U.S. patent application number 17/386266 was filed with the patent office on 2021-11-18 for use of microbial communities for human and animal health.
The applicant listed for this patent is MICROBIAL RESOURC MANAGEMENT HEALTH NV (MRM HEALTH), Universiteit Gent. Invention is credited to Selin Bolca, Davide Gottardi, Massimo Marzorati, Sam Possemiers, Ilse Scheirlinck, Tom Van De Wiele, Pieter Van Den Abeele.
Application Number | 20210353694 17/386266 |
Document ID | / |
Family ID | 1000005738527 |
Filed Date | 2021-11-18 |
United States Patent
Application |
20210353694 |
Kind Code |
A1 |
Possemiers; Sam ; et
al. |
November 18, 2021 |
USE OF MICROBIAL COMMUNITIES FOR HUMAN AND ANIMAL HEALTH
Abstract
The disclosure relates to a mixture of bacteria belonging to at
least six or seven different and specific bacterial species
preferably for use in preventing or treating gastro-intestinal
disorders. Preferably, the mixture of bacteria is grown together in
a fermenter prior to administering the mixture to a subject in
order to prevent or treat the disorder.
Inventors: |
Possemiers; Sam;
(Zwijnaarde, BE) ; Marzorati; Massimo; (Brussel,
BE) ; Van De Wiele; Tom; (Merelbeke, BE) ;
Scheirlinck; Ilse; (Gentbrugge, BE) ; Van Den Abeele;
Pieter; (Lokeren, BE) ; Bolca; Selin;
(Zwijnaarde, BE) ; Gottardi; Davide; (Gent,
BE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Universiteit Gent
MICROBIAL RESOURC MANAGEMENT HEALTH NV (MRM HEALTH) |
Gent
Ghent |
|
BE
BE |
|
|
Family ID: |
1000005738527 |
Appl. No.: |
17/386266 |
Filed: |
July 27, 2021 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
16068470 |
Jul 6, 2018 |
11096971 |
|
|
PCT/EP2017/052422 |
Feb 3, 2017 |
|
|
|
17386266 |
|
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A23Y 2300/19 20130101;
A61K 9/0056 20130101; A61K 35/744 20130101; A61P 1/14 20180101;
A61K 9/0031 20130101; A61K 35/747 20130101; A61K 35/741 20130101;
A61K 35/745 20130101; A23L 33/135 20160801; A61K 35/74 20130101;
Y02A 50/30 20180101; A23Y 2220/67 20130101; A61K 2035/115 20130101;
C12N 1/20 20130101; A23V 2002/00 20130101; A23Y 2300/55 20130101;
A61K 9/0053 20130101 |
International
Class: |
A61K 35/747 20060101
A61K035/747; C12N 1/20 20060101 C12N001/20; A61K 35/741 20060101
A61K035/741; A23L 33/135 20060101 A23L033/135; A61P 1/14 20060101
A61P001/14; A61K 9/00 20060101 A61K009/00; A61K 35/74 20060101
A61K035/74; A61K 35/744 20060101 A61K035/744; A61K 35/745 20060101
A61K035/745 |
Foreign Application Data
Date |
Code |
Application Number |
Feb 4, 2016 |
EP |
16154288.1 |
Claims
1. A method of treating a subject to reduce symptoms associated
with a gastro-intestinal disorder, the method comprising:
administering to the subject a composition consisting of: bacteria
belonging to the species Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila, Lactobacillus plantarum, and
Anaerostipes caccae, and optionally, a pharmaceutically acceptable
excipient or excipient(s), so as to increase butyrate production or
increase protective effects towards gut barrier function in the
subject and thus reduce symptoms associated with the
gastro-intestinal disorder in the subject.
2. The method according to claim 1, wherein the gastro-intestinal
disorder is a disruption of the barrier function of the gut,
diarrhea, constipation, irritable bowel syndrome, inflammatory
bowel disease, Crohn's disease, ulcerative colitis, coeliac
disease, pouchitis, mucositis, an infection of the gut, gut
microbiota dysbiosis, and any combination thereof.
3. A method of treating a subject to reduce symptoms associated
with a gastro-intestinal disorder, the method comprising:
administering to the subject a composition consisting of: bacteria
belonging to the species Faecalibacterium prausnitzii,
Butyricicocccus pullicaecorum, Roseburia inulinivorans, Akkermansia
muciniphila, Lactobacillus plantarum, and Anaerostipes caccae, and
optionally, a pharmaceutically acceptable excipient or
excipient(s), so as to increase butyrate production or increase
protective effects towards gut barrier function in the subject and
thus reduce symptoms associated with the gastro-intestinal disorder
in the subject.
4. The method according to claim 3, wherein the composition further
includes one or more prebiotics.
5. The method according to claim 3, wherein the bacteria are grown
together in a fermenter prior to administration of the composition
to the subject.
6. The method according to claim 5, wherein the fermenter is a
dynamic simulator of the gastrointestinal tract.
7. The method according to claim 3, wherein the gastro-intestinal
disorder is a disruption of the barrier function of the gut,
diarrhea, constipation, irritable bowel syndrome, inflammatory
bowel disease, Crohn's disease, ulcerative colitis, coeliac
disease, pouchitis, mucositis, an infection of the gut, gut
microbiota dysbiosis, and any combination thereof.
8. The method according to claim 3, wherein the composition further
includes bacteria belonging to the species Escherichia coli,
Enterococcus faecium, Lactobacillus mucosae, Bifidobacterium
adolescentis, Bifidobacterium longum, Bacteroides thetaiotaomicron
and Bacteroides vulgatus.
9. The method according to claim 3, wherein the bacteria are
selected from the group consisting of Faecalibacterium prausnitzii
LMG P-29362, Faecalibacterium prausnitzii DSMZ 17677,
Butyricicoccus pullicaecorum LMG P-29360, Butyricicoccus
pullicaecorum LMG24109, Roseburia 10 inulinivorans LMG P-29365,
Roseburia inulinivorans DSMZ 16841, Akkermansia muciniphila LMG
P-29361, Akkermansia muciniphila DSMZ 22959, Lactobacillus
plantarum LMG P-29366, Lactobacillus plantarum ZJ316, Anaerostipes
caccae LMG P-29359, Anaerostipes caccae DSMZ 15 14662 and strains
showing at least 97% sequence identity to the 16S rRNA sequences of
at least one of the strains.
10. A method of treating a subject to reduce symptoms associated
with a gastro-intestinal disorder, the method comprising:
administering to the subject a composition consisting of: bacteria
belonging to the species Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Akkermansia
muciniphila, Lactobacillus plantarum, Anaerostipes caccae,
Escherichia coli, Enterococcus faecium, Lactobacillus mucosae,
Bifidobacterium adolescentis, Bifidobacterium longum, Bacteroides
thetaiotaomicron, and Bacteroides vulgatus, and optionally, a
pharmaceutically acceptable excipient or excipient(s), so as to
increase butyrate production or increase protective effects towards
gut barrier function in the subject and thus reduce symptoms
associated with the gastro-intestinal disorder in the subject.
11. The method according to claim 5, wherein the bacteria, after
having been grown together, have been frozen and subsequently
thawed for administration to the subject.
12. A method of treating a subject to reduce symptoms associated
with a gastro-intestinal disorder, the method comprising:
administering to the subject a composition consisting of: bacteria
belonging to the species Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila, Lactobacillus plantarum,
Anaerostipes caccae, Escherichia coli, Enterococcus faecium,
Lactobacillus mucosae, Bifidobacterium adolescentis,
Bifidobacterium longum, Bacteroides thetaiotaomicron, and
Bacteroides vulgatus and optionally, a pharmaceutically acceptable
excipient or excipient(s), so as to increase butyrate production or
increase protective effects towards gut barrier function in the
subject and thus reduce symptoms associated with the
gastro-intestinal disorder in the subject.
13. The method according to claim 12, wherein the composition
further includes one or more prebiotics.
14. The method according to claim 12, wherein the bacteria are
grown together in a fermenter prior to administration of the
composition to the subject.
15. The method according to claim 14, wherein the fermenter is a
dynamic simulator of the gastrointestinal tract.
16. The method according to claim 15, wherein the bacteria, after
having been grown together, have been frozen and subsequently
thawed for administration to the subject.
17. The method according to claim 12, wherein the bacteria are
selected from the group consisting of Faecalibacterium prausnitzii
LMG P-29362, Faecalibacterium prausnitzii DSMZ 17677,
Butyricicoccus pullicaecorum LMG P-29360, Butyricicoccus
pullicaecorum LMG24109, Roseburia 10 inulinivorans LMG P-29365,
Roseburia inulinivorans DSMZ 16841, Roseburia hominis LMG P-29364,
Roseburia hominis DSMZ 16839, Akkermansia muciniphila LMG P-29361,
Akkermansia muciniphila DSMZ 22959, Lactobacillus plantarum LMG
P-29366, Lactobacillus plantarum ZJ316, Anaerostipes caccae LMG
P-29359, Anaerostipes caccae DSMZ 15 14662 and strains showing at
least 97% sequence identity to the 16S rRNA sequences of at least
one of the strains.
18. A reactor comprising: a composition consisting of from 5 to 20
distinct bacterial members, wherein when the composition resides in
the reactor under standardized conditions representative of the
gastrointestinal (GI) tract for a time of between 3 and 14 days, a
functionally stable collaborome is obtained, and wherein the
standardized conditions representative of the GI tract comprise: a
pH range of between 1.5 and 8; carbon sources; a retention time of
between 10 minutes and 200 hours; an oxygen availability of between
0 g/L and 8 g/L; micronutrients; optional antibiotic(s); an
optional bile salt concentration of less than or equal to 20 mM;
heavy metals; and host factors as immune molecules.
19. The reactor of claim 18, wherein the composition consists of
from 5 to 15 distinct bacterial members.
20. The reactor of claim 19, wherein the composition consists of
from 6 to 14 distinct bacterial members.
21. The reactor of claim 18, wherein when the composition resides
in the reactor under standardized conditions representative of the
GI tract for a time of between 3 and 10 days, a functionally stable
collaborome is obtained.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of co-pending U.S. patent
application Ser. No. 16/068,470, filed Jul. 6, 2018, now U.S.
patent ______, which is a national phase entry under 35 U.S.C.
.sctn. 371 of International Patent Application PCT/EP2017/052422,
filed Feb. 3, 2017, designating the United States of America and
published as International Patent Publication WO 2017/134240 A1 on
Aug. 10, 2017, which claims the benefit under Article 8 of the
Patent Cooperation Treaty to European Patent Application Serial No.
EP16154288.1, filed Feb. 4, 2016, the contents of the entirety of
each of which are incorporated herein by this reference.
TECHNICAL FIELD
[0002] This application relates to a mixture of bacteria belonging
to at least six or seven different and specific bacterial species,
preferably for use to prevent or treat gastro-intestinal disorders.
More preferably, the mixture of bacteria is grown together in a
fermenter prior to administering the mixture to a subject in order
to prevent or treat the disorder.
STATEMENT ACCORDING TO 37 C.F.R. .sctn. 1.821(c) or (e)-SEQUENCE
LISTING SUBMITTED AS ASCII TEXT FILE
[0003] Pursuant to 37 C.F.R. .sctn. 1.821(c) or (e), a file
containing an ASCII text version of the Sequence Listing has been
submitted concomitant with this application, the contents of which
are hereby incorporated by reference.
BACKGROUND
[0004] The human and animal gut ecosystem consists of a variety of
different habitats and metabolic niches that are colonized by the
so-called microbiota that contain more than 10.sup.11
micro-organisms per gram wet weight of contents, predominantly
anaerobes (Macfarlane & Macfarlane, 1997). It is nowadays
well-recognized that the human or animal gut microbiome plays a
crucial role in human health and well-being by contributing to
energy harvest, modulating the immune system and establishing
colonization resistance against opportunistic pathogens (Fuller
& Gibson, 1997; Cummings & Macfarlane, 1997). Evidence
exists that the interaction of bacteria and their metabolites with
the mucus layer and/or with the intestinal gut wall is important
(Barnett et al. 2012). Although the gut microbiome is generally
stable over time, its composition is altered by external
perturbations, such as dietary changes, antibiotic use, increasing
hygienization and stress. This leads to an unbalanced condition in
the gastrointestinal tract, called dysbiosis (Clemente et al.
2012). Dysbiosis is characterized by moderate or severe disruptions
in the normal gut microbiome composition, thereby causing the lack
of key microbial species, gaps in specific microbial functions and,
as a consequence, an impaired modulation of the gut wall activity.
This may lead to the colonization of pathogenic
microorganisms--causing diarrhea or necrotizing enteritis (Sekirov
et al. 2008). One of the extreme forms of such pathogenesis is CDAD
(Clostridium difficile associated diarrhea) for which classic
antibiotic therapy is more and more falling short of curing the
patient. Other consequences of microbial dysbiosis may be a
compromised immune response, resulting in chronic inflammation
(Willing et al. 2009) or food allergies, or an increased gut
permeability, nutrient malabsorption or even bacteremia. The
adverse effects of dysbiosis toward microbial functionality and gut
wall physiology may thus undermine human health. In fact,
constipation, IBS, IBD, pouchitis, metabolic syndrome, obesity,
diabetes, cardiovascular diseases, mental conditions, impaired
cognitive function, a neurodegenerative disease, different types of
cancers (e.g., colon cancer), inflammation of the female
reproductive apparatus, CDAD, rheumatism or rheumatoid arthritis
are all associated with changes in the activity/composition of the
gut microbiota. It is, therefore, clear that dysbiosis should be
avoided or remedied upon occurrence.
[0005] When dysbiosis is associated with the presence of pathogens,
an obvious strategy to get rid of health-detrimental microorganisms
is the application of antibiotic agents. However, widespread and
improper use of broad-spectrum antibiotics over the last decades
has dramatically increased antibiotic resistance (Brandi et al.
2008). Moreover, antibiotics also tackle the indigenous gut
microorganisms, many of which fulfill crucial functions and deliver
health benefits, therefore worsening the condition of dysbiosis. As
a result, the last two decades have seen a tremendous increase in
functional food research, particularly the development of prebiotic
and probiotic products. Although the prebiotic concept is
attractive as it concerns the dietary modulation of indigenous gut
microorganisms that are already adapted to the host (Van Loo et al.
1999), it is primarily used in a preventive manner. For a
therapeutic application, a severely disrupted gut microbiome would
benefit more from the introduction of key microbial species, rather
than the provision of substrates that benefit health-promoting
species that are less abundant or even absent in a diseased
individual. A possible solution is the introduction of viable,
health-promoting microorganisms, termed probiotics (Iannitti and
Palmieri, 2010). Probiotic products are mostly comprised of one to
a couple of not interconnected microbial strains (mostly lactic
acid-producing bacteria) with a specific functionality. However,
survival of probiotic strains during the harsh conditions of the
upper digestive tract is challenging and competition with the vast
indigenous microbiome is often negligible. Yet, the concept of
introducing new species in a compromised gut ecosystem has gained
momentum in recent years through the application of fecal microbial
transplants (FMT) (Khoruts et al. 2010). This entails the transfer
of a fecal microbial slurry from a healthy donor to a diseased
recipient. This form of bacteriotherapy is mostly applied to treat
antibiotic-resistant infections and has cure rates of 90% and
higher. FMT is currently being considered for treating many other
pathologies that have their origin in gastrointestinal dysbiosis
(Crohn's disease, obesity, irritable bowel syndrome, etc.). FMT
seems to efficiently work where single probiotic strains frequently
fail. Yet, the badly characterized nature of fecal transplants
comes with transmission risks of infectious diseases and currently
raises questions over its widespread applicability in less acute
and life-threatening pathologies (De Vrieze 2013).
[0006] Early 2013, an alternative for fecal microbial transplants
entered the field with the publication of a scientific paper
(Petrof et al. 2013) and patent application (WO 2013/037068--Method
for treatment of disorders of the gastrointestinal system) on the
use of a synthetic mixture of microbes that were isolated from an
individual based on their culturability as therapeutic agent to
cure CDAD. Such product is also composed of a known set of
microorganisms, which would take away the concerns of disease
transmission from fecal transplants, when QPS criteria are
respected. However, mixing together microorganisms does not
guarantee them to interact with one another and to occupy
functional niches that require microbial networking. Product
stability, standardization and performance of important functions
can, therefore, not be guaranteed.
[0007] In the patent application WO 2014/145958A2 (Network-based
microbial compositions and methods), it is proposed to administer
to a mammalian subject, in need of an effective amount of a
therapeutic bacterial composition, a plurality of isolated bacteria
or a purified bacterial preparation. The plurality of isolated
bacteria or the purified bacterial preparation is able to form a
so-called network ecology. The bacteria belonging to this
preparation are selected based on genomic information and are
provided to the mammalian subject as a loosely assembled set of
strains.
[0008] In a publication of Becker et al. (2011), a community is
described consisting of eight different strains: Anaerostipes
caccae, Bacteroides thetaiotaomicron, Bifidobacterium longum,
Blautia producta, Clostridium butyricum, Clostridium ramosum,
Escherichia coli, and Lactobacillus plantarum. The community is
referred to as SIHUMIx (Simplified Human Microbiota extended). This
artificial microbial community was tested in rat studies, comparing
SIHUMIx-inoculated rats with conventional human-associated and
germ-free rats. The authors claim the community is representative
for the human colon-associated microbiota in terms of composition
and functionality. The microbial community evolved depending on the
age of the rats, but reached a stable composition over time.
