Metagenomic analysis of bile salt biotransformation in the human gut microbiome

• Published in: BMC genomics Vol. 20; no. 1; pp. 517 - 12
• Main Authors: Das, Promi, Marcišauskas, Simonas, Ji, Boyang, Nielsen, Jens
• Format: Journal Article
• Language: English
• Published: London BioMed Central 25.06.2019; BioMed Central Ltd; BMC
• Subjects: and bile salt biotransformation genes; Animal Genetics and Genomics; Bacteria - classification; Bacteria - genetics; Bacteria - metabolism; Bacterial Proteins - genetics; Bile acids; Bile Acids and Salts - metabolism; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Biotransformation; Biotransformation - genetics; Computational biology; Deoxycholic acid; Dysbiