Mouse gastrointestinal tract Transcriptome or Gene expression. mouse gut metagenome

Alterations in microbiota composition during acute colitis have been repeatedly observed, but the recovery from dysbiosis and gene expression during and after colitis have received little attention. In this study, we investigated the response of the microbiota during acute inflammation and recovery in a murine dextran sodium sulfate-colitis model using metatranscriptomics, 16S rRNA gene amplicon sequencing, and monitoring of selected host markers of inflammation. Parallel to an increase of markers of inflammation during acute colitis, we observed abundance shifts of the dominant bacterial orders Clostridiales and Bacteroidales, alterations in phylotype composition therein and the increase of low abundant families. During recovery, the microbial community began to resemble bacterial populations before inflammation, but did not reach its original composition even at day 25. In contrast, disturbances of microbial gene expression ceased after acute colitis. The decrease of Clostridiales correlated with a reduction of transcripts related to pyruvate metabolism and butyrate formation suggesting a disturbance in host-microbe signalling and nutrient provision for the mucosal tissue. The impact of acute inflammation on the Clostridiales was also characterized by a significant reduction of their major transcripts encoding flagellin subunits. Comparison of abundance levels of flagellin genes and transcripts hinted that the decrease of flagellins was not only due the decrease of Clostridiales but also due to a downregulation of flagellin expression. Concurrently, abundance of the Bacteroidales increased accompagnied by the enhanced presence of transcripts related to mucin degradation. We propose that a selective reaction of the immune system against commensal members of the microbiota temporarily altered murine microbiota composition and its function and thereby impacted host-microbiota interactions. However, the host-microbiota homeostasis revealed a significant ability for a fast recovery.