[0009] Van den Abbeele et al. (2013) suggested the possibility of
creating a glycan-degrading community by using conventional in
vitro fermenters that can be inoculated with relevant keystone
species and a mixture of cross-feeding microbes. After inoculation
and stabilization, such a microbial network unit for specific
functions can be attained and produced at a large scale.
[0010] Finally, Newton et al. (1998) made use of anaerobic
chemostats to create reproducible defined bacterial communities
comprising fourteen different saccharolytic and amino
acid-fermenting species (i.e., Bifidobacterium longum, Bif.
adolescentis, Bif. pseudolongum, Bif. infantis, Bacteroides
thetaiotaomicron, Bact. vulgatus, Lactobacillus acidophilus,
Enterococcus faecalis, Ent. faecium, Escherichia coli, Clostridium
perfringens, Cl. butyricum, Cl. innocuum, Cl. Bifermentans) to
study the effect of the sulphate-reducing bacterium (SRB)
Desulfovibrio desulfuricans on other intestinal organisms.
[0011] However, there is still a need to design alternative and
specific mixtures of bacterial species that can be effectively used
to prevent or treat gastro-intestinal disorders. Moreover, it is
completely unknown whether pre-adapted mixtures perform
therapeutically as well, worse or better when compared to
administering the loosely assembled and non-pre-adapted mixtures of
the same bacterial species.
BRIEF SUMMARY
[0012] This disclosure relates in the first instance to a
composition consisting essentially of bacteria belonging to the
species Faecalibacterium prausnitzii, Butyricicoccus pullicaecorum,
Roseburia inulinivorans, Roseburia hominis, Akkermansia
muciniphila, Lactobacillus plantarum and Anaerostipes caccae
preferably for use to prevent or treat symptoms associated with a
gastro-intestinal disorder.
[0013] In other words, the disclosure relates to a method of
preventing or treating symptoms associated with a gastro-intestinal
disorder in a subject in need thereof, the method comprising
administering to the subject a therapeutically effective amount of
a composition consisting essentially of bacteria belonging to the
species Faecalibacterium prausnitzii, Butyricicoccus pullicaecorum,
Roseburia inulinivorans, Roseburia hominis, Akkermansia
muciniphila, Lactobacillus plantarum and Anaerostipes caccae.
[0014] This disclosure further relates to a composition as
described wherein the gastro-intestinal disorder is a disruption of
the barrier function of the gut, diarrhea, constipation, irritable
bowel syndrome, inflammatory bowel disease, Crohn's disease,
ulcerative colitis, coeliac disease, pouchitis, mucositis, an
infection of the gut, gut microbiota dysbiosis, or any combination
thereof.
[0015] Also disclosed is a composition as described herein, wherein
the gastro-intestinal disorder is prevented or treated via: a)
stimulating growth and/or activity of one or a limited number of
beneficial bacteria in the intestinal tract, b) inhibiting growth
and/or activity of one or a limited number of pathogenic bacteria
in the intestinal tract, c) relatively increasing the attachment of
non-pathogenic bacteria to the mucosa of the gastrointestinal
surface, d) reducing uncontrolled uptake of antigens,
pro-inflammatory, bacteria or bacterial products by the gut, e)
providing anti-inflammatory activity at the intestinal surface, f)
increasing gut barrier functioning, g) producing bacterial
metabolites or h) any combination of a) to g).
[0016] The disclosure also relates to a composition as described
herein wherein bacteria belonging to the species Roseburia hominis
are eliminated from the composition.
[0017] The disclosure further relates to a composition as described
herein wherein bacteria belonging to the species Escherichia coli,
Enterococcus faecium, Lactobacillus mucosae, Bifidobacterium
adolescentis, Bifidobacterium longum, Bacteroides thetaiotaomicron
and Bacteroides vulgatus are further added to the composition.
[0018] The disclosure further relates to a composition as described
herein further comprising one or more prebiotics.
[0019] In a preferred embodiment, this disclosure relates to a
composition as described herein wherein the bacteria are preadapted
by growing them together in a fermenter prior to administering the
composition to the subject to prevent or treat the
gastro-intestinal disorders.
[0020] In this regard, the disclosure further relates to a
composition as described herein wherein the fermenter is a dynamic
simulator of the gastro-intestinal tract.
[0021] More specifically, this disclosure relates to a composition
as described herein wherein the bacteria are chosen from the list
of the following strains: Faecalibacterium prausnitzii LMG P-29362,
Faecalibacterium prausnitzii DSMZ 17677, Butyricicoccus
pullicaecorum LMG P-29360, Butyricicoccus pullicaecorum LMG 24109,
Roseburia inulinivorans LMG P-29365, Roseburia inulinivorans DSMZ
16841, Roseburia hominis LMG P-29364, Roseburia hominis DSMZ 16839,
Akkermansia muciniphila LMG P-29361, Akkermansia muciniphila DSMZ
22959, Lactobacillus plantarum LMG P-29366, Lactobacillus plantarum
ZJ316, Anaerostipes caccae LMG P-29359, Anaerostipes caccae DSMZ
14662 and/or strains showing at least 97% sequence identity to the
16SrRNA sequences of at least one of the strains.
[0022] The disclosure further relates to a composition as described
herein wherein the composition is a pharmaceutical composition
formulated either as a rectally administrated form or an orally
ingestible form.
[0023] In this regard, the disclosure further relates to a
composition as described herein wherein the orally ingestible form
is a capsule, microcapsule, tablet, granule, powder, troche, pill,
suspension or syrup.
[0024] The disclosure further relates to a composition as described
herein that is incorporated in a food, drink, food supplement or
nutraceutical.
[0025] This disclosure more specifically relates to a composition
as described herein wherein the composition comprises between
10.sup.5 and 10.sup.11 colony-forming units of bacteria.
[0026] The gut microbiome comprises hundreds of microbial species
that co-exist within different subjects and that interact with each
other and the host. Nowadays, it is generally believed that the gut
microbiota play a key role in human health and disease by
regulating metabolic functions and immune homeostasis (Cent et al.
2014). Several studies have investigated these complex gut
microbial communities in an attempt to define a "core microbiome,"
implying that all human individuals share a key number of essential
species or strains that define the functional capabilities of a
healthy gut microbiome (Kinross et al., 2011). Based on this
concept (i.e., that all humans are populated by a core microbiome),
the extensive literature that is available on the composition and
function of the gut microbiota (e.g., keystone species, mucosal
versus luminal microbiota, proximal versus distal colon bacteria,
etc.) and functional genome analysis, a list of microbial
candidates could be identified that covers the main functionalities
of the complex human gut microbiome.
[0027] The disclosure relates in the first instance to a specific
selection of a subgroup of bacterial species of the human gut
microbiome that have a particular and surprising effect. More
specifically, the disclosure relates to a composition consisting
essentially of bacteria belonging to the species Faecalibacterium
prausnitzii, Butyricicoccus pullicaecorum, Roseburia inulinivorans,
Roseburia hominis, Akkermansia muciniphila, Lactobacillus plantarum
and Anaerostipes caccae preferably for use to prevent or treat
symptoms associated with a gastro-intestinal disorder. The term
"consisting essentially of" indicates that the composition may
include other bacterial species and/or other components provided
they do not negatively affect the effect (i.e., preventing or
treating symptoms associated with a gastro-intestinal disorder) of
the composition. In an embodiment, a composition of the disclosure
comprises bacteria belonging to the species Faecalibacterium
prausnitzii, Butyricicoccus pullicaecorum, Roseburia inulinivorans,
Roseburia hominis, Akkermansia muciniphila, Lactobacillus plantarum
and Anaerostipes caccae.
[0028] In another embodiment, a composition of the disclosure
consists of bacteria belonging to the species Faecalibacterium
prausnitzii, Butyricicoccus pullicaecorum, Roseburia inulinivorans,
Roseburia hominis, Akkermansia muciniphila, Lactobacillus plantarum
and Anaerostipes caccae.
[0029] The bacterial species Faecalibacterium prausnitzii (Duncan
et al. 2002), Butyricicoccus pullicaecorum (Eeckhaut et al. 2008),
Roseburia inulinivorans (Duncan et al. 2006), Roseburia hominis
(Duncan et al. 2006), Akkermansia muciniphila (Derrien et al.
2004), Lactobacillus plantarum (Walter 2008) and Anaerostipes
caccae (Schwiertz et al. 2002) are well-known bacterial species to
a skilled person. The terms "symptoms associated with a
gastro-intestinal disorder" refer to health problems in humans and
animals. The use of a composition of the disclosure leads more
specifically to prevention/recovery from dysbiosis resulting in a
positive modulation of the interaction between bacteria and
intestinal surface. As a result, an improved functioning of the
intestinal surface is obtained: e.g., barrier, hormonal, immune
functioning. The onset of the effect on the intestinal surface is
quicker when a "pre-adapted composition" is dosed as compared to a
"loosely assembled set of the same strains" (see further). As used
herein, modulating or improving the barrier, hormonal or immune
function of the intestinal surface is meant to include altering any
parameter that affects the normal homeostasis of the intestinal
surface and, in particular, its role in the first line of defense
against the invasion by pathogens, antigens or other harmful
substances and its role to produce substances (e.g., immune
molecules, hormones) that have systemic influences on the host. The
parameters include, but are not limited to: [0030] a stimulation of
the growth and/or activity of one or a limited number of beneficial
bacteria in the intestinal tract (e.g., lactobacilli,
bifidobacteria, butyrate- or propionate-producing bacteria,
others); [0031] an inhibition of the growth and/or activity of one
or a number of pathogenic bacteria in the intestinal tract; [0032]
a relative increase in the attachment of non-pathogenic bacteria to
the mucosa of the intestinal surface; [0033] a reduction in the
uncontrolled uptake from the gut of antigens, pro-inflammatory
molecules, bacteria or bacterial products; [0034] modulation of the
gut-associated lymphoid tissue (GALT) and the host systemic immune
system; [0035] production of specific bacterial metabolites (e.g.,
propionate, butyrate); and [0036] modulation of the production of
certain intestinal signaling molecules that directly or indirectly
modulate metabolic homeostasis (e.g., pro-glucagon, GLP-1, GLP-2,
FIAF).
[0037] This disclosure thus relates to a composition as described
herein wherein the gastro-intestinal disorder is prevented or
treated via: a) stimulating growth and/or activity of one or a
limited number of beneficial bacteria in the intestinal tract, b)
inhibiting growth and/or activity of one or a limited number of
pathogenic bacteria in the intestinal tract, c) relatively
increasing the attachment of non-pathogenic bacteria to the mucosa
of the gastrointestinal surface, d) reducing uncontrolled uptake of
antigens, pro-inflammatory, bacteria or bacterial products by the
gut, e) providing anti-inflammatory activity at the intestinal
surface, f) increasing gut barrier functioning, g) producing
bacterial metabolites or h) any combination of a) to g).
[0038] Health conditions that may be associated with general
gastro-intestinal disorders include, but are not limited to,
constipation, Irritable Bowel Syndrome (IBS), Inflammatory Bowel
Diseases (IBD), gut microbiota dysbiosis, mucositis, metabolic
syndrome, obesity, diabetes, a cardiovascular disease, chronic
fatigue syndrome, a mental condition, impaired cognitive function,
a neurodegenerative disease, a form of cancer, an autoimmune
condition, impaired immune functioning, rheumatism, rheumatoid
arthritis, inflammation of the female reproductive apparatus, and
infection of pathogens (bacteria, viruses and fungi). Examples of
neurodegenerative diseases include, but are not limited to, ALS,
dementia, Alzheimer's, Parkinson's and Huntington's disease.
Examples of types of cancers include, but are not limited to, lung
cancer, breast cancer, prostate cancer, pancreatic cancer and
particularly colorectal cancer. Examples of autoimmune diseases
include, but are not limited to, multiple sclerosis, atopic
dermatitis, celiac disease, psoriasis and lupus.
[0039] Based on the observation that the compositions of the
disclosure enhance the interaction and/or activity of
non-pathogenic bacteria to the mucosal layer of the
gastrointestinal epithelium, it is envisaged that the preparations
are particularly useful to improve the barrier function of the
intestinal surface, such as, for example, to prevent or reduce the
uncontrolled uptake from the gut of antigens, pro-inflammatory
molecules, pathogenic bacteria or bacterial products. One such
indication with an impaired mucosal barrier is Inflammatory Bowel
Disease. As it is generally accepted that in Inflammatory Bowel
Diseases, mucosal injury with an impaired resolution of the lesions
is one of the key elements that lead to these chronic indications,
the compositions of the disclosure have a beneficial effect in that
indication. Provided is the use of the compositions of the
disclosure in the prevention and treatment of conditions associated
with an impaired barrier function and characterized by the
uncontrolled uptake from the gut of antigens, pro-inflammatory
molecules, pathogenic bacteria or bacterial products.
[0040] "Inflammatory bowel diseases," also referred to as "chronic
colonic diseases," as used herein include any condition
characterized by persistent mucosal inflammation at different
levels of the gastrointestinal tract, such as, for example,
inflammatory bowel syndrome, mucositis, gastric ulcers, Crohn's
disease, ulcerative colitis, colorectal cancer and pouchitis.
[0041] As mucositis is generally recognized as being essentially
characterized by inflammation of the mucosal surface lining the
mouth and gastrointestinal tract, typically as adverse event of
chemotherapy and radiotherapy or stem cell transplantation, it is
also to be envisaged that the application of the compositions of
the disclosure have a beneficial effect in that indication. Thus,
also provided herein is the use of the compositions of the
disclosure in the prevention and treatment of conditions associated
with mucositis. Mucositis can occur anywhere along the
gastrointestinal tract. In the case of occurring in the oral
cavity, it is typically referred to as oral mucositis.
[0042] It is also to be envisaged that the application of the
compositions of the disclosure provide protection against
introduction of antigens that cause allergic reactions, whereby
such allergens may comprise certain food substances, chemicals and
other molecules. Thus, in a further embodiment, provided is the use
of compositions in the prevention and treatment of conditions
associated with the introduction of antigens leading to allergic
reactions (e.g., food allergies, asthma, and eczema).
[0043] It is furthermore also envisaged that the application of the
compositions to influence both the gut-associated lymphoid tissue
(GALT) as well as the systemic immune system. Among other effects,
this may result in decreased expression of pro-inflammatory
cytokines and increased production of immunoregulatory factors and
improved activity of lymphocytes. It is, therefore, envisaged that
the compositions be particularly useful in improving the
development and functioning of the host immune system.
[0044] In another aspect of the disclosure, based on the
observation that the compositions of the disclosure modulate the
epithelial barrier and subsequently decrease chronic inflammation,
it is envisaged that the compositions be particularly useful in
controlling and improving metabolic homeostasis. Non-limiting
effects of the preparations on metabolic homeostasis include
control of food intake and fat and glucose metabolism, improvement
of insulin secretion and sensitivity and control of cholesterol
synthesis and metabolism. Thus, also provided herein is the use of
the compositions of the disclosure in the management of food
uptake, induction of satiety, weight management, and the prevention
and treatment of conditions associated with an impaired metabolic
homeostasis, such as obesity and type 2 diabetes.
[0045] Based on the observation that a composition of the
disclosure decreases several established causal risk factors of
cardiovascular diseases (CVD), it is to be envisaged in another
aspect of the disclosure that the compositions be particularly
useful for the prevention of CVD. CVD technically refers to any
disease that affects the cardiovascular system, yet is usually used
to refer to those related to atherosclerosis. The latter is a
syndrome affecting arterial blood vessels, a chronic inflammatory
response in the walls of arteries, in large part due to the
accumulation of macrophage white blood cells and promoted by low
density lipoproteins. CVD development depends on multiple
mechanisms and a number of clear causal risk factors have been
identified. These factors include, yet are not limited to, elevated
LDL cholesterol, plasma triglycerides, metabolic diseases (obesity,
diabetes, etc.), chronic inflammation and oxidative stress. The
latter two factors are especially of utmost importance.
Atherosclerosis develops from LDL becoming oxidized (LDL-ox) by
free radicals, particularly oxygen free radicals, in situations of
oxidative stress. Excessive response of the immune system, in case
of chronic inflammation, to damage caused by LDL-ox further
promotes the expansion of the disease. Thus, also provided herein
is the use of the compositions of the disclosure in the prevention
or treatment of CVD.
