Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

First Advisor

Christopher A. Lowry

Second Advisor

Pei-San Tsai

Third Advisor

Noah Fierer

Fourth Advisor

Andrew Hoisington

Fifth Advisor

Matthew McQueen


The human microbiota is a term that is used to describe the microorganisms (archaea, bacteria, eukaryotes, and viruses) within the human body. The past decade has been characterized by a number of landmark surveys of the human microbiome such as The Human Microbiome Project. The main objective of these surveys was to generate a point of reference and large databases of comparators. Nevertheless, in-depth analyses of the human microbiome in association with validated measures of human general, physical, and mental health are lacking, especially the latter.

The main goal of this dissertation was to assess the skin, oral, and fecal microbiomes in association with validated measures of general health, physical health, insomnia, and mental health in a cohort of U.S. Veterans. We sought to study this select group of individuals with unique environmental exposures and health outcomes, to determine if there were identifiable microbial signatures associated with specific health measures. We collected microbiome samples from three anatomical sites (skin, oral, and fecal) from 188 U.S. Veterans. From our results, we detail the general characteristics of the sample types (skin, oral and fecal) as they relate to each other and as they relate to gender, race, and age. We then characterized the microbiome of all three sample types (skin, oral and fecal) as they relate to metadata collected in three main categories: general and physical health, insomnia, and mental health.

Overall, our results comparing the microbiome at the three anatomical sites with respect to gender, race, and age were consistent with previous studies of different cohorts with different demographics. Measures of general and physical health displayed similar relationships to the fecal microbiome; specifically, we observed increased alpha diversity of the fecal microbiome in association with “healthy” states. We found that severe insomnia symptoms and several measures of mental health were associated with microbial feature from the various sampling sites. Further analyses are needed to understand the biological basis of the associations between the skin, oral, and fecal microbiomes and measures of physical health, insomnia, mental health, and if microbiome-based interventions can be developed in order to improve these health outcomes.

Available for download on Sunday, October 10, 2021