Evaluation of Skin, Colonic, and Oral Microbiome and Effect of Time and Antibiotic Treatment on Organism Diversity at Each Site

The study of infectious agents and their role in disease is not new. Most efforts in this
area have focused on specific agents, such as human papillomaviruses and cervical cancer,
Helicobacter pylori (HP) and gastric diseases and carcinoma, hepatitis B and C virus and
liver cancer, to name a few. The body's skin and mucosal surface's play host to microbial
communities (the microbiome) whose membership outnumbers our own somatic and germ cells by
an order of magnitude or more. The skin, oral, and gastrointestinal (GI) tract are all
densely colonized surfaces . Recent technological advances, however, have made exploration
of the microbiome, an understudied area, feasible. It is reasonable to hypothesize that
some of the infectious agents that naturally reside in the body may impact health, or that
perhaps the balance between the various micro-organisms has an effect on health. This new
field of study has much promise that could lead to important new discoveries of how
infectious agents are associated with disease and how environmental (e.g., diet) and host
responses (e.g., immune response and genetics) to these agents determine chronic patterns of
colonization and subsequent disease risk.

However, because the study of the human microbiome is a new area of research, much remains
to be learned regarding: a) the extent and pattern of the microbiome at various sites, b)
determinants of these patterns (e.g., consistency over time), and c) optimal assay
techniques.

Prior to launching large-scale epidemiological studies to evaluate the association between
microbiome and disease (including cancer), it is crucial to conduct well-designed,
systematic, methodological studies to address some of the issues listed above. These
methodological studies will begin to provide the baseline information that could be used to
plan for, and conduct disease association studies.

We propose to initiate a study to collect oral, skin, vaginal (only women), penile (men
only) and colonic samples at enrollment and again 6 months later on up to 150 individuals.
Our objectives are:

1. To evaluate the microbiome heterogeneity between individuals across specimen types -
colonic/oral/skin/vaginal/penile.

2. To evaluate the microbiome heterogeneity within individuals (over time and across
specimen types - colonic/oral/skin/vaginal/penile).

3. To evaluate the effect of self-reported antibiotic treatment on the oral, colonic,
skin, penile and vaginal microbiomes diversity and richness.

4. To evaluate the associations between colonic microbiome and gastrointestinal symptom
disorders (assessed by the Rome III questionnaire - a detailed diagnostic questionnaire
for adult functional gastrointestinal disorder), inflammatory markers (initially using
measures of C-reactive protein (CRP)), and demographic factors.

5. To evaluate the reproducibility of assays used to measure the microbiota and compare
the diversity and abundance determined by the different assays.

- ELIGIBILITY CRITERIA:

Individuals who meet the age criteria of 18 years and older and are interested in the
study will be asked to provide written informed consent. Participants must be willing to
reside in the study area for the study duration (6 months). Those individuals with any
known medical conditions that may limit life expectancy in the short term (including but
not limited to: congestive heart failure, renal failure, prior malignancy, or any other
chronic disease that limits functional status to the extent that the individual cannot
perform light work or the usual activities of daily self care) are ineligible for
inclusion in the study. Female participants must not be pregnant.

Individuals who report recent antibiotic use will be deferred and enrolled after they have
been at least 6 weeks without antibiotic use.

In Hojancha, region of Guanacaste, Costa Rica, where our study will be conducted, a
population based census was completed in March 2009 and will serve as the basis for
enrollment, allowing for recruitment of a representative sample of the population. The
same census was used to identify participants for another study in the same area.
Therefore, because we will use the same census, we will exclude participants that were
enrolled in the other study. Eligible participants must be willing to return for one
follow-up visit: 6 months after the initial enrollment visit and willing to allow
submission of blood for assays of serum immune markers, host genetic susceptibility and
environmental factors, and to provide consent for use of the specimens.