[0046] In a further aspect, given the beneficial effect of the
compositions of the disclosure on the adherence of the normal
microbiota to the mucosal layer, it is envisaged that the
application of the compositions provides protection against mucosal
attachment and invasion by pathogens. Examples of pathogens
include, but are not limited to, Bacillus anthracis, Bacillus
cereus, Bordetella pertussis, Borrelia burgdorferi, Brucella
abortus, Brucella canis, Brucella melitensis, Brucella suis,
Campylobacter jejuni, Chlamydia pneumonia, Chlamydia trachomatis,
Chlamydophila psittaci, Clostridium botulinum, Clostridium
difficile, Clostridium perfringens, Clostridium tetani,
Corynebacterium diphtheria, Enterotoxigenic Escherichia coli
(ETEC), Enteropathogenic E. coli, E. coli O157:H7, Francisella
tularensis, Haemophilus influenza, Helicobacter pylori, Legionella
pneumophila, Leptospira interrogans, Listeria monocytogenes,
Mycobacterium leprae, Mycobacterium tuberculosis, Mycoplasma
pneumonia, Neisseria gonorrhoeae, Neisseria meningitides,
Pseudomonas aeruginosa, Rickettsia rickettsii, Salmonella typhi,
Salmonella typhimurium, Shigella sonnei, Staphylococcus aureus,
Staphylococcus epidermidis, Staphylococcus saprophyticus,
Streptococcus agalactiae, Streptococcus pneumonia, Streptococcus
pyogenes, Treponema pallidum, Vibrio cholera, Yersinia pestis,
Candida spp., Norovirus (Norwalk Virus), and Hepatitis A, and
viruses inducing smallpox, influenza, mumps, measles, chickenpox,
ebola, and rubella. Thus, in a further embodiment, the disclosure
provides the use of the compositions of the disclosure in the
prevention and treatment of conditions associated with the mucosal
attachment and invasion by pathogens, in particular, in the
treatment and prevention of acquired diarrhea and traveler's
diarrhea.
[0047] The disclosure thus relates to a method to prevent or treat
symptoms associated with a gastro-intestinal disorder in a subject
in need thereof comprising administering a therapeutically
effective amount of a composition consisting essentially of
bacteria belonging to the species Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila, Lactobacillus plantarum and
Anaerostipes caccae.
[0048] The term "subject in need" refers to a human or a non-human
animal having a gastro-intestinal disorder as described herein.
[0049] The terms "a therapeutically effective amount" refers to a
minimum of the combined total amount of the seven bacterial species
that is capable of exerting its prophylactic or therapeutic effect.
The seven bacteria species are Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila, Lactobacillus plantarum and
Anaerostipes caccae.
[0050] However, "a therapeutically effective amount" may also refer
to a minimum of a combined total amount of six bacteria species:
Faecalibacterium prausnitzii, Butyricicoccus pullicaecorum,
Roseburia inulinivorans, Akkermansia muciniphila, Lactobacillus
plantarum and Anaerostipes caccae.
[0051] Depending on the final application, the combined total
amount can be the result of equal amounts of each of the seven
bacterial species or unequal amounts of the seven bacterial
species, in which each single species of the seven bacterial
species has a minimum abundance of 0.0001% of the combined total
amount, more preferably a minimum abundance of 0.001% of the
combined total amount and most preferably a minimum abundance of
0.01% of the combined total amount. If thus, for example, six
species have an abundance of 10.00% of the combined total amount,
then the seventh species has an abundance of 40.00% of the combined
total amount. Depending on the final application, the combined
total amount ranges between a daily dose of 10.sup.2 and 10.sup.14
bacterial cells, preferably ranging between a daily dose of
10.sup.3 and 10.sup.13 bacterial cells, more preferably ranging
between a daily dose of 10.sup.4 and 10.sup.12 bacterial cells and
most preferably ranging between a daily dose of 10.sup.5 and
10.sup.11 bacterial cells.
[0052] The disclosure further relates to a composition as described
herein wherein bacteria belonging to the species Roseburia hominis
are eliminated from the composition. The term "eliminated" refers,
in particular, to making a composition of six bacterial species as
is indicated further in the Examples section without adding or
removing the species Roseburia hominis as a seventh species.
[0053] The disclosure further relates to a composition as described
herein wherein bacteria belonging to the species Escherichia coli,
Enterococcus faecium, Lactobacillus mucosae, Bifidobacterium
adolescentis, Bifidobacterium longum, Bacteroides thetaiotaomicron
and Bacteroides vulgatus are further added to the composition.
[0054] The bacterial species Escherichia coli (Rath et al. 1999),
Enterococcus faecium (Schleifer et al. 1984), Lactobacillus mucosae
(Roos et al. 2000), Bifidobacterium adolescentis (Scharek et al.
2000), Bifidobacterium longum (Bahaka et al. 1993), Bacteroides
thetaiotaomicron (Scharek et al. 2000) and Bacteroides vulgatus
(Rath et al. 1999) are well known bacterial species to a skilled
person. The disclosure further relates to a composition as
described herein further comprising one or more prebiotics.
[0055] The term "prebiotic" refers to any chemical that induces the
growth or activity of microorganisms (e.g., bacteria) that
contribute to the well-being of their host. Hence, prebiotics can
influence or alter the composition of organisms in the gut
microbiome. However, in principle, it is a more general term that
can refer to other areas of the body as well. Typical, but
non-limiting, prebiotics are non-digestible fiber compounds that at
least partially pass undigested through the upper part of the
gastrointestinal tract and stimulate the growth or activity of
advantageous bacteria that colonize the large bowel by acting as
substrate for them.
[0056] In a preferred embodiment, the disclosure relates to a
composition as described herein wherein the bacteria are grown
together in a fermenter prior to administering the composition to
prevent or treat the gastro-intestinal disorders. The latter
compositions are also referred to (see further) as the "Collaborome
strategy" or as the "Alternative collaborome strategy." In
contrast, compositions wherein the bacteria are not grown together
in a fermenter prior to administration are referred to (see
further) as the "Assembly strategy."
[0057] In this regard, this disclosure further relates to a
composition as described herein wherein the fermenter is a dynamic
simulator of the gastro-intestinal tract. In this specific case,
the latter compositions are also referred to (see further) as the
"Collaborome strategy."
[0058] The SHIME.RTM. (Simulator of the Human Microbial Ecosystem)
is a dynamic in vitro model of the human gastrointestinal tract
that is composed of five double jacketed vessels, simulating the
stomach, small intestine, and the three colon regions (ascending,
transverse, and descending colon), with a total retention time of
72 hours (FIG. 1). Three times per day, 140 ml SHIME.RTM. feed and
60 ml pancreatic juice were added to the stomach and small
intestine compartments, respectively (Van den Abbeele et al.,
2010). After an initial two-week stabilization period, which allows
the microbiota to adapt to the imposed in vitro conditions, the
isolation procedure was started. The selected microbial strains of
the disclosure can thus be inoculated in single-stage (alternative
collaborome strategy) or multi-stage reactors or dynamic simulators
of the gastrointestinal tract (e.g., SHIME.RTM. or M-SHIME.RTM.,
collaborome strategy) under standardized conditions representative
for the GI tract. Accordingly, the disclosure relates to a reactor
comprising a composition comprising, consisting of or consisting
essentially of bacteria belonging to six or seven or up to fourteen
species as defined herein and further listed below: [0059]
comprising a composition comprising, consisting of or consisting
essentially of bacteria belonging to the species Faecalibacterium
prausnitzii, Butyricicoccus pullicaecorum, Roseburia inulinivorans,
Roseburia hominis, Akkermansia muciniphila, Lactobacillus
plantarum, and Anaerostipes caccae, or [0060] comprising a
composition comprising, consisting of or consisting essentially of
bacteria belonging to the species Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Akkermansia
muciniphila, Lactobacillus plantarum, and Anaerostipes caccae or,
[0061] comprising a composition comprising, consisting of or
consisting essentially of bacteria belonging to the species
Faecalibacterium prausnitzii, Butyricicoccus pullicaecorum,
Roseburia inulinivorans, Roseburia hominis, Akkermansia
muciniphila, Lactobacillus plantarum, Anaerostipes caccae,
Escherichia coli, Enterococcus faecium, Lactobacillus mucosae,
Bifidobacterium adolescentis, Bifidobacterium longum, Bacteroides
thetaiotaomicron, and Bacteroides vulgatus.
[0062] In a preferred embodiment, this reactor comprising the
composition is under standardized conditions representative for the
GI tract as defined below.
[0063] The parameters characterizing the standardized conditions
include, but are not limited to, pH (ranging between 1.5 and 8);
availability of carbon sources (either carbohydrate or proteins or
a combination thereof); retention time in a specific reactor
(ranging between 10 minutes and 200 hours); oxygen availability
(ranging between 0 and 8 g/L); availability of micronutrients;
presence/absence of antibiotics; concentration of bile salts
(ranging between 0 and 20 mM); presence of heavy metals; and
presence of host factors as immune molecules. In a preferred
embodiment, the parameters characterizing the standardized
conditions comprise pH, retention time in a specific reactor and
concentration of bile salts, all as earlier defined herein.
Depending on the complexity of the collaborome, a period of 1 to 15
days is needed to obtain a functionally stable collaborome. On
average, in order to develop a collaborome composed of 7 to 14
members, a time between 3 and 10 days is sufficient to obtain a
functionally stable collaborome (depending on the environmental
conditions). A composition as defined herein is, therefore,
obtainable after having been trained or cultured during a time
between 3 and 10 days under conditions wherein pH, retention time
in a specific reactor, and concentration of bile salts have been
set as defined herein. Such a process allows the production of a
composition or collaborome that is functionally stable.
[0064] Within the context of the disclosure, "a functionally stable
collaborome" is a composition as defined herein still comprising
the initial different number of species of bacteria after at least
3 or 5 or 10 days of culture.
[0065] In a further aspect, there is provided a reactor operating
under standardized conditions representative for the GI tract,
comprising: pH ranging between 1.5 and 8; availability of carbon
sources; retention time between 10 minutes and 200 hours; oxygen
availability between 0 and 8 g/L; availability of micronutrients;
presence/absence of antibiotics; concentration of bile salts
between 0 and 20 mM; presence of heavy metals; and presence of host
factors as immune molecules. In an embodiment, the reactor is such
that the parameters characterizing the standardized conditions
comprise pH, retention time in a specific reactor and concentration
of bile salts as defined in the previous paragraph. In an
embodiment, such reactor comprises a composition of 5 and 20
distinct bacteria members, or 6 to 14 distinct bacteria members or
5 to 15 distinct bacteria members. In a preferred embodiment, such
composition resides for a time between 3 and 14 days or 3 and 10
days in such a reactor to obtain a functionally stable
collaborome.
[0066] The disclosure more specifically relates to the composition
and use of a set of microbial strains having specific functional
characteristics and pre-adapted to function together in order to
prevent or treat health problems in humans and animals and
obtaining a faster biotherapeutic onset and higher efficiency as
compared to a loosely assembled set of the same strains (="assembly
strategy"). Such a set of microorganisms pre-adapted to function
together takes the name of the "collaborome strategy" or
"alternative collaborome strategy."
[0067] In other words, the disclosure relates to pre-adapted
compositions of sets of microbial strains preferably for use to
significantly decrease the time of biotherapeutic onset and/or to
significantly increase the effect of treatment of dysbiosis as
compared to a loosely assembled set of the same microbial
strains.
[0068] The terms "significantly decrease the time of biotherapeutic
onset" mean that, by being pre-adapted, the set of microorganisms
can exert their functionality at least 5% quicker (on a temporal
scale), preferably at least 10% quicker, more preferably at least
20% quicker and most preferably at least 30% quicker as compared to
a loosely assembled set of the same strains. Any value below 5% is
considered physiologically not relevant.
[0069] The terms "significantly increase the effect of treatment"
mean that, by being pre-adapted, the set of microorganisms can
exert their functionality with at least a 5% higher efficacy,
preferably at least 10% more efficient, more preferably at least
20% and most preferably at least 30% more efficient. The efficacy
depends on the endpoint for which the set of microorganisms has
been designed. Possible functionalities include, but are not
limited to, Short Chain Fatty Acid (SCFA) production, improvement
in gut barrier permeability, decrease/increase in pro-inflammatory
cytokines, increase in anti-inflammatory cytokines, decrease in
pathogen concentration (at least 0.5 log), decrease in gas
production, and stimulation of specific gut-wall receptors, etc.
Any value below 5% is considered physiologically not relevant.
[0070] Hence, the disclosure more specifically relates to a method
to prevent or treat dysbiosis of humans and animals in need thereof
comprising administering a therapeutic amount of a pre-adapted
composition of a set of microbial strains to the humans or animals
wherein the treatment results in a faster biotherapeutic onset
and/or increased efficiency as compared to the administration of a
loosely assembled set of the same microbial strains.
[0071] More specifically, the disclosure relates to a composition
as described herein wherein the bacteria are chosen from the list
of the following strains: Faecalibacterium prausnitzii LMG P-29362,
Faecalibacterium prausnitzii DSMZ 17677, Butyricicoccus
pullicaecorum LMG P-29360, Butyricicoccus pullicaecorum LMG 24109,
Roseburia inulinivorans LMG P-29365, Roseburia inulinivorans DSMZ
16841, Roseburia hominis LMG P-29364, Roseburia hominis DSMZ 16839,
Akkermansia muciniphila LMG P-29361, Akkermansia muciniphila DSMZ
22959, Lactobacillus plantarum LMG P-29366, Lactobacillus plantarum
ZJ316, Anaerostipes caccae LMG P-29359, Anaerostipes caccae DSMZ
14662 and/or strains showing at least 97% sequence identity to the
16SrRNA sequences of at least one of the strains.
[0072] The above-indicated strains having accession numbers LMG
P-29362 (date of deposit: Jan. 18, 2016), LMG P-29360 (date of
deposit: Jan. 18, 2016), LMG P-29365 (date of deposit: Jan. 18,
2016), LMG P-29364 (date of deposit: Jan. 18, 2016), LMG P-29361
(date of deposit: Jan. 18, 2016), LMG P-29366 (date of deposit:
Jan. 18, 2016) and LMG P-29359 (date of deposit: Jan. 18, 2016)
have been deposited with BCCM/LMG Laboratorium voor Microbiologie,
Universiteit Gent (UGent), having an address of K. L.
Ledeganckstraat 35, B-9000 Gent, Belgium.
[0073] The above-indicated strains having accession numbers DSMZ
17677, LMG24109, DSMZ 16841, DSMZ 16839, DSMZ 22959, ZJ316 and DSMZ
14662 have been deposited in public collections, have been
described intensively and are accessible to skilled persons
worldwide.
[0074] It should be further clear that variants of each of the
strains showing at least 97% (i.e., 97, 98, 99%) sequence homology
to the 16S rRNA sequence of each of the corresponding strains are
also part of this disclosure. An example to determine such sequence
"homology" is, for instance, described by Eeckhaut et al. (2008).
As used herein, the term "16S rRNA" refers to a nucleic acid
sequence of about 1542 nucleotides, which is a component of the
small prokaryotic ribosomal subunit (30S). The 16S rRNA is known to
act as a scaffold defining the positions of the ribosomal proteins.
The 16S rRNA sequence is commonly used for phylogenetic studies, as
it is known to be a highly conserved sequence. Comparative analysis
of 16S rRNA sequences from thousands of organisms has demonstrated
the presence of oligonucleotide signature sequences. As used
herein, the term "homology" refers to the sequence similarity of
the nucleic acids. For example, in general, if two nucleic acids
have identical sequences they show 100% homology. A change in the
nucleotide sequence of one of the nucleic acids reduces the
percentage of homology. In general, the percentage homology
quantifies the degree of identity between two nucleic acid
sentences.
[0075] Sequence identity or sequence homology is herein defined as
a relationship between two or more amino acid (polypeptide or
protein) sequences or two or more nucleic acid (polynucleotide)
sequences, as determined by comparing the sequences. Usually,
sequence identities or similarities are compared over the whole
length of the sequences compared. In the art, "identity" also means
the degree of sequence relatedness between amino acid or nucleic
acid sequences, as the case may be, as determined by the match
between strings of such sequences. "Similarity" between two amino
acid sequences is determined by comparing the amino acid sequence
and its conserved amino acid substitutes of one polypeptide to the
sequence of a second polypeptide. "Identity" and "similarity" can
be readily calculated by various methods, known to those skilled in
the art. In a preferred embodiment, sequence identity is determined
by comparing the whole length of the sequences as identified
herein.
[0076] Preferred methods to determine identity are designed to give
the largest match between the sequences tested. Methods to
determine identity and similarity are codified in publicly
available computer programs. Preferred computer program methods to
determine identity and similarity between two sequences include,
e.g., the BestFit, BLASTP, BLASTN, and FASTA (S. F. Altschul et
al., J. Mol. Biol. 215:403-410 (1990), publicly available from NCBI
and other sources (BLAST Manual, S. Altschul et al., NCBI NLM NIH
Bethesda, Md. 20894). A most preferred algorithm used is EMBOSS (on
the World Wide Web at ebi.ac.uk/emboss/align). Preferred parameters
for amino acid sequences comparison using EMBOSS are gap open 10.0,
gap extend 0.5, Blosum 62 matrix. Preferred parameters for nucleic
acid sequences comparison using EMBOSS are gap open 10.0, gap
extend 0.5, DNA full matrix (DNA identity matrix).
[0077] Optionally, in determining the degree of amino acid
similarity, the skilled person may also take into account so-called
"conservative" amino acid substitutions, as will be clear to the
skilled person. Conservative amino acid substitutions refer to the
interchangeability of residues having similar side chains. For
example, a group of amino acids having aliphatic side chains is
glycine, alanine, valine, leucine, and isoleucine; a group of amino
acids having aliphatic-hydroxyl side chains is serine and
threonine; a group of amino acids having amide-containing side
chains is asparagine and glutamine; a group of amino acids having
aromatic side chains is phenylalanine, tyrosine, and tryptophan; a
group of amino acids having basic side chains is lysine, arginine,
and histidine; and a group of amino acids having sulphur-containing
side chains is cysteine and methionine. Preferred conservative
amino acids substitution groups are: valine-leucine-isoleucine,
phenylalanine-tyrosine, lysine-arginine, alanine-valine, and
asparagine-glutamine. Substitutional variants of the amino acid
sequence disclosed herein are those in which at least one residue
in the disclosed sequences has been removed and a different residue
inserted in its place. Preferably, the amino acid change is
conservative. Preferred conservative substitutions for each of the
naturally occurring amino acids are as follows: Ala to ser; Arg to
lys; Asn to gln or his; Asp to glu; Cys to ser or ala; Gln to asn;
Glu to asp; Gly to pro; His to asn or gln; Ile to leu or val; Leu
to ile or val; Lys to arg; gln or glu; Met to leu or ile; Phe to
met, leu or tyr; Ser to thr; Thr to ser; Trp to tyr; Tyr to trp or
phe; and Val to ile or leu.
[0078] It is well known to a person skilled in the art that 16s
rRNA sequences can be deposited online, for example, at GenBank (on
the World Wide Web at ncbi.nlm.nih.gov/genbank/) and that they can
be retrieved based on their unique accession number for use as
reference 16S rRNA sequence in evaluation of sequence homology,
such as, for example, described by Eeckhaut et al. (2008). The
GenBank accession numbers for the 16S rRNA sequences of seven
bacterial species of the composition are listed below. These
accession numbers can be used to retrieve the respective 16S rRNA
sequences from the World Wide Web at ncbi.nlm.nih.gov/genbank/ for
assessment of sequence homology.
TABLE-US-00001 GenBank accession number Species Strain
(ncbi.nlm.nih.gov/genbank/) Roseburia hominis DSMZ 16839 AJ270482.2
(SEQ ID NO:1) Roseburia inulinivorans DSMZ 16841 AJ270473.3 (SEQ ID
NO:2) Akkermansia muciniphila DSMZ 22959 AY271254.1 (SEQ ID NO:3)
Anaerostipes caccae DSMZ 14662 AJ270487.2 (SEQ ID NO:4)
Faecalibacterium DSMZ 17677 AJ270469.2 (SEQ ID NO:5) prausnitzii
Lactobacillus plantarum ZJ316 JN126052.1 (SEQ ID NO:6)
Butyricicoccus LMG 24109 HH793440.1 (SEQ ID NO:7) pullicaecorum
[0079] The disclosure further relates to a composition as described
herein wherein the composition is a pharmaceutical composition
formulated either as a rectally administrated form or an orally
ingestible form.
[0080] In this regard, the disclosure further relates to a
composition as described herein wherein the orally ingestible form
is a capsule, microcapsule, tablet, granule, powder, troche, pill,
suspension or syrup.
[0081] This disclosure further relates to a composition as
described herein that is incorporated in a food, drink, food
supplement or nutraceutical.
[0082] The disclosure thus relates to a composition as described
herein that is used as food, food supplement or medicine for a
human, a non-human domestic or farmed land animal or an aquatic
animal. The composition can thus be introduced in food, functional
foods, food supplements, cosmetics, nutraceutical formulations,
probiotic composition or pharmaceutical. A food is typically an
edible material composed primarily of one or more of the
macronutrients protein, carbohydrate and fat. A food may also
contain one or more micronutrients such as vitamins or minerals.
The term food as used herein also covers a beverage. Examples of
foods in which the composition may be incorporated include snack
bars, cereals, buns, muffins, biscuits, cakes, pastries, processed
vegetables, sweets, probiotic formulations including yogurts,
beverages, plant oil-based liquids, animal fat-based liquids,
frozen confections and cheeses. Preferred foods include yogurts,
cheeses and other dairy products. Examples of beverages include
soft beverages, syrups, squashes, dry drink mixes and nutritional
beverages. A nutraceutical is a food ingredient, food supplement or
food product that is considered to provide a medical or health
benefit, including the prevention and treatment of disease. A
functional food is a food that is typically marketed as providing a
health benefit beyond that of supplying pure nutrition to the
consumer.
[0083] Also provided is a probiotic comprising a composition as
discussed herein. A probiotic is typically a live supplement that
can enhance the intestinal microbiota. Such probiotics may be given
in particular to humans but also to farm and domestic animals and
to aquatic organisms. The probiotic may additionally comprise one
or more acceptable excipients or flavorings, which are suitable for
ingestion by a human or animal.
[0084] A composition of the disclosure may be used in the
production of pharmaceutical compositions. Thus, further provided
is a pharmaceutical composition comprising a composition of the
disclosure and a pharmaceutically acceptable excipient or
carrier.
[0085] Compositions comprising compounds of the disclosure may be
in diverse forms, for example, in the form of a tablet, capsule, or
powder. Examples of excipients that may be present in such
compositions include diluents (e.g., starch, cellulose derivatives
or sugar derivatives), a stabilizer (e.g., hygroscopic excipients
such as silica or maltodextrin), a lubricant (e.g., magnesium
stearate), a buffer (e.g., phosphate buffer), a binder, coating,
preservative or suspension agent. Suitable excipients are well
known to those skilled in the art.
[0086] This disclosure more specifically relates to a composition
as described herein wherein the composition comprises a total
between 10.sup.5 and 10.sup.11 colony-forming units of bacteria of
the disclosure.
[0087] In this document and in its claims, the verb "to comprise"
and its conjugations is used in its non-limiting sense to mean that
items following the word are included, but items not specifically
mentioned are not excluded. In addition, the verb "to consist" may
be replaced by "to consist essentially of" meaning that a
composition as defined herein may comprise additional component(s)
than the ones specifically identified, the additional component(s)
not altering the unique characteristic of the disclosure. In
addition, reference to an element by the indefinite article "a" or
"an" does not exclude the possibility that more than one of the
elements are present, unless the context clearly requires that
there be one and only one of the elements. The indefinite article
"a" or "an" thus usually means "at least one."
[0088] All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety. The included examples are offered for illustrative
purposes only, and are not intended to limit the scope of the
disclosure in any way.
BRIEF DESCRIPTION OF THE DRAWINGS
[0089] FIG. 1: Schematic representation of a SHIME.RTM. unit that
consists of stomach, small intestine, and the three different colon
regions. Liquid SHIME.RTM. nutritional medium and pancreatic juice
enter the compartments, which simulate the stomach and small
intestine, respectively. After a defined residence time in these
sterile compartments, the suspension goes to three consecutive
colon compartments, the ascending, transverse, and descending colon
compartments, each characterized by distinct pHs and residence
times. These compartments are inoculated with human fecal
microbiota. All vessels are kept anaerobic by flushing the
headspace with N2, continuously stirred, and kept at 37.degree.
C.
[0090] FIG. 2: Butyrate production by 23 different compositions
upon 24-hour incubation (top panel) and effect on the
transepithelial electrical resistance (TEER) of Caco-2 cells
cultured in the presence of THP1 cells (bottom panel). For the
latter, samples collected from the 23 incubations after 24 were
sterile-filtered and added (1:5 v/v) for 24 hours to the apical
compartment of Caco-2 cells grown for fourteen days on
semipermeable inserts and placed on top of PMA-stimulated
THP1-derived macrophages (co-cultures). Growth medium alone (DMEM)
was used as control. THP1 cells cultured in the presence of PMA for
48 hours induce damage on the Caco-2 cells as measured by a
decrease in TEER in the DMEM control. TEER values have been
normalized to the values measured before co-culture (0 hour) and
are expressed as percentage from the initial value. The coding of
the different compositions was as follows: MX-Y, in which X=number
of isolates present in the composition and Y=unique composition A,
B, C, etc., with X isolates.
[0091] FIG. 3: Butyrate production upon 24-hour and 48-hour
incubation in conditioned SHIME.RTM. nutritional medium by either
the complete composition of seven species or compositions of six
species, in which each time one of the seven original species was
omitted. Results are presented as the percentage of butyrate
production detected in each incubation with a composition of six
species, as opposed to the composition consisting of all seven
species. Compositions are referred to as "Total" (all seven
species) or "Total-X," with X being the species omitted from the
total composition. *: p<0.05 as compared to "Total" at 24 hours;
#: p<0.05 as compared to "Total" at 48 hours.
[0092] FIG. 4: Levels (mM) of butyrate, propionate and acetate
produced by the composition throughout a five-day anaerobic
incubation in conditioned SHIME.RTM. nutritional medium. The
composition was either produced through the "Assembly" strategy
(left panel) or the "Collaborome" strategy (right panel).
[0093] FIG. 5: Evolution of the levels (mM) of propionate (left
panel) and butyrate (right panel) over a fourteen-day time period
in three independent production cycles of the composition through
the "Collaborome" strategy. Upon initial growth in appropriate
culture medium, the strains of the composition were mixed,
inoculated and cultured for fourteen days in triplicate in a
SHIME.RTM. setup, consisting of a single colon region at a pH of
6.15-6.4.
[0094] FIG. 6: Evolution of SCFA levels expressed as mol % of
acetate, propionate and butyrate over time, upon production of the
composition through the alternative "Collaborome" strategy. Upon
initial growth in appropriate culture medium, the strains of the
composition were mixed, inoculated and cultured for eight days in
triplicate in single fermenters operated in a fed-batch mode. At
specific intervals of 16 hours, 40% (v:v) of the growth medium was
replaced with conditioned SHIME.RTM. nutritional medium.
[0095] FIG. 7: Production (mM) of acetate, propionate, butyrate and
total short-chain fatty acids (SCFA) in 24-hour incubations with
(i) sterile basal medium (top panel), or sterile medium supplied
with (ii) microbiota derived from a SHIME.RTM. colon region (middle
panel) or (iii) fecal microbiota (lower panel). Different
treatments with the composition, produced through the "Collaborome"
strategy, were applied ranging from 0% to 4% and 20% of the total
incubation volume.
[0096] FIG. 8: Evolution of levels (mM) of acetate (top panel),
propionate (middle panel) and butyrate (lower panel) in an
antibiotic recovery experiment in the M-SHIME.RTM.. Upon dysbiosis
induction of the SHIME.RTM.-derived colon microbiota through
administration of a cocktail of antibiotics (40/40/10 mg/L of
amoxicillin/ciprofloxacin/tetracycline, respectively), the
dysbiosed microbiota was treated for five days with the
composition, produced either through the "Assembly" strategy or the
"Collaborome" strategy (day 1=start of administration of the
composition). The results are expressed as the delta of SCFA levels
in the SHIME.RTM. at each time point vs. the values before
antibiotic administration.
[0097] FIG. 9: Levels (mM) of acetate (top panel), propionate
(middle panel) and butyrate (lower panel) in an IBD-associated
dysbiosis recovery experiment in the M-SHIME.RTM.. Three
independent SHIME.RTM. colon vessels were inoculated with fecal
material from an Ulcerative Colitis patient. Simultaneously, a
single dose of the composition, produced either through the
"Assembly" strategy or the "Collaborome" strategy, was added to a
respective SHIME.RTM. colon vessel. A third experiment ran in
parallel as control experiment without administration of the
composition. Production of acetate, propionate and butyrate was
followed one and two days after administration of the
composition.
[0098] FIG. 10: Evolution of levels (mol %) of acetate, propionate
and butyrate in an antibiotic recovery experiment in C57/BL6 mice.
After a control period in which the mice were fed a standard diet,
gut microbiota dysbiosis was induced by adding clindamycin (250
mg/L) to the drinking water for five days. After this, the mice
(n=10/group) were orally gavaged for five days with either saline
solution (no bacterial intervention control; left panel), the
composition, produced through the "Collaborome" strategy (middle
panel) or the extended composition, produced through the
"Collaborome" strategy (right panel). Mice fecal samples obtained
from the same intervention group were pooled and levels of acetate,
propionate and butyrate were quantified.
[0099] FIG. 11: Evolution of the Disease Activity Index (DAI) and
weight change in a TNBS-induced colitis experiment in C57/BL6 mice.
After a one-week acclimatization period in which the mice were fed
a standard diet, the experiment was started. Each group (n=9/group)
was treated for five consecutive days by means of oral gavage.
Preventive dosing of all treatments started one day before the
rectal administration of 2 mg TNBS/50% EtOH and lasted for four
days after TNBS administration, before mice were sacrificed. The
following treatments were included: TNBS+saline solution (vehicle
TNBS control); TNBS+composition, produced through the "Assembly"
strategy, and TNBS+composition, produced through the "Collaborome"
strategy. A conventional group (without TNBS treatment but treated
with saline solution) was included as vehicle control.
[0100] FIG. 12: Evolution of the Disease Activity Index (DAI) in a
DSS-induced chronic colitis experiment in C57/BL6 mice. After a
one-week acclimatization period in which the mice were fed a
standard diet, the experiment was started. Each group (n=10/group)
was treated three times per week for eight consecutive weeks, by
means of oral gavage. Preventive dosing of all treatments started
one week before the first DSS cycle. The first DSS cycle started on
week 2 and included one week of DSS administration (0.25% in
drinking water) followed by two weeks of recovery. This first cycle
was followed by an identical second DSS cycle. The third DSS cycle
consisted of one week of DSS administration followed by one week of
recovery, after which the animals were sacrificed. The following
treatments were included: DSS+saline solution (vehicle DSS
control); DSS+composition, produced through the "Collaborome"
strategy. A conventional group (without DSS treatment but treated
with saline solution) was included as vehicle control.
DETAILED DESCRIPTION
Examples
Example 1: Establishment of a Composition
1.1 Isolation of Bacteria for the Composition
[0101] A young, healthy donor with no prior exposure to antibiotic
therapy was selected to inoculate the SHIME.RTM. model. By
controlling several operational parameters of the SHIME.RTM. model
(FIG. 1, Van den Abbeele et al., 2010), one can enrich and select
for networks of gut microbiota that have a beneficial impact on
human health such as microbiota involved in dietary fiber
fermentation, bile acids metabolism, lactose degradation, etc. The
SHIME.RTM. setup was used for isolation of bacterial strains with
different functional properties, such as fiber degraders (e.g.,
Bifidobacteria, Bacteroides), fermentative (e.g., Escherichia coli)
or lactate producers (e.g., Lactobacilli, Pediococci and
Enterococci), butyrate producers (e.g., Anaerostipes caccae,
Butyricicoccus pullicaecorum, Faecalibacterium prausnitzii,
Roseburia hominis, Roseburia inulinivorans, Clostridium butyricum)
and propionate producers (e.g., Bacteroides thetaiotaomicron,
Bacteroides vulgatus, Roseburia inulinivorans, Akkermansia
muciniphila). For this purpose, certain media were selected such as
LAMVAB (lactobacilli; Hartemink et al. 1997), RB (bifidobacteria;
Hartemink et al. 1996), Enterococcus medium (Enterococci;
Possemiers et al. 2004), TBX (Escherichia coli; Le Bon et al.
2010), BBE (Bacteroides fragilis group; Livingston et al. 1978),
Mucin minimal medium (Akkermansia; Derrien et al. 2004), M2GSC
(butyrate producers; Barcenilla et al. 2000) or lactate-containing
minimal SHIME.RTM. medium (butyrate producers), succinate- and
fucose-containing minimal SHIME.RTM. media (propionate producers),
sulphate-enriched minimal media (sulphate reducers),
arabinoxylan-containing minimal SHIME.RTM. medium and Blood agar
plates (Prevotella). In addition to the SHIME.RTM., bacteria were
also isolated directly from a fresh fecal sample from a healthy
donor, using the same strategy.
[0102] In practice, ten-fold dilutions of samples collected from
the colonic compartments of the SHIME.RTM. or homogenized fecal
samples were made and spread on agar plates with the specific
medium composition as described herein. Plates were incubated at
37.degree. C., taking into account the respective growth conditions
of the different bacterial groups. Upon incubation, approximately
30 colonies were picked up per bacterial group and incubated in the
respective liquid growth media under appropriate conditions. The
short-chain fatty acid concentrations in the overnight cultures
were analyzed using gas chromatography as described in Possemiers
et al. (2004). Furthermore, a sample of the liquid cultures was
used for phylogenetic analysis. DNA was extracted as described in
Possemiers et al. 2004 and the near-entire 16S rRNA sequences were
amplified for each isolate using the universal eubacterial primers
fD1 and rD1 (Weisburg et al. 1991). Upon purification, the DNA
samples were sent out for sequencing. The obtained sequences were
aligned with existing sequences for identification of each isolate
using the BLAST toolbox (on the World Wide Web at
blast.ncbi.nlm.nih.gov/Blast.cgi).
1.2 Design of the Composition
[0103] To combine different bacterial strains into actual
functional microbial networks, the pure cultures isolated from the
SHIME.RTM. reactor and fecal were used (as described in Example
1.1). Additionally, pure cultures were sourced from culture
collections such as BCCM/LMG (World Wide Web at bccm.belspo.be) and
DSMZ (World Wide Web at dsmz.de).
[0104] Short-chain fatty acids (SCFA) are the end products of
dietary fibers fermentation by the intestinal microbiota and are
known to exert several beneficial effects on host health. The main
SCFA produced are acetate, butyrate and propionate in an
approximate 60:20:20 molar ratio. Whereas acetate can be absorbed
from the gut and used as energy substrate by the host, butyrate
acts as the main energy source for the gut epithelium and has
proven protective effects against inflammation and colon cancer.
