The human gut microbiome is believed to play an integral role in host health and disease. In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, from fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were also constructed using these signature species revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional differences. Next, multiple external healthy controls from the same geographical regions (American population) were compared to Inflammatory Bowel Disease (IBD) samples from the American population using shotgun sequencing data. We identified 34 bacterial species that were significantly elevated in IBD samples, relative to all control groups. These species elevated in IBD appear to play important roles in the healthy control groups, but it is possible that their over-abundance has deleterious effects on the host, possibly due to many of these bacteria being involved in mucin degradation, immune modulation, antibiotic resistance, and inflammation. We also identified differences in functional capacities between IBD and healthy controls and linked the changes in the functional capacity to previously published clinical research and to symptoms that commonly occur in IBD, such as rectal bleeding, diarrhea, vitamin K deficiency, and inflammation.


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Graduation Date





Yooseph, Shibu


Doctor of Philosophy (Ph.D.)


College of Medicine


Burnett School of Biomedical Sciences

Degree Program

Biomedical Sciences




CFE0009108; DP0026441





Release Date

February 2022

Length of Campus-only Access


Access Status

Doctoral Dissertation (Open Access)

Restricted to the UCF community until February 2022; it will then be open access.