidence of allergic reaction as
described in Example 4. The data (see FIGS. 22 B-H) clearly show
that unlike animals receiving no bacteria, germ-free animals
administered the GP-I and GP-II consortia experienced substantially
no allergic reaction upon challenge with the sensitizing food
allergen.
Example 6. GP-I and GP-II Consortia Cure Food Allergy in
Conventional IL4RA F709 Mice; Negative Control Consortium does
not
[0465] To test whether animals that had been sensitized to food
allergen before treatment with consortia shown herein to be
protective against the development of food allergy could be cured
of allergic sensitivity, conventional (i.e., non-germ-free) IL4RA
F709 mice were sensitized to ovalbumin by 8 weekly treatments with
OVA-SEB as performed in the experiments described above (see FIG.
23A for the experimental timeline). The animals were then treated
with antibiotics to knock out their natural gut bacteria, before
being treated with the GP-I, GP-II or NCC consortia using four
weekly doses. After the fourth weekly dose of the test consortia,
the animals were challenged with OVA. The data, which examined the
same criteria examined in Examples 4 and 5, show that animals
treated with the GP-I (Clostridiales) and GP-II (Bacteroidetes)
consortia were substantially protected against allergic reaction,
while those receiving the negative control (Proteobacteria)
consortium were not (see FIG. 23B-H). These data demonstrate that
not only can food allergy be prevented from developing through
administration of the microbial consortia described herein, but
established food allergy can also be treated by administration of
the same protective consortia.
Example 7. GP-II Consortium (Bacteroidetes) Protects Against Food
Allergy without Prior Antibiotic Knockdown of the Flora
[0466] To examine whether it is necessary to first knock down the
natural gut microbiota via antibiotic treatment in order to obtain
protection in conventional mice, such animals were administered 8
weekly doses of GP-I and GP-II consortia or no additional bacterial
treatment, while sensitizing mice to OVA with weekly OVA-SEB
treatments over the course of 8 weeks (see FIG. 24A for the
experimental timeline). Subsequent challenge with OVA demonstrated
that, in the absence of natural flora knockdown prior to treatment
with GP-I or GP-II, the Bacteroidetes consortium, GP-II, provided
protection against the development of food allergy (see FIG.
24B-L). It is specifically contemplated that the administration of
a combination of GP-II with one or more, or even all of the species
of GP-I would provide an improved effect, in terms of initial
response or protection and/or in terms of the persistence of such
protection.
Example 8. The GP-I Consortium (Clostridiales) can Cure Food
Allergy without the Use of Antibiotics in Conventional Mice
[0467] To examine whether it is necessary to knock down the natural
gut microbiota in order to cure food allergy in conventional mice,
conventional wild-type and IL4RA F709 mutant mice were sensitized
to ovalbumin via 8 weekly doses of OVA-SEB, followed by
twice-weekly administration of the GP-I (Clostridiales) consortium
for 4 weeks, without prior antibiotic knockdown of the natural gut
microbiota (see FIG. 25A for the experimental timeline). When
challenged after the four weeks of GP-I administration, the data
show that the GP-I consortium was effective to reduce allergic
symptoms by all measures examined in both the wild-type and
allergy-prone animals (See FIG. 25B-I). The data indicate that the
administration of the GP-I consortium is able to cure food allergy
in the presence of the natural gut flora--that is, it is not
necessary to first knock down the natural gut microbiota to
effectively treat food allergy using protective microbial consortia
such as the GP-I consortium.
* * * * *