Description:

Understanding the Permissivity of Microbe-Modified Environments to Clostridioides difficile

The gastrointestinal tract contains a complex community of microbes that utilize and transform nutrients to shape the intestinal metabolic landscape. This metabolism determines whether foreign microbes, including the spore-forming pathogen Clostridioides difficile, colonize the gut environment. C. difficile colonization occurs following disturbances, such as antibiotic treatment, that disrupt these microbial metabolic networks. Here, we seek to understand the microbial functions that mediate C. difficile colonization resistance. Specifically, we aim to study how microbe-modified environments affect C. difficile at distinct phases of its life cycle, namely spore germination and vegetative cell growth.

To assess how microbe-modified environments affect C. difficile spore germination, we used ex vivo germination assays in fluid obtained from the small intestine of healthy, human adults. We characterized the microbes and bile salts present within this fluid using 16S rRNA-gene sequencing and LC-MS/MS, respectively. We found that fluid from all sections of the small intestine supported C. difficile germination with 50% of spores germinating in the duodenum and 99.7% germinating in the proximal jejunum. Germination significantly correlated with concentrations of bile salts, which either promote or inhibit germination depending on microbe-mediated modifications.

To investigate relationships between gut microbes and C. difficile vegetative cell growth, we established microbial communities derived from human feces in bioreactors and altered those communities by antibiotic treatment or fecal inoculum dilution. We added C. difficile vegetative cells to the bioreactors and measured colonization by plating on selective media to obtain colony-forming units (CFUs). We characterized the microbial community through 16S rRNA-gene sequencing and qPCR of a bile salt metabolism gene. Bacterial communities established in the bioreactors resisted C. difficile colonization unless perturbed by antibiotic treatment or dilution. While microbiota diversity is an indicator of colonization resistance, our data suggest that C. difficile’s ability to colonize seems to be associated with metabolic characteristics of the microbiota.

Microbes regulate gut permissivity to C. difficile at both the spore and vegetative cell stages. The upper gut is permissive to spores, supporting their germination. By modelling the lower gut, we see that permissivity depends on how well microbes can compete with C. difficile. From these findings, we will be able to model specific microbial functions that affect C. difficile physiology, which may lead to novel microbiota-based treatment methods.

Matt Schnizlein is a Ph.D. candidate in the Department of Microbiology & Immunology at the University of Michigan-Ann Arbor. He is interested in questions related to how microbes interact with each other in host-associated and host-independent environments. As a member of Vincent Young’s lab, he has pursued these questions through several projects investigating how the mammalian gut affects Clostridioides difficile physiology using mouse and bioreactor models.