Propionate has similar local activity in the gut as compared to
butyrate, yet it is also transported to the liver where it was
shown to have positive cholesterol-lowering effects and effects on
glycemic control.
[0105] Considering the important and diverse physiological roles of
SCFA, disruption of this gut microbial function (e.g., in
gastrointestinal disorders) can have a significant impact on host
health. Consequently, in this example, a screening was performed to
design a composition that can induce the highest total SCFA
production and most interesting relative SCFA production ratios.
For the latter, butyrate was considered the most interesting among
the different SCFA produced. Furthermore, the effect of the
different compositions on gut barrier integrity was assessed by
means of a co-culture of epithelial and immune cells.
[0106] In practice, a total 20 isolates with the most interesting
fermentation profiles, obtained from the isolation and selection
round as described in 1.1 (referred to as "Isolate-X") or ordered
from culture collections, were retrieved from their glycerol stocks
and grown under their respective optimal growth conditions to
obtain homogeneous suspensions of the bacterial strains.
TABLE-US-00002 Ref Species Strain 1 Lactobacillus plantarum
Isolate-1 2 Clostridium bolteae Isolate-2 3 Desulfovibrio
desulfuricans Isolate-3 4 Akkermansia muciniphila Isolate-4 5
Coprococcus spp. Isolate-5 6 Roseburia hominis Isolate-6 7
Bacteroides Isolate-7 thetaiotaomicron 8 Clostridium butyricum
Isolate-8 9 Anaerostripes caccae Isolate-9 10 Bifidobacterium
Isolate-10 adolescentis 11 Faecalibacterium Isolate-11 prausnitzii
12 Roseburia inulinivorans Isolate-12 13 Ruminococcus spp.
Isolate-13 14 Lactobacillus acidophilus Isolate-14 15 Enterococcus
faecium Isolate-15 16 Butyrivibrio fibrisolvens Isolate-16 17
Eubacterium limosum DSM20543 Nissle 18 Escherichia coli 1917 19
Eubacterium rectale DSM17629 20 Butyricicoccus Isolate-17
pullicaecorum
[0107] Isolates were combined in numbers ranging from 2 to 10 in a
set of 98 individual initial screening experiments. For each
experiment, fermentation was started in sterile incubation bottles
containing sterilized SHIME.RTM. nutritional medium adjusted to pH
6.8 with KH.sub.2PO.sub.4/K.sub.2HPO.sub.4 and flushed with
nitrogen. Then, the sterilized medium was inoculated with 10% (v/v)
of mixed inoculum consisting of equal volumes of the selected
species. Incubation bottles were flushed with nitrogen to ensure
anaerobic conditions and were incubated at 37.degree. C. (90 rpm).
Samples were analyzed after 24 hours for SCFA production.
Compositions with the highest butyrate production were then
selected and further used in the final experiment with 23 different
sets of bacteria (referred to as MX-Y, in which X=number of
isolates present in the composition and Y=unique composition A, B,
C, etc. with X isolates).
TABLE-US-00003 Identification number Composition M2-A 10, 12 M3-A
1, 9, 11 M4-A 1, 5, 10, 11 M4-B 8, 10, 11, 17 M4-C 9, 10, 11, 13
M5-A 5, 8, 10, 13, 18 M5-B 6, 9, 10, 11, 18 M6-A 5, 6, 9, 10, 12,
14 M6-B 2, 4, 8, 11, 13, 19 M6-C 1, 4, 9, 11, 12, 17 M6-D 1, 6, 11,
13, 16, 20 M7-A 1, 3, 6, 9, 12, 16, 20 M7-B 1, 4, 6, 9, 11, 12, 20
M7-C 6, 7, 13, 14, 16, 17, 20 M8-A 4, 5, 6, 9, 10, 11, 13, 17 M8-B
4, 6, 7, 8, 11, 14, 16, 18 M8-C 1, 4, 8, 11, 12, 15, 17, 20 M9-A 3,
6, 7, 11, 13, 14, 15, 17, 20 M9-B 3, 4, 6, 7, 14, 15, 16, 18, 20
M9-C 2, 3, 5, 6, 7, 8, 12, 14, 20 M10-A 1, 3 ,4, 7, 8, 9, 10, 12,
14, 15 M10-B 3, 4, 5, 7, 8, 9, 12, 14, 15, 16, 19 M10-C 2, 4, 6, 8,
10, 11, 12, 13, 16, 18
[0108] These 23 combinations were again incubated as described
before. After 24 hours, samples were collected for SCFA analysis
and for combination with the co-culture model of Caco-2 and THP1
cells, as described in Possemiers et al. (2013). Endpoint of the
latter experiment was Trans-Epithelial Electrical Resistance (TEER)
as measured for protective effects toward gut barrier function.
[0109] FIG. 2 describes butyrate levels obtained upon 24-hour
incubation of the 23 different compositions as well as their effect
on the TEER values. Strong variation was observed in both butyrate
levels and effects on gut barrier functioning and combinations with
highest butyrate levels did not necessarily induce highest
protective effects on TEER levels, as shown by different ranking.
Surprisingly, one composition of seven different isolates (referred
to as M7-B in FIG. 2) was ranked first on both butyrate levels
after 24 hours and especially on protective effects toward gut
barrier function. This composition contained six isolates from the
SHIME.RTM. and one culture obtained from a human fecal sample. 16S
rRNA gene sequencing and comparison of the sequence with the NCBI
BLAST database revealed that M7-B was composed of novel SHIME.RTM.
isolates of Lactobacillus plantarum, Faecalibacterium prausnitzii,
Roseburia inulinivorans, Roseburia hominis, Akkermansia muciniphila
and Anaerostipes caccae and of a novel fecal isolate of
Butyricicoccus pullicaecorum. Interestingly, the novel isolates
were all present in at least one of the other compositions shown in
FIG. 2, yet none of the other compositions reached the same
effectivity with respect to butyrate production and protection of
TEER values. This shows that the observed effect is not related to
one of the specific species present in the composition, but that
only the specific combination of these seven bacteria leads to the
surprising positive results.
[0110] The seven novel isolates were deposited at the BCCM/LMG
Bacteria collection (Ghent Belgium), with accession numbers:
Faecalibacterium prausnitzii LMG P-29362, Butyricicoccus
pullicaecorum LMG P-29360, Roseburia inulinivorans LMG P-29365,
Roseburia hominis LMG P-29364, Akkermansia muciniphila LMG P-29361,
Lactobacillus plantarum LMG P-29366 and Anaerostipes caccae LMG
P-29359.
[0111] As additional experimental evidence of the surprising
synergy between the seven isolates and the need for presence of
each of the species, an experiment was set up in which each time
one of the isolates was removed (i.e., eliminated) from the
original composition of seven isolates. In practice, fermentation
was started again in sterile incubation bottles containing
sterilized SHIME.RTM. nutritional medium adjusted to pH 6.8 with
KH.sub.2PO.sub.4/K.sub.2HPO.sub.4 and flushed with nitrogen. Then,
the sterilized medium was inoculated with 10% (v/v) of mixed
inoculum consisting of equal volumes of six of the seven isolates.
The complete composition of seven isolates acted as control,
resulting in a total of eight parallel incubations. Incubation
bottles were flushed with nitrogen to ensure anaerobic conditions
and were incubated at 37.degree. C. (90 rpm). Samples were analyzed
after 24 hours and 48 hours for butyrate production. As shown in
FIG. 3, removal of only one species out of the original composition
significantly decreased butyrate production levels after 24 hours
for all compositions of six species to below 80% of the butyrate
production of the original composition. Also, after 48 hours of
incubation, butyrate levels were significantly lower for all
compositions of six species, with the exception of the composition
excluding Roseburia hominis. This confirms that all isolates of the
composition are essential to reach the full potential of the
composition. As only the composition excluding Roseburia hominis
still resulted in a similar functionality of the complete
composition after 48 hours of incubation, one can also envisage, as
second best, the use of the composition of six species, consisting
essentially of Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Akkermansia muciniphila,
Lactobacillus plantarum and Anaerostipes caccae.
1.3 Production of the Composition
[0112] A composition consisting of the species Lactobacillus
plantarum, Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Roseburia hominis,
Akkermansia muciniphila and Anaerostipes caccae is produced using
three different strategies. These strategies include either 1)
growing the species of the composition separately, followed by
mixing them together, 2) growing the species of the composition
together in a multi-stage fermenter (i.e., the in vitro SHIME.RTM.
model as described herein) and 3) growing the species of the
composition together in a single-stage fermenter.
[0113] In the first strategy (the "assembly" strategy), the
selected species were retrieved from their glycerol stocks and
grown under their respective optimal growth conditions to obtain
homogeneous suspensions of the bacterial strains. To evaluate their
functional activity, a mixed inoculum was created consisting of
equal volumes of the selected species. This inoculum was added at
10% (v/v) to sterile incubation bottles containing sterilized
SHIME.RTM. nutritional medium adjusted to pH 6.8 with
KH.sub.2PO.sub.4/K.sub.2HPO.sub.4. Incubation bottles were flushed
with nitrogen to ensure anaerobic conditions and were incubated at
37.degree. C. (90 rpm). At specific intervals of 16 hours, 40%
(v:v) of the growth medium was replaced with conditioned SHIME.RTM.
nutritional medium. Conditioned SHIME.RTM. nutritional medium was
prepared by incubating 700 mL of normal SHIME.RTM. feed (pH 2) for
one hour at 37.degree. C., after which 300 mL of pancreatic juice
(pH 6.8)--supplemented with 25 g/L NaHCO.sub.3, 23.6 g/L
KH.sub.2PO.sub.4 and 4.7 g/L K.sub.2HPO.sub.4--was added. Samples
were analyzed over a period of five days for SCFA production (FIG.
4). Butyrate levels reached 7 mM upon 24 hours incubation of the
assembly and a maximum of 14 mM after five days.
[0114] In the second strategy (i.e., the "Collaborome" strategy or
the strategy "wherein the bacteria are grown together in a dynamic
simulator of the gastro-intestinal tract prior to administration"),
the selected species were retrieved from their glycerol stocks and
grown under their respective optimal growth conditions to obtain
homogeneous suspensions of the bacterial strains. Then, the strains
were mixed and inoculated in triplicate in a SHIME.RTM. setup (Van
den Abeele et al., 2010) consisting of a single colon region at a
pH of 6.15-6.4. A two-week adaptation period was implemented to
create a functional collaborome composition. The need and relevance
of such an adaptation period is clearly demonstrated by the
evolution of SCFA profiles during the cultivation of the
composition of selected species (FIG. 5). Initially, the
composition requires time to adapt to one another and to become
active in converting the supplied substrates to SCFA. However, four
to six days after inoculation, the production of SCFA by the
composition started to stabilize and high levels of butyrate were
measured. On the final day of incubation (day 14), each of the
triplicate incubations resulted in a highly similar, stable and
strongly active functional composition with butyrate levels
reaching 19 mM.
[0115] When the stabilized Collaborome was frozen at -80.degree. C.
as glycerol stock and subsequently thawed for use as inoculum in
the same way as for the assembly strategy, butyrate levels
surprisingly increased faster and reached 25% higher levels under
the same incubation conditions as for the assembly of individual
species (FIG. 4). Butyrate levels already reached 12 mM upon
24-hour incubation of the assembly and a maximum of 19 mM was
already reached after two days.
[0116] In the third strategy, the production of the composition was
undertaken using an optimized single-stage fermenter approach,
operated in fed-batch mode (i.e., the alternative "Collaborome"
strategy or the strategy "wherein the bacteria are grown together
in "a fermenter prior to administration"). The selected species
were retrieved from their glycerol stocks and grown under their
respective optimal growth conditions to obtain homogeneous
suspensions of the bacterial strains. Fermentation was started in
sterile incubation bottles containing sterilized SHIME.RTM. feed
adjusted to pH 6.8 with KH.sub.2PO.sub.4/K.sub.2HPO.sub.4 and
flushed with nitrogen. Then, the sterilized medium was inoculated
with 10% (v/v) of mixed inoculum consisting of equal volumes of the
selected species. Incubation bottles were flushed with nitrogen to
ensure anaerobic conditions and were incubated at 37.degree. C. (90
rpm). At specific intervals of 16 hours, 40% (v:v) of the growth
medium was replaced with conditioned SHIME.RTM. nutritional medium.
Conditioned SHIME.RTM. nutritional medium was prepared by
incubating 700 mL of normal SHIME.RTM. feed (pH 2) for one hour at
37.degree. C., after which 300 mL of pancreatic juice (pH
6.8)--supplemented with 25 g/L NaHCO.sub.3, 23.6 g/L
KH.sub.2PO.sub.4 and 4.7 g/L K.sub.2HPO.sub.4--was added.
[0117] As shown in FIG. 6, the total SCFA production and the ratio
of SCFA produced by the composition was stable after six
replacement cycles. When re-inoculated in the same strategy as
described before, the stabilized Collaborome led to a maximized
SCFA production (acetate/propionate/butyrate ratio was around
14/12/74) two days earlier as compared to the same set of species
in the assembly strategy and a 25% higher butyrate production.
Example 2: In Vitro Experiments
2.1 Effect of Adding the Functional Composition to Complex
Microbial Gut Communities
[0118] This experiment demonstrates that the functional composition
is active when inoculated in a mixed microbial gut community, where
there is a strong competition for colonic substrates with members
of this complex intestinal community that is estimated to consist
of 500 to 1000 microbial species. To address this issue, an
experiment was performed in small incubation bottles using the
composition, containing Lactobacillus plantarum, Faecalibacterium
prausnitzii, Butyricicoccus pullicaecorum, Roseburia inulinivorans,
Roseburia hominis, Akkermansia muciniphila and Anaerostipes caccae
and produced through the Collaborome strategy from Example 1.3. An
increasing concentration of the pre-adapted composition (0%, 4% and
20%) was washed in PBS and added to three different media: [0119]
1) Sterile basal medium [2 g/L pepton, 2 g/L yeast extract, 2 mL/L
TWEEN.RTM. 80, 10 .mu.L/L, vitamin K1, 500 mg/L L-cysteine HCl, 100
mg/L NaCl, 40 mg/L K.sub.2HPO.sub.4, 40 mg/L KH.sub.2PO.sub.4, 10
mg/L MgSO.sub.4.7H.sub.2O, 6.7 mg/L CaCl.sub.2.2H.sub.2O, 1.5 mg/L
resazurin, 50 mg/L hemin (50 mg/L)-pH 5.5]+starch 6 g/L; [0120] 2)
Basal medium+20% fecal slurry (prepared as described in De Boever
et al., 2000); [0121] 3) Basal medium+20% SHIME.RTM. colon
suspension, containing the complete microbiota.
[0122] The increasing concentration of the pre-adapted
butyrate-producing consortium from 0% to 4% and 20% resulted in a
proportional increase of absolute butyrate levels (FIG. 7). This
was not only observed in sterile medium, but also for media
supplemented with a mixed microbiota derived from both a fecal
sample or a SHIME.RTM. colon region. This experiment thus
demonstrates that composition is not only active when present in a
non-competing colonic environment, but that it also results in
higher butyrate levels when administered to a mixed microbiota
where many gut microbes are competing for the same nutrients.
Furthermore, not only butyrate production increased, but also
propionate production strongly increased. The combination of these
increases and the decrease of acetate in the incubation stipulates
that the composition can modulate general microbial fermentation
profiles into a more health-beneficial profile.
2.2 Efficiency of the Functional Composition to Restore the
Metabolic Functions of an Antibiotic-Induced Dysbiosed Gut
Microbial Community
[0123] The use of antibiotics is believed to cause major
disruptions of the gut microbiota community. It has been shown that
a dysbiosed microbial composition is more susceptible to infections
by pathogens. Furthermore, a number of gastrointestinal diseases
have been correlated with a dysbiosed microbial composition, such
as inflammatory bowel diseases, underlining the importance of a
healthy gut microbiome. Recovery of the taxonomic composition and
especially functionality after long-term antibiotic intake usually
takes three months to reach the pre-treatment state, a healthy gut
microbial community (Panda et al., 2014). A decrease in the
recovery time after exposure to antibiotic therapy could thus
reduce the risk of severe infections and promote host health in
general. In that respect, the observed functional activity of the
selected composition could be a promising strategy to enhance
restoration of microbial communities upon antibiotics-induced
dysbiosis and reduce infection risks.
[0124] In this example, antibiotics-induced dysbiosis was modeled
in the in vitro SHIME.RTM. model by dosing the appropriate
antibiotics. The aim of this experiment was to evaluate the
recovery of the typical "healthy" metabolite profiles in the
simulated intestinal colon environments upon administration of the
functional composition. Furthermore, the experiment aimed to
differentiate the effectivity of the composition, when either
produced through the "Assembly" strategy or the "Collaborome"
strategy (see Example 1.3). The experiment was again performed with
the composition, containing Lactobacillus plantarum,
Faecalibacterium prausnitzii, Butyricicoccus pullicaecorum,
Roseburia inulinivorans, Roseburia hominis, Akkermansia muciniphila
and Anaerostipes caccae. To better mimic the complete functionality
profile of the intestinal microbiome, the composition was in this
specific experiment further supplemented with E. coli, Enterococcus
faecium, Lactobacillus mucosae, Bifidobacterium adolescentis,
Bifidobacterium longum, Bacteroides thetaiotaomicron and
Bacteroides vulgatus.
