Date of Award


Degree Name

Biomedical Sciences


Joan C. Edwards School of Medicine

Type of Degree


Document Type


First Advisor

Dr. Hongwei Yu, Committee Chairperson

Second Advisor

Dr. James Denvir

Third Advisor

Dr. Joseph Horzempa

Fourth Advisor

Dr. Jeremy McAleer

Fifth Advisor

Dr. Timothy Long


The microbial community harbored by the mammalian gastrointestinal tract, collectively called the gut microbiota, plays a critical role in host health, metabolism, and immunity. Quantifiable changes in the gut microbiota have been implicated in a myriad of pathologies, including autoimmune, metabolic, and neurodegenerative diseases. Because of the gut microbiota’s plasticity, manipulating this community for therapeutic benefit presents as a novel strategy to combat modern diseases. Yet, only a fraction of the total microbial diversity that exists within the gut has been successfully cultured in a laboratory, leaving the clinical implications and functional attributes of many gut microbes undetermined. To address this issue, studies in this dissertation focused on bioinformatically investigating (i) the role of dietary and genetic factors on the gut microbiota in metabolic syndrome and (ii) the anatomic niche and immunomodulating antigens of the culture-resistant commensal, Segmented Filamentous Bacteria (SFB). Comprehensive characterization of the cecal microbial community in normal and metabolic syndrome-susceptible mice revealed that dietary factors overshadow the effects of host genetics and are determinist of the microbial patterns that emerge in metabolically healthy or diseased hosts. Moreover, we identified a microbial community proximal to the Peyer’s Patches that was phylogenetically distinct from the cecum. Through a multi-omics approach, we show that independent of mouse genetics, vendor, age, or gender, SFB are highly abundant in the Peyer’s Patches mucosa. Our in silico antigen prediction analyses identified thirty-five potential antigens within the reference proteome of SFB. Shotgun proteomics of the murine ileal mucosa confirmed the in situ presence of several potential antigens expressed by SFB, of which included multiple flagellar proteins. To experimentally valid bioinformatically-inferred antigen targets, we developed a collection of broad-host bacterial vectors to enable microbial products of interest to be precisely expressed in vitro, ex vivo, and in vivo. Collectively, our studies reveal important findings about the mechanisms by which (i) exogenous factors modulate the gut microbiota and (ii) an endogenous microbe modulates the host immune system and provides a novel molecular platform by which microbial products of interest can be causally investigated in polymicrobial communities.


Microbiology – Research.

Intestines – Microbiology.

Microorganisms – Research.