U.S. patent application number 15/794337 was filed with the patent office on 2018-02-15 for devices for continual monitoring and introduction of gastrointestinal microbes.
The applicant listed for this patent is Gearbox, LLC. Invention is credited to Mahalaxmi Gita Bangera, Edward S. Boyden, Roderick A. Hyde, Jordin T. Kare, Eric C. Leuthardt, Dennis J. Rivet, Lowell L. Wood, JR..
Application Number | 20180042467 15/794337 |
Document ID | / |
Family ID | 43381478 |
Filed Date | 2018-02-15 |
United States Patent
Application |
20180042467 |
Kind Code |
A1 |
Bangera; Mahalaxmi Gita ; et
al. |
February 15, 2018 |
DEVICES FOR CONTINUAL MONITORING AND INTRODUCTION OF
GASTROINTESTINAL MICROBES
Abstract
Systems and methods described herein include those for the
continual modification of intestinal microbes. Described herein are
systems including sampling devices, analysis devices, computational
devices and user interface devices as well as methods for the use
of such devices in combination.
Inventors: |
Bangera; Mahalaxmi Gita;
(Renton, WA) ; Boyden; Edward S.; (Chestnut Hill,
MA) ; Hyde; Roderick A.; (Redmond, WA) ; Kare;
Jordin T.; (San Jose, CA) ; Leuthardt; Eric C.;
(St. Louis, MO) ; Rivet; Dennis J.; (Richmond,
VA) ; Wood, JR.; Lowell L.; (Bellevue, WA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Gearbox, LLC |
Bellevue |
WA |
US |
|
|
Family ID: |
43381478 |
Appl. No.: |
15/794337 |
Filed: |
October 26, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12459388 |
Jun 29, 2009 |
9848760 |
|
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15794337 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61B 5/411 20130101;
A61B 1/041 20130101; Y02A 90/26 20180101; A61B 5/0002 20130101;
G16B 5/00 20190201; G16B 20/00 20190201; A61B 5/42 20130101; Y02A
90/10 20180101; G16H 10/40 20180101 |
International
Class: |
A61B 1/04 20060101
A61B001/04; A61B 5/00 20060101 A61B005/00; G06F 19/00 20110101
G06F019/00; G06F 19/12 20110101 G06F019/12 |
Claims
1.-48. (canceled)
49. A system for monitoring and introducing gastrointestinal
microbes into a mammalian gastrointestinal tract over time,
comprising: two or more sampling devices; one or more analysis
device; at least one computational device configured to receive
information from the one or more analysis device; at least one user
interface operably connected to the at least one computational
device; and at least one dispenser operably connected to the at
least one computational device.
50. The system of claim 49, wherein the two or more sampling
devices comprise: one or more dietary sampling devices.
51. The system of claim 49, wherein the two or more sampling
devices comprise: two or more passive sampling devices.
52. The system of claim 49, wherein the two or more sampling
devices comprise: one or more additional devices configured to
yield additional information about a sample collection.
53. The system of claim 49, wherein the two or more sampling
devices comprise: an antenna.
54. The system of claim 49, wherein the two or more sampling
devices comprise: one or more electronic detector.
55. The system of claim 49, wherein the one or more analysis device
is configured to come in direct contact with each of the two or
more sampling devices for analysis of a sample.
56. The system of claim 49, wherein the one or more analysis device
is configured for nucleic acid analysis of the microbes present in
a sample.
57. The system of claim 49, wherein the one or more analysis device
and the at least one computational device are integrated into a
single unit.
58. The system of claim 49, wherein the at least one computational
device is configured to accept data regarding an analysis of at
least one sample and compare the accepted data to a standard
profile.
59. The system of claim 49, wherein the at least one dispenser is
configured to dispense at least one microbe, antibiotic,
antifungal, prebiotic agent, probiotic agent, or nutritional
supplement.
60. The system of claim 49, wherein the at least one dispenser
comprises: an antenna.
61. The system of claim 49, wherein the at least one dispenser
comprises: a database of potential agents possible to dispense.
62. The system of claim 49, wherein the at least one dispenser
comprises: a database of codes to signal or indicate when a
specific dispensation protocol should be initiated.
63. A system for monitoring and introducing gastrointestinal
microbes into a mammalian gastrointestinal tract over time,
comprising: two or more sampling devices; one or more analysis
device; at least one computational device configured to receive
information from the one or more analysis device and configured to
signal a dispensing device information relating to time, quantity,
location or identity of material to dispense; and at least one
dispenser operably connected to the at least one computational
device, the at least one dispenser configured to receive
information relating to time, quantity, location or identity of
material to dispense from the at least one computational
device.
64. The system of claim 63, wherein the two or more sampling
devices comprise: one or more dietary sampling devices.
65. The system of claim 63, wherein the two or more sampling
devices comprise: two or more passive sampling devices.
66. The system of claim 63, wherein the two or more sampling
devices comprise: one or more additional devices configured to
yield additional information about a sample collection.
67. The system of claim 63, wherein the two or more sampling
devices comprise: an antenna.
68. The system of claim 63, wherein the two or more sampling
devices comprise: one or more electronic detector.
69. The system of claim 63, wherein the one or more analysis device
is configured to come in direct contact with each of the two or
more sampling devices for analysis of a sample.
70. The system of claim 63, wherein the one or more analysis device
is configured for nucleic acid analysis of the microbes present in
a sample.
71. The system of claim 63, wherein the one or more analysis device
and the at least one computational device are integrated into a
single unit.
72. The system of claim 63, wherein the at least one computational
device is configured to accept data regarding an analysis of at
least one sample and compare the accepted data to a standard
profile.
73. The system of claim 63, wherein the at least one dispenser is
configured to dispense at least one microbe, antibiotic,
antifungal, prebiotic agent, probiotic agent, or nutritional
supplement.
74. The system of claim 63, wherein the at least one dispenser
comprises: an antenna.
75. The system of claim 63, wherein the at least one dispenser
comprises: a database of potential agents possible to dispense.
76. The system of claim 63, wherein the at least one dispenser
comprises: a database of codes to signal or indicate when a
specific dispensation protocol should be initiated.
77. A system for monitoring and introducing gastrointestinal
microbes into a mammalian gastrointestinal tract, comprising: at
least one gastrointestinal microbe analysis device; at least one
computational device; at least one user interface operably
connected to the at least one computational device; and at least
one dispenser operably connected to the at least one computational
device.
78. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device comprises: a dietary
sampling device.
79. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device comprises: a passive
sampling device.
80. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device comprises: one or more
additional devices configured to yield additional information about
a sample collection.
81. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device comprises: an antenna.
82. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device comprises: one or more
electronic detector.
83. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device is configured for nucleic
acid analysis of the microbes present in a sample.
84. The system of claim 77, wherein the at least one
gastrointestinal microbe analysis device and the at least one
computational device are integrated into a single unit.
85. The system of claim 77, wherein the at least one computational
device is configured to accept data regarding an analysis of at
least one sample and compare the accepted data to a standard
profile.
86. The system of claim 77, wherein the at least one dispenser is
configured to dispense at least one microbe, antibiotic,
antifungal, prebiotic agent, probiotic agent, or nutritional
supplement.
87. The system of claim 77, wherein the at least one dispenser
comprises: an antenna.
88. The system of claim 77, wherein the at least one dispenser
comprises: a database of potential agents possible to dispense.
89. The system of claim 77, wherein the at least one dispenser
comprises: a database of codes to signal or indicate when a
specific dispensation protocol should be initiated.
Description
SUMMARY
[0001] In one aspect, a system includes but is not limited to a
system for continual modification of intestinal microbes including
a set of devices. The devices include: at least one sampling device
operable for taking at least one sample of an individual's
gastrointestinal microbes; at least one analysis device operable
for analysis of the at least one sample; at least one computational
device operable for accepting data regarding the analysis of the at
least one sample and comparing the data to a standard profile; and
at least one user interface device operably connected to the at
least one computational device. In one aspect, a system includes
but is not limited to a system for monitoring and introducing
gastrointestinal microbes into a mammalian gastrointestinal tract
over time, including a set of devices. The devices include: at
least one gastrointestinal microbe analysis device; at least one
computational device; at least one user interface operably
connected to the at least one computational device; and at least
one dispenser operably connected to the at least one computational
device. In addition to the foregoing, other system aspects are
described in the claims, drawings, and text forming a part of the
present disclosure.
[0002] In an aspect, a method includes but is not limited to a
computer-implemented method including: accepting data describing at
least one aspect of an individual's gastrointestinal microbes
present at a particular time; accepting data regarding at least one
aspect of the individual's health status at the particular time;
integrating, on a computing device, the accepted data regarding the
individual's gastrointestinal microbes and the accepted data
regarding the individual's health status into an individual profile
for the particular time; comparing the individual profile for the
particular time to a standard profile; and indicating, to at least
one system user, one or more interventions relating to
gastrointestinal microbes associated with directing the individual
profile for the particular time to approximate the standard
profile. In one aspect, a method includes but is not limited to a
computer-implemented method for suggesting adjustments to
gastrointestinal microbe profiles over time, including: accepting
data relating to at least one aspect of an individual's
gastrointestinal tract microbial composition at an initial time;
comparing, on a computing device, the data relating to at least one
aspect of an individual's gastrointestinal tract microbial
composition at an initial time to at least one standard
gastrointestinal tract microbial composition; identifying
differences, if any, between the data relating to the at least one
aspect of the individual's gastrointestinal tract microbial
composition at an initial time and one or more of the at least one
standard gastrointestinal tract microbial composition; creating an
initial difference listing of the identified differences between
the data relating to the individual's gastrointestinal tract
microbial composition at an initial time and one or more of the at
least one standard gastrointestinal tract microbial composition;
creating at least one initial action plan to alter at least one
aspect of the individual's gastrointestinal tract microbial
composition to minimize the initial difference listing; and
indicating one or more of the at least one initial action plan to
at least one system user. In addition to the foregoing, other
method aspects are described in the claims, drawings, and text
forming a part of the present disclosure.
[0003] In one or more various aspects, related systems include but
are not limited to circuitry and/or programming for effecting the
herein-referenced method aspects; the circuitry and/or programming
can be virtually any combination of hardware, software, and/or
firmware configured to effect the herein-referenced method aspects
depending upon the design choices of the system designer.
[0004] The foregoing summary is illustrative only and is not
intended to be in any way limiting. In addition to the illustrative
aspects, embodiments, and features described above, further
aspects, embodiments, and features will become apparent by
reference to the drawings and the following detailed
description.
BRIEF DESCRIPTION OF THE FIGURES
[0005] FIG. 1 is a schematic of a system including multiple
devices.
[0006] FIG. 2 is a schematic of a system including multiple
devices.
[0007] FIG. 3 is a schematic of a system including multiple
devices.
[0008] FIG. 4 is a flowchart of a computer-implemented method.
[0009] FIG. 5 depicts alternate embodiments of the method shown in
FIG. 4.
[0010] FIG. 6 shows alternate embodiments of the method shown in
FIG. 4.
[0011] FIG. 7 illustrates alternate embodiments of the method shown
in FIG. 4.
[0012] FIG. 8 is a flowchart of a computer-implemented method.
[0013] FIG. 9 depicts alternate embodiments of the method shown in
FIG. 8.
[0014] FIG. 10 illustrates alternate embodiments of the method
shown in FIG. 8.
[0015] FIG. 11 illustrates alternate embodiments of the method
shown in FIG. 8.
[0016] FIG. 12 depicts the number of cells detected by real-time
PCR in clinical samples from five healthy control patients.
[0017] FIG. 13 depicts linear regression coefficients for bacterial
counts and odds ratios for the presence of gut bacteria, with
respect to determinants in multivariate analyses.
[0018] FIG. 14 depicts variation in total fecal bacterial density
and specific taxa for an infant treated with antibiotics.
[0019] FIG. 15 illustrates changes in microbial profiles in
individuals consuming different diets over time.
[0020] FIG. 16 illustrates the comparison of 16S rRNA gene
libraries derived from healthy controls and FMF patients in
remission and attack.
[0021] FIG. 17 depicts minimum inhibitory concentrations (MIC) of
antimicrobials for a list of enteropathogens.
DETAILED DESCRIPTION
[0022] In the following detailed description, reference is made to
the accompanying drawings, which form a part hereof. In the
drawings, similar symbols typically identify similar components,
unless context dictates otherwise. The illustrative embodiments
described in the detailed description, drawings, and claims are not
meant to be limiting. Other embodiments may be utilized, and other
changes may be made, without departing from the spirit or scope of
the subject matter presented here.
[0023] Aspects of the systems and methods described herein are
illustrated in FIG. 1. Systems and methods as described herein are
intended for use in relation with the mammalian gastrointestinal
tract system. As an overview, the mammalian gastrointestinal tract
system 100 includes multiple sub-systems, such as the nasal system
102, oral system 110, esophageal system 130, gastric system 120,
small and large intestine systems 140 and 150, and rectal system
160. In some contexts as used herein the small and large intestine
systems 140, 150 will be described collectively as the intestine
system. Although a human gastrointestinal tract system is depicted
in FIG. 1, in some embodiments the methods and systems described
herein may be used with other mammals, such as domesticated
animals, for example cats, dogs, cattle, pigs, horses, sheep or
goats. Normally in mammals microbial populations reside within all
sub-systems of the gastrointestinal tract system. As used herein,
"microbe" includes one or more species or strain of microscopic
agents from the three domains eubacteria, eukarya and archaea as
well as viruses. For example, the oral system, which includes
structures such as the mouth, tongue, teeth, oral cavity and
salivary glands, hosts a varied microbial population. For example,
in humans microbes from saliva have been shown to be diverse
between individuals, with each individual's oral cavity hosting
multiple bacterial genera. See Nasidze et al., "Global Diversity in
the Human Salivary Microbiome," Genome Research published online
Feb. 27, 2009, and ScienceNOW Daily News "What your spit says about
you," 26 Feb. 2009, each of which is incorporated herein by
reference. For example, the gastrointestinal microbes of an
individual have been demonstrated to adapt and change over time,
see Adlerberth, "Factors influencing the establishment of the
intestinal microbiota in infancy," Nestle Nutr Workshop Ser Pediatr
Program, 62:13-33 (2008), which is herein incorporated by
reference. For example, the intestine system 140, 150 and the
rectal system 160 host an array of prokaryotic and eukaryotic
diversity both within and between individuals. See Scanlan and
Marchesi, "Micro-eukaryotic diversity of the human distal gut
microbiota: qualitative assessment using culture-dependent and
-independent analysis of faeces," The ISME Journal, 1-11 (2008),
which is herein incorporated by reference. Within a given
individual at a particular time, there may be a mixture of microbes
in each region of the gastrointestinal tract and the mixtures may
have some overlap between regions. For example, in some instances,
microbes from the nasal system may pass into the oral system or
other regions of the gastrointestinal system, for example during
sneezing or coughing. For example, microbes from the nasal system
or the oral system may pass into other portions of the
gastrointestinal system through swallowing or the normal flow of
matter during digestion. Generally, microbial populations would
tend to move through the entirety of the gastrointestinal system
from the oral system through to the rectal system due to normal
physiological action of an individual body. Although the same
microbes are unlikely to colonize every portion of the
gastrointestinal system in an individual, microbes that colonize
other regions may be present in a given region through routine
physiological activity.
[0024] The specific types and relative quantities of microbes
present in an individual's gastrointestinal system have been linked
to the health and well-being of the individual. As used herein, a
group of microbes, or a microbial population, taken as a whole is
referred to as a "microbiota," and when the group is quantitated or
measured in some manner it is referred to as a "microbiome."
However these terms may be used interchangeably in some contexts,
as a microbiome is often taken as representative of a microbiota.
For example, the microbes present in an individual's
gastrointestinal system, taken as a whole, constitute that
individual's "gut microbiota." A balanced gut microbiota is
required for intestinal health, and there is an emerging view that
specific diseases are characterized by specific gut microbiota
imbalances, see for example the slides of Leroy and De Vuyst,
titled "New insights in the gut microbiota: a key to good health,"
from Alimentation & Sante: Microbiotica, etc. in Liege, Sep.
