ABSTRACTAntibiotics alter the gut microbiota and decrease resistance toClostridium difficilecolonization; however, the mechanisms driving colonization resistance are not well understood. Loss of resistance toC. difficilecolonization due to antibiotic treatment is associated with alterations in the gut metabolome, specifically, with increases in levels of nutrients thatC. difficilecan utilize for growthin vitro. To define the nutrients thatC. difficilerequires for colonization and pathogenesisin vivo, we used a combination of mass spectrometry and RNA sequencing (RNA Seq) to model the gut metabolome andC. difficiletranscriptome throughout an acute infection in a mouse model at the following time points: 0, 12, 24, and 30 h. We also performed multivariate-based integration of the omics data to define the signatures that were most important throughout colonization and infection. Here we show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time in the mouse cecum and thatC. difficilegene expression is consistent with their utilizationin vivo. This was also reinforced by the multivariate-based integration of the omics data where we were able to discriminate the metabolites and transcripts that supportC. difficilephysiology between the different time points throughout colonization and infection. This report illustrates how important the availability of amino acids and other nutrients is for the initial stages ofC. difficilecolonization and progression of disease. Future studies identifying the source of the nutrients and engineering bacteria capable of outcompetingC. difficilein the gut will be important for developing new targeted bacterial therapeutics.IMPORTANCEClostridium difficileis a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoringC. difficilegrowth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages ofC. difficilecolonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and thatC. difficilegene expression is consistent with their utilization by the bacteriumin vivo. We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential forC. difficilecolonization and disease.
Posttranscriptional regulation of albumin gene expression by branched-chain amino acids in rats with acute liver injury
