Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

Abstract

The gut microbiota plays a critical role in pathogen defense. Studies using antibiotic-treated mice reveal mechanisms that increase susceptibility to Clostridioides difficile infection (CDI), but risk factors associated with CDI in humans extend beyond antibiotic use. Here, we studied the dysbiotic gut microbiota of a subset of patients with diarrhea and modeled the gut microbiota of these patients by fecal transplantation into germ-free mice. When challenged with C. difficile, the germ-free mice transplanted with fecal samples from patients with dysbiotic microbial communities showed increased gut amino acid concentrations and greater susceptibility to CDI. A C. difficile mutant that was unable to use proline as an energy source was unable to robustly infect germ-free mice transplanted with a dysbiotic or healthy human gut microbiota. Prophylactic dietary intervention using a low-proline or low-protein diet in germ-free mice colonized by a dysbiotic human gut microbiota resulted in decreased expansion of wild-type C. difficile after challenge, suggesting that amino acid availability might be important for CDI. Furthermore, a prophylactic fecal microbiota transplant in mice with dysbiosis reduced proline availability and protected the mice from CDI. Last, we identified clinical risk factors that could potentially predict gut microbial dysbiosis and thus greater susceptibility to CDI in a retrospective cohort of patients with diarrhea. Identifying at-risk individuals and reducing their susceptibility to CDI through gut microbiota–targeted therapies could be a new approach to preventing C. difficile infection in susceptible patients.

A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides ( Clostridium ) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects

“…A high-fat diet was also observed to intensify CDI in a hamster model of infection (31); however, to our knowledge, a high-fat/high-protein diet has never been explored in animal models of CDI, as typical diets used for mouse and hamster models of CDI have Յ10% kcal from fat and Յ30% kcal from protein. The poor CDI outcome observed here for mice fed the high-fat/highprotein diet compared with the high-fat/low-protein diet is consistent with known relationships between dietary protein and CDI in both laboratory mice with native murine microbiota (13) and humanized mice fed a defined amino acid diet deficient in the Stickland electron acceptor proline (11). The major diets used in these other studies used relatively low (Յ20%) concentrations of protein provided as casein.…”

Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice

“…A growing body of evidence points to dietary intervention as a promising new approach to prevent CDI colonization (4, 15) . One recent study showed that a diet poor in proline (an essential amino acid for C. difficile growth) prevented C. difficile carriage (4) . Another study demonstrated that mice fed a diet deficient in MACs (e.g.…”

“…While dietary fiber content can result in microbial metabolites that are protective against CDI, other diet-influenced metabolites seem to promote the pathogenesis of CDI. For instance, consistent with C. difficile being auxotrophic for the amino acid proline, experiments conducted in gnotobiotic mice have supported that mice were protected from C. difficile colonization with low-proline diets (4) .…”

“…A complex gut microbiome has been shown to be protective against CDI (4) . Broad spectrum antibiotic usage, such as clindamycin, beta-lactams, and fluoroquinolones (5, 6) increase risk of CDI as do other illnesses associated with reduced gut microbiome diversity, such as Inflammatory Bowel Diseases (7) .…”

Role of Bile in Infectious Disease: the Gall of 7α-Dehydroxylating Gut Bacteria

“…In the reductive branch, glycine and/or proline are reduced by the selenium-containing glycine and proline reductases to acetate or 5-aminovalerate, respectively, to regenerate the NAD+ pool (Bouillaut et al, 2015). Proline is a highly relevant amino acid for C. difficile growth and a recent study by Battaglioli et al (Battaglioli et al, 2018) found that the proline reductase is required for a robust infection in gnotobiotic mice colonized with a dysbiotic patient microbiota that is susceptible to CDI. These findings combined indicate that proline metabolism by C. difficile impacts multiple facets of the C. difficile lifestyle – from colonization and growth to the production of toxic molecules to potentiate a C. difficile growth advantage (Bouillaut et al, 2015; Kang et al, 2018).…”