25, 2008, which is herein incorporated by reference. For example,
some microbes have been associated with differential daily
requirements of nutrients, see Hrdina et al., "The gastrointestinal
microbiota affects the selenium status and selenoprotein expression
in mice," Journal of Nutritional Biochemistry, available online 30
Sep. 2008, which is herein incorporated by reference. For example,
some microbes have been linked to obesity, see DiBaise et al., "Gut
microbiota and its possible relationship with obesity," Mayo Clin
Proc 83(4):460-469 (2008), and Turnbaugh et al., "An
obesity-associated gut microbiome with increased capacity for
energy harvest," Nature 444:1027-1031 (2006), which are herein
incorporated by reference. It has been suggested that the relative
levels of some microbial species in the gastrointestinal system may
be manipulated as an approach to obesity; see Ley et al., "Human
gut microbes associated with obesity," Nature 444:1022-1023,
(2006), and Bajzer and Seeley, "Obesity and gut flora," Nature News
and Views 444: 1009-1010 (2006), and WO 2008076696 titled "The gut
microbiome as a biomarker and therapeutic target for treating
obesity or an obesity-related disorder," which are herein
incorporated by reference. Genetic factors of an individual also
affect the microbial population in the individual's
gastrointestinal system, see for example Khachatryan et al.,
"Predominant role of host genetics in controlling the composition
of gut microbiota," PLoS ONE, 3:e3064 (2008), which is herein
incorporated by reference. More specifically, the activity of
proteins and other metabolites in individual hosts have been shown
to be affected by the presence of some species of microbes in the
gut, see Samuel et al., "Effects of the gut microbiota on host
adiposity are modulated by the short-chain fatty acid binding G
protein-coupled receptor, Gpr41," PNAS-USA 105(43): 16767-16772
(2008), which is incorporated herein by reference. Although the
gastrointestinal system microbial population is complex, it has
been suggested that key functional members of the microbiome most
influence host metabolism and thus health, a concept which has been
termed "functional metagenomics," see for example Li et al.,
"Symbiotic gut microbes modulate human metabolic phenotypes,"
PNAS-USA, 105(6):2117-2122 (2008), which is incorporated herein by
reference. For example, certain molecules of the bacterial
microbiota have been indicated as protective for inflammatory bowel
disease (IBD), see Mazmanian "A microbial symbiosis factor prevents
intestinal inflammatory disease," Nature 453: 620-625 (2008), which
is herein incorporated by reference. For example, interaction of
gastrointestinal microbes with an individual's immune system have
been suggested to be a critical epigenetic factor modifying type I
diabetes predisposition, see Wen et al., "Innate immunity and
intestinal microbiota in the development of Type I diabetes,"
Nature 455: 1109-1113 (2008), which is incorporated herein by
reference.
[0025] Systems described herein include devices operable for
sampling microbial populations from regions of the gastrointestinal
system. In some embodiments, the sampling device is configured to
directly sample the microbial population in a region, while in
others the sampling device is configured to sample a product of the
microbes, such as metabolic waste products or cellular debris of
the microbial population. In some embodiments, the sampling devices
operate internally to the body, including one or more sampling
device 104 for the nasal system 102, one or more sampling device
115 for the oral system 110, one or more sampling device 135 for
the esophageal system 130, one or more sampling device 125 for the
gastric system 120, one or more sampling device 145, 155 for the
intestine system 140, 150 and one or more sampling device 165 for
the rectal system 160. For example, one or more sampling device 104
for the nasal system 102 may include one or more sampling device
that is configured to operate after being placed in the upper nasal
passages, nose, or in the back of the throat in the lower nasal
passages. For example, an endoscopy instrument may be placed in the
nasal system and used to sample mucus or tissue. For example, an
elongated swab or similar object may be placed in the nasal system
and used to sample mucus or tissue. For example, one or more
sampling device 115 for the oral system 110 may include one or more
sampling device that is configured to be operable after being
placed into the oral cavity. Examples of sampling devices for the
oral system include, but are not limited to, absorbent pads, tubes
for collection of salivary fluid, and scrapings from the interior
of the mouth. In some instances, a specialized device for sampling
the oral system may be implemented such as described in European
Patent Application Publication EP1397997 to Groschl and Rauh,
titled "Detection Device," which is herein incorporated by
reference. For example, one or more sampling device 115 for the
oral system 110 may include a device that is configured to sample
breath. See, for example, U.S. Pat. No. 7,255,677 to Burch et al.,
titled "Detection, diagnosis and monitoring of a medical condition
or disease with artificial olfactometry," which is herein
incorporated by reference. For example, one or more sampling device
115 for the oral system 110, one or more sampling device 135 for
the esophageal system 130, one or more sampling device 125 for the
gastric system 120, one or more sampling device 145, 155 for the
intestine system 140, 150 and one or more sampling device 165 for
the rectal system 160 may include one or more sampling device that
is operable after being swallowed and passed through the
gastrointestinal tract system 100 during the operation of an
individual's gastrointestinal physiology. See, for example, US
patent application to Boyden et al., titled "Adaptive dispensation
in a digestive tract," filed on Oct. 23, 2007 and US Patent
Application No. 2009/0112191 to Boyden et al. titled "Medical or
veterinary digestive tract utilization systems and methods" which
are herein incorporated by reference. For example, one or more
sampling device 135 for the esophageal system 130 may include a
tethering component, and configured to be withdrawn through the
mouth at an appropriate time point after being swallowed or
inserted into the esophagus. For example, a sampling device for the
esophageal system may include an endoscopy device. For example, one
or more sampling device 165 for the intestinal system or rectal
system 160 may be configured to be inserted anally. In some
embodiments, sampling devices operate externally to an individual's
body, 175, 185. For example, sampling devices 175, 185 may retain
gastrointestinal tract samples external to the body. For example,
sampling devices may retain salivary fluid, mucus, vomit,
intestinal matter, or fecal matter collected after exit from an
individual body.
[0026] The types and targeted locations of sampling devices in a
particular embodiment may depend on, for example, user preference,
cost, accuracy, comfort of the individual, safety, speed, duration
or durability. The types and targeted locations of sampling devices
may also depend on what species of mammal the system is intended
for use with. For example, when sampling from human infants, fecal
matter may be easily obtainable with minimal invasion. Or example,
in individuals undergoing routine endoscopy, tissue and mucus may
be sampled as part of the endoscopy process with minimal additional
discomfort and inconvenience to the individual. For example, when
sampling from domesticated animals, salivary fluid may be
obtainable during routine daily animal care, such as during
cleaning or feeding, or fecal matter may be obtainable from a
stall, box or cage. Various sampling devices implemented together
or singly are envisioned for use in different embodiments. Some
systems may include sampling devices configured to operate in a
single organ system while others may include sampling devices
configured to operate in two or more organ systems. For example, an
oral system 110 sampling device 115 may be used in addition to or
in conjunction with a gastric system 120 sampling device 125. In
some aspects, a sampling device may obtain samples from more than
one organ system. For example, an ingestible sampling device may
sample from multiple locations, such as the oral system 110,
esophageal system 130, intestine system 140, 150 and rectal system
160 as it moves through the gastrointestinal tract system 100 as
part of an individual's physiological processes. See, for example,
US patent application to Boyden et al., titled "Adaptive
dispensation in a digestive tract, filed on Oct. 23, 2007 and US
Patent Application No. 2009/0112191 to Boyden et al. titled
"Medical or veterinary digestive tract utilization systems and
methods" which are herein incorporated by reference. For example, a
sampling device may include a tethering mechanism for the
withdrawal of the sampling device after passing through more than
one region of the gastrointestinal tract system 100, such as a
sampling device that is placed in the mouth to sample the oral
system 110 before being swallowed and thereafter sampling the
esophageal system 130 before retraction and removal from the
gastrointestinal tract system 100. In some systems, multiple
sampling devices targeting a single system may be included. For
example, two or more oral system 110 sampling devices 115 may be
implemented at the same time or in series.
[0027] It is envisioned that the systems as described herein will
be used to take multiple samples from the gastrointestinal system
of an individual over time. In some embodiments, the systems as
described herein may be configured to operate continually, or
repeatedly with time breaks in between samples being taken. For
example, systems as described herein may operate over a period of
days, with sampling devices operating daily, every other day, or in
periodic intervals of days. For example, systems as described
herein may be implemented to take samples from an individual weekly
or monthly. It may be desirable in some situations to monitor an
individual in shorter intervals for some time period followed by
longer intervals between samples being taken. In some situations,
sampling may occur on a schedule set by other events, such as
medical testing, routine care, or accessibility of an individual.
For example, a domestic animal may be easily sampled during daily
routines such as feeding or cleaning. In some embodiments, sampling
from the gastrointestinal system of an individual over time may be
implemented through the use of multiple single use sampling
devices. In some embodiments, sampling from the gastrointestinal
system of an individual over time may be implemented through the
use of a sampling device that may be used more than once, for
example a sampling device that may be recharged, refurbished or
reused. In some embodiments, sampling from the gastrointestinal
system of an individual over time may be implemented through the
use of a sampling device that may be ingested and durably persist
in the gastrointestinal tract of an individual, with sufficient
time to take multiple samples before the device leaves the
individual's gastrointestinal system.
[0028] As all regions and sub-systems of the gastrointestinal tract
system 100 normally contain microbes, in various embodiments the
types of samples retained by the one or more sampling devices 104,
115, 135, 125, 145, 155, 165, 175 and 185 may include samples from
all regions and sub-systems of the gastrointestinal tract system
100. The types of samples retained by the one or more sampling
devices may be tissue, secretory or waste product samples of the
gastrointestinal system 100. Such samples would be analyzed as
described herein to yield information relating to the microbial
composition of regions or sub-systems of the gastrointestinal tract
system 100, or the gastrointestinal tract system 100 generally. For
example, one or more samples may include breath. For example, one
or more samples may include mucus secretions from the nasal system
102. For example, one or more samples may include salivary fluid
from the oral system 110, or the esophageal system 130. For
example, one or more samples may include mucus secretions from the
esophageal system 130. For example, one or more samples may include
gastric fluid from the gastric system 120. For example, one or more
samples may include intestinal contents from the intestine system
140, 150. For example, one or more samples may include fecal matter
from the rectal system 160. In some embodiments, the samples may
also include tissue from the gastrointestinal tract system 100
wherein the tissue contains a microbial population as part of its
cellular structure or secretions. Samples may also include tissue
or cell debris that has been sloughed off or removed from the
surface of the gastrointestinal tract system 100, such as
intestinal tissue or cell debris that has sloughed off during
physiological processes, or cell debris that has been scraped off
by a sampling device, such as during oral or nasal sampling with
swabs or endoscopy of any portion of the gastrointestinal
system.
[0029] Sampling devices that would be suitable for implementation
in the systems as described herein include passive devices that
enclose, attach or support a sample. Examples include containers,
sampling swabs or sticks, and absorbent pads which may be used as
sampling devices for mucus, secretions, salivary fluids or fecal
matter. In some embodiments, samples may be retained internally to
the sampling device, such as diagrammed by sample 180 and sampling
device 185 in FIG. 1. For example, a sampling device may include a
cup, reservoir, indentation, receptacle, tank or other form of
storage internal to the sampling device. See, for example, European
Patent Application Publication EP1397997 to Groschl and Rauh,
titled "Detection Device," which is herein incorporated by
reference. In some embodiments, samples may be retained externally
to the sampling device, such as diagrammed by sample 170 and
sampling device 175 in FIG. 1. For example, a sampling device may
include a surface area that adheres or attaches to a sample
material. See, for example, U.S. Pat. No. 6,102,892 to Putzer et
al., titled "Diaper with pleats for containment of liquid and solid
wastes," and U.S. Pat. No. 6,423,884 to Oehmen, titled "Absorbent
article having apertures for fecal material," which are
incorporated by reference herein.
[0030] Systems and methods described herein include one or more
analysis device. As shown in FIG. 1, an analysis device 177, 187
may come in direct contact with or be integrated with the sampling
device 175, 185 for analysis of a sample. For example, a sampling
device including a swab or absorbent material may be placed
directly into an analysis device. In some embodiments, a portion or
component of a sample may be extracted prior to analysis. For
example, excess fluid may be removed from a sample prior to
analysis. For example, a portion of a sample may be concentrated in
a gradient or by centrifugation prior to analysis. For example,
proteins or nucleic acids may be purified from a sample prior to
analysis.
[0031] An analysis device may analyze a sample by any number of
techniques, depending on the type of sample and parameters of the
assays utilized. For example, the analysis device may include
culturing microbes from the sample and then testing them for one or
more characteristics such as growth rate, visual appearance,
antibiotic resistance, antibiotic susceptibility, culturing
parameters including but not limited to growth on specific nutrient
sources, or culture staining. For example, one or more samples may
be cultured in an analysis device that also allows for testing in
vitro response to antimicrobial agents, such as described in U.S.
Pat. No. 7,384,778 to Chen et al., titled "Methods and devices for
the detection of pathogenic microorganisms and their antimicrobial
susceptibility," which is incorporated herein by reference. For
example, one or more samples may be cultured in a microplate
analysis such as the MicroLog.TM. system available from BIOLOG,
Inc, (Hayward Calif.), the brochure for which (Part #00A022, Rev A
01/2007) is herein incorporated by reference. In some embodiments,
the microbes present in a sample may be difficult or impossible to
culture using standard techniques and therefore must be analyzed
using techniques that do not require cell culture. See, for
example, US Patent Application No. 2007/0264636 to Crosby and
Criddle, titled "Capture and random amplification protocol for
identification and monitoring of microbial diversity," and Scanlan
and Marchesi Ibid, which are herein incorporated by reference. For
example, a sample may be subjected to Gram staining, or florescent
in situ hybridization ("FISH") analysis, or total DNA staining with
an agent such as SYBR green. See, for example, Ivanov et al.,
"Specific microbiota direct the differentiation of IL-17-producing
T-helper cells in the mucosa of the small intestine," Cell Host and
Microbe, 4:377-349 (2008), and Penders et al., "Factors influencing
the composition of the intestinal microbiota in early infancy,"
Pediatrics 118(2): 511-521 (2006), which are herein incorporated by
reference. For example, the analysis device may include nucleic
acid analysis of the microbes present in the sample. Depending on
the embodiment, nucleic acids may be analyzed directly, or may be
purified from the sample prior to examination by the analysis
device. In some embodiments, DNA from a sample may be purified and
then a profile of the sample generated by denaturing gradient gel
electrophoresis, or a specific DNA fragment or set of fragments may
be profiled using appropriate molecular biology techniques
including, but not limited to, "real-time" PCR analysis or
sequencing. See, for example, Iapichino et al., "Impact of
antibiotics on the gut microbiota of critically ill patients,"
Journal of Medical Microbiology 57: 1007-1014, (2008), Scalan and
Marchesi Ibid, and Penders et al, Ibid, which are herein
incorporated by reference. In some embodiments, a normalized global
estimation of the major contributing microbial species may be based
on real-time PCR assays, such as described in Ott et al.,
"Quantification of intestinal bacterial populations by real-time
PCR with a universal primer set and minor groove binder probes: a
global approach to the enteric flora," Journal of Clinical
Microbiology, 42(6):2566-2572 (2004), which is herein incorporated
by reference. In some embodiments, breath may be analyzed, such as
described in U.S. Pat. No. 7,255,677 to Burch et al., titled
"Detection, diagnosis and monitoring of a medical condition or
disease with artificial olfactometry," which is herein incorporated
by reference.
[0032] In some embodiments, a carrier or challenge compound may be
administered to an individual prior to sample collection and
analysis to improve assay sensitivity. For example, an individual
may be given a controlled dosage of a sugar-containing compound
prior to sampling of breath as part of a test for small intestine
bacterial overgrowth. See, for example, US Patent applications Nos.
2008/0014184 and 2008/0014185 to Lin and Pimentel, titled "Methods
of treating fibormyalgia caused by small intestinal bacterial
overgrowth," and "Methods of treating diarrhea and bloating caused
by small intestinal bacterial overgrowth" respectively, which are
herein incorporated by reference. For example, an individual may be
administered carbon isotopes as part of a test for H. Pylori
infection, see Pathak et al., "Urea breath test for Helicobacter
pylori detection: present status," Tropical Gastroenterology
25:156-161 (2004), which is incorporated by reference herein.
[0033] In some embodiments, a sampling device 104, 115, 125, 135,
145, 155, 165 may include one or more additional device which may
yield additional information about the sample collection. For
example, the sampling device may include a stopwatch or timekeeping
device and record the time when one or more samples are taken, the
date of sample collection, or the time interval between samples
being collected. The sampling device may also include a temperature
monitor or pH monitor and record the temperature or pH at the time
a sample is taken.
[0034] In some embodiments, a sampling device 104, 115, 125, 135,
145, 155, 165 may communicate with an analysis device 105 remotely,
including through wireless transmissions 107. See US patent
application to Boyden et al., titled "Adaptive dispensation in a
digestive tract, filed on Oct. 23, 2007 and US Patent Application
No. 2009/0112191 to Boyden et al. titled "Medical or veterinary
digestive tract utilization systems and methods" which are herein
incorporated by reference. Such wireless transmissions may assist a
user in locating a sampling device located within an individual
body at a given time point. An analysis device may also receive
crude or incomplete data from one or more sampling device and act
to analyze the crude data into a full analysis as described herein.
For example, a sampling device may signal remotely, from within a
gastrointestinal tract system, information such as the time, date,
pH or temperature, and such information may be integrated with data
from the analysis of a sample during information processing.
[0035] Information from one or more analysis devices may be
communicated to at least one computational device for integration
into a profile at one or more time points. One or more analysis
device may be operably attached to at least one computational
device. For example, an analysis device may be operably attached to
a computational device through a wire or network connection. In
some embodiments, the analysis device and the computational device
may be integrated into a single unit. For example, an analysis
device may operate such that data from the analysis device
automatically outputs to a computational device. Although a laptop
computer is shown as computational device 190 in FIG. 1, it is
envisioned that in some embodiments there may be a group of
computational devices, such as a network or large computer system.
A computational device may include digital memory and a user input
device such as a mouse, touchpad, touch screen or auditory signal
converter. A computational device 190 is operably attached to at
least one user interface device 195, such as a monitor, auditory
signal generator, light emitter, or electronic ink device.
[0036] Although user 197 is shown/described herein as a single
illustrated figure, those skilled in the art will appreciate that
user 197 may be representative of a human user, a robotic user
(e.g., computational entity), and/or substantially any combination
thereof (e.g., a user may be assisted by one or more robotic
agents) unless context dictates otherwise. In some embodiments,
user 197 may be part of a larger medical system, such as a medical
team, clinic, hospital, HMO, or office as individual people or as
computer-based systems or networks. In some embodiments, a user 197
may be an individual whose gastrointestinal microbes are being
evaluated, or a relative, associate or caregiver of such an
individual. In some contexts, the user 197 may be a patient. In
general, the same may be said of "sender" and/or other
entity-oriented terms as such terms are used herein unless context
dictates otherwise. As used herein, the user may include, for
example, a doctor, nurse, medical personnel, researcher, caregiver,
patient or individual, using the system either singly or
collectively.
[0037] FIG. 2 shows aspects of systems such as those described
herein. A system 200 for continual modification of intestinal
microbes includes at least one sampling device 210 operable for
taking at least one sample of an individual's gastrointestinal
microbes and at least one analysis device 250 operable for analysis
of at least one sample. The system 200 also includes at least one
computational device 190, operable for accepting data regarding the
analysis of the at least one sample and comparing the data to a
standard profile, and at least one user interface device 195
operably connected to the at least one computational device. In
some embodiments, the at least one computational device and the at
least one user interface device are an integrated unit. A system
user 197 may, for example, interface with the system, input data
into the system, recognize an indication from the system, or
receive output from the system through a user interface (UI) device
that may include one or more monitor, keyboard, mouse, voice
recognition system or auditory signal generator. In some
embodiments, the system 200 may include a sampling device 210
including one or more electronic detector 220. The electronic
detector 220 may include an electronic detector 225 operable for
sampling internal to a body. See US patent application to Boyden et
al., titled "Adaptive dispensation in a digestive tract," filed on
Oct. 23, 2007 and US Patent Application No. 2009/0112191 to Boyden
et al. titled "Medical or veterinary digestive tract utilization
systems and methods" which are herein incorporated by reference.
The sampling device 210 may include one or more physical sample
collector 230. The sampling device 210 may include at least one
antenna 235, such as an antenna operable for sending or receiving
data from other parts of the system or external to the system. For
example, a sampling device may transmit information relating to
sample collection such as time, pH, temperature or sample
identification information. For example, a sampling device may
receive a signal to take a sample at a specific location within the
gastrointestinal system or at a specific time point. One or more
sampling device 210 may include at least one ingestible sampling
device 240. One or more sampling device 210 may include one or more
dispensing devices 245. The analysis device 250 may include one or
more nucleic acid analysis device 252. For example, one or more
nucleic acid analysis device may include one or more DNA sequencer,
PCR machine, "real-time" (RT) PCR machine, mass spectrophotometer,
gradient gel device (including denaturing gradient gels) or
microscope for examination of stained nucleic acids in a sample.
For example, one or more nucleic acid analysis device may include
an analysis device that analyses at the metagenomic level,
including at the level of analyzing composite characteristics of a
group of microbes. The analysis device 250 may include one or more
protein analysis device 254. For example, a protein analysis device
may include a protein sequencer, a mass spectrophotometer, one or
more antibodies forming recognition elements, or a gradient gel
device. For example, a protein analysis device may include
detecting specific proteins, such as described in U.S. Pat. No.
7,214,479 to Welch et al., titled "E. coli O157:H7 C1-INH-binding
protein and methods of use," which is incorporated herein by
reference. The analysis device 250 may include one or more chemical
analysis device 256. A chemical analysis device may detect
volatiles, organic compounds, secondary metabolites or enzymes
indicative of a microbial population. For example, a chemical
analysis device may include a chemical component detector, such as
a mass spectrophotometer. The analysis device 250 may include one
or more electronic detector 258. For example, an electronic
detector may include an "electronic nose" or "electronic tongue"
device. See, for example, U.S. Pat. No. 7,255,677 to Burch et al.,
titled "Detection, diagnosis and monitoring of a medical condition
or disease with artificial olfactometry," and U.S. Pat. Nos.
5,571,401 and 5,698,089 to Lewis and Freund, titled "Sensor arrays
for detecting analytes in fluids," and US Patent Application
2008/0293997 to Buhlmann and Boswell, titled "Chemical sensor,"
which are herein incorporated by reference.
[0038] In some embodiments, the system receives input from a system
user such as a patient, individual, or caregiver and incorporates
that information into the analysis parameters or stored
information. Input from a system user may be incorporated with data
from one or more analysis device, and may form metadata. A system
user may input information relating to a specific event, such as an
individual going on antibiotic medication, or changing diet, and
incorporate that information along with the data generated from an
analysis device during that time period to generate relevant
metadata. For example, where an individual is undergoing a specific
course of antibiotic treatment, that individual or another person
may enter the dates and details about the antibiotic treatment into
the system, and the system may incorporate this into metadata for
the relevant time period. For example, an individual may eat an
unusually fatty or sugary meal before a sample is taken, and an
individual may input the relevant details of their recent diet into
the system. For example, an individual who is undergoing a series
of sampling procedures may change diet (such as become a
vegetarian, or go on a low-fat diet) at some point during the
series. Information relating to the diet change may be input into
the system and incorporated into the stored information as, for
example, metadata.
[0039] A system such as the one diagrammed in FIG. 2 may also
include additional elements as desired for a particular embodiment.
For example, a system 200 may include at least one additional
sampling device, including multiple sampling devices 210, 260, 262.
For example, a system 200 may include one or more dietary sampling
devices 270, 275. At least one dietary sampling device may be
operably connected to the at least one computational device. A
dietary sampling device may sample a portion of foodstuffs intended
for ingestion by the individual for analysis, such as to yield data
on the composition of the foodstuffs. For example, a dietary
sampling device may sample a foodstuff for caloric analysis. For
example, a dietary sampling device may sample a foodstuff for
composition analysis, such as what components are included in a
foodstuff mixture. For example, a dietary sampling device may
sample a foodstuff for microbial analysis, such as microbial
analysis of a fermented or microbe-containing foodstuff such as
yogurt, tofu or cheese products. For example, a dietary sampling
device may sample partially digested foodstuffs from any region of
the gastrointestinal tract for completeness of digestion, rates of
digestion, or dietary byproducts. A system 200 may include one or
more dispensing devices 280, 285, which may dispense, for example,
one or more microbes, antimicrobial agent, prebiotic, prebiotic,
synbiotic, or nutritional supplement. For more information on the
terms "probiotic" and "prebiotic," and "synbiotic" see Schrezenmeir
and de Vrese, "Probiotics, prebiotics, and synbiotics--approaching
a definition," American Journal of Clinical Nutrition 73(suppl.):
361S-364S (2001), which is herein incorporated by reference.
Briefly, a "probiotic" may be described as "a preparation of or a
product containing viable, defined microorganisms in sufficient
numbers, which alter the microflora (by implantation or
colonization) in a compartment of the host and that exert
beneficial health effects on this host," while "prebiotic" may be
described as "a non-digestible food ingredient that beneficially
affects the host by selectively stimulating the growth and/or
activity of one or a limited number of bacteria," see Schrezenmeir
and de Vrese, Ibid. For example, the one or more dispensing devices
may dispense one or more specific antimicrobial compounds, such as
those described in U.S. Pat. No. 7,211,426 to Bruessow et al.,
titled "Isolated phages and their use in food or pet food
products," and U.S. Pat. No. 7,371,375 to Zimmer et al., titled
"Protein," and US Patent Application No. 2008/0146609 to Guiles et
al., titled "Substituted Thienopyridone Compounds With
Antibacterial Activity," and US Patent Application No. 2008/0170991
to Shi et al., titled "Selectively targeted antimicrobial peptides
and the use thereof," and US Patent Application No. 2008/0171376 to
Scholl and Williams, titled "Modified bacteriocins and methods for
their use," and US Patent Application No. 2008/0220103 to Birnbaum
et al., titled "Method for treating/controlling/killing fungi and
bacteria on living animals," all of which are herein incorporated
by reference. For example, the one or more dispensing devices 280,
285 may dispense a pharmaceutical composition such as those
described in U.S. Pat. No. 6,706,287 to Ranganathan et al, titled
"Prebiotic and probiotic compositions and methods for their use in
gut-based therapies," or as described in US Patent Application No.
2004/0028689 to Borody, titled "Probiotic recolonisation therapy,"
which are herein incorporated by reference. For example, the one or
more dispensing devices may dispense slowly digestible starch and
fermentable dietary fiber compounds such as those described in US
Patent Application No. 2007/0196437 to Hamaker et al., titled
"Slowly digesting starch and fermentable fiber," and in Napolitano
et al., "Potential prebiotic activity of oligosaccharides obtained
by enzymatic conversion of durum wheat insoluble dietary fibre into
soluble dietary fibre," Nutrition, Metabolism & Cardiovascular
Diseases, in press, available online as of 20 Sep. 2008, DOI:
10.1016/j.numecd.2008.07.005, which are incorporated herein by
reference. For example, the one or more dispensing devices may
dispense at least one lactose-reduced dairy composition, such as
those described in US Patent Application No. 2007/0196439 to Catani
and Robinson, titled "Lactose-reduced dairy compositions and
related methods," which is incorporated herein by reference. At
least one dispensing device may be operably connected to the at
least one computational device. For example, the at least one
computational device may receive information from a dispensing
device relating to time, quantity and identity of material
dispensed. For example, the at least one computational device may
signal a dispensing device relating to time, quantity, location or
identity of material to dispense. A system 200 may include one or
more antenna 290 configured for signaling between parts of the
system or with elements outside of the system. A system 200 may
include data storage 292, such as digital data storage including
recordable type medium formats such as floppy disk, hard disk
drive, digital tape, computer memory, etc. A system 200 may include
a database 294. For example, a database may include information on
previous samples taken from a specific individual, or information
regarding the health history or status of an individual or metadata
such as comments from the individual or physician. A database may
also contain information relating to a set of standard profiles or
possible interventions that may be suggested by the system to at
least one system user. A system 200 may include at least one user
interface 296, for example at least one display, touch screen,
auditory response system, keypad, mouse, or other interface device.
A system 200 may include control circuitry 298, which may include
electronic circuitry having one or more paths of electrical current
constructed and arranged to implement various functions as
described herein. A system 200 may include one or more elements 299
selected by the system designer.
[0040] FIG. 3 depicts aspects of a system 300. A system for
monitoring and introducing gastrointestinal microbes into a
mammalian gastrointestinal tract over time includes at least one
gastrointestinal microbe analysis device 310, at least one
computational device 350, at least one user interface 360 operably
connected to the at least one computational device 350, and at
least one dispenser 370 operably connected to the at least one
computational device 350. In some embodiments, the at least one
gastrointestinal microbe analysis device may be reusable, such as
an endoscopy device that may be recharged or refurbished before
reuse. In some embodiments, the at least one gastrointestinal
microbe analysis device may be modular, such as a device that may
have one or more modules removed and replaced or swapped for
another module. In some embodiments, the at least one
gastrointestinal microbe analysis device 310 may include one or
more nucleic acid analysis device 330. In some embodiments, the at
least one gastrointestinal microbe analysis device 310 may include
one or more protein analysis device 325. In some embodiments, the
at least one gastrointestinal microbe analysis device 310 may
include one or more chemical analysis device 345. In some
embodiments, the at least one gastrointestinal microbe analysis
device 310 may include one or more electronic detector 320. In some
embodiments, the at least one computational device 350 is operably
connected to the at least one gastrointestinal microbe analysis
device 310. For example, the at least one computational device may
be operably connected to the at least one gastrointestinal microbe
analysis device through a wired or wireless connection, or a
network. In some embodiments, the at least one computational device
may be integrated with the at least one gastrointestinal microbe
analysis device, such as an analysis device that is integrated with
a computer system as part of its standard operation. In some
embodiments, the at least one gastrointestinal microbe analysis
device 310 includes at least one antenna 315, such as an antenna
operable for sending or receiving communications from other parts
of the system or external to the system. An antenna may be
configured to send or receive communications from various parts of
the system or from one or more devices external to the system. In
some embodiments, a gastrointestinal microbe analysis device 310
may be an ingestible sampling device 340.
[0041] Depending on the embodiment, the at least one dispenser 370
may be configured to dispense one or more materials. For example,
at least one dispenser may be configured to dispense at least one
microbe, antibiotic, antifungal, prebiotic agent, probiotic agent,
or nutritional supplement. For more information regarding
probiotics, see Blandino et al., "Probiotics: overview of
microbiological and immunological characteristics," Expert Rev
Infect Ther 6(4):497-508 (2008), which is herein incorporated by
reference. The at least one dispenser 370 may include a database
372, for example a database of potential agents possible to
dispense, or of codes to signal or indicate when a specific
dispensation protocol should be initiated. The at least one
dispenser 370 may include at least one data storage unit 374, for
example a look-up table including sequences of events involved in
certain dispensation protocols. In some embodiments, the at least
one dispenser 370 may include at least one antenna 376. For
example, the antenna may be configured to send a signal when the
dispensation begins or ends, or may be configured to receive a
signal initiating a dispensation protocol. In some embodiments, the
at least one dispenser 370 may include circuitry 377, for example
control circuitry for the dispenser. In some embodiments, the at
least one dispenser 370 may include logic 378, such as dispensing
protocols implemented as hardware, software or firmware.
[0042] Depending on the embodiment, the at least one computational
device 350 may include at least one database 352, for example
containing information regarding an individual or group of
individuals, one or more individual or standard profiles, or
operating parameters of the system. In some embodiments, the at
least one computational device 350 may include at least one data
storage unit 354, for example data storage in a hard disk drive, a
digital tape, or a computer memory. The data storage may be
operable for storing data input during operation of the system, for
example information from the analysis device or the user interface.
The data storage may be operable for storing data preexisting to
the system operation, for example one or more standard profiles or
individual identifiers. In some embodiments, the at least one
computational device 350 may include at least one antenna 356, for
example at least one antenna operable for transmitting information
relating to the analysis device or the dispensing device. The at
least one antenna may also receive input from an outside source,
such as an external network or database. In some embodiments, the
at least one computational device 350 may include circuitry 357.
