RT Journal Article SR Electronic T1 Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes JF bioRxiv FD Cold Spring Harbor Laboratory SP 092304 DO 10.1101/092304 A1 Matthew L. Jenior A1 Jhansi L. Leslie A1 Vincent B. Young A1 Patrick D. Schloss YR 2017 UL http://biorxiv.org/content/early/2017/04/19/092304.abstract AB Clostridium difficile is the largest single cause of hospital-acquired infection in the United States. A major risk factor for Clostridium difficile infection (CDI) is prior exposure to antibiotics, as they disrupt the gut bacterial community which protects from C. difficile colonization. Multiple antibiotic classes have been associated with CDI susceptibility; many leading to distinct community structures stemming from variation in bacterial targets of action. These microbiomes present separate metabolic challenges to C. difficile, therefore we hypothesized that the pathogen adapts its physiology to available nutrients within different gut environments. Utilizing an in vivo CDI model, we demonstrated C. difficile highly colonized ceca of mice pretreated with any of three antibiotics from distinct classes. Levels of C. difficile spore formation and toxin activity varied between animals based on the antibiotic administered. These physiologic processes in C. difficile are partially regulated by environmental nutrient concentrations. To investigate metabolic responses of the bacterium in vivo, we performed transcriptomic analysis of C. difficile from ceca of infected mice across pretreatments. This revealed heterogeneous expression in numerous catabolic pathways for diverse growth substrates. To assess which resources C. difficile exploited, we developed a genome-scale metabolic model with a transcriptomic-enabled metabolite scoring algorithm integrating network architecture. This platform identified nutrients C. difficile used preferentially between infections. These findings were validated through untargeted mass spectrometry of each microbiome. Our results supported the hypothesis that C. difficile inhabits alternative nutrient niches across cecal microbiomes with increased preference for nitrogen-containing carbon sources, particularly Stickland fermentation substrates and host-derived aminoglycans.Importance Infection by the bacterium Clostridium difficile causes an inflammatory diarrheal disease which can become life-threatening, and has grown to be the most prevalent nosocomial infection. Susceptibility to C. difficile infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study we demonstrated that C. difficile altered pathogenesis between hosts pretreated with antibiotics from separate classes, as well as exploited different nutrient sources across these environments. Our metabolite importance calculation also provides a platform to study nutrient requirements of pathogens during the context of infection. Our results suggest that C. difficile colonization 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 is the most effective treatment to date. This work could ultimately contribute to the identification of targeted measures that prevent or reduce C. difficile colonization including pre- and probiotic therapies.