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.