[0125] In practice, SHIME.RTM. vessels (pH 6.15-6.40) were
inoculated with fecal material and allowed to stabilize for
fourteen days (M-SHIME.RTM. setup--Van den Abbeele et al., 2012).
After a control period of two weeks, the SHIME.RTM.-derived colon
microbiota was treated with a cocktail of antibiotics (40/40/10
mg/L of amoxicillin/ciprofloxacin/tetracycline, respectively) to
induce dysbiosis. One day later, the dysbiosed microbiota was
treated for five days with the functional composition, produced
either through the "Assembly" strategy or the "Collaborome"
strategy. Endpoint of the study was to evaluate the recovery of the
typical "healthy" SCFA metabolite profiles in the simulated
intestinal colon environments. A control SHIME.RTM. vessel was
included to simulate spontaneous recovery of the metabolic activity
of the gut community after antibiotic exposure, without
administration of the composition. The results are expressed as the
delta of SCFA levels in the SHIME.RTM. at each time point vs. the
values before antibiotic administration (FIG. 8).
[0126] Upon antibiotic treatment of the SHIME.RTM. vessels, a
significant drop in acetate, propionate and butyrate production was
observed. This finding confirms the disruption of the gut microbial
community. Recovery of the metabolite profile (in terms of SCFA
production) to the pre-treatment state is shown in FIG. 8 as the
evolution of acetate, propionate and butyrate over a 5-day period.
This shows that recovery of the functionality was slow in the
control situation (no administration of composition) and no full
recovery could be observed for acetate and propionate within five
days. Interestingly, treatment with the composition resulted in a
faster recovery as compared to the control condition for all three
SCFA. Furthermore, while the composition of the Assembly strategy
induced full recovery of propionate and butyrate after five days
and three days, respectively, the composition of the Collaborome
strategy induced a faster recovery as opposed to the Assembly
strategy with full recovery of propionate and butyrate after four
days and 2.5 days, respectively. Finally, the Collaborome strategy
also resulted in an increased final activity with increased
propionate and butyrate levels as opposed to the Assembly strategy.
These results emphasize the potential of the composition for the
recovery of antibiotic-mediated microbial dysbiosis. Moreover, this
finding clearly demonstrates that the preadaptation through the
Collaborome strategy results in a more efficient recovery of
microbial SCFA production after antibiotic exposure as compared to
the Assembly strategy.
2.3 Efficiency of the Functional Composition to Restore the
Metabolic Functions of a Dysbiosed Gut Microbial Community in
Inflammatory Bowel Diseases
[0127] Inflammatory Bowel Diseases (IBD) have been associated with
impaired host-microbe interactions, which is related, at least
partially, to a state of gut microbiota dysbiosis. The latter, for
instance, includes a lower abundance of butyryl CoA:acetate CoA
transferase and propionate kinase (Vermeiren et al., FEMS 2011),
which, in turn, negatively affects the production of a balanced
SCFA production capacity. Given the important effects of SCFA on
normal intestinal development and maintenance, restoration of the
microbiota composition and functionality in terms of SCFA
production can positively impact IBD-associated symptoms. In that
respect, the observed functional activity of the selected
composition could be a promising strategy to enhance restoration of
microbial communities in IBD dysbiosis as a basis for restoration
and maintenance of a healthy gut barrier.
[0128] In this example, IBD-associated dysbiosis was modeled in the
in vitro M-SHIME.RTM. model, as described before (Vigsnaes et al.
2013). The aim of this experiment was to evaluate the recovery of
the microbiota in terms of SCFA profiles in the simulated
intestinal colon environment upon administration of the functional
composition. Furthermore, the experiment aimed to differentiate the
effectivity of the composition, when either produced through the
"Assembly" strategy or the "Collaborome" strategy (see Example
1.3). The experiment was again performed with the composition,
containing Lactobacillus plantarum, Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila and Anaerostipes caccae.
[0129] In practice, SHIME.RTM. vessels (pH 6.15-6.40) were
inoculated with fecal material from an Ulcerative Colitis patient
(M-SHIME.RTM. setup--Van den Abbeele et al., 2012). Simultaneously,
a single dose of the functional composition, produced either
through the "Assembly" strategy or the "Collaborome" strategy, was
added to the colon region to simulate administration. A third
experiment ran in parallel as control experiment without
administration of the composition. Production of acetate,
propionate and butyrate was followed one and two days after
administration of the composition.
[0130] The results are presented in FIG. 9: administration of the
composition, produced in the Assembly strategy, resulted in an
increased SCFA production (mainly acetate and butyrate) on day 1,
yet this effect was no longer apparent on day 2. This indicates
that the composition is functionally active in the IBD microbiome
environment. Interestingly, the effect on propionate and butyrate
production was much more pronounced upon administration of the
composition of the Collaborome strategy, with a four-fold and
three-fold increase in propionate and butyrate production,
respectively, as opposed to the IBD control. In contrast with the
composition of the Assembly strategy, the effect was still
pronounced on day 2 and coincided with a lower acetate production
(indication of increased cross-feeding and, therefore, improved
networking). These results emphasize the potential of the
composition for the recovery of IBD-associated microbial dysbiosis.
Moreover, this finding clearly demonstrates that the preadaptation
through the Collaborome strategy results in a more efficient
recovery of microbial SCFA production under IBD conditions as
compared to the Assembly strategy.
2.4 Efficiency of the Functional Composition to Inhibit Growth of
Vegetative Clostridium difficile in an In Vitro Simulation
Assay
[0131] In this example, a Clostridium difficile challenge test was
performed aiming to evaluate whether the functional composition is
not only functionally active under intestinal conditions, yet can
also protect the intestinal environment against infections. In such
challenge test, the composition is challenged with vegetative
Clostridium difficile (Cdif) cells to assess its capacity to
inhibit growth of Cdif under simulated gastro-intestinal
conditions. Furthermore, the experiment aimed to differentiate the
effectivity of the composition, when either produced through the
"Assembly" strategy or the "Collaborome" strategy (see Example
1.3). The experiment was again performed with the composition,
containing Lactobacillus plantarum, Faecalibacterium prausnitzii,
Butyricicoccus pullicaecorum, Roseburia inulinivorans, Roseburia
hominis, Akkermansia muciniphila and Anaerostipes caccae.
[0132] In practice, a glycerol stock of Clostridium difficile (LMG
21717.sup.T) was thawed and inoculated in a bottle containing
Reinforced Clostridial Medium (RCM) broth that was flushed with
nitrogen to ensure anaerobic conditions. The bottle was incubated
in a shaking incubator (90 rpm) for 24 hours and 10% of the grown
culture was again inoculated in RCM broth. After 24 hours of
growth, the homogenized C. difficile culture was aliquoted (in
triplicate) in bottles (10% v:v) containing: [0133] 1) Basal medium
(blank); [0134] 2) Basal medium containing the composition of the
Assembly strategy; [0135] 3) Basal medium containing composition of
the Collaborome strategy; [0136] 4) Basal medium containing
SHIME.RTM. colon suspension.
[0137] Bottles were incubated at 37.degree. C. in a shaking
incubator (90 rpm). At regular time points, a sample was collected
and immediately frozen at -80.degree. C. before quantifying C.
difficile by means of a qPCR assay based on the detection and
quantification of the triose phosphate isomerase gene. For this
purpose, genomic DNA was extracted according to Boon et al. (2003).
The amplification reaction included forward and reverse
oligonucleotide: 5'-TATGGACTATGTTGTAATAGGAC-3' (forward) (SEQ ID
NO:8) and 5'-CATAATATTGGGTCTATTCCTAC-3' (reverse) (SEQ ID NO:9).
Absolute quantification of the PCR product was obtained by creating
a standard curve.
[0138] In this controlled in vitro simulation assay, growth of C.
difficile was observed in the basal medium after 48 hours of
incubation, confirming the validity of the blank in the in vitro
simulation assay. The SHIME.RTM. colon suspension (as simulation of
an actual fecal transplant) showed the highest C. difficile growth
inhibition after 48 hours of incubation (i.e., 58%). Interestingly,
a similar result was obtained for the composition of the
Collaborome strategy, showing approximately 53% of C. difficile
growth inhibition. The lowest effect was observed when the
composition of the Assembly strategy was added (i.e., 23% of growth
inhibition). This experiment clearly demonstrates that C. difficile
is significantly inhibited in its growth by the composition and
that this inhibition is most pronounced in case of preadaptation of
the composition through the Collaborome strategy.
2.5 Effect of the Functional Composition on Host Biomarkers of Gut
Barrier Functioning and Intestinal Immunity
[0139] Examples 2.1 to 2.3 showed that the composition is
functionally active under complex intestinal conditions and can
restore intestinal metabolite profiles, with highest activity in
the case of the production through the Collaborome strategy. This
may, in turn, beneficially influence the intestinal epithelium and
thereby gut barrier functioning and local immunity.
[0140] To evaluate that possibility, this example describes the
combination of samples collected from the previous experiments on
an established co-culture cell model of enterocytes (Caco-2 cells)
and macrophages (THP1) (Possemiers et al. 2013). In this model,
stimulation of THP1 cells with LPS results in increased production
of pro-inflammatory cytokines, which, in turn, tends to disrupt the
enterocyte layer creating a so-called "leaky gut" condition. The
effect on the "leaky gut" is measured by assessing the effect of
the transepithelial electrical resistance (TEER) [measurement for
gut barrier efficiency] and inflammatory cytokine production, as
compared to a control condition.
[0141] In practice, samples collected on day 1 from the
M-SHIME.RTM. experiment from Example 2.3 were combined with the
co-culture leaky gut model.
2.6 Impact of Variations in Strain Identity on Functional Activity
of the Composition
[0142] To assess whether the surprising synergistic effect between
the seven isolates in the composition is strain specific or can
also be reached with other strains of the same species, an
additional experiment was performed. In this example, two different
compositions are produced through the "Collaborome" strategy (see
Example 1.3). While composition 1 contains the specific isolates
described in Example 1.2, composition 2 is composed of strains from
the same species obtained from culture collections: [0143]
Composition 1: Faecalibacterium prausnitzii LMG P-29362,
Butyricicoccus pullicaecorum LMG P-29360, Roseburia inulinivorans
LMG P-29365, Roseburia hominis LMG P-29364, Akkermansia muciniphila
LMG P-29361, Lactobacillus plantarum LMG P-29366 and Anaerostipes
caccae LMG P-29359 [0144] Composition 2: Lactobacillus plantarum
ZJ316, Faecalibacterium prausnitzii (DSMZ 17677), Butyricicoccus
pullicaecorum (LMG 24109), Roseburia inulinivorans (DSMZ 16841),
Roseburia hominis (DSMZ 16839), Akkermansia muciniphila (DSMZ
22959) and Anaerostipes caccae (DSMZ 14662)
[0145] In practice, the selected species were retrieved from their
glycerol stocks and grown under their respective optimal growth
conditions to obtain homogeneous suspensions of the bacterial
strains. Then, the strains were mixed into Composition 1 and
Composition 2, respectively, and each inoculated in triplicate in a
SHIME.RTM. setup (Van den Abbeele et al., 2010) consisting of a
single colon region at a pH of 6.15-6.4. Butyrate production
profiles were followed up for a period of fourteen days.
[0146] Interestingly, the dynamics in butyrate production were
highly similar for both Compositions, with initial strong
fluctuations, followed by stabilization of butyrate levels after
approximately six days. At the end of the experiment (d14),
butyrate levels for Composition 1 reached 19.3 mM, while levels for
Composition 2 were 18.8 mM. This shows that the synergistic effect
observed in the composition from Example 1.2 could be replicated by
using different strains obtained from the same species.
Example 3: In Vivo Experiments
3.1 Mouse Model of Antibiotic-Induced Gastrointestinal Microbiota
Disruption
[0147] The goal of the experiment in this example was to assess
whether the functional composition can also in an in vivo setting
restore the metabolic capacity of the gut microbiome after
antibiotic-induced dysbiosis.
[0148] In this example, the composition, containing Lactobacillus
plantarum, Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Roseburia hominis,
Akkermansia muciniphila and Anaerostipes caccae, was used and
produced via the "Collaborome" strategy of Example 1.3.
Furthermore, to evaluate the need for more complete mimicking of
the complete functionality profile of the intestinal microbiome, an
extra experiment was performed in which the composition was further
supplemented with Escherichia coli, Enterococcus faecium,
Lactobacillus mucosae, Bifidobacterium adolescentis,
Bifidobacterium longum, Bacteroides thetaiotaomicron and
Bacteroides vulgatus (referred to as "extended composition").
[0149] In practice, the "composition" and "extended composition"
were prepared fresh according to the Collaborome strategy, washed
twice in PBS (in an anaerobic chamber to ensure anaerobic
conditions), concentrated in 100 .mu.L and administered to the mice
via oral gavage as soon as possible. Mice (C57/BL6) of at least
five weeks old were purchased, kept under pathogen-free conditions
and fed a standard diet. Mouse experiments were performed in
accordance with protocols approved by the Ethics Committee of
Animal Trials of Ghent University, Belgium. To induce
antibiotic-induced dysbiosis, the antibiotic clindamycin was dosed
to the drinking water at a concentration of 250 mg/L. After five
days of antibiotic treatment, the stomach content of the mice was
neutralized with NaHCO.sub.3 after which the mice (ten mice per
group) are orally gavaged for five consecutive days with: [0150] 1)
the composition in saline solution; [0151] 2) the extended
composition in saline solution and [0152] 3) saline solution
(control).
[0153] A conventional group (without antibiotic treatment but
treated with saline solution) is included as control to exclude
variability arising from the gavage procedure. During the
experiment, fecal samples (approximately 100 mg/mouse) were
collected and stored at -80.degree. C. for future analyses.
[0154] The SCFA profiles, obtained from pooled mice fecal samples
originating from the same groups, demonstrate that five days of
antibiotic treatment significantly reduce butyrate and propionate
production up to the extent that only acetate remained (FIG. 10).
As it is shown in FIG. 10, spontaneous recovery of the metabolic
functions is slow and only started about five days (d10) after the
last antibiotic treatment, although the molar ratios of the three
major SCFA (acetate, propionate and butyrate) did not yet return to
the pre-antibiotic state. When mice were, however, treated with
either the composition or extended composition of the Collaborome
strategy, recovery of butyrate metabolism already started
approximately three days (d8) after antibiotic treatment.
Furthermore, the metabolic activity of the mice treated with both
compositions showed almost complete recovery five days after the
last dose of antibiotics (d10), with good production of both
propionate and butyrate. The extended composition contained a
higher diversity of acetate and propionate producers as compared to
the composition, which is also reflected by the slightly different
fermentation profile at d10 of the experiment. In conclusion, this
example provides an in vivo confirmation that the functional
composition is effective in obtaining a faster and more potent
recovery of intestinal metabolic profiles upon antibiotic-induced
dysbiosis. Furthermore variations in the exact species combinations
in the composition allows tuning the end result into specific
metabolic profiles.
3.2 TNBS Mouse Model for Inflammation
[0155] The TNBS (2,4,6-trinitrobenzenesulfonic acid) model is a
commonly used model for colitis that mimics some of the features of
Crohn's disease (Scheiffele et al. 2001), including weight loss,
bloody diarrhea and intestinal wall thickening. On histopathology,
TNBS causes patchy transmural inflammation of the gut with the
formation of deep ulcers, classical features found in patients with
CD. This makes the TNBS model a good candidate for in vivo
evaluation of the capacity of the functional composition to prevent
and/or restore damage to the intestinal mucosa in IBD and to assist
in maintaining/developing a healthy gut barrier.
[0156] In this example, the composition, containing Lactobacillus
plantarum, Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Roseburia hominis,
Akkermansia muciniphila and Anaerostipes caccae was used to
evaluate the beneficial effects upon evaluation in the TNBS model.
Furthermore, the experiment aimed to differentiate the effectivity
of the composition, when either produced through the "Assembly"
strategy or the "Collaborome" strategy (see Example 1.3). Colitis
was evoked in the animals by rectal instillation of TNBS, a mucosal
sensitizing agent diluted in ethanol. The administration of ethanol
is a prerequisite to break the colonic mucosal barrier to allow
penetration of TNBS into the lamina propria. TNBS haptenizes the
localized colonic and gut microbial proteins to become immunogenic,
thereby triggering the host innate and adaptive immune
responses.
[0157] In practice, eight- to ten-week-old male C57BL6/J mice were
housed in a temperature-controlled room at 20.degree. C. with a
12:12-hour light-dark cycle. The animals had free access to water
and to a commercial chow. Mice were randomized among cages to avoid
cage effects. After one week of acclimatization, the experiment was
started. Each group (n=9/group) was treated for five consecutive
days by means of oral gavage. Preventive dosing of all treatments
started one day before the administration of 2 mg TNBS/50% EtOH
rectally and lasted for four days after TNBS administration before
mice were sacrificed. The following treatments were included:
[0158] 1) TNBS+the composition of the Assembly strategy in saline
solution; [0159] 2) TNBS+the composition of the Collaborome
strategy in saline solution and [0160] 3) TNBS+saline solution
(control).
