Donor and Recipient Microbiome Interactions Determine Functional Outcomes of Fecal Microbiota Transplantation for Clostridioides difficile Infection

Author

• Sophie A. Millard, Clemson UniversityFollow

Date of Award

5-2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biological Sciences

Committee Chair/Advisor

Dr. Anna Seekatz

Committee Member

Dr. Min Cao

Committee Member

Dr. Vince Richards

Committee Member

Dr. Emily Rosowski

Committee Member

Dr. Kristi Whitehead

Abstract

Clostridioides difficile is a major cause of healthcare-associated diarrhea. Infection typically occurs after antibiotic treatment disrupts the gut microbiome, allowing C. difficile to colonize and produce toxins leading to disease (CDI). Standard antibiotic treatments can resolve acute infection but frequently lead to recurrence, highlighting the need for alternative strategies that restore the gut ecosystem. Fecal microbiota transplantation (FMT), the transfer of stool from a healthy donor, has emerged as an effective therapy for recurrent C. difficile infection (rCDI). Understanding the mechanisms underlying the success of FMT for treatment of rCDI could lead to safer, more defined microbial mixtures.

This dissertation investigates how microbial community structure, function, and host context, influence the ability of transplanted microbial communities to clear C. difficile. Using a combination of mouse models and sequencing-based analyses to examine the microbiome, we found that successful colonization alone does not guarantee C. difficile clearance. Instead, functional integration, how microbes express genes and interact metabolically within the host, was critical. First, we found that human-derived microbes readily colonize specific-pathogen-free (SPF) mice but failed to achieve C. difficile clearance, revealing that microbial activity is likely influenced by the environment and ecological context of the recipient gut. Second, we clarified the role of short-chain fatty acids in FMT-based treatment of rCDI in a mouse model of rCDI, identifying that butyrate supplementation was not sufficient to clear C. difficile despite a previously demonstrated role in disease attenuation. Third, we observed that prior colonization of a microbial community in a host (pre-adaptation) promoted transcriptional profiles associated with steady-state growth and maintenance, which correlated with more effective C. difficile clearance.

Collectively, these findings suggest that both donor and recipient factors, including microbial traits, host immune status, and the existing gut ecosystem, shape the outcome of microbiome-based therapies. This work provides a framework for understanding the ecological and functional principles that govern microbial transplantation and offers insights for the rational design of microbiome therapeutics aimed at safely and effectively modulating gut health.

Recommended Citation

Millard, Sophie A., "Donor and Recipient Microbiome Interactions Determine Functional Outcomes of Fecal Microbiota Transplantation for Clostridioides difficile Infection" (2026). All Dissertations. 4193.
https://open.clemson.edu/all_dissertations/4193

Author ORCID Identifier

0009-0001-5522-9262