Clostridium difficilecolonizes alternative nutrient niches during infection across distinct murine gut microbiomes
Authors: Jenior Matthew L. , Leslie Jhansi L. , Young Vincent B. , Schloss Patrick D. 
Published: December 2016

AbstractClostridium difficileis the largest single cause of hospital-acquired infection in the United States. A major risk factor forClostridium difficileinfection (CDI) is prior exposure to antibiotics, as they disrupt the gut bacterial community which protects fromC. difficilecolonization. Multiple antibiotic classes have been associated with CDI susceptibility; many leading to distinct community structures stemming from variation in bacterial targets of action. These community structures present separate metabolic challenges toC. difficile.Therefore we hypothesized that the pathogen adapts its physiology to the nutrients within different gut environments. Utilizing anin vivoCDI model, we demonstratedC. difficilehighly colonized ceca of mice pretreated with any of three antibiotics from distinct classes. Levels ofC. difficilespore formation and toxin activity varied between animals based on the antibiotic pretreatment. These physiologic processes inC. difficileare partially regulated by environmental nutrient concentrations. To investigate metabolic responses of the bacteriumin vivo, we performed transcriptomic analysis ofC. difficilefrom ceca of infected mice across pretreatments. This revealed heterogeneous expression in numerous catabolic pathways for diverse growth substrates. To assess which resourcesC. difficileexploited, we developed a genome-scale metabolic model with a transcriptome-enabled metabolite scoring algorithm integrating network architecture. This platform identified nutrientsC. difficileused preferentially between pretreatments, which were validated through untargeted mass spectrometry of each microbiome. Our results supported the hypothesis thatC. difficileinhabits alternative nutrient niches across cecal microbiomes with increased preference for nitrogen-containing carbon sources, particularly Stickland fermentation substrates and host-derived glycans.ImportanceInfection by the bacteriumClostridium difficilecauses an inflammatory diarrheal disease which can become life-threatening, and has grown to be the most prevalent nosocomial infection. Susceptibility toC. difficileinfection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study we demonstrated thatC. difficilealtered pathogenesis between hosts pretreated with antibiotics from separate classes, and exploited different nutrient sources across these environments. Our metabolite score calculation also provides a platform to study nutrient requirements of pathogens during an infection. Our results suggest thatC. difficilecolonization resistance is mediated by multiple groups of bacteria competing for several subsets of nutrients and could explain why total reintroduction of competitors through fecal microbial transplant currently is the most effective treatment for recurrent CDI. This work could ultimately contribute to the identification of targeted, context-dependent measures that prevent or reduceC. difficilecolonization including pre- and probiotic therapies.