Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent <i>Clostridioides difficile</i> infection.

Abstract

Faecal microbiota transplant (FMT) effectively treats recurrent <i>Clostridioides difficile</i> infection (rCDI), but its mechanisms of action remain poorly defined. Certain bile acids affect <i>C. difficile</i> germination or vegetative growth. We hypothesised that loss of gut microbiota-derived bile salt hydrolases (BSHs) predisposes to CDI by perturbing gut bile metabolism, and that BSH restitution is a key mediator of FMT's efficacy in treating the condition. Using stool collected from patients and donors pre-FMT/post-FMT for rCDI, we performed 16S rRNA gene sequencing, ultra performance liquid chromatography mass spectrometry (UPLC-MS) bile acid profiling, BSH activity measurement, and qPCR of <i>bsh</i>/<i>bai</i>CD genes involved in bile metabolism. Human data were validated in <i>C. difficile</i> batch cultures and a C57BL/6 mouse model of rCDI. From metataxonomics, pre-FMT stool demonstrated a reduced proportion of BSH-producing bacterial species compared with donors/post-FMT. Pre-FMT stool was enriched in taurocholic acid (TCA, a potent <i>C. difficile</i> germinant); TCA levels negatively correlated with key bacterial genera containing BSH-producing organisms. Post-FMT samples demonstrated recovered BSH activity and <i>bsh</i>/<i>bai</i>CD gene copy number compared with pretreatment (p<0.05). In batch cultures, supernatant from engineered <i>bsh</i>-expressing <i>E. coli</i> and naturally BSH-producing organisms (<i>Bacteroides ovatus, Collinsella aerofaciens, Bacteroides vulgatus</i> and <i>Blautia obeum</i>) reduced TCA-mediated <i>C. difficile</i> germination relative to culture supernatant of wild-type (BSH-negative) <i>E. coli. C. difficile</i> total viable counts were ~70% reduced in an rCDI mouse model after administration of <i>E. coli</i> expressing highly active BSH relative to mice administered BSH-negative <i>E. coli</i> (p<0.05). Restoration of gut BSH functionality contributes to the efficacy of FMT in treating rCDI.