Theriot and colleagues at NC State and the University of North Carolina at Chapel Hill used metagenomics and a sophisticated metabolomic platform called LC-IMS-MS to examine the stool microbiota and metabolome of 15 patients before and after FMTs. The microbiota refers to bacteria and their genetic information, while the metabolome refers to small molecules such as lipids, bile acids and amino acids.

The analysis found that the pre-transplant microbiota was composed primarily of Enterobacteriaceae, a group of bacteria with genes that make them antibiotic resistant. Post-transplant samples showed a decrease in Enterobacteriaceae and an increase in Lachnospiraceae, a group of bacteria which contain enzymes called bile salt hydrolases (BSHs) that allow them to alter bile acids.

Bile acids are key players in gut health, having a hand in everything from controlling cholesterol to dictating what kinds of bacteria can inhabit the gut. BSHs alter bile acids by separating or attaching – conjugating or reconjugating – them from attached amino acids, allowing other bacteria to further transform the bile acids as they continue through the colon. These transformations affect the bile acids’ toxicity, which in turn affects the ability of different bacteria to survive in the gut.

“Lachnospiraceae and C. diff may eat the same things and occupy the same niche in the gut microbiome, but Lachnospiraceae don’t produce the toxin that C. diff does,” Theriot says.

“We think the increase in Lachnospiraceae post-transplant has the effect of out-competing C. diff for resources and, through their ability to alter bile acids, creating an environment that is favorable for other good bacteria to live in. But now we have to prove this.”

The researchers identified multiple BSHs from Lachnospiraceae strains associated with microbial conjugated bile acids, and their next steps include looking at the different genomes of these strains to understand their role in the gut microbiome and bile acid metabolism.

“This is one of the first studies to show that microbial conjugated bile acids increase post-FMT,” Theriot says. “The evidence points toward Lachnospiraceae driving this surge, especially with secondary bile acids. So if we can isolate and define what each strain does in the gut then we may be able to use them in targeted therapies for recurrent C. diff infections and move away from FMTs.”

The work appears in mSphere and was supported by the National Institutes of Health (grants T32 DK007634, R35GM119438 and R35GM149222); the National Institute of Environmental Health Sciences (P42 ES027704), the National Institute of General Medical Sciences (R01 GM141277 and RM1 GM145416), and a cooperative agreement with the Environmental Protection Agency (STAR RD 84003201). Former NC State Ph.D. student Sam McMillan is first author. Postdoctoral fellow Guozhi Zhang, Associate Professor of Chemistry Erin Baker, and Drs. Michael Dougherty, Sarah McGill and Anjay Gulati of UNC-CH also contributed to the work. Zhang and Baker developed the LC-IMS-MS platform used in the work.