[0161] A conventional group (without TNBS treatment but treated
with saline solution) is included as control to exclude variability
arising from the gavage procedure. As study endpoint, Disease
Activity was monitored daily (before the daily treatment) by
measuring body weight, fecal blood loss (ColoScreen) and general
appearance.
[0162] The results of this example are presented in FIG. 11. No
effects on weight nor Disease Activity were observed for the
Vehicle (saline) control group without TNBS, while the control
group that received TNBS showed an immediate weight loss on dl of
8% and a strong increase in Disease Activity. Both weight loss and
Disease activity were partially restored by the end of the study.
Interestingly, a potent protective effect of the composition was
observed on both weight loss and Disease Activity, yet the extent
of this protective effect depended on the production strategy of
the composition. While an initial mild protection was observed on
dl for the Assembly strategy as shown to be lower weight loss and
Disease Activity, this protective effect was no longer observed on
the next study days. In contrast, the administration of the
composition produced through the Collaborome strategy led to a
potent preventive effect toward weight loss and Disease Activity on
dl, as compared to the TNBS control, and a faster and complete
restoration by the end of the study, as shown by the return of the
disease activity to the level of the Vehicle control. In
conclusion, this example provides an in vivo confirmation that the
functional composition is effective in obtaining a stronger
prevention of, and faster and more potent recovery from, intestinal
inflammation and Disease Activity upon TNBS-induced colitis
induction. Moreover, this finding clearly demonstrates that the
preadaptation through the Collaborome strategy results in a more
efficient activity as compared to the Assembly strategy.
3.3 DSS Mouse Model for Inflammation
[0163] The chronic DSS model is a commonly used model for colitis
that mimics some of the features of Crohn's disease, including
weight loss and bloody diarrhea. On histopathology, chronic DSS
administration causes inflammation of the gut with typical
architectural changes such as crypt distortion, (sub)mucosal
infiltration of inflammatory cells and fibrosis, features found in
patients with CD. This makes the DSS model a good candidate for in
vivo evaluation of the capacity of the functional composition to
prevent and/or restore damage to the intestinal mucosa in IBD and
to assist in maintaining/developing a healthy gut barrier.
[0164] In this example, the composition, containing Lactobacillus
plantarum, Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Roseburia hominis,
Akkermansia muciniphila and Anaerostipes caccae, and produced
through the "Collaborome" strategy (see Example 1.3), is used to
evaluate the beneficial effects upon evaluation in the chronic DSS
model. Colitis is evoked in the animals by repeated administration
of DSS in the drinking water (0.25% challenge). The experiment is
performed over a total of eight weeks, with three cycles of DSS
administration and recovery.
[0165] In practice, six-week-old male C57BL6/J mice are housed in a
temperature-controlled room at 20.degree. C. with a 12:12-hour
light-dark cycle. The animals have free access to water and to a
commercial chow. Mice are randomized among cages to avoid cage
effects. After one week of acclimatization, the experiment is
started. Each group (n=10/group) is treated three times per week
for eight consecutive weeks, by means of oral gavage. Preventive
dosing of all treatments starts one week before the first DSS
cycle. The first DSS cycle starts on week 2 and includes one week
of DSS administration (0.25% in drinking water) followed by two
weeks of recovery. This first cycle is followed by an identical
second DSS cycle. The third DSS cycle consists of one week of DSS
administration followed by one week of recovery, after which the
animals are sacrificed. The following treatments are included:
[0166] 1) non-DSS control [0167] 2) DSS+the composition of the
Collaborome strategy in saline solution (three times/week) and
[0168] 3) DSS+saline solution (DSS control).
[0169] As study endpoint, the Disease Activity Index (DAI) was
monitored during each DSS cycle, three times per week (before the
daily treatment) by monitoring body weight, fecal blood loss
(ColoScreen) and general appearance. As shown in FIG. 12, no
effects on DAI were observed for the Vehicle (saline) control group
without DSS, while the control group that received DSS showed a
strong increase in DAI at each administration cycle. Interestingly,
a potent protective effect (approximately 25% lower DAI at each
cycle) of the composition was observed on Disease Activity. This
further demonstrates that the functional composition is effective
in obtaining a strong protective effect from intestinal
inflammation and Disease Activity upon DSS-induced colitis
induction.
3.4 Mucositis Model
[0170] Mucositis is a clinical term used to describe damage to
mucous membranes after anticancer therapies. It occurs throughout
the entire gastrointestinal tract (GT) (including the mouth) and
genito-urinary tract, and to a lesser extent in other mucosal
surfaces. Its severity and duration varies with the dose and the
type of drug used. The importance of mucositis is that it limits
the dose of chemotherapy. The GI crypt epithelium is particularly
vulnerable to chemotherapeutic toxicity, with symptoms including
nausea and vomiting, abdominal pain, distension, and diarrhea due
to direct effects of the cytotoxics on the mucosa. The
5-fluorouracyl (5FU)-induced gut mucositis rat model was
established by Keefe et al. for assessment of the effects of
chemotherapy on the GI tract and it is now one of the most
extensively used models to investigate chemotherapy-induced
mucositis in rats (Keefe 2004).
[0171] In this example, the composition, comprising Lactobacillus
plantarum, Faecalibacterium prausnitzii, Butyricicoccus
pullicaecorum, Roseburia inulinivorans, Akkermansia muciniphila and
Anaerostipes caccae, was used as the basis for the experiment and
produced via the "Collaborome" strategy of Example 1.3. Mucositis
is induced by means of a single intraperitoneal dose of 5FU.
[0172] In practice, a total of 30 rats were randomly assigned to
either a control or experimental group according to a specific time
point. All rats in the experimental groups received a single
intraperitoneal dose of 5FU (150 mg 5FU/kg BW). Rats in the control
groups received treatment with the solvent vehicle
(dimethylsulphoxide). Subsequent to administration of the
chemotherapy drugs, study endpoints such as mortality, diarrhea,
and general clinical condition were assessed four times per 24-hour
period. Subgroups of the rats were killed by exsanguination and
cervical dislocation at 24, 48, and 72 hours following
administration of the drug. Primary endpoints of interest were
evolution of weight, diarrhea and general wellbeing (sickness
score). Secondary endpoints included histology of intestinal
samples and stool and gut mucosal microbiota analysis.
[0173] To assess the effect of the composition on prevention or
reducing the evaluated symptoms, part of the rats were administered
for eight consecutive days with the composition by means of oral
gavage. Preventive dosing started five days before the
administration of 5FU and lasted for three days after 5FU
administration or until rats were sacrificed. Control animals did
not receive the composition.
REFERENCES
[0174] Bahaka et al. 1993--Phenotypic and genomic analyses of human
strains belonging or related to Bifidobacterium longum,
Bifidobacterium infantis, and Bifidobacterium breve.--Int. J. Syst.
Evol. Microbiol. 43:565-573. [0175] Barcenilla et al.
2000--Phylogenetic relationships of butyrate-producing bacteria
from the human gut--Appl. Environ. Microbiol. 66:1654-1661. [0176]
Barnett et al. 2012--The interactions between endogenous bacteria,
dietary components and the mucus layer of the large bowel.--Food
Funct. 3:690-9. [0177] Becker et al. 2011--Human intestinal
microbiota: characterization of a simplified and stable gnotobiotic
rat model--Gut Microbes 2:25-33. [0178] Boon et al.
2003--Bioaugmentation as a tool to protect the structure and
function of an activated-sludge microbial community against a
3-chloroaniline shock load--Appl. Environ. Microbiol. 69:1511-1520.
[0179] Brandl et al. 2008--Vancomycin-resistant enterococci exploit
antibiotic-induced innate immune deficits--Nature 455:804-7. [0180]
Cenit et al. 2014--Rapidly expanding knowledge on the role of the
gut microbiome in health and disease--Biochim. Biophys. Acta.
1842:1984-1992. [0181] Clemente et al. 2012--The impact of the gut
microbiota on human health: an integrative view--Cell 148:1258-70.
[0182] Cummings & Macfarlane, 1997--Role of intestinal bacteria
in nutrient metabolism--J. Parenter. Enteral. Nutr. 21:357-65.
[0183] Derrien et al. 2004--Akkermansia muciniphila gen. nov., sp.
nov., a human intestinal mucin-degrading bacterium--Int. J. Syst.
Evol. Microbiol. 54:1469-1476. [0184] De Vrieze 2013--Medical
research. The promise of poop--Science 341:954-7. [0185] Duncan et
al. (2002)--Growth requirements and fermentation products of
Fusobacterium prausnitzii, and a proposal to reclassify it as
Faecalibacterium prausnitzii gen. nov., comb. nov.--Int. J. Syst.
Evol. Microbiol. 52:2141-2146. [0186] Duncan et al.
(2006)--Proposal of Roseburia faecis sp. nov., Roseburia hominis
sp. nov. and Roseburia inulinivorans sp. nov., based on isolates
from human faeces--Int. J. Syst. Evol. Microbiol. 56:2437-2441.
[0187] Eeckhaut et al. (2008)--Butyricicoccus pullicaecorum gen.
nov., sp. nov., an anaerobic, butyrate-producing bacterium isolated
from the caecal content of a broiler chicken--Int. J. Syst. Evol.
Microbiol. 58:2799-2802. [0188] Fuller & Gibson,
1997--Modification of the intestinal microflora using probiotics
and prebiotics--Scand. J. Gastroenterol. Suppl. 222:28-31. [0189]
Hartemink et al. 1996--Raffinose-Bifidobacterium (RB) agar, a new
selective medium for bifidobacteria--J. Microbiol. Methods
27:33-43. [0190] Hartemink et al. 1997--LAMVAB--A new selective
medium for the isolation of lactobacilli from faeces--J. Microbiol.
Methods 29:77-84. [0191] Iannitti and Palmieri, 2010--Therapeutical
use of probiotic formulations in clinical practice--Clin. Nutr.
29:701-25. [0192] Le Bon et al. 2010--Influence of probiotics on
gut health in the weaned pig--Livestock Sci. 133:179-181. [0193]
Livingston et al. 1978--New medium for selection and presumptive
identification of the Bacteroides fragilis group--J. Clin.
Microbiol. 7:448-453. [0194] Keefe 2004--Gastrointestinal
mucositis: a new biological model--Supp. Care Canc. 12:6-9. [0195]
Khoruts et al. 2010--Changes in the composition of the human fecal
microbiome after bacteriotherapy for recurrent Clostridium
difficile-associated diarrhea--J. Clin. Gastroenterol. 44:3 54-60.
[0196] Kinross et al. 2011--Gut microbiome-host interactions in
health and disease--Genome Med. 3:14. [0197] Macfarlane &
Macfarlane, 1997--Human colonic microbiota: ecology, physiology and
metabolic potential of intestinal bacteria--Scand. J.
Gastroenterol. 32:3-9. [0198] Newton et al. 1998--Growth of a human
intestinal Desulfovibrio desulfuricans in continuous cultures
containing defined populations of saccharolytic and amino acid
fermenting bacteria--J. Appl. Microbiol. 85:372-380. [0199] Panda
et al. 2014--Short-Term Effect of Antibiotics on Human Gut
Microbiota--PloS One 9: e95476. [0200] Petrof et al. 2013--Stool
substitute transplant therapy for the eradication of Clostridium
difficile infection: "RePOOPulating" the gut--Microbiome 1:3-10.
[0201] Possemiers et al. 2004--PCR-DGGE-based quantification of
stability of the microbial community in a simulator of the human
intestinal microbial ecosystem--FEMS Microbiol. Ecol. 49:495-507.
[0202] Possemiers et al. 2013--A dried yeast fermentate selectively
modulates both the luminal and mucosal gut microbiota, enhances
butyrate production and protects against inflammation, as studied
in an integrated in vitro approach--J. Agric. Food Chem.
61:9380-9392. [0203] Rath et al. 1999--Differential induction of
colitis and gastritis in HLA-B27 transgenic rats selectively
colonized with Bacteroides vulgatus or Escherichia coli.--Infect.
Immun. 67:2969-2974. [0204] Roos et al. 2000--Lactobacillus mucosae
sp. nov., a new species with in vitro mucus-binding activity
isolated from pig intestine--Int. J. Syst. Evol. Microbiol.
50:251-258. [0205] Scharek et al. 2000--Bifidobacterium
adolescentis Modulates the Specific Immune Response to Another
Human Gut Bacterium, Bacteroides thetaiotaomicron, in Gnotobiotic
Rats--Immunobiology 5:429-441. [0206] Scheiffele and Fuss
2002--Induction of TNBS colitis in mice--Curr. Protocols Immunol.
doi: 10.1002/0471142735.im1519s49. [0207] Schleifer et al.
1984--Transfer of Streptococcus faecalis and Streptococcus faecium
to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb.
nov. and Enterococcus faecium comb. nov.--Int. J. Syst. Evol.
Microbiol. 34:31-34. [0208] Schwiertz et al. 2002--Anaerostipes
caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising,
butyrate-producing bacterium from human faeces--Syst. Appl.
Microbiol. 25:46-51. [0209] Sekirov et al. 2008--Antibiotic-induced
perturbations of the intestinal microbiota alter host
susceptibility to enteric infection--Infect. Immun. 76:4726-36.
[0210] Van den Abbeele et al. 2010--Microbial community development
in a dynamic gut model is reproducible, colon region specific, and
selective for Bacteroidetes and Clostridium cluster IX--Appl.
Environ. Microbiol. 76:5237-5246. [0211] Van den Abbeele et al.
2013--Prebiotics, faecal transplants and microbial network units to
stimulate biodiversity of the human gut microbiome--Microb.
Biotechnol. 6:335-40. [0212] Van Loo et al. 1999--Functional food
properties of non-digestible oligosaccharides: a consensus report
from the ENDO project (DGXII AIRII-CT94-1095)--Br. J. Nutr.
81:121-32. [0213] Vermeiren et al. 2011--Decreased colonization of
fecal Clostridium coccoides/Eubacterium rectale species from
ulcerative colitis patients in an in vitro dynamic gut model with
mucin environment--FEMS Microbiol. Ecol. 79:685-696. [0214]
Vigsnaes et al. 2013--Microbiotas from UC patients display altered
metabolism and reduced ability of LAB to colonize mucus--Sci. Rep.
3:1110. [0215] Walter 2008--Ecological Role of Lactobacilli in the
Gastrointestinal Tract: Implications for Fundamental and Biomedical
Research--Appl. Environ. Microbiol. 74:4985-4996. [0216] Weisburg
et al. 1991--16S ribosomal DNA amplification for phylogenetic
study--J. Bacteriol. 173:697-703. [0217] Willing et al. 2009--Twin
studies reveal specific imbalances in the mucosa-associated
microbiota of patients with ileal Crohn's disease--Inflamm. Bowel
Dis. 15:653-60. [0218] WO 2013/037068--Method for treatment of
disorders of the gastrointestinal system (Allen-Vercoe and Petrof,
2013). [0219] WO 2014/145958A2--Network-based microbial
compositions and methods (Henn et al. 2014).