For example, the circuitry may include control circuitry for the
system as a unit. In some embodiments, the at least one
computational device 350 may include logic 358, for example
integration protocols to integrate information relating to the
individual and information from the sample analysis into a profile
for a time point. The at least one computational device 350 may
include logic 358 which includes protocols for the comparison of an
individual profile to a standard profile.
[0043] In some embodiments, the at least one user interface 360 may
include any type of user interface (UI) configured to be operable
for a particular embodiment. For example, the at least one user
interface 360 may include at least one keyboard 362, at least one
monitor 364 (which may be a touch-sensitive monitor or an E-ink
device), at least one sound generator 365 (such as a sound signal
generator for beeps, hums, alarms or the like, or a sound generator
operable for production of artificial human speech), and at least
one mouse 366. The at least one user interface 360 may also include
at least one antenna 368, for example an antenna operable for
receiving transmitted signals that may be translated into an
indicator for at least one system user.
[0044] In addition, a system 300 may include at least one
additional gastrointestinal microbe analysis device 388. For
example, a system 300 may be operable to include input from two or
more distinct types of gastrointestinal microbe analysis devices.
For example, a system 300 may be operable to include input from two
or more gastrointestinal microbe analysis devices of the same type
analyzing samples at distinct times. A gastrointestinal microbe
sampling device may be ingestible. A system 300 may include at
least one dietary sampling device 382. The at least one dietary
sampling device 382 may be operably connected to the at least one
computational device 350, for example for the transmission of
information between the at least one computational device 350 and
the at least one dietary sampling device 382. A system 300 may
include at least one gastrointestinal microbe sampling device 384.
A system 300 may include control circuitry 380, for example
circuitry for integrating the operation of the components of the
system. A system 300 may include a sampling device 386, for example
a sampling device for sampling extra-gastrointestinal samples from
an individual such as blood or urine samples. A system 300 may
include at least one antenna 390, such as for transmitting
information to or receiving information from outside of the system.
A system 300 may include at least one additional element 392.
[0045] Following are a series of flowcharts depicting
implementations. For ease of understanding, the flowcharts are
organized such that the initial flowcharts present implementations
via an example implementation and thereafter the following
flowcharts present alternate implementations and/or expansions of
the initial flowchart(s) as either sub-component operations or
additional component operations building on one or more
earlier-presented flowcharts. Those having skill in the art will
appreciate that the style of presentation utilized herein (e.g.,
beginning with a presentation of a flowchart(s) presenting an
example implementation and thereafter providing additions to and/or
further details in subsequent flowcharts) generally allows for a
rapid and easy understanding of the various process
implementations. In addition, those skilled in the art will further
appreciate that the style of presentation used herein also lends
itself well to modular and/or object-oriented program design
paradigms.
[0046] FIG. 4 illustrates some aspects of the systems and methods
as described herein. A computer-implemented method 400 may include:
accepting data describing an individual's gastrointestinal microbes
present at a first time 410; accepting data regarding the
individual's status at the first time 420; integrating, on a
computing device, the accepted data regarding an individual's
gastrointestinal microbes and the accepted data regarding the
individual's health status into an individual profile for the first
time 430; comparing the individual profile for the first time to a
standard profile 440; and indicating, to at least one system user,
one or more interventions relating to gastrointestinal microbes
associated with directing the individual profile for the first time
to be closer to the standard profile 450. The method steps may be
repeated multiple times at time intervals appropriate to the
particular embodiment, for example daily while an individual is
undergoing a course of antibiotic therapy, or weekly while an
individual is undergoing chemotherapy. The method steps may be
repeated daily, weekly, monthly or in other periodic intervals. The
method steps may be repeated at intervals selected to be convenient
for the individual, such as during regular medical exams or routine
screening events. The computer-implemented method may be
implemented on a system with a user interface (UI) to at least one
system user 460. A system user may include, for example, the
individual, a healthcare worker, a physician, nurse, occupational
therapist, counselor, dietician, family member or caregiver. A
system user may include a group of individuals or a computational
or robotic entity such as a network or a health-related system. An
individual's health status may include, for example, information
relating to the individual's medical history, metabolic status,
indicators of health or disease, body mass index (BMI), family
medical history, genomic data, mitochondrial genomic data, or
epigenomic data. Accepted data regarding an individual's
gastrointestinal microbes may include, for example, estimated
numbers of various types of gastrointestinal microbes in one or
more particular regions of the gastrointestinal system, or
estimated relative levels of different species, classes or groups
of microbes. Accepted data regarding an individual's
gastrointestinal microbes may include minimum or maximum values or
ranges of data. Accepted data regarding an individual's
gastrointestinal microbes may include extrapolations based on
indirect microbial analysis, such as analysis of metabolites of
microbial populations or dietary products or digestion products
from the gastrointestinal tract. Accepted data regarding an
individual's gastrointestinal microbes may include extrapolations
based on an individual's diet, such as their dietary intake of
microbe-containing foodstuffs, such as probiotics, yogurts,
cheeses, or fermented foods. Accepted data regarding an
individual's gastrointestinal microbes may include extrapolations
based on an individual's recent medical treatments, such as drug
therapies or surgical events. Accepted data regarding an
individual's gastrointestinal microbes may include extrapolations
based on an individual's environmental exposure from an outside
source, such as family members, other individuals in an institution
or care facility, or other members of the regional population.
Accepted data may include "metadata" such as comments explaining
anomalies.
[0047] A standard profile, as used herein, refers to an
extrapolated gastrointestinal microbial profile from a hypothetical
standard healthy individual, such as a hypothetical individual with
similar personal history as the sampled individual. A standard
profile may include a range or scale of values for various
parameters of the profile. For example, a standard profile may be
an idealized profile based on information from a group of
individuals. A standard profile may be extrapolated based on
information from a group of individuals of the same or similar
ethnic group, age, medical history, gender, national origin, or
genomic status. For example, a standard profile may be extrapolated
from healthy infants born at full term with a similar ethnic
background or born in a single hospital. For example, a standard
profile may be extrapolated from healthy infants born at full term
who are exclusively breastfed. For example, a standard profile may
be extrapolated from information regarding the individual
gastrointestinal microbial profiles of a group of healthy
individuals of one gender in a certain age range of a particular
ethnic group. For example, a standard profile may be extrapolated
from information regarding the individual gastrointestinal
microbial profiles of a group of healthy men aged 50-60 who are all
African-American. For example, a standard profile may be
extrapolated from information regarding the individual
gastrointestinal microbial profiles of a group of healthy women
aged 35-40 who are all of Chinese descent. For example, a standard
profile may be extrapolated from information regarding the
individual gastrointestinal microbial profiles of a group of
healthy men aged 60-70 who were all born in India but immigrated to
North America as young adults. For example, a standard profile may
be extrapolated from information regarding the individual
gastrointestinal microbial profiles of a group of individuals in an
extended family, such as siblings, children, grandchildren,
parents, aunts, uncles, cousins and grandparents. For example, a
standard profile may be extrapolated from information regarding the
individual gastrointestinal microbial profiles of a group of
individuals who share one or more genetic or genomic traits, such
as DNA sequences, single-nucleotide polymorphic (SNP) alleles,
restriction fragment polymorphism alleles (RFLP) alleles, karyotype
characteristics, or cDNA assay results. An individual's genetic
information may include, for example, information from one or more
medical tests that incorporates one or more genetic assay, one or
more nucleic acid array, or one or more specific locus assay. In
some embodiments, a standard profile may be based on earlier assay
data from the same individual, such as when the individual was in a
healthy or pre-medical intervention state, while in others it may
be based on assay data from other individuals as a composite or
theoretical ideal.
[0048] It is envisioned that the one or more interventions relating
to gastrointestinal microbes associated with directing the
individual profile for the first time to approximate or be closer
to the standard profile may be determined by calculating, on a
computing device, the relative differences between the individual
profile for the first time and the standard profile, then
indicating which differences may be amenable to specific
interventions. For example, where the individual profile includes a
reduction in total diversity of microbial population, an
intervention may include the dispensation of a group of microbes,
each of which is reduced in the individual profile relative to the
standard profile. Such a situation may exist, for example, in an
individual who has recently undergone a medical procedure including
the administration of antibiotics, antifungals, or suppression of
the gastrointestinal system, such as surgery, chemotherapy, or
anesthesia. For example, where an individual profile includes a
reduction in a group or class of gastrointestinal microbes relative
to the standard profile, a suggested intervention may include the
reintroduction of one or more group or class of gastrointestinal
microbes that is reduced in the individual profile, or the addition
of one or more probiotic (or prebiotic or synbiotic) associated
with increased growth of the desired group or class of microbes.
For example, where the individual profile includes an increase in
total diversity of microbial population, an intervention may
include the dispensation of at least one antimicrobial agent
associated with decreasing the diversity to be closer to the
diversity seen in the standard profile. For example, where an
individual profile includes an increase in a group or class of
gastrointestinal microbes relative to the standard profile, a
suggested intervention may include the introduction of one or more
antimicrobial agents that are associated with the reduction in
numbers of the elevated group or class. For example, an
intervention may include one or more specific antibiotic,
antifungal or chemical agents predicted to selectively reduce the
population of a group or subset of microbes. In some embodiments, a
combination of the selective increase and the selective decrease of
microbial groups or classes may be indicated. In some embodiments,
one or more intervention may include additional suggested
components associated with an increase in the health of the
individual. One or more indicated intervention may include
interventions such as the inclusion or reduction of prebiotics,
probiotics, synbiotics, or nutritional therapies to an individual's
diet. One or more indicated intervention may include one or more
antibiotics, antimicrobials or antifungal agents. One or more
indicated intervention may include one or more suggestion of
additional hydration measures, such as increasing water drunk by
the individual. One or more indicated intervention may include
avoidance of some foodstuffs, such as those containing dairy
products, wheat gluten, processed or cured meats, salts, some
spices, or those with excessive fat content. One or more indicated
intervention may include avoidance of some beverages, such as
alcoholic beverages, caffeinated beverages, beverages with a high
sugar content, or beverages containing fermented products like tofu
or yogurt.
[0049] FIG. 5 depicts variations of the methods illustrated in FIG.
4. In some embodiments, accepting data regarding the individual's
health status at the first time 420 may include accepting data
regarding the individual's diet 500. For example, accepting data
regarding the individual's diet 500 may include accepting data as
to the individual's recent diet, planned diet or standard diet. For
example, accepting data regarding the individual's diet 500 may
include accepting data indicating that the individual is a
vegetarian, or does not eat dairy products, or generally eats
salads for lunch. In some embodiments, accepting data regarding the
individual's health status at the first time 420 may include
accepting data regarding at least one metabolic state of the
individual 510. For example, accepting data regarding at least one
metabolic state of the individual may include accepting data
regarding a disease state such as autoimmune disease, infectious
disease, or cancer incidence. For example, accepting data regarding
at least one metabolic state of the individual may include
accepting data regarding a non-ideal state, such as metabolic
syndrome, hypertension, poor circulation, immune suppression, or
recent history of serial or chronic infectious disease.
[0050] In reference to FIG. 5, in some embodiments integrating, on
a computing device, the accepted data regarding an individual's
gastrointestinal microbes and the accepted data regarding the
individual's health status into an individual profile for the first
time 430 may include integrating the accepted data into an
individual profile which includes a range of values for the data
520. For example, if an individual has had multiple
gastrointestinal samples taken and analyzed at the same or
different time points, the subsequent data may yield a range of
values that are integrated into an individual profile as a standard
range of values for that individual.
[0051] FIG. 6 illustrates variations of the method depicted in FIG.
4. For example, some embodiments may include signaling for release
of one or more gastrointestinal microbe 600. For example, where the
method is implemented on a system including a dispensing device,
the dispensing device may be sent a signal triggering the release
of one or more species or class of gastrointestinal microbe. For
example, some embodiments may include signaling for release of one
or more probiotic agent 610. For example, some embodiments may
include associating the individual profile with one or more
interventions relating to gastrointestinal microbes to direct the
individual profile for the first time to be closer to the standard
profile 620.
[0052] FIG. 7 depicts optional embodiments of the method shown in
FIG. 4. Some embodiments may include accepting data describing an
individual's gastrointestinal microbes present at a second time,
accepting data regarding the individual's health status at the
second time, integrating, on a computing device, the accepted data
regarding an individual's gastrointestinal microbes and the
accepted data regarding the individual's health status into an
individual profile for the second time, comparing the individual
profile for the second time to the standard profile, and indicating
one or more alterations in gastrointestinal microbes associated
with directing the individual profile for the second time to be
closer to the standard profile 700. For example, an individual may
be sampled a second or subsequent time and the individual profile
for the second time may be distinct from the individual profile at
the first time, and so any intervention may be revised relative to
the new information. Some embodiments may include accepting at
least one personal parameter relating to the individual, and
selecting the standard profile to correspond with one or more of
the at least one personal parameter 710. Personal parameters may
include, for example, age, gender, ethnicity, nationality,
birthplace, genetic status, genomic status, disease state or
metabolic state. For example in some embodiments, a standard
profile may be selected based on a shared personal parameter
between the standard profile and the individual. For example, the
standard profile may be a composite profile based on information
derived from gastrointestinal samples taken from healthy, full-term
breast-fed infants and the sampled individual may also be an
infant. For more information regarding factors influencing the
establishment of gastrointestinal microbes in infants, see
Adlerberth, "Factors influencing the establishment of the
intestinal microbiota in infancy," Nestle Nutr Workshop Ser Pediatr
Program, 62:13-33 (2008), and Penders et al., "Factors influencing
the composition of the intestinal microbiota in early infancy,"
Pediatrics 118(2):511-521 (2006), which are herein incorporated by
reference. For example, the standard profile may be derived from
information relating to gastrointestinal samples taken from a group
of healthy men aged 70-80 and the individual may be a 75 year old
man. For example, the standard profile may be based on information
from gastrointestinal samples taken from Caucasian women in their
20s, and the individual may be a Caucasian woman in her 50s. For
example, the standard profile may be based on data obtained from
gastrointestinal samples taken from healthy immigrants from India
who have lived in North America at least 10 years and the
individual may have recently emigrated from India, such as perhaps
within the past six months. For example, the standard profile may
be derived from information relating to gastrointestinal samples
taken from persons who have otherwise tested positive for a
particular allele or set of alleles, such as specific alleles of
surface receptor proteins, and the sampled individual may also have
tested positive for the same allele or a subset of relevant
alleles. For example, the standard profile may be derived from
information relating to gastrointestinal samples taken from persons
who independently have a distinct set of attributes in a specific
assay, such as a DNA-based genetic assay or a set of antibody
tests, and the sampled individual may also have the same distinct
set of attributes when tested by the same assay.
[0053] FIG. 8 illustrates aspects of the method depicted in FIG. 4.
