Date of Award

4-4-2025

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Microbiology & Microbial Pathogenesis)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

The human gut microbiome is a consortium of trillions of bacteria, archaea, fungi, and viruses that colonizes the gastrointestinal tract and promotes health under homeostatic conditions. This microbial community trains the immune system, modulates inflammation and anticancer immunity, promotes cardiometabolic health, enables nutrient extraction, and prevents pathogen overgrowth. The latter function manifests through colonization resistance, in which microbes occupy spatial and nutritional niches thereby excluding pathogens from the community entirely, and through limiting pathogen population growth if colonization occurs. These roles are facilitated by complex host-microbe and microbe-microbe interactions that underlie differences in susceptibility to microbiome-mediated infectious diseases. The strain-level diversity of commensal and potentially pathogenic organisms, which determines their functional potential, is an important aspect of these microbe-microbe relationships and their impact on pathogen colonization outcomes. This thesis work delves into the gut commensal-pathogen-host dynamics that affect bacterial infections across different patient populations with the goal of advancing therapies and prevention efforts for microbiome-mediated infections. In Chapter 2, I present results from a study investigating whether the gut microbiome is a reservoir of serious extraintestinal bacterial infections (EBIs) in infants, who are at heightened risk. The most common EBI pathogens in infancy are aerobic and facultatively anaerobic bacteria that commonly inhabit the early life microbiome, but a direct link between these sites has not been established using strain-level genomics. We selected participants with and without EBI from a multi-center cohort of febrile term infants presenting to the emergency department. Based on genome assemblies from cultured isolates and gut metagenomic sequencing, we established that a strain isogenic to the extraintestinal pathogen was present in the intestine of 25/40 cases at the time of infection. The pathogen species was often more abundant and prevalent in the gut of infants with EBI, and for 18/25 cases colonized by the EBI-causing strain, its DNA was at sufficient abundance to be detected via metagenomic reads alone. For infants with E. coli EBI, E. coli strains from phylogroup B2 were significantly more abundant in the gut of cases whose EBI-causing E. coli strain was detected in the gut rather than E. coli-colonized controls, as were several virulence factor genes associated with adhesion, nutrient acquisition, and exotoxin production. These results point to the intestine as a potential source of EBI in young infants, and they raise the potential for microbiome screening as a diagnostic and clinical risk assessment tool for this population. Chapter 3 focuses on understanding why many people colonized by the enteric pathogen Clostridioides difficile do not get sick, while in others it causes severe infection (CDI). C. difficile remains a global public health burden despite advances in infection prevention practices and antimicrobial stewardship programs. We analyzed stool samples and pathogen genomes from two cohorts of hospitalized patients colonized by C. difficile. Using a random forest classifier, we found that microbiome-related features were more discriminatory between patients with CDI and asymptomatic carriers than pathogen strain and demographic features. By engrafting stool communities from carriers into germ-free mice, we observed that both the colonizing C. difficile strain and commensal taxa, including those from Lachnospiraceae, influenced disease severity in vivo. We next designed two defined communities of bacteria that recapitulated microbiome structures of C. difficile-colonized patients and performed C. difficile challenge experiments in mice engrafted with either community. Clinically prevalent C. difficile strains showed a range of virulence in vivo that was suppressed in the background of the more diverse community, possibly through enhanced nutrient availability. These results provide support for commensal-pathogen interactions being a key driver of C. difficile carriage that may be leveraged to develop antibiotic-sparing strategies to prevent CDI in colonized patients.

Language

English (en)

Chair and Committee

Gautam Dantas

Committee Members

Barbara Warner; Drew Schwartz; Matthew Ciorba; Megan Baldridge; Tamara Doering

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Microbiology Commons

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