Abstract
Every living organism exists together in a delicate balance. People, animals, and microbial species all live connected to each other through complex interactions, both direct and indirect. One Health is a multi-disciplinary framework for understanding these interactions, gathering insights from public health, veterinary medicine, environmental science, and more. With this lens, the microbiome, all the bacteria, fungi, viruses, and other microbes in a given location, becomes an important mediator in understanding human, animal, and environmental health. Microbes can play a beneficial or detrimental role to their host. Given their health impact, a deeper understanding of microbial composition and variability in different conditions is needed. In one study, we examined the microbiome of an indoor built environment, a hospital. The human health impact of these microbial dynamics has potential to be significant due to the vulnerability of patients in this setting. We took thirty-seven surface samples in the neonatal intensive care unit (NICU) both before and after the hospital first opened, and healthcare workers collected 160 surface samples from five additional areas of the hospital after opening. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. We found complex dynamics of the microbiome, which we believe to have risen from the occupants and their interactions. The initiation of inpatient care had little effect on the NICU microbiome, and separate areas of the hospital had distinct microbiomes. Machine learning models, including least absolute shrinkage and selection operator (LASSO), support vector machine (SVM), and random forest models, identified bacteria which were associated with each area. These findings shed light on potential drivers of microbial variability in hospitals and can inform infection control practices. In another study, we examined the microbiomes of free-living three-toed box turtles (Terrapene mexicana triunguis) in outdoor environments. Host-associated microbiomes are key influencers in host health, but studies of wildlife microbiomes and how they vary with environmental conditions are limited. We sampled fifteen turtles in a rural site and an urban site monthly for six months and collected 1157 oral, foot, and cloacal samples. Two hundred and sixty-seven oral, foot, and cloacal samples were processed for 16S rRNA sequencing, and 89 cloacal samples were processed for long and short shotgun metagenomic sequencing. The alpha and beta diversities between each of the body parts were significantly different suggesting a distinction between body parts. Within each body part, the alpha diversity of the microbiome was significantly different between individuals, months, and sites. Principal coordinate analysis (PCoA) of the beta diversity indicated that the months clustered into seasons. In cloacal samples, metagenomic sequencing revealed that the profile of antibiotic resistant genes (ARGs) varied slightly with season. Additionally, genomes from potentially novel bacteria, including eleven from unclassified genera, were assembled. Using a combination of LASSO classification models, MaAsLin models, and gene set enrichment analysis (GSEA), we identified specific bacteria and their functions which varied with season, site, and home range. Lastly, we identified a higher rate of strain sharing among urban turtles, potentially indicating a higher rate of transmission. The knowledge gained from this study can be applied to conservation efforts for this species of box turtle as well as other chelonian species which may have similar microbial dynamics. There are countless conditions which can cause variations in the microbiome, which in turn potentially impact human and animal health. By examining a hospital microbiome and box turtle microbiome, I added to the collective understanding of these conditions and variabilities. With this knowledge, the microbiome can be better incorporated into future efforts to safeguard the health of humans, animals, and the environment.
Committee Chair
Fangqiong Ling
Committee Members
Jay Turner; Jenna Ditto; Likai Chen; Sharon Deem
Degree
Doctor of Philosophy (PhD)
Author's Department
Energy, Environmental & Chemical Engineering
Document Type
Dissertation
Date of Award
8-17-2026
Language
English (en)
DOI
https://doi.org/10.7936/8jat-8038
Recommended Citation
Chibwe, Kaseba, "Characterizing Microbial Communities in the Context of One Health" (2026). McKelvey School of Engineering Graduate Student Theses & Dissertations. 1425.
The definitive version is available at https://doi.org/10.7936/8jat-8038