The method may include, in some embodiments, creating, on a
computing device, at least one difference listing between the
individual profile for the first time and the standard profile,
associating at least one intervention with minimizing the at least
one difference listing, and indicating, to at least one system
user, at least one intervention associated with minimizing the at
least one difference listing 800. For example, if the difference
listing indicates an overgrowth of a class or group of microbes in
the individual profile relative to the standard or reference
profile, an intervention may include suggesting one or more
antimicrobial agent that is known to affect the excess class or
group of microbes relative to other microbes, or an intervention
may include suggesting a prebiotic which encourages growth of other
classes or groups of microbes relative to the excess group and
therefore adjust their relative levels. For example, if a
difference listing indicates a relative lack of a class of group of
microbes relative to the standard or reference profile, an
intervention may include suggesting one or more prebiotic that is
expected to encourage growth of the reduced group, or a probiotic
containing the lacked microbes or a synbiotic with the appropriate
combination of the two. It is envisioned that an intervention may
also include aspects that support the primary components, such as
suggestions to avoid foods that may contain microbes that appear to
be in overabundance relative to the standard profile, or foods that
would otherwise interfere with the suggested intervention such as
excessively spicy foods, highly sugary foods or beverages,
alcoholic beverages, highly processed foods, or foods containing
high levels of preservatives. As shown in FIG. 8, the method may
include, in some embodiments, accepting data describing an
individual's gastrointestinal microbes present at a second time,
accepting data regarding the individual's health status at the
second time, integrating, on a computing device, the accepted data
regarding an individual's gastrointestinal microbes and the
accepted data regarding the individual's health status into an
individual profile for the second time, comparing the individual
profile for the second time to the individual profile for the first
time, and indicating to at least one system user at least one
difference between the individual profile for the second time and
the individual profile for the first time 810. For example, a
system carrying out the method may indicate to a system user how
the relative levels of at least one group or class of microbes may
have changed between a first sampling and a second or subsequent
sampling. In some embodiments, the first time of sampling may be a
reference time point, with an associated reference sample to set a
baseline profile and therefore monitor individual profile
progressions from the initial time forward. In some embodiments, an
individual profile for a second or subsequent time may be used to
evaluate the effectiveness of any intervention. For example, if a
specific prebiotic agent was suggested as part of the initial
intervention strategy and the second or subsequent profile does not
indicate a relative change in microbe levels, a different prebiotic
agent may be suggested. For example, if a specific antibiotic agent
was suggested as part of the initial intervention strategy and the
second or subsequent profile does not indicate a relative change in
microbe levels, a different antibiotic agent may be suggested. For
example, if a specific antibiotic agent was suggested as part of
the initial intervention strategy and the intervention had to be
discontinued due to allergic reaction or other ill affects, a
different intervention strategy may be suggested after a subsequent
profile. In some embodiments, the method includes comparing the
individual profile for the second time to the standard profile, and
indicating to at least one system user at least one difference
between the individual profile for the second time and the standard
profile 820. For example, a relative increase or decrease in a
specific group or class of microbes may be indicated. Such
information may be of use, for example, in evaluating the
effectiveness of any intervention strategy or agent.
[0054] FIG. 9 depicts a computer-implemented method 900 for
suggesting adjustments to gastrointestinal microbe profiles over
time. The method includes accepting data describing an individual's
gastrointestinal microbes present at an initial time 910. For
example, the data may relate to a sample taken at a first or
initial time. The method includes comparing, on a computing device,
the data relating to an individual's gastrointestinal tract
microbial composition at an initial time with at least one standard
gastrointestinal tract microbial composition 920. For example, the
computing device may use graphing methods, tabular formats, or
statistical methods to compare the data sets. In some instances,
the data may include ranges or sets of values. The method includes
identifying differences between the data relating to the
individual's gastrointestinal tract microbial composition at an
initial time and one or more of the at least one standard
gastrointestinal tract microbial composition 930. For example,
absolute differences or relative differences may be identified. In
some instances, a lack of differences or unity between the data
sets may also be identified. The method includes creating an
initial difference listing of the identified differences between
the data relating to the individual's gastrointestinal tract
microbial composition at an initial time and one or more of the at
least one standard gastrointestinal tract microbial composition
940. The initial difference listing may be communicated to a system
user. The method includes creating at least one initial action plan
to alter the individual's gastrointestinal tract microbial
composition to minimize the difference listing 950. For example,
the action plan may include one or more intervention strategies. An
action plan may include suggesting the ingestion of prebiotic
agents, probiotic agents, or antimicrobial agents by the
individual. An action plan may include suggesting the avoidance of
certain foods or beverages, or increasing intake of some foods and
beverages. An action plan may include suggesting that the
individual drink sufficient fluids, exercise regularly, or include
nutritional supplements. In some instances, the action plan may
include the removal and replacement of gastrointestinal flora such
as described in U.S. Pat. No. 6,645,530 to Borody, titled
"Treatment of gastro-intestinal disorders," which is herein
incorporated by reference. The method includes indicating one or
more of the at least one initial action plan to at least one system
user 960. For example, if the system user 970 is a healthcare
professional, he or she may integrate the action plan into any
medical care plans for the individual. For example, if the system
user 970 is a dietician or therapist, he or she may explain at
least one action plan to the individual and make specific
suggestions regarding diet and therapy that includes the action
plan. In some instances, more than one action plan may be indicated
and the system user may evaluate the indicated plans based on other
criteria, such as ease of implementation, personal preference of
the individual, cost, or other individual factors.
[0055] FIG. 10 illustrates embodiments of the method shown in FIG.
9. In some embodiments, creating at least one initial action plan
to alter the individual's gastrointestinal tract microbial
composition to minimize the difference listing 950 may include
wherein the at least one initial action plan includes one or more
dietary suggestions 1000. For example, an action plan may include
suggesting the avoidance of certain foods or beverages, or
increasing intake of some foods and beverages. In some embodiments,
the method may include accepting data relating to an individual's
gastrointestinal tract microbial composition at a second time,
comparing, on a computing device, the data relating to an
individual's gastrointestinal tract microbial composition at a
second time with the initial difference listing, creating a second
difference listing, creating at least one second action plan to
alter the individual's gastrointestinal tract microbial
composition, and suggesting one or more of the at least one second
action plan to the system user 1010. For example, the method may be
implemented over time and an individual may provide serial samples
over time, with the goal of evaluating the gastrointestinal
microbial profile of the individual on a recurring basis, or for
the evaluation of the effectiveness of an intervention.
[0056] FIG. 11 shows embodiments of the method diagrammed in FIG.
9. A method may include accepting data relating to the individual's
personal history, and selecting one or more of the at least one
standard gastrointestinal tract microbial composition in relation
to the individual's personal history 1100. For example, if a
specific standard gastrointestinal tract microbial composition
originates from data obtained from persons with a particular
personal history and the individual shares that personal history,
the specific standard gastrointestinal tract microbial composition
may be selected for comparison. For example, personal history may
include residence type (such as institutional or private home),
country of origin, medical history, diagnosis, usual dietary habits
(such as vegetarianism or habitual red meat eating), or usual
exercise habits. A method may include accepting data regarding at
least one personal parameter of the individual, creating an action
plan in relation to the accepted data regarding the at least one
personal parameter of the individual, and indicating the action
plan in relation to the accepted data regarding the at least one
personal parameter of the individual to a system user 1110. For
example, a personal parameter of an individual may include a factor
or preference of the individual that may influence the
effectiveness of an action plan. A personal parameter may include,
for example, age, dietary restrictions based on medical, social or
religious indications, known allergies or sensitivities, weight or
size of the individual, availability of components of the action
plan to the individual, cost, or other medical therapies which the
individual is currently taking or may be taking in the future. Some
potential components of an action plan will not be suitable for
some individuals based on one or more personal parameters of the
individual. For example, a diabetic may have dietary restrictions
that any action plan for a diabetic individual would ideally take
into account. For example, some components of an action plan may
not be available to an individual, such as an individual with
limited mobility who is unable to obtain or consume some
foodstuffs. For example, an individual may have surgery scheduled
in the foreseeable future, and any action plan would have to be
able to be implemented in conjunction with any restrictions
relative to the surgery. For example, individuals being treated
with the anticoagulant Warfarin (i.e. Coumadin or Waran) should
maintain a steady rate of vitamin K intake and any action plan for
individuals prescribed Warfarin should incorporate the estimated
vitamin K levels of any suggested dietary changes. A system user
such as a healthcare professional or caregiver may enter data
regarding at least one personal parameter of the individual into a
computer system implementing this method and the system may rank,
prioritize or highlight a group of potential action plans for
indication to the system user that take into account the personal
parameter. For example, an action plan for an obese individual may
include in part compositions such as those described in U.S. Pat.
No. 6,565,847 to Gorsek, titled "Thermogenic weight management
composition," and U.S. Pat. No. 6,641,808 to Bojrab, titled
"Composition for treatment of obesity," and US Patent Application
No. 2005/0239706 to Backhed et al, titled "Modulation of fiaf and
the gastrointestinal microbiota as a means to control energy
storage in a subject," which are all herein incorporated by
reference. For example, an action plan for an individual concerned
about intestinal gas production in relation to the intervention may
include a composition such as described in US Patent Application
No. 2006/0193845 to Watson et al., titled "Combination therapy for
controlled carbohydrate digestion," which is herein incorporated by
reference. For example, an action plan for an individual otherwise
prescribed antibiotics such as ampicillin or piperacillin may
include in part compositions such as those described in Stiefel et
al., "Orally administered .beta.-lactamase enzymes represent a
novel strategy to prevent colonization by Clostridium difficile,"
Journal of Antimicrobial Chemotherapy, 62:1105-1108 (2008), which
is incorporated herein by reference. For example, if an individual
has been diagnosed with inflammatory bowel disease (IBD), the
action plan may include administration of compositions such as
those described in US Patent Application No. 2007/0104712 to
Ashkenazi and Ward, titled "Treatment of Inflammatory Bowel Disease
with IFN-Gamma Inhibitors," and US Patent Application No.
2007/0123460 to Chang and Petrof, titled "Probiotic compounds from
Lactobacillus GG and uses therefore," and US Patent Application No.
2007/0128303 to Chang and Petrof, titled "Anti-inflammatory,
cytoprotective factor derivable from a probiotic organism," and US
Patent Application No. 2007/0178078 to Khoo, titled "Method for
modifying gut flora in animals," which are herein incorporated by
reference. For example, an action plan for an infant or child may
include formula or milk supplements containing oligosaccharide
mixtures such as those described in US Patent Application No.
2009/0092729 to Sprenger et al., titled "Oligosaccharide mixture,"
which is herein incorporated by reference. For example, if an
individual has been diagnosed with a neurodegenerative disease, the
action plan may include administration of nutritional compositions
such as those described in US Patent Application No. 2008/0145451
to Hageman and Bindels, titled "Composition for relieving
discomfort," which is herein incorporated by reference. For
example, an action plan for an individual with a history of lactic
acidosis may include a composition such as described in U.S. Pat.
No. 7,011,826 to Rowe and Al Jassim, titled "Control of acidosis,"
which is herein incorporated by reference. For example, if an
individual has been diagnosed with an autoimmune disease, the
action plan may include administration of nutritional compositions
such as those described in US Patent Application No. 2008/0146510
to Wong and Lam which is herein incorporated by reference. The
method may include signaling at least some portion of the indicated
one or more action plans to one or more dispenser 1120. For
example, if the method is implemented as part of a healthcare
system, a portion of the action plan may include specific
medications and the system may signal for dispensation of those
medications. For example, if the method is implemented as part of
an institutional dietary program, the food providers may be
signaled to provide specific foods to the individual. For example,
a food provider may be signaled to include nutritional additives in
the food preparation, such as those described in US Patent
Application No. 2008/0102162 to Delcour et al., titled "Prebiotic
preparation," which is herein incorporated by reference. For
example, the method may include signaling for dispensation of at
least one pharmaceutical composition such as those described in
U.S. Pat. No. 6,706,287 to Ranganathan et al, titled "Prebiotic and
probiotic compositions and methods for their use in gut-based
therapies," which is herein incorporated by reference. For example,
if the individual is also taking a course of antibiotics, the
method may include signaling for the dispensation of pharmaceutical
compounds such as those described in US Patent Application No.
2007/0105791 to Sears et al., titled "Method of treating
clostridium difficile-associated diarrhea," which is herein
incorporated by reference.
[0057] Systems and methods as described herein may be used for
continual modification of intestinal microbes, for example to
monitor and influence the growth of subpopulations of intestinal
microbes over time. Other aspects of the systems and methods
described herein are described in the examples below.
EXAMPLES
Example 1
[0058] To improve infant health by evaluating and modifying
intestinal microbial flora, a system is described to: 1)
periodically determine the microbial flora present (microbial
profile) in an individual infant's intestine; 2) integrate medical
data related to the infant such as genotype, epigenotype,
mitochondrial genotype, gender, race, gestational age, birth
weight, mode of delivery, type of infant feeding, antibiotic use,
viral infections, bacterial infections, and family history; 3)
determine and select a reference microbial profile that integrates
data regarding the abundance and diversity of intestinal microbes
with medical information, such as genotype, epigenotype,
mitochondrial genotype, gender, race, gestational age, birth
weight, mode of delivery, type of infant feeding, antibiotic use,
viral infections, bacterial infections, and family history; 4)
analyze changes or differences in the abundance of specific
microbes or groups or divisions of microbes in the individual
infant with respect to reference microbial profiles (established
for the individual at an earlier time point or derived from the
medical information of healthy infants); 5) provide an indicator to
recommend treatments to change the microbial profile and achieve
congruency with the selected reference microbial profile; and 6)
periodically monitor the individual infant's microbial profile over
time and recommend treatment when indicated.
[0059] Feces specimens collected from infant diapers are a ready
source of intestinal microbes that are processed to identify and
enumerate the bacterial classes, divisions and species inhabiting
the lower intestine. To collect stool samples, sanitary napkins are
placed in diapers (to prevent absorption of feces by the diaper),
or feces tubes with a spoon (Sarstedt, Numbrecht, Germany) are used
to obtain a standardized amount of material (see, for example,
Penders et al, "Factors influencing the composition of intestinal
micorbiota in early infancy," Pediatrics, 118: 511-521 (2006) which
is incorporated herein by reference). Diapers suitable for stool
collection may also be used, such as are described in U.S. Pat. No.
6,102,892 to Putzer, titled "Diaper with pleats for containment of
liquid and solid waste," and U.S. Pat. No. 6,423,884 to Oehmen,
titled "Absorbent article having apertures for fecal material,"
each of which is incorporated herein by reference. DNA for analysis
is purified from feces specimens using a QIAamp DNA stool minikit
(Qiagen, Hilden, Germany).
[0060] To determine the abundance of microbial species,
quantitative real time polymerase chain reaction (PCR) is used.
Quantitative analysis of bacterial species is performed using PCR
amplification of genes encoding 16s ribosomal RNA (rRNA) using
feces-derived genomic DNA as template and PCR primers specific for
different bacterial species. Examples of primer sequences and
reaction conditions are described in Ott et al, "Quantification of
intestinal bacterial populations by real-time PCR with a universal
primer set and minor groove binder probes: a global approach to the
enteric flora," J. Clinical Microbiology, 42: 2566-2572 (2004)
which is herein incorporated by reference. Using 96-well optical
plates and an ABI Prism 7700 sequence detector (Applied Biosystems,
Foster City, Calif.) (as shown by Ott et al, Ibid.) 16s ribosomal
RNA genes are amplified with primers specific for bacterial
species, group and genus, and intestinal flora are quantitated,
with sensitivities ranging from 10 to 1000 bacterial cells.
Exemplary data (from Ott et al, Ibid.) listing the number of
Bacteroides, Porphyromonas, and Prevotella cells present in five
clinical samples is shown in FIG. 12.
[0061] FIG. 12 depicts the number of cells detected by real-time
PCR in clinical samples from five healthy control patients.
Normalized mean values of two independent experiments.+-.standard
deviation. (Taken from Ott et al, Ibid.) *C.sub.T=threshold
cycle.
[0062] Alternatively or in addition to enumerate and identify
classes, groups or species of infant intestinal microbes, stool
samples are processed to obtain microbial DNA using established
protocols and reagents (Qiagen Inc., Valencia, Calif.) and analyzed
on microarrays. Microarrays containing probes for 16s rRNA genes
that are specific for phyla, classes or species are constructed
using the teachings of Palmer et al, "Development of the human
infant intestinal microbiota," PLoS Biology, 5: 1556-1573 (2007)
which is incorporated herein by reference. Microarrays with probes
for 9121 unique taxonomically specific probes are constructed using
40 nucleotide sequences derived from 16s rRNA genes. The selection
of 16s rRNA probe sequences and synthesizing surface-attached
oligonucleotide probes in situ is as described (see Palmer et al,
Ibid.). To interrogate microbial DNA derived from infant stool
specimens, rRNA gene sequences are amplified using PCR using broad
range bacterial primers that amplify more than 90% of bacterial 16s
rRNA genes and also provide a promoter sequence for T7 RNA
polymerase. Broad range bacterial-specific PCR primers, PCR
reaction conditions and methods to purify amplified rDNA are as
described in Palmer et al, Ibid. In vitro transcription with T7
polymerase, using the amplified bacterial rDNA as template, is used
to prepare fluorescently-labeled RNA for hybridization to
microarrays. Protocols and reagents for in vitro transcription and
purification of RNA are available from Ambion, Inc., (Austin,
Tex.). RNA is fluorescently-labeled with Cy5 using commercially
available reagents and protocols (for example, the Minis Bio Label:
Cy5 Labeling Kit available from Fisher Scientific, Pittsburgh,
Pa.). Reaction conditions for hybridization of
fluorescently-labeled RNA to microarrays are as described in Palmer
et al, Ibid. Equipment and instruments for hybridization and
analysis of microarrays are available from Agilent Technologies,
Inc., (Santa Clara, Calif.).
[0063] Information obtained using microarrays or quantitative PCR
(as described above) is incorporated into a profile of intestinal
microbe abundance and integrated with medical data for each infant.
A system that integrates an infant's microbial profile with, for
example, factors such as gestational age, route of delivery
(vaginal or Caesarian section), weight, nutrition, diet, antibiotic
use, drug use, viral (e.g. HIV) or bacterial exposure, genotype,
epigenetics and family history is used to associate environmental,
genetic, epigenetic and medical factors with microbial diversity
and abundance. For example, as shown by Penders et al, Ibid., using
multivariate analysis "beneficial microbes" (e.g. bifidobacteria
and Bacteroides) are identifiable that associate with full-term
infants, and the factors of breast feeding and vaginal birth. An
example, (taken from Penders et al, Ibid.) of linear regression
analysis that associates microbial numbers with medical data is
shown in FIG. 13. FIG. 13 depicts linear regression coefficients
for bacterial counts and odds ratios for the presence of gut
bacteria, with respect to determinants in multivariate analyses.
Coefficients are regression coefficients of association between
determinants and counts, determined with linear regression
analyses. Odds ratios (ORs) of association between determinants and
prevalence of colonization (colonized compared with not colonized)
are determined with logistic regression analyses. ND indicates not
determined (logistic regression analysis of prevalence of
bifidobacteria was not performed because 99% of infants were
colonized). Adapted from Penders et al, Ibid. .sup.aStatistically
significant results (at P=0.01, 2-sided). Moreover, analysis of
medical data such as on antibiotic use, prematurity and
hospitalization shows associations with specific potential
pathogens such as Clostridium difficile and E. coli (see Penders et
al, Ibid.).
[0064] To establish a reference microbial profile, the microbial
profile for a number (e.g. 14-1000) of healthy infants is
determined. Information from these microbial profiles is then used
to generate a standard microbial profile for healthy infants.
Integration of microbial profiles and medical data allows for the
calculation of microbial profiles whose microbial diversity and
abundance associate with healthy infants displaying normal weight
gain, digestion and clinical parameters relating to health and
illness. For example, a "healthy" intestinal microbial profile is
delineated at the level of prokaryotic phyla by analysis of stool
samples from healthy infants. For example, Palmer et al, Ibid. have
observed a "preponderance of Bacteroides and Firmicutes, common
occurrence of Verrucomicrobia, and very low abundance of
Proteobacteria and aerobic Gram-negative bacteria in general."
[0065] Alternatively or in addition, a reference microbial profile
is established for an infant by integrating medical data and a
microbial profile observed at a first time point. Data from stool
samples collected and analyzed at later time points are compared to
the initial reference microbial profile. Stool samples collected at
birth and then at later time points such as daily, weekly and
monthly are used to analyze the temporal development of microbial
flora following birth (for example, see Palmer et al, Ibid.).
Integration of medical data obtained at the time of each sampling
allows for the association of factors such as therapies, medical
procedures, illnesses, infections, diet and environmental, genetic,
epigenetic and other factors with microbial abundance and diversity
over time. For example, changes in the density and composition of
intestinal microbes are associated with antibiotic administration.
Microbial profiling of an infant treated with amoxicillin at 4
months of age detects a decrease in total bacterial density and
altered bacterial composition in stool samples relative to a
reference microbial profile established at 1 month of age as shown
by Palmer et al, Ibid. Also amoxicillin treatment is associated
with changes in the abundance of specific bacterial groups, for
example, reductions in gamma proteobacteria, and increases in
bacilli as shown by Palmer et al, Ibid.
[0066] FIG. 14 depicts variation in total fecal bacterial density
and specific taxa for an infant treated with antibiotics. Taken
from Palmer et al, Ibid. Estimated rRNA gene copies per gram of
feces (y-axis) are plotted as a function of days of life (x-axis).
Both axes are on a logarithmic scale. Episodes of antibacterial
treatment are indicated on the temporal axis by gray bars. Within a
few days of the antibiotic treatment, a sharp increase in the
levels of Bacteroides and Cytophaga were observed (from less than
40 rRNA gene copies per gram of feces to over 80 rRNA gene copies
per gram). Similarly, levels of Bacilli and related species sharply
increased during the time of antibiotic treatment, from a
pre-treatment low of negligible levels to a high of over 60 rRNA
gene copies per gram of feces. After antibiotic treatment, the
levels of Bacilli and related species returned to negligible
levels. However, levels of Clostridia and related species, which
had been negligible or under 20 rRNA gene copies per gram of feces
from birth until the time of antibiotic treatment, increased after
antibiotic treatment to approximately 20 rRNA gene copies per gram
of feces and maintained this increase for the duration of the study
period. Systems as those described herein monitor such
post-antibiotic use increases in specific pathogen species or
classes and suggest interventions to improve health after the end
of an antibiotic course.
[0067] To modify an infant's microbial profile, the system suggests
treatments to increase or decrease specific divisions, classes or
species of intestinal microbes. For example, infants treated with
antibiotics display reduced numbers of bifidobacteria and
Bacteroides (see Penders et al, Ibid.). One potential recommended
treatment is administration of in vitro cultures of Bacteroides and
bifidobacteria (obtained from healthy, untreated infant feces) and
reconstituted with saline to be administered using an enema or by
colonoscope. A potential treatment includes liquid cultures of
Bacteroides and bifidobacteria lyophilized and reconstituted in
appropriate diluent before enteric or colonic administration, as
described in U.S. Pat. No. 6,645,530 to Borody titled "Treatment of
gastro-intestinal disorders," which is incorporated herein by
reference. In addition, recommended treatments include prebiotics
which promote the growth of specific groups of bacteria. For
example, to promote the growth of bifidobacteria, prebiotics such
as fructooligosaccharides, inulin, soybean oligosaccharides, and
transgalactosylated oligosaccharides are administered orally. See,
for example, Schrezenmeir et al, "Probiotics, prebiotics, and
synbiotics--approaching a definition," Am. J. Clin. Nutr., 73
(suppl): 361S-364S (2001) and U.S. Pat. No. 6,706,287 to
Ranganathan et al. titled "Prebiotic and probiotic compositions and
methods for their use in gut-based therapies," which are herein
incorporated by reference.
[0068] To reduce the number of undesirable or pathogenic bacteria,
treatment with antibacterials are suggested. For example, lytic
bacteriophage are isolated and propagated in vitro that are
suitable for treating pediatric gastroenteritis. "T4-like"
bacteriophage with a broad host range for pathogenic E. coli and
Salmonella are propagated, purified and given orally to infants in
infant formula. See, for example, U.S. Pat. No. 7,211,426 to
Bruessow et al. titled "Isolated phages and their use in food or
pet food products," which is herein incorporated by reference.
Methods and compositions for propagating, isolating, purifying,
formulating and administering "T4-like" bacteriophage with lytic
activity for pathogenic E. coli and Salmonella are described in
U.S. Pat. No. 7,211,426, to Bruessow et al. titled "Isolated phages
and their use in food or pet food products," which is herein
incorporated by reference. Alternatively or in addition,
antibacterial treatment includes antimicrobial peptides, such as
those described in U.S. Patent Application No. 2008/0170991 to Shi
et al., titled "Selectively targeted antimicrobial peptides and the
use thereof," which is incorporated herein by reference. For
example, andropin, apidaecin, bactencin, clavanin, dodecappeptide,
defensin, and indolicidin are antimicrobial peptides having
antibacterial activities. Also tachyplesins are known to have
antifungal and antibacterial activities. Buforin, nisin and
cecropin peptides have antimicrobial effects on Escherichia coli,
Shigella disenteriae, Salmonella typhimurium, Streptococcus
pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa.
Magainin and ranalexin peptides have antimicrobial effects on the
same organisms, and in addition have such effects on Candida
albicans, Cryptococcus neoformans, Candida krusei, and Helicobacter
pylori. Alexomycin peptides have antimicrobial effects on
Campylobacter jejuni, Moraxella catarrhalis and Haemophilus
influenzae, while defensin and .beta.-pleated sheet defensin
peptides have antimicrobial effects on Streptococcus pneumoniae.
Antimicrobial peptides are fused to targeting peptides to create
antimicrobials with specificity for microbial pathogens that spare
beneficial gut microbes. Methods for creating targeted
antimicrobial peptides are described in U.S. Patent Application No.
20080170991, to Shi et al., titled "Selectively targeted
antimicrobial peptides and the use thereof," which is incorporated
herein by reference. Following suggestions for the treatment of
infants to modify their microbial profile, the system periodically
monitors their microbial flora and analyzes changes in microbial
profiles, and may recommend additional treatment for restoration or
establishment of a beneficial microbial composition.
Example 2
[0069] A system that analyzes, identifies and lists changes in a
patient's microbiome or microbial profile, with respect to a
reference microbial profile, indicates potential treatments to
promote cardiovascular health. Some possible treatment suggestions
are: nutritional changes, probiotics, prebiotics, synbiotics,
enzymes, bacterial phyla, bacterial species, fungal species,
therapeutics, antifungals, antibacterials, antimicrobials, and
antibiotics. Patients with specific microbial profiles are at
increased risk for cardiovascular disease, and treatment
suggestions are indicated in regard to such patients by a system
that compares a patient's microbial profile to one or more
reference microbial profiles derived from information associated
with individuals in good cardiovascular health. Reference microbial
profiles relative to cardiovascular health, for example, integrate
factors such as plasma ferulic acid levels, plasma C-reactive
protein levels, and plasma lipid levels. The system lists, for
example, differences in intestinal microbial diversity and
abundance. The system evaluates and indicates a need for treatment,
and recommends a treatment such as a prebiotic to modify the
microbial profile. For example, where indicated the system suggests
treatment of intestinal microbiota with a prebiotic, such as
enzymatically-digested durum wheat fiber, to modify the numbers of
specific microbiota groups (e.g. bifidobacteria and lactobacilli)
and result in the increased release of the antioxidant ferulic
acid, which has been suggested to promote cardiovascular health.
See Napolitano et al, "Potential prebiotic activity of
oligosaccharides obtained by enzymatic conversion of durum wheat
insoluble dietary fibre into soluble dietary fibre," Nutrition,
Metabolism Cardiovascular Diseases (2008), in press, available
online as of 20 Sep. 2008, DOI: 10.1016/j.numecd.2008.07.005, which
is herein incorporated by reference. Alternatively or in addition,
a system may recommend a synbiotic comprised of a prebiotic (e.g.
oligofructose, enzyme-digested durum wheat fiber) and a probiotic
(e.g. bifidobacteria such as B. adolescentis, B. animalis spp.
lactis, B. breve, B. longum) (see Schrezenmeir et al, et al,
"Probiotics, prebiotics, and synbiotics--approaching a definition,"
Am. J. Clin. Nutr., 73 (suppl): 361S-364S (2001), which is herein
incorporated by reference). In addition, repeated determinations of
patient microbial profiles pre- and post-treatment are compared to
at least one reference microbial profile and analyzed with respect
to time in order to monitor modifications to microbial abundance
and diversity over time, such as in response to one or more
therapies. The system also continuously monitors microbial profiles
including parameters of cardiovascular health, and calculates and
lists differences in comparison to a reference microbial profile.
Periodically, the system may indicate a need for treatment and
recommend the dispensation of a treatment, for example a prebiotic
such as enzyme-digested wheat fiber.
[0070] A system for monitoring microbial profiles and integrating
data (e.g. diet, microbial exposure from food, digestion,
regularity of bowel movements, and metabolic parameters such as
blood glucose levels and insulin levels) into individual profiles
indicates potential adverse changes in intestinal microbial
composition and makes dietary recommendations to restore microbial
compositions and promote health. To monitor the intestinal
microbial flora, bacterial cellular fatty acids are extracted from
stool samples and analyzed using gas-liquid chromatography (GLC).
Fatty acid GLC profiles are used to represent the microbial flora
present in the stool samples and allow for the detection of
differences or changes in the microbial flora of individuals or
groups. Initially, bacteria present in stool samples are isolated
by sedimentation and centrifugation to yield a bacterial pellet.
Prior to GLC, the bacterial samples are saponified, methylated and
extracted to isolate fatty acids. See, Peltonen et al, "An uncooked
vegan diet shifts the profile of human fecal microflora:
computerized analysis of direct stool sample gas-liquid
chromatography profiles of bacterial cellular fatty acids," Applied
Environmental Microbiology, 58:3660-3666 (1992) which is herein
incorporated by reference. GLC is performed with a gas
chromatograph (such as those available from Thermo Fisher
Scientific, Inc., Waltham, Mass.). Detailed protocols and materials
for GLC analysis of fatty acids from fecal bacteria are described
in Peltonen et al, Ibid. GLC data analysis of stool specimens are
based on GLC spectra from bacterial species analyzed in isolation.
Computer analysis allows calculation of similarity indices for each
pair of samples; in addition mean indices for sample groups are
calculated to allow comparison of test groups or control groups.
For example, one can detect significant changes in mean fatty acid
similarity indices for a test group fed an uncooked vegan diet when
compared to a control group fed an omnivorous Western diet. See
FIG. 15, taken from Peltonen et al, Ibid. Data on microbial flora,
as indicated by fatty acid profiles and similarity indices, is
integrated with medical data to indicate changes associated with
health and disease and diet. Microbial profiles associated with
disease and poor health are used to indicate a need for treatment
and to recommend dietary changes to modify microbial profiles to
benefit health.
[0071] FIG. 15 shows that a vegan diet alters fecal microflora as
measured by GLC fatty acid profile analysis. The mean value of
similarity indices (.+-.standard deviation) are calculated by
comparison to pretest profiles for control group (squares, solid
line) and vegan diet group (circles, dotted line). * indicates
statistically significant (P<0.05) difference from pretest
profiles and from control group samples collected on the same day.
Taken from Peltonen et al, Ibid.
[0072] A system that integrates microbial profiles, metabolic data,
medical data, genetics and diet indicates desirable alterations in
diet and recommends appropriate treatments to modify microbial
profiles. By integrating data regarding metabolites present in
plasma and urine with other medical data relating to individuals,
cometabolites (i.e. metabolites arising from the combined action of
host and commensal microbe metabolism) are associated with disease
states. See, for example, Dumas et al, "Metabolic profiling reveals
a contribution of gut microbiota to fatty liver phenotype in
insulin-resistant mice," Proc. Natl. Acad. Sci. USA, 103:
12511-12516 (2006) which is herein incorporated by reference. Using
.sup.1H nuclear magnetic resonance (NMR) spectroscopy and
multivariate statistical modeling, Dumas et al, Ibid. shows that
impaired glucose homeostasis and nonalcoholic fatty liver disease
(NAFLD) induced by a high-fat diet in mouse strain 129S6 are
associated with disruptions of choline metabolism. Specifically,
low circulating levels of plasma phosphatidylcholine and high
urinary secretion of methylamines, cometabolites of choline
resulting from gut microbe processing, are associated with NAFLD
and insulin resistance (see Dumas et al, Ibid.). Data from glucose
tolerance testing, insulin secretion studies, liver histopathology,
liver triglyceride testing, plasma aspartate aminotransferase
testing, and plasma alanine aminotransferase testing shows that a
high fat diet induces NAFLD, impaired glucose tolerance, and
dyslipidemia in 129S6 mice but not in Balb/c control mice. As shown
by Dumas et al, Ibid., .sup.1H NMR analysis of plasma samples from
129S6 mice fed a high-fat diet indicates a reduction in
phosphatidyl choline and a significant increase in
microbiota-derived methylamines including dimethylamine,
trimethylamine and trimethylamine-N-oxide.
