species in the gut.
So how does the AGP work? As a participant, your involvement is easy as you simply fill out a questionnaire about your
background and dietary information, mail a stool sample to
the AGP using a provided collection kit, and pay a fee ($99) to
cover sequencing and analysis costs. (For the AGA initiative,
these fees were reduced for nontrainee members or waived
altogether for trainee member volunteers.) Once your sample
arrives at the lab in San Diego, the bacterial DNA is extracted,
and a portion of the 16S ribosomal RNA gene is amplified and
sequenced on Illumina® machines, and the resulting sequences are analyzed. You will then receive an alert to obtain your
results online. Clicking through the online portal provides a
graphical summary and compares the percent make-up of your
microbial phyla with others of similar diet, gender, age, and
BMI. Eventually, you will be provided with a summary graphical representation that compares how similar your gut bacteria
are to people of different nationalities or to microbial communities analyzed from other body sites. You also receive information on your four most abundant microbes, four most enriched
microbes compared to the average population, and (most fun
of all) the rare species that are present in your microbiome.
For data-minded individuals, the raw sequencing data for your
sample is available with a few extra clicks online.
Do gastroenterologists and other AGA members who work in
the GI field develop a distinct microbial population? At DDW®
2016, an active learning discussion was held with AGA mem-
bers and attended by many participants in the stool sample ini-
tiative. Dr. Lee Kaplan (Harvard Medical School), Dr. Rob Knight
(UC San Diego), and Dr. Gary Wu (University of Pennsylvania)
discussed the samples and analysis, and the next steps toward
making this knowledge useful. The major findings revealed that
AGA volunteer microbiotas are widely distributed and resem-
ble a random sampling of the entire AGP population of healthy
individuals and patients. So breathe a sigh of relief, gastroen-
terologists, your microbiome has likely not been drastically
altered by your profession. How this information will become
useful is the interesting question that labs around the world
are now racing to address.
An intriguing finding from this explosion of research is that
your gut microbiota, which begins to develop as soon as you
are born, is malleable and shaped by a variety of factors. Individuals harbor a thriving bacterial community that matures
throughout life, and responds to antibiotic insults, as well as
dietary and lifestyle changes. As a result, distinct microbiotas
are observed between many populations. What can we do with
this information? This is the exciting part. Exactly how these
different microbial communities impact health and disease and
whether they can be precisely shaped for optimal health are
actively being studied. There is hope that modifying your gut
microbiota, perhaps through installation of defined microbial
communities, may prevent antibiotic-associated predisposition
to disease as well as prevent or treat inflammatory or metabolic diseases and even adverse health outcomes like obesity.
By embarking on this journey now, our field is setting the
stage for a microbe revolution in medicine. Are we headed
toward a future where defined microbial communities are
introduced to patients to reinforce their microbial armor?
Which species are providing this benefit and through what
mechanism? In the (possibly near!) future, a patient may be
tested for their microbial make-up and pose the question
“what does it all mean and what can I do about it?” And there
may actually be an answer. n
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2. Nicholson J.K., et al. Science 2012;336:1262-7.
3. Yoshimoto S., et al. Nature 2013;499:97-101.
4. Ridaura V.K., et al. Science 2013;341:1241214.
American Gut Project fecal samples
Analysis of the data; the more data
collected, the more detailed the picture.
An Illumina® sequencer, which
sequences some of the bacterial DNA in