Faculty Mentor: Daniel Leung (Internal Medicine, University of Utah)

Background

The gut microbiota plays a key role in maintaining host health, supporting immune function, and resisting pathogen colonization. Disruption of the microbiota (dysbiosis) can lead to overgrowth of pathobionts–commensal microbes with disease-causing potential under certain conditions. Clostridium difficile infections (CDI) are a prime example of a disease linked to dysbiosis and excessive pathobiont carriage. Fecal Microbiota Transplantation (FMT) has shown clinical success in restoring microbial balance and treating current CDI. Understanding how FMT alters microbial diversity and reduces pathobiont abundance is critical for optimizing therapeutic outcomes.

Purpose of Research

Microbiota diversity refers to the variety and abundance of microorganisms in specific environments, including the human gut. Although microbiota diversity plays an important role in health, its significance is still not well understood and explored. Our study aims to investigate the shifts in microbiota diversity following Fecal Microbiota Transplant (FMT). We utilized a metagenomic approach to analyze differences in microbiota diversity between human subjects undergoing FMT procedures and healthy controls.

Methods

We collected stool samples from C. difficile-infected individuals pre-FMT (day 0), and post-FMT (days, 14, and 56), and healthy controls (at days 0 and 14). We prepared DNA sequencing libraries using the NEBNext Ultra II FS DNA Library Prep for Small Genomes Kit, and performed Whole Genome Sequencing at 150×150 bp, 20M reads, and sampling on an Ilumina NovaSeq. We processed the reads with Prinseq, Trim Galore, and BWA to remove reads that map to the human genome. We analyzed microbiome diversity and taxonomic profiling with Kraken2 and Shannon- index using custom code in Python.

Results

We demonstrate a markedly lower microbial diversity and higher pathobiont carriage in FMT recipients prior to transplantation, compared to healthy control individuals. However, by Day 14 post- transplantation, microbial diversity had risen, and pathobiont carriage reduced, relative to Day 0. These shifts suggest that the gut microbiota began to recover, restoring ecological balance and reducing pathobiont carriage.

Conclusion

Diversity significantly increased in FMT recipients by Day 14 post-transplant, approaching levels seen in healthy controls. The microbiome shift may support gut immune homeostasis by reducing pro-inflammatory pathobionts and increasing commensal diversity. Maintaining microbial diversity is important in preventing the overgrowth of harmful species. Overall, this study complements prior studies showing clinical efficacy of Fecal Microbiota Transplant (FMT). We show that FMT restores persons with lower microbiota diversity to levels of healthy controls by 14 days and highlights its therapeutic potential in microbiota-associated diseases.

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