[0073] Systems and methods such as those described herein integrate
data regarding microbial profiles associated with urinary
metabolites with metabolite data and medical data from specific
individuals and list differences between control (i.e. healthy)
subjects and patients. Metabolic indicators of impaired glucose
metabolism or NAFLD are possible factors leading to the suggestion
of specific treatments. For example, an individual exhibiting
elevated urinary methylamines and reduced plasma PC is indicated as
at risk for NAFLD and recommended treatments include a low fat diet
as well as modification of the individual's microbial profile.
Example 3
[0074] A microbial monitoring system is used to identify and
recommend treatments for genetic diseases such as Familial
Mediterranean Fever (FMF). FMF is caused by mutations in a single
gene, MEFV (Mediterranean Fever), that encodes a protein, pyrin,
which is involved in regulating innate immunity and inflammation. A
gastrointestinal microbial profile that integrates an individual's
genotype for MEFV with clinical symptoms of FMF, including markers
of remission and attack, is used to identify microbial imbalances
associated with FMF symptoms and to recommend treatments to modify
microbial profiles and reduce inflammation in individual FMF
patients. Profiles of gastrointestinal microbial diversity and
abundance are determined for clinically diagnosed FMF patients as
well as for healthy volunteers that are matched with respect to
ethnic information associated with the patients and volunteers in a
personal information database.
[0075] To evaluate microbial diversity and abundance, microbial 16s
ribosomal DNA (rDNA) sequences are determined from gastrointestinal
samples taken from individual patients and volunteers. Fecal
samples are extracted to obtain microbial genomic DNA (methods and
reagents from Qiagen, Inc., Valencia, Calif.). Microbial 16s
ribosomal RNA (rRNA) gene fragments are amplified from the
extracted DNA using polymerase chain reaction (PCR) and universal
primers for microbial 16s rRNA genes as described in Khachatryan et
al, "Predominant role of host genetics in controlling the
composition of gut microbiota," PLoS ONE, 3:e3064 (2008) which is
herein incorporated by reference. Amplified 16s rDNA fragments are
isolated, purified and cloned in a plasmid vector such as pCR-4 in
E. coli TOP10 (available from Invitrogen Corp., Carlsbad, Calif.).
The library of cloned 16s rDNA fragments is sequenced using an
automated capillary sequencer (Beckman Instruments, Fullerton,
Calif.) and the rDNA sequences aligned, edited, and evaluated for
similarity and phylogenetics using bioinformatics programs such as
CLUSTALX, BLAST, DNADIST, DOTUR and RDP-II (see Khachatryan et al,
Ibid. for more information regarding these programs).
[0076] Systems comparing 16s rDNA libraries from healthy controls
and FMF patients (in remission or attack) indicate differences in
microbial composition between healthy individuals and FMF
individuals. For example, FIG. 16 illustrates the comparison of 16S
rRNA gene libraries derived from healthy controls and FMF patients
in remission and attack. (*p, 0.01, comparison of remission vs.
control libraries. **p, 0.01, comparison of attack vs. control
libraries. ***p, 0.01, comparison of remission vs. attack
libraries.) Data shown in FIG. 16 taken from Khachatryan et al,
"Predominant role of host genetics in controlling the composition
of gut microbiota," PLoS ONE, 3:e3064 (2008) which is herein
incorporated by reference. As indicated by the data presented in
FIG. 16, in asymptomatic FMF patients in remission, the proportion
of Enterobacteriaceae, Acidaminococcaceae, Ruminococcus and
Megasphaera is significantly increased in comparison with control
subjects, while Roseburia is significantly reduced. In FMF patients
with active disease, the percentages of Porphyromonadaceae
Phascolarctobacterium, Faecalibacterium, and Parabacteroides are
increased relative to control subjects, and the percentages of
Prevotellaceae, Dialister and Prevotella are decreased.
[0077] Another approach to generating microbial profiles is using
fluorescent in situ hybridization (FISH) to identify and enumerate
fecal bacteria. Microbial profiles based on FISH results may
augment those obtained by cloning and sequencing (as above) or
FISH-based data may be used to generate profiles independently. The
predominant groups of bacteria in fecal samples are quantified
using Cy3-labelled oligonucleotide probes for 16s rRNA genes
hybridized to bacterial DNA in cells fixed on microscope slides to
generate FISH data. Hybridization in bacterial cells is counted
automatically using image analysis software, such as with Quantimet
HR600 and a Leica DMRXA epifluorescence microscope (Wetzlar,
Germany). Detailed methods and materials including Cy3-labeled
oligonucleotide probes, hybridization conditions, preparation of
fixed bacteria on microscope slides and data analysis techniques
are described in Khachatryan et al, Ibid. Microbial profiles from
fecal specimens derived from healthy controls and patients with
genetic diseases such as FMF are based on data generated using
techniques including FISH and DNA sequencing of 16s rDNA
libraries.
[0078] To create an informative reference microbial profile and to
associate microbial profiles with genetic disease information, a
microbial monitoring system incorporates genetic data from
individuals. For example, an individual's genotype, including
alleles, cDNA or gDNA sequence, for MEFV is determined using PCR
amplification and sequencing of gDNA or cDNA derived from blood or
tissue samples. Where such testing has been done previously, an
individual's genotype may also be obtained from information
existing as part of an individual's medical record. Genomic DNA and
RNA are isolated from blood or tissue samples using reagents and
protocols available from Qiagen Inc., (Valencia, Calif.). The
FlexiGene DNA kit is used for samples of whole blood between 1 and
5 mL, while the DNeasy Blood and Tissue Kit is used for tissue or
smaller blood volumes (Qiagen Inc., Valencia, Calif.). PCR primers
and reaction conditions specific for exon 10 and exon 2 (the sites
of known mutations) of the MEFV gene are as described in
Khachatryan et al, Ibid. PCR-amplified fragments from the MEFV gene
are purified using Qiagen reagents and sequenced using an automated
capillary DNA sequencer (Beckman Instruments Inc., Fullerton,
Calif.).
[0079] Information regarding mutations in the MEFV gene of specific
individuals relative to sequences derived from healthy control
subjects is incorporated into a microbial reference profile and
represented to a system user as particular combinations of alleles,
including heterozygous or homozygous mutations. The system also
accepts medical data relating to inflammatory symptoms such as
fever, influx of polymorphonuclear leukocytes, neutrophilia, and
acute-phase response. In addition, clinical data such as blood
levels of C-reactive protein, SAA, and interferon gamma are
integrated into individual profiles.
[0080] A microbial monitoring system is used to profile subjects
who are suspected to have FMF in addition to profiling known FMF
patients. For example, the system is used generate microbial
profiles for individuals exhibiting clinical symptoms of FMF (e.g.
repeated episodes of fever and polyseritis) but lacking genotype
information and specific diagnosis, or individuals that are related
to an MEFV carrier or an FMF patient but have displayed
inconclusive symptoms. Individuals who have tested positive for a
mutant MEFV gene allele but do not display clinical symptoms are
also profiled. A system that integrates clinical and genotype
information with microbial diversity and abundance data assists
caregivers in diagnosing FMF and also indicates potential
treatments and recommends treatments. For example, a fecal
microbial profile associated with FMF patients during attack (i.e.
fever and inflammation) displays low proportions of the bacterial
taxa Prevotellaceae, Dialister and Prevotella relative to healthy
control subjects (see FIG. 16 and Khachatryan et al, Ibid.).
Identification of such a microbial profile in a patient suspected
of having FMF in conjunction with genotype and clinical information
increases confidence in the diagnosis of FMF and assists in
suggesting appropriate treatments for FMF in individual patients. A
system may suggest treatment including a probiotic containing the
depleted bacteria Prevotellaceae, Dialister and Prevotella in the
appropriate proportions to be administered orally along with
anti-inflammatory drugs such as aspirin and acetaminophen. There is
increased confidence in diagnosis when suspected FMF patients
display a microbial profile associated with FMF patients, and
furthermore can facilitate treatment at the time of future acute
episodes. FMF patients in remission display a microbial profile
with increased proportions of Enterobacteriaceae,
Acidaminococcaceae, Ruminococcus and Megasphaera in comparison with
control subjects, while Roseburia is significantly reduced (see
FIG. 16 and Khachatryan et al, Ibid.). For suspected FMF patients,
a microbial monitoring system integrates genotypic data, clinical
data, family history and at least one microbial profile to assist
medical personnel in the diagnosis and effective treatment of FMF.
For example, any specific bacterial species that are
overrepresented in FMF individuals may be targeted with
antibacterial agents.
Example 4
[0081] A microbial monitoring system assists in the evaluation and
treatment of elderly patients and travelers exposed to new
environmental microbial flora. The system assists individuals and
health care professionals to make informed decisions regarding
possible interventions to improve the health of immigrants.
Genetics, age, environment, diet and drugs are important
determinants of the microbial composition of gut flora in healthy
and diseased individuals. Individuals who have recently moved into
a new environment (for example, elderly immigrants, such as parents
or grandparents of Chinese-Americans, Japanese-Americans and
Latin-Americans) benefit from a system which monitors microbial
flora and recommends treatments to improve health in the new
locale. For example, an elderly immigrant will benefit from
modification of his or her gastrointestinal microbial profile to
align it with a reference profile based on data from individuals of
a similar ethnic background who have been living in the new locale
for some time or to maintain their original profile in spite of the
change in the diet. Microbial samples from the gastrointestinal
tract are obtained using an ingested sampling device (see, for
example, US patent application to Boyden et al., titled "Adaptive
dispensation in a digestive tract, filed on Oct. 23, 2007 and US
Patent Application No. 2009/0112191 to Boyden et al. titled
"Medical or veterinary digestive tract utilization systems and
methods" which are herein incorporated by reference). Alternatively
or in addition, samples from the digestive tract are obtained with
an endoscopic device. The choice of sampling method for any
individual patient may depend on personal choice of the medical
staff relative to other medical indications, or the needs and
preferences of the individual patient. Analysis of microbial
diversity and abundance may be made using DNA sequencing of 16s
rDNA clone libraries (as above).
[0082] Analysis of microbial diversity and abundance may also be
generated using denaturing gradient gel electrophoresis (DGGE) data
integrated into the systems and methods described herein. For
example, DGGE analysis of fecal samples from a Chinese family has
reveals differences in microbial composition at the species level
relative to American individuals (see Li et al, "Symbiotic gut
microbes modulate human metabolic phenotypes," Proc. Natl. Acad.
Sci. USA, 105: 2117-2122 (2008), which is herein incorporated by
reference).
[0083] In addition, microbial monitoring of single individuals over
time indicates the stability of an individual's microbial profile
over time, or changes that may result from a new environment, new
diet or ageing (see Li et al, Ibid.). For example, travelers from
industrialized nations to tropical developing countries contract
traveler's diarrhea that is associated with enteric microbial
pathogens, and it has been noted that "approximately 80% of
traveler's diarrhea cases with an identified pathogen are caused by
bacteria, including enterotoxigenic Escherichia coli (ETEC),
recently identified enteroaggregative E. coli (EAEC), Salmonella
spp., Shigella spp., Campylobacter spp., Plesiomonas shigelloides,
Aeromonas spp., and non-cholera-causing vibrios" (quoted from Gomi
et al, "In vitro antimicrobial susceptibility testing of bacterial
enteropathogens causing traveler's diarrhea in four geographic
regions," Antimicrobial Agents and Chemotherapy, 45: 212-216 (2001)
which is herein incorporated by reference).
[0084] A microbial monitoring system accepts data on the abundance
of bacterial pathogens such as enterotoxigenic Escherichia coli
(ETEC) and enteroaggregative E. coli (EAEC) (see Gomi et al, Ibid.
for methods), and integrates data on the susceptibility of
microbial pathogens to antimicrobials such as ampicillin (AMP;
Sigma Chemical Co., St. Louis, Mo.), trimethoprim (TMP; Sigma),
TMP/sulfamethoxazole (SXT; Sigma), doxycycline (DOX; Sigma),
nalidixic acid (NAL; Sigma), amdinocillin (MEC; Leo Pharmaceutical
Products, Copenhagen, Denmark), ceftriaxone (CRO; Sigma),
ciprofloxacin (CIP; Medlatech Inc., Herndon, Va.), levofloxacin
(LVX; Pharmaceutical Research Institute, Spring House, Pa.),
azithromycin (AZM; Pfizer Inc., Brooklyn, N.Y.), and rifaximin
(RFX; Alfa Wassermann, Bologna, Italy). Such integrated data is
used by the system to suggest treatments specific to individuals
based on their profiles.
[0085] The susceptibility of bacterial pathogens associated with
traveler's diarrhea to antibiotics is shown in FIG. 17. FIG. 17
depicts the minimum inhibitory concentration (MIC) of
antimicrobials for enteropathogens at the MIC.sub.90 level. Table
reference (a) denotes MIC.sub.90, which is the MIC required to
inhibit the growth of 90% of the strains tested. Table reference
(b) indicates that data for CRO and AZM are based on 268 pathogens.
Table reference (c) indicates that the column headed "Others"
denotes other pathogens, including non-cholera-causing vibrios, P.
shigelloides, and Aeromonas sp. Isolates. Taken from Gomi et al,
Ibid.
[0086] A microbial monitoring system indicates when treatment is
needed and recommends treatments to caregivers and individuals. For
example, a patient with an ETEC infection is indicated as
potentially benefitting from treatment and the system recommends
AZM or CIP or CRO based on the MIC values for these antimicrobials
(see FIG. 17). Conversely, AMP, TMP and SXT would be disfavored due
to their high MIC values as extremely high doses of antibiotics are
generally less medically desirable treatments. Such antibiotics are
suggested with an indication of high dosages needed relative to the
MIC levels for specific pathogens so that a healthcare professional
may make a final treatment choice. The system also integrates data
regarding an individual's complete intestinal microbial profile and
medical data such as age, existing diseases, antibiotic allergies,
and current medications to indicate and recommend treatments for
traveler's diarrhea and other enteric microbial diseases. Repeated
microbial profiling is used to monitor an individual's health over
time and evaluate treatment efficacy. For example, changes in
microbial profile, especially changes in abundance of
enteropathogens and a reduction in normal microbial flora resulting
from antimicrobial treatment, indicates a need for further
treatment and/or alternate treatments such as different
antimicrobials or probiotics to restore a normal microbial flora
balance.
[0087] Elderly individuals often display changes in the composition
of their microbial flora that can directly cause disease or make
them susceptible to disease. A microbial monitoring system that
accepts and integrates data on age, microbial composition and
abundance, antibiotic use and environmental data is used to detect
and indicate changes in gastrointestinal microbial flora and to
recommend treatments to rebalance the microbiota of elderly
individuals. Ageing is generally accompanied by changes in an
individual's gastrointestinal tract as well as in their diet and
immune system responses. For example, ageing is associated with
increased numbers of facultative anaerobes and decreased numbers of
beneficial anaerobes such as bifidobacteria and lactobacilli as
well as a general reduction in the species diversity for most
bacterial groups (see, for example, Woodmansey et al, "Intestinal
bacteria and aging," J. Appl. Microb., 102: 1178-1186 (2007), which
is herein incorporated by reference). Ageing individuals often
display decreased intestinal motility and consequent increased
intestinal transit times that can make them more susceptible to
disease. Decreased numbers of Bacteroides are associated with
increased age and this is magnified following antibiotic therapy.
Species diversity within Bacteroides is also often reduced in the
elderly. Changes in Bacteroides abundance and diversity correlates
with a reduction in amylolitic activity (Woodmansey et al, Ibid.),
and microbial profiles with reduced numbers of Bacteroides are
associated with obesity, which is undesirable at any age (see Ley
et al, "Human gut microbes associated with obesity," Nature 444:
1022-1023 (2006) which is herein incorporated by reference).
Furthermore, elderly individuals often display increased intestinal
proteolytic activity associated with increased numbers of
Fusobacteria, Propionibacteria and Clostridia. Elderly individuals
treated with antibiotics display increased abundance and diversity
of clostridia species including: Clostridium bifermentans,
Clostridium clostridioforme, Clostridium sordellii and Clostridium
malenominatum and the pathogen Clostridium difficile (Woodmansey et
al, Ibid.). Yet the abundance and diversity of beneficial
Bifidobacteria tend to be reduced in elderly individuals, so that
frequently only a few species remain, for example, Bifidobacterium
adolescentis, Bifidobacterium angulatum, and Bifidobacterium longum
(Woodmansey et al, Ibid.).
[0088] A system monitoring the changes in microbial abundance and
diversity with age to detect and indicate changes in the abundance
of bacterial divisions and the diversity of bacterial species which
accompany the ageing process also suggests interventions to modify
these effects. Reference microbial profiles established, for
example, with samples and medical data from healthy elderly
subjects, younger individuals, sick elderly patients, patients
receiving antibiotics and data from the biomedical literature are
used to analyze changes and recommend treatments. As with all
systems described herein, the choice of appropriate reference
profile individuals and data is at the option of the system user
and/or programmer. Elderly patients may be sampled periodically
such as annually, semi-annually, monthly or weekly to establish a
reference microbial profile from a particular individual that can
be used for difference analysis. Microbial samples may be taken
during regular medical events such as check-ups or evaluations. A
microbial profile system recommends treatments as indicated to
restore a healthy microbial profile or to eliminate microbial
pathogens. For example, reduced beneficial bacteria such as
Bifidobacteria may be supplemented with probiotics (e.g.
Bifidobacterium bifidum and Bifidobacterium longum) and prebiotics
(e.g. oligofructose) to specifically increase their abundance and
promote diversity (Woodmansey et al, Ibid.). In situations wherein
the microbial profile system detects a bacterial pathogen such as
C. difficile, or indicates a significant change in C. difficile
abundance, they system recommends treatment with probiotics such as
Lactobacillus plantarum and B. bifidum combined with prebiotics
such as fructooligosaccharides, inulin and xylooligosaccharides
(Woodmansey et al, Ibid.).
[0089] Those having skill in the art will recognize that the state
of the art has progressed to the point where there is little
distinction left between hardware, software, and/or firmware
implementations of aspects of systems; the use of hardware,
software, and/or firmware is generally (but not always, in that in
certain contexts the choice between hardware and software can
become significant) a design choice representing cost vs.
efficiency tradeoffs. Those having skill in the art will appreciate
that there are various vehicles by which processes and/or systems
and/or other technologies described herein can be effected (e.g.,
hardware, software, and/or firmware), and that the preferred
vehicle will vary with the context in which the processes and/or
systems and/or other technologies are deployed. For example, if an
implementer determines that speed and accuracy are paramount, the
implementer may opt for a mainly hardware and/or firmware vehicle;
alternatively, if flexibility is paramount, the implementer may opt
for a mainly software implementation; or, yet again alternatively,
the implementer may opt for some combination of hardware, software,
and/or firmware. Hence, there are several possible vehicles by
which the processes and/or devices and/or other technologies
described herein may be effected, none of which is inherently
superior to the other in that any vehicle to be utilized is a
choice dependent upon the context in which the vehicle will be
deployed and the specific concerns (e.g., speed, flexibility, or
predictability) of the implementer, any of which may vary. For
example, those skilled in the art will recognize that optical
aspects of implementations will typically employ optically-oriented
hardware, software, and or firmware.
[0090] In some implementations described herein, logic and similar
implementations may include software or other control structures.
Electronic circuitry, for example, may have one or more paths of
electrical current constructed and arranged to implement various
functions as described herein. In some implementations, one or more
media may be configured to bear a device-detectable implementation
when such media hold or transmit device detectable instructions
operable to perform as described herein. In some variants, for
example, implementations may include an update or modification of
existing software or firmware, or of gate arrays or programmable
hardware, such as by performing a reception of or a transmission of
one or more instructions in relation to one or more operations
described herein. Alternatively or additionally, in some variants,
an implementation may include special-purpose hardware, software,
firmware components, and/or general-purpose components executing or
otherwise invoking special-purpose components. Specifications or
other implementations may be transmitted by one or more instances
of tangible transmission media as described herein, optionally by
packet transmission or otherwise by passing through distributed
media at various times.
[0091] Alternatively or additionally, implementations may include
executing a special-purpose instruction sequence or invoking
circuitry for enabling, triggering, coordinating, requesting, or
otherwise causing one or more occurrences of virtually any
functional operations described herein. In some variants,
operational or other logical descriptions herein may be expressed
as source code and compiled or otherwise invoked as an executable
instruction sequence. In some contexts, for example,
implementations may be provided, in whole or in part, by source
code, such as C++, or other code sequences. In other
implementations, source or other code implementation, using
commercially available and/or techniques in the art, may be
compiled/implemented/translated/converted into a high-level
descriptor language (e.g., initially implementing described
technologies in C or C++ programming language and thereafter
converting the programming language implementation into a
logic-synthesizable language implementation, a hardware description
language implementation, a hardware design simulation
implementation, and/or other such similar mode(s) of expression).
For example, some or all of a logical expression (e.g., computer
programming language implementation) may be manifested as a
Verilog-type hardware description (e.g., via Hardware Description
Language (HDL) and/or Very High Speed Integrated Circuit Hardware
Descriptor Language (VHDL)) or other circuitry model which may then
be used to create a physical implementation having hardware (e.g.,
an Application Specific Integrated Circuit). Those skilled in the
art will recognize how to obtain, configure, and optimize suitable
transmission or computational elements, material supplies,
actuators, or other structures in light of these teachings.
[0092] The foregoing detailed description has set forth various
embodiments of the devices and/or processes via the use of block
diagrams, flowcharts, and/or examples. Insofar as such block
diagrams, flowcharts, and/or examples contain one or more functions
and/or operations, it will be understood by those within the art
that each function and/or operation within such block diagrams,
flowcharts, or examples can be implemented, individually and/or
collectively, by a wide range of hardware, software, firmware, or
virtually any combination thereof. In one embodiment, several
portions of the subject matter described herein may be implemented
via Application Specific Integrated Circuits (ASICs), Field
Programmable Gate Arrays (FPGAs), digital signal processors (DSPs),
or other integrated formats. However, those skilled in the art will
recognize that some aspects of the embodiments disclosed herein, in
whole or in part, can be equivalently implemented in integrated
circuits, as one or more computer programs running on one or more
computers (e.g., as one or more programs running on one or more
computer systems), as one or more programs running on one or more
processors (e.g., as one or more programs running on one or more
microprocessors), as firmware, or as virtually any combination
thereof, and that designing the circuitry and/or writing the code
for the software and or firmware would be well within the skill of
one of skill in the art in light of this disclosure. In addition,
those skilled in the art will appreciate that the mechanisms of the
subject matter described herein are capable of being distributed as
a program product in a variety of forms, and that an illustrative
embodiment of the subject matter described herein applies
regardless of the particular type of signal bearing medium used to
actually carry out the distribution. Examples of a signal bearing
medium include, but are not limited to, the following: a recordable
type medium such as a floppy disk, a hard disk drive, a Compact
Disc (CD), a Digital Video Disk (DVD), a digital tape, a computer
memory, etc.; and a transmission type medium such as a digital
and/or an analog communication medium (e.g., a fiber optic cable, a
waveguide, a wired communications link, a wireless communication
link (e.g., transmitter, receiver, transmission logic, reception
logic, etc.), etc.).
[0093] In a general sense, those skilled in the art will recognize
that the various aspects described herein which can be implemented,
individually and/or collectively, by a wide range of hardware,
software, firmware, and/or any combination thereof can be viewed as
being composed of various types of "electrical circuitry."
Consequently, as used herein "electrical circuitry" includes, but
is not limited to, electrical circuitry having at least one
discrete electrical circuit, electrical circuitry having at least
one integrated circuit, electrical circuitry having at least one
application specific integrated circuit, electrical circuitry
forming a general purpose computing device configured by a computer
program (e.g., a general purpose computer configured by a computer
program which at least partially carries out processes and/or
devices described herein, or a microprocessor configured by a
computer program which at least partially carries out processes
and/or devices described herein), electrical circuitry forming a
memory device (e.g., forms of memory (e.g., random access, flash,
read only, etc.)), and/or electrical circuitry forming a
communications device (e.g., a modem, communications switch,
optical-electrical equipment, etc.). Those having skill in the art
will recognize that the subject matter described herein may be
implemented in an analog or digital fashion or some combination
thereof.
[0094] Those skilled in the art will recognize that at least a
portion of the devices and/or processes described herein can be
integrated into a data processing system. Those having skill in the
art will recognize that a data processing system generally includes
one or more of a system unit housing, a video display device,
memory such as volatile or non-volatile memory, processors such as
microprocessors or digital signal processors, computational
entities such as operating systems, drivers, graphical user
interfaces, and applications programs, one or more interaction
devices (e.g., a touch pad, a touch screen, an antenna, etc.),
and/or control systems including feedback loops and control motors
(e.g., feedback for sensing position and/or velocity; control
motors for moving and/or adjusting components and/or quantities). A
data processing system may be implemented utilizing suitable
commercially available components, such as those typically found in
data computing/communication and/or network computing/communication
systems.
[0095] In a general sense, those skilled in the art will recognize
that the various embodiments described herein can be implemented,
individually and/or collectively, by various types of
electro-mechanical systems having a wide range of electrical
components such as hardware, software, firmware, and/or virtually
any combination thereof; and a wide range of components that may
impart mechanical force or motion such as rigid bodies, spring or
torsional bodies, hydraulics, electro-magnetically actuated
devices, and/or virtually any combination thereof. Consequently, as
used herein "electro-mechanical system" includes, but is not
limited to, electrical circuitry operably coupled with a transducer
(e.g., an actuator, a motor, a piezoelectric crystal, a Micro
Electro Mechanical System (MEMS), etc.), electrical circuitry
having at least one discrete electrical circuit, electrical
circuitry having at least one integrated circuit, electrical
circuitry having at least one application specific integrated
circuit, electrical circuitry forming a general purpose computing
device configured by a computer program (e.g., a general purpose
computer configured by a computer program which at least partially
carries out processes and/or devices described herein, or a
microprocessor configured by a computer program which at least
partially carries out processes and/or devices described herein),
electrical circuitry forming a memory device (e.g., forms of memory
(e.g., random access, flash, read only, etc.)), electrical
circuitry forming a communications device (e.g., a modem,
communications switch, optical-electrical equipment, etc.), and/or
any non-electrical analog thereto, such as optical or other
analogs. Those skilled in the art will also appreciate that
examples of electro-mechanical systems include but are not limited
to a variety of consumer electronics systems, medical devices, as
well as other systems such as motorized transport systems, factory
automation systems, security systems, and/or
communication/computing systems. Those skilled in the art will
recognize that electro-mechanical as used herein is not necessarily
limited to a system that has both electrical and mechanical
actuation except as context may dictate otherwise.
[0096] The herein described subject matter sometimes illustrates
different components contained within, or connected with, different
other components. It is to be understood that such depicted
architectures are merely exemplary, and that in fact many other
architectures may be implemented which achieve the same
functionality. In a conceptual sense, any arrangement of components
to achieve the same functionality is effectively "associated" such
that the desired functionality is achieved. Hence, any two
components herein combined to achieve a particular functionality
can be seen as "associated with" each other such that the desired
functionality is achieved, irrespective of architectures or
intermedial components. Likewise, any two components so associated
can also be viewed as being "operably connected", or "operably
coupled," to each other to achieve the desired functionality, and
any two components capable of being so associated can also be
viewed as being "operably couplable," to each other to achieve the
desired functionality. Specific examples of operably couplable
include but are not limited to physically mateable and/or
physically interacting components, and/or wirelessly interactable,
and/or wirelessly interacting components, and/or logically
interacting, and/or logically interactable components.
[0097] In some instances, one or more components may be referred to
herein as "configured to," "configured by," "configurable to,"
"operable/operative to," "adapted/adaptable," "able to,"
"conformable/conformed to," etc. Those skilled in the art will
recognize that such terms (e.g. "configured to") can generally
encompass active-state components and/or inactive-state components
and/or standby-state components, unless context requires
otherwise.
[0098] All of the above U.S. patents, U.S. patent application
publications, U.S. patent applications, foreign patents, foreign
patent applications and non-patent publications referred to in this
specification and/or listed in any Application Data Sheet, are
incorporated herein by reference, to the extent not inconsistent
herewith.
[0099] While particular aspects of the present subject matter
described herein have been shown and described, it will be apparent
to those skilled in the art that, based upon the teachings herein,
changes and modifications may be made without departing from the
subject matter described herein and its broader aspects and,
therefore, the appended claims are to encompass within their scope
all such changes and modifications as are within the true spirit
and scope of the subject matter described herein. It will be
understood by those within the art that, in general, terms used
herein, and especially in the appended claims (e.g., bodies of the
appended claims) are generally intended as "open" terms (e.g., the
term "including" should be interpreted as "including but not
limited to," the term "having" should be interpreted as "having at
least," the term "includes" should be interpreted as "includes but
is not limited to," etc.). It will be further understood by those
within the art that if a specific number of an introduced claim
recitation is intended, such an intent will be explicitly recited
in the claim, and in the absence of such recitation no such intent
is present. For example, as an aid to understanding, the following
appended claims may contain usage of the introductory phrases "at
least one" and "one or more" to introduce claim recitations.
However, the use of such phrases should not be construed to imply
that the introduction of a claim recitation by the indefinite
articles "a" or "an" limits any particular claim containing such
introduced claim recitation to claims containing only one such
recitation, even when the same claim includes the introductory
phrases "one or more" or "at least one" and indefinite articles
such as "a" or "an" (e.g., "a" and/or "an" should typically be
interpreted to mean "at least one" or "one or more"); the same
holds true for the use of definite articles used to introduce claim
recitations. In addition, even if a specific number of an
introduced claim recitation is explicitly recited, those skilled in
the art will recognize that such recitation should typically be
interpreted to mean at least the recited number (e.g., the bare
recitation of "two recitations," without other modifiers, typically
means at least two recitations, or two or more recitations).
Furthermore, in those instances where a convention analogous to "at
least one of A, B, and C, etc." is used, in general such a
construction is intended in the sense one having skill in the art
would understand the convention (e.g., "a system having at least
one of A, B, and C" would include but not be limited to systems
that have A alone, B alone, C alone, A and B together, A and C
together, B and C together, and/or A, B, and C together, etc.). In
those instances where a convention analogous to "at least one of A,
B, or C, etc." is used, in general such a construction is intended
in the sense one having skill in the art would understand the
convention (e.g., "a system having at least one of A, B, or C"
would include but not be limited to systems that have A alone, B
alone, C alone, A and B together, A and C together, B and C
together, and/or A, B, and C together, etc.). It will be further
understood by those within the art that typically a disjunctive
word and/or phrase presenting two or more alternative terms,
whether in the description, claims, or drawings, should be
understood to contemplate the possibilities of including one of the
terms, either of the terms, or both terms unless context dictates
otherwise. For example, the phrase "A or B" will be typically
understood to include the possibilities of "A" or "B" or "A and
B."
[0100] With respect to the appended claims, those skilled in the
art will appreciate that recited operations therein may generally
be performed in any order. Also, although various operational flows
are presented in a sequence(s), it should be understood that the
various operations may be performed in other orders than those
which are illustrated, or may be performed concurrently. Examples
of such alternate orderings may include overlapping, interleaved,
interrupted, reordered, incremental, preparatory, supplemental,
simultaneous, reverse, or other variant orderings, unless context
dictates otherwise. Furthermore, terms like "responsive to,"
"related to," or other past-tense adjectives are generally not
intended to exclude such variants, unless context dictates
otherwise.
[0101] One skilled in the art will recognize that the herein
described components (e.g., operations), devices, objects, and the
discussion accompanying them are used as examples for the sake of
conceptual clarity and that various configuration modifications are
contemplated. Consequently, as used herein, the specific exemplars
set forth and the accompanying discussion are intended to be
representative of their more general classes. In general, use of
any specific exemplar is intended to be representative of its
class, and the non-inclusion of specific components (e.g.,
operations), devices, and objects should not be taken limiting.
[0102] While various aspects and embodiments have been disclosed
herein, other aspects and embodiments will be apparent to those
skilled in the art. The various aspects and embodiments disclosed
herein are for purposes of illustration and are not intended to be
limiting, with the true scope and spirit being indicated by the
following claims.
* * * * *