Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain (hybrid MAG data)

The dramatically increased risk of symptomatic C. difficile infection (CDI) following use of antibiotics, as well as the ability of fecal microbiota transplant (FMT) prevent disease recurrence, highlights the role of the commensal microbiota in keeping this pathogen in-check. Yet, how microbiota impede C. difficile (C. diff) colonization is unclear, in part due to lack of reductionist in vivo models. Antibiotic-based models of C. diff are influenced by microbiota composition, which can be quite heterogenous both basally and in response to antibiotics making them particularly difficult for mechanistic studies. Germfree (GF) mice circumvent this complexity but their abnormal gut physiology and immunology call into question their physiological relevance. Hence, we utilized mice harboring the 8-species of bacteria referred to as the Altered Schaedler Flora (ASF), which correct many of the abnormalities of GF mice. We observed that, like GF mice, ASF mice were highly prone to rapid lethal CDI (without antibiotics) even when given relatively low doses of this pathogen, although very low doses resulted in most ASF mice surviving the challenge and developing chronic symptomatic CDI. Administering such chronic CDI mice an undefined preparation of Clostridia lowered C. diff levels by several logs and restored health. Such resolution of CDI was associated with colonization of Lachnospiraceae. Fractionation of the Clostridia prep prior to its administration led to appreciation that its ability to impede CDI strongly associated with a specific Lachnospiraceae stain, namely UBA3401. UBA3401 was recalcitrant to being propagated as a pure culture, both in vitro and in monoassociated mice, but could be maintained in ASF mice, wherein it comprised up to 50% of the gut microbiome, which was sufficient to generate high-quality genomic sequence of this bacteria. Sequence analysis and ex vivo study of UBA3401 indicated it had direct ability to secrete substances that impeded C. diff growth. In vivo, administration of UBA3401/ASF feces provided strong protection to a high-dose C. diff challenge that was otherwise uniformly lethal. Thus, UBA3401 may serve as a CDI therapeutic and a tractable platform for study of microbiota-mediated CDI resistance.