Sequence CWU 1
1
911485DNARoseburia hominis 1gatcctggct caggatgaac gctggcggcg
tgcttaacac atgcaagtcg aacgaagcac 60tttaattgat ttcttcggaa tgaagttttt
gtgactgagt ggcggacggg tgagtaacgc 120gtgggtaacc tgcctcatac
agggggataa cagttggaaa cgactgctaa taccgcataa 180gcgcacagga
ttgcatgatc cagtgtgaaa aactccggtg gtatgagatg gacccgcgtc
240tgattagcca gttggcgggg taacggccca ccaaagcgac gatcagtagc
cgacctgaga 300gggtgaccgg ccacattggg actgagacac ggcccaaact
cctacgggag gcagcagtgg 360ggaatattgc acaatggggg aaaccctgat
gcagcgacgc cgcgtgagcg aagaagtatt 420tcggtatgta aagctctatc
agcagggaag aagaatgcgg tacctgacta agaagcaccg 480gctaaatacg
tgccagcagc cgcggtaata cgtatggtgc aagcgttatc cggatttact
540gggtgtaaag ggagcgcagg cggtacggca agtctgatgt gaaatcccgg
ggctcaaccc 600cggtactgca ttggaaactg tcggactaga gtgtcggagg
ggtaagtgga attcctagtg 660tagcggtgaa atgcgtagat attaggagga
acaccagtgg cgaaggcggc ttactggacg 720attactgacg ctgaggctcg
aaagcgtggg gagcaaacag gattagatac cctggtagtc 780cacgccgtaa
acgatgaata ctaggtgtcg gggagcattg ctcttcggtg ccgcagcaaa
840cgcaataagt attccacctg gggagtacgt tcgcaagaat gaaactcaaa
ggaattgacg 900gggacccgca caagcggtgg agcatgtggt ttaattcgaa
gcaacgcgaa gaaccttacc 960aagtcttgac atcccactga cagagtatgt
aatgtacttt ctcttcggag cagtggtgac 1020aggtggtgca tggttgtcgt
cagctcgtgt cgtgagatgt tgggttaagt cccgcaacga 1080gcgcaacccc
tattcttagt agccagcggt tcggccgggc actctaggga gactgccagg
1140gataacctgg aggaaggtgg ggatgacgtc aaatcatcat gccccttatg
acttgggcta 1200cacacgtgct acaatggcgt aaacaaaggg aagcaatccc
gcgaggggga gcaaatctca 1260aaaataacgt ctcagttcgg actgtagtct
gcaactcgac tacacgaagc tggaatcgct 1320agtaatcgcg aatcagaatg
tcgcggtgaa tacgttcccg ggtcttgtac acaccgcccg 1380tcacaccatg
ggagttggta atgcccgaag tcagtgaccc aaccgcaagg agggagctgc
1440cgaaggcagg actgataact ggggtgaagt cgtaacaagg gtacg
148521454DNARoseburia inulinivorans 2ttgatcctgg ctcaggatga
acgctggcgg cgtgcttaac acatgcaagt cgaacgaagc 60acttttacag atttcttcgg
aatgaagttt tagtgactga gtggcggacg ggtgagtaac 120gcgtgggtaa
cctgcctcac acagggggat aacagttgga aacggctgct aataccgcat
180aagcgcacag taccgcatgg tacagtgtga aaaactccgg tggtgtgaga
tggacccgcg 240tctgattagc tagttggcag ggcaacggcc taccaaggcg
acgatcagta gccgacctga 300gagggtgacc ggccacattg ggactgagac
acggcccaaa ctcctacggg aggcagcagt 360ggggaatatt gcacaatggg
ggaaaccctg atgcagcgac gccgcgtgag cgaagaagta 420tttcggtatg
taaagctcta tcagcaggga agaagaaatg acggtacctg actaagaagc
480accggctaaa tacgtgccag cagccgcggt aatacgtatg gtgcaagcgt
tatccggatt 540tactgggtgt aaagggagcg caggcggaag gctaagtctg
atgtgaaagc ccggggctca 600accccggtac tgcattggaa actggtcatc
tagagtgtcg gaggggtaag tggaattcct 660agtgtagcgg tgaaatgcgt
agatattagg aggaacacca gtggcgaagg cggcttactg 720gacgataact
gacgctgagg ctcgaaagcg tggggagcaa acaggattag ataccctggt
780agtccacgcc gtaaacgatg aatactaggt gtcggaaagc acagcttttc
ggtgccgccg 840caaacgcatt aagtattcca cctggggagt acgttcgcaa
gaatgaaact caaaggaatt 900gacggggacc cgcacaagcg gtggagcatg
tggtttaatt cgaagcaacg cgaagaacct 960taccaagtct tgacatcctt
ctgaccggac agtaatgtgt cctttccttc gggacagaag 1020tgacaggtgg
tgcatggttg tcgtcagctc gtgtcgtgag atgttgggtt aagtcccgca
1080acgagcgcaa cccttatccc cagtagccag cggttcggac gggcactctg
aggagactgc 1140cagggataac ctggaggaag gtggggatga cgtcaaatca
tcatgcccct tatgacttgg 1200gctacacacg tgctacaatg gcgtaaacaa
agggaagcga gaccgtgagg tggagcaaat 1260cccaaaaata acgtctcagt
tcggactgta gtctgcaacc cgactacacg aagctggaat 1320cgctagtaat
cgcagatcag aatgctgcgg tgaatacgtt cccgggtctt gtacacaccg
1380cccgtcacac catgggagtt ggaaatgccc gaagtcagtg acccaaccgc
aaggagggag 1440ctgcgaaggc aggt 145431433DNAAkkermansia muciniphila
3aacgaacgct ggcggcgtgg ataagacatg caagtcgaac gagagaattg ctagcttgct
60aataattctc tagtggcgca cgggtgagta acacgtgagt aacctgcccc cgagagcggg
120atagccctgg gaaactggga ttaataccgc atagtatcga aagattaaag
cagcaatgcg 180cttggggatg ggctcgcggc ctattagtta gttggtgagg
taacggctca ccaaggcgat 240gacgggtagc cggtctgaga ggatgtccgg
ccacactgga actgagacac ggtccagaca 300cctacgggtg gcagcagtcg
agaatcattc acaatggggg aaaccctgat ggtgcgacgc 360cgcgtggggg
aatgaaggtc ttcggattgt aaacccctgt catgtgggag caaattaaaa
420agatagtacc acaagaggaa gagacggcta actctgtgcc agcagccgcg
gtaatacaga 480ggtctcaagc gttgttcgga atcactgggc gtaaagcgtg
cgtaggctgt ttcgtaagtc 540gtgtgtgaaa ggcgcgggct caacccgcgg
acggcacatg atactgcgag actagagtaa 600tggaggggga accggaattc
tcggtgtagc agtgaaatgc gtagatatcg agaggaacac 660tcgtggcgaa
ggcgggttcc tggacattaa ctgacgctga ggcacgaagg ccaggggagc
720gaaagggatt agatacccct gtagtcctgg cagtaaacgg tgcacgcttg
gtgtgcgggg 780aatcgacccc ctgcgtgccg gagtaacgcg ttaagcgtgc
cgcctgggga gtacggtcgc 840aagattaaaa ctcaaagaaa ttgacgggga
cccgcacaag cggtggagta tgtggcttaa 900ttcgatgcaa cgcgaagaac
cttacctggg cttgacatgt aatgaacaac atgtgaaagc 960atgcgactct
tcggaggcgt tacacaggtg ctgcatggcc gtcgtcagct cgtgtcgtga
1020gatgtttggt taagtccagc aacgagcgca acccctgttg ccagttacca
gcacgtgaag 1080gtggggactc tggcgagact gcccagatca actgggagga
aggtggggac gacgtcaggt 1140cagtatggcc cttatgccca gggctgcaca
cgtactacaa tgcccagtac agagggggcc 1200gaagccgcga ggcggaggaa
atcctaaaaa ctgggcccag ttcggactgt aggctgcaac 1260ccgcctacac
gaagccggaa tcgctagtaa tggcgcatca gctacggcgc cgtgaatacg
1320ttcccgggtc ttgtacacac cgcccgtcac atcatggaag ctggtcgcac
ccgaagtatc 1380tgaagccaac cgcaaggagg cagggtccta aggtgagact
ggtaactggg atg 143341456DNAAnaerostipes caccae 4gcgcttaata
catgtcaagt cgaacgaagc atttaggatt gaagttttcg gatggatttc 60ctatatgact
gagtggcgga cgggtgagta acgcgtgggg aacctgccct atacaggggg
120ataacagctg gaaacggctg ctaataccgc ataagcgcac agaatcgcat
gattcagtgt 180gaaaagccct ggcagtatag gatggtcccg cgtctgatta
gctggttggt gaggtaacgg 240ctcaccaagg cgacgatcag tagccggctt
gagagagtga acggccacat tgggactgag 300acacggccca aactcctacg
ggaggcagca gtggggaata ttgcacaatg ggggtaaacc 360ctgatgcagc
gacgccgcgt gagtgaagaa gtatttcggt atgtaaagct ctatcagcag
420ggaagaaaac agacggtacc tgactaagaa gccccggcta actacgtgcc
agcagccgcg 480gtaatacgta gggggcaagc gttatccgga attactgggt
gtaaagggtg cgtaggtggc 540atggtaagtc agaagtgaaa gcccggggct
taaccccggg actgcttttg aaactgtcat 600gctggagtgc aggagaggta
agcggaattc ctagtgtagc ggtgaaatgc gtagatatta 660ggaggaacac
cagtggcgaa ggcggcttac tggactgtca ctgacactga tgcacgaaag
720cgtggggagc aaacaggatt agataccctg gtagtccacg ccgtaaacga
tgaatactag 780gtgtcggggc cgtagaggct tcggtgccgc agcaaacgca
gtaagtattc cacctgggga 840gtacgttcgc aagaatgaaa ctcaaaggaa
ttgacgggga cccgcacaag cggtggagca 900tgtggtttaa ttcgaagcaa
cgcgaagaac cttacctggt cttgacatcc caatgaccga 960accttaaccg
gttttttctt tcgagacatt ggagacaggt ggtgcatggt tgtcgtcagc
1020tcgtgtcgtg agatgttggg ttaagtcccg caacgagcgc aacccctatc
tttagtagcc 1080agcatttaag gtgggcactc tagagagact gccagggata
acctggagga aggtggggac 1140gacgtcaaat catcatgccc cttatggcca
gggctacaca cgtgctacaa tggcgtaaac 1200aaagggaagc gaagtcgtga
ggcgaagcaa atcccagaaa taacgtctca gttcggattg 1260tagtctgcaa
ctcgactaca tgaagctgga atcgctagta atcgtgaatc agaatgtcac
1320ggtgaatacg ttcccgggtc ttgtacacac cgcccgtcac accatgggag
tcagtaacgc 1380ccgaagtcag tgacccaacc gcaaggaggg agctgccgaa
ggtgggaccg ataactgggg 1440tgaagtcgta acaagg
145651466DNAFaecalibacterium prausnitzii 5gttgatcctg gctcaggacg
aacgctggcg gcgcgcctaa cacatgcaag tcgaacgagc 60gagagagagc ttgctttctc
gagcgagtgg cgaacgggtg agtaacgcgt gaggaacctg 120cctcaaagag
ggggacaaca gttggaaacg actgctaata ccgcataagc ccacagctcg
180gcatcgagca gagggaaaag gagcaatccg ctttgagatg gcctcgcgtc
cgattagcta 240gttggtgagg taatggccca ccaaggcaac gatcggtagc
cggactgaga ggttgaacgg 300ccacattggg actgagacac ggcccagact
cctacgggag gcagcagtgg ggaatattgc 360acaatggggg aaaccctgat
gcagcgacgc cgcgtggagg aagaaggtct tcggattgta 420aactcctgtt
gttgaggaag ataatgacgg tactcaacaa ggaagtgacg gctaactacg
480tgccagcagc cgcggtaaaa cgtaggtcac aagcgttgtc cggaattact
gggtgtaaag 540ggagcgcagg cgggaagaca agttggaagt gaaatctatg
ggctcaaccc ataaactgct 600ttcaaaactg tttttcttga gtagtgcaga
ggtaggcgga attcccggtg tagcggtgga 660atgcgtagat atcgggagga
acaccagtgg cgaaggcggc ctactgggca ccaactgacg 720ctgaggctcg
aaagtgtggg tagcaaacag gattagatac cctggtagtc cacaccgtaa
780acgatgatta ctaggtgttg gaggattgac cccttcagtg ccgcagttaa
cacaataagt 840aatccacctg gggagtacga ccgcaaggtt gaaactcaaa
ggaattgacg ggggcccgca 900caagcagtgg agtatgtggt ttaattcgac
gcaacgcgaa gaaccttacc aagtcttgac 960atcctgcgac gatgctggaa
acagtatttt ccttcgggac gcagagacag gtggtgcatg 1020gttgtcgtca
gctcgtgtcg tgagatgttg ggttaagtcc cgcaacgagc gcaaccctta
1080ctgtcagtta ctacgcaaga ggactctggc aggactgccg ttgacaaaac
ggaggaaggt 1140ggggatgacg tcaaatcatc atgcccttta tgacttgggc
tacacacgta ctacaatggc 1200gttaaacaaa gagaagcaag accgcgaggt
ggagcaaaac tcagaaacaa cgtcccagtt 1260cggactgcag gctgcaactc
gcctgcacga agtcggaatt gctagtaatc gtggatcagc 1320atgccacggt
gaatacgttc ccgggccttg tacacaccgc ccgtcacacc atgagagccg
1380gggggacccg aagtcggtag tctaaccgca aggaggacgc cgccgaaggt
aaaactggtg 1440attggggtga agtcgtaaca aggtac
146661586DNALactobacillus plantarum 6gggacatgct gcagtcgacg
attagagttt gatcctggct caggacgaac gctggcggcg 60tgcctaatac atgcaagtcg
aacgaactct ggtattgatt ggtgcttgca tcatgattta 120catttgagtg
agtggcgaac tggtgagtaa cacgtgggaa acctgcccag aagcggggga
180taacacctgg aaacagatgc taataccgca taacaacttg gaccgcatgg
tccgagtttg 240aaagatggct tcggctatca cttttggatg gtcccgcggc
gtattagcta gatggtgagg 300taacggctta ccatggcaat gatacgtagc
cgacctgaga gggtaatcgg ccacattggg 360actgagacac ggcccaaact
cctacgggag gcagcagtag ggaatcttcc acaatggacg 420aaagtctgat
ggagcaacgc cgcgtgagtg aagaagggtt tcggctcgta aaactctgtt
480gttaaagaag aacatatctg agagtaactg ttcaggtatt gacggtattt
aaccagaaag 540ccacggctaa ctacgtgcca gcagccgcgg taatacgtag
gtggcaagcg ttgtccggat 600ttattgggcg taaagcgagc gcaggcggtt
ttttaagtct gatgtgaaag ccttcggctc 660aaccgaagaa gtgcatcgga
aactgggaaa cttgagtgca gaagaggaca gtggaactcc 720atgtgtagcg
gtgaaatgcg tagatatatg gaagaacacc agtggcgaag gcggctgtct
780ggtctgtaac tgacgctgag gctcgaaagt atgggtagca aacaggatta
gataccctgg 840tagtccatac cgtaaacgat gaatgctaag tgttggaggg
tttccgccct tcagtgctgc 900agctaacgca ttaagcattc cgcctgggga
gtacggccgc aaggctgaaa ctcaaaggaa 960ttgacggggg cccgcacaag
cggtggagca tgtggtttaa ttcgaagcta cgcgaagaac 1020cttaccaggt
cttgacatac tatgcaaatc taagagatta gacgttccct tcggggacat
1080ggatacaggt ggtgcatggt tgtcgtcagc tcgtgtcgtg agatgttggg
ttaagtcccg 1140caacgagcgc aacccttatt atcagttgcc agcattaagt
tgggcactct ggtgagactg 1200ccggtgacaa accggaggaa ggtggggatg
acgtcaaatc atcatgcccc ttatgacctg 1260ggctacacac gtgctacaat
ggatggtaca acgagttgcg aactcgcgag agtaagctaa 1320tctcttaaag
ccattctcag ttcggattgt aggctgcaac tcgcctacat gaagtcggaa
1380tcgctagtaa tcgcggatca gcatgccgcg gtgaatacgt tcccgggcct
tgtacacacc 1440gcccgtcaca ccatgagagt ttgtaacacc caaagtcggt
ggggtaacct tttaggaacc 1500agccgcctaa ggtgggacag atgattaggg
tgaagtcgta acaaggtaac caatctctag 1560aggtccccgg gaccgagctg acgcaa
158671482DNAButyricicoccus pullicaecorum 7tagtttgatc ctggctcagg
atgaacgctg gcggcgtgcc taacacatgc aagtcgaacg 60gagttgtttg aggaaatcct
tcgggatgga atcttccaac ttagtggcgg acgggtgagt 120aacgcgtgag
caatctgcct ttcagagggg gataacagcc ggaaacggct gctaataccg
180cataatgcat tgaattcgca tgtttttgat gccaaagatt ttatcgctga
aagatgagct 240cgcgtctgat tagctagttg gcggggtaac ggcccaccaa
ggcgacgatc agtagccgga 300ctgagaggtt gaacggccac attgggactg
aggacacggc ccagactcct accgggaggc 360agcagtgggg aatattgcgc
aatgggggca accctgacgc agcaacgccg cgtgattgat 420gaaggtcttc
ggattgtaaa aatctttaat cagggacgaa acaaatgacg gtacctgaag
480aataagctcc ggctaactac gtgccagcag ccgcggtaat acgtagggag
caagcgttat 540ccggatttac tgggtgtaaa gggcgtgtag gcgggcttgt
aagttggaag tgaaatctcg 600gggcttaacc ccgaaactgc tttcaaaact
gcgagtcttg agtgatggag aggcaggcgg 660aattcccagt gtagcggtga
aatgcgtaga tattgggagg aacaccagtg gcgaaggcgg 720cctgctggac
attaactgac gctgaggcgc gaaagcgtgg ggagcaaaca ggattagata
780ccctggtagt ccacgccgta aacgatggat actaggtgtg ggaggtattg
accccttccg 840tgccggagtt aacacaataa gtatcccacc tggggagtac
ggccgcaagg ttgaaactca 900aaggaattga cgggggcccg cacaagcagt
ggagtatgtg gtttaattcg aagcaacgcg 960caagaacctt accaagtctt
gacatcccga tgaccgctcy agagataggg cttttcttcg 1020gaacatcggt
gacaggtggt gcatggttgt cgtcagctcg tgtcgtgaga tgttgggtta
1080agtcccgcaa cgagcgcaac ccttacgggt tagttgctac gcaagagcac
tctagccgga 1140ctgccgttga caaaacggag gaaggtgggg acgacgtcaa
atcatcatgc cccttatgac 1200ttgggctaca cacgtactac aatggcagtc
atacagaggg aagcaaaacc gcgaggtgga 1260gcaaatccct aaaagctgtc
ccagttcaga ttgcaggctg caactcgcct gcatgaagtc 1320ggaattgcta
gtaatcgcgg atcagcatgc cgcggtgaat acgttcccgg gccttgtaca
1380caccgcccgt cacaccatga gagccggtaa tacccgaagt ccgtagtcta
accgcaagga 1440ggacgcggcc gaaggtagga ctggtaattg ggacgaagtc gt
1482823DNAArtificial SequenceDNA primer 8tatggactat gttgtaatag gac
23923DNAArtificial SequenceDNA primer 9cataatattg ggtctattcc tac
23
* * * * *