Abstract

INTRODUCTION. The role in immune regulation of gut microbes involved in bile acid metabolism is beginning to be appreciated. For instance, changes in microbial bile salt hydrolase (BSH) activity in the gastrointestinal tract of gnotobiotic mice alters the mucosal transcriptomic pattern. Moreover, bile acid dysmetabolism may contribute to chronic inflammation in inflammatory bowel disease (IBD). AIM. To elucidate associations between microbial bile-acid metabolizing genes and host genes involved in bile acid metabolism and intestinal inflammation. METHODS. We carried out an integrated gut microbiome-host transcriptome analysis utilizing Crohn’s disease (CD), ulcerative colitis (UC), IBD unclassified (IBDU) patients and healthy controls (HC) who were recruited during routine care and screening colonoscopy. Microbial DNA and human RNA were extracted from terminal ileum (TI), ascending colon (AC) and sigmoid colon (SC) biopsies. The V4 region of 16S rRNA gene was sequenced and relative abundance of bile acid-metabolizing genes were inferred using PICRUSt. Additionally, bacterial bsh genes abundance was further validated by qPCR. RNA-seq was used to sequence total human RNA and a supervised transcript reduction focused upon 65 genes previously associated with bile acid metabolism and intestinal inflammation was selected. A segmental simple endoscopic score >2 and a segmental Mayo endoscopic score >0 were considered inflamed mucosa in CD and UC/IBDU, respectively. Associations between microbiome, transcriptome, type of diagnosis (CD vs UC/IBDU), inflammation and biopsy location were analyzed using linear mixed-effects model with lmer4 function in R. A q-value <0.05 was considered significant. RESULTS. A total of 264 samples from 157 subjects were analyzed corresponding to 51 CD, 61 UC/IBDU and 45 HC. Mean age for the cohort was 40.2 ± 14 years and 51% were females. In IBD patients, 13 (22%) samples from TI, 12 (37%) from AC and 52 (52%) from SC were obtained from inflamed mucosa. There was a significant inverse association between increased abundance of bacterial bsh genes evaluated through PICRUSt (COG3049) and host RORγT expression (q = 0.02). Similarly, abundance of bsh gene from Bifidobacterium bifidum assessed by qPCR was inversely correlated to RORγT gene expression (q = 0.04). These associations were independent of type of diagnosis, biopsy location and status of inflammation. CONCLUSION. In this integrative microbiome-host transcriptomic analysis we identified new evidence linking microbial bile acid deconjugation (bsh) genes using two different approaches and gene expression in the mucosal-luminal interface. Nuclear receptor RORγT is pivotal in the T-helper 17 cell functions. Modulation of this pathway by bile acids or bacteria involved in their metabolism such as Bifidobacterium bifidum could shed light on the immune role of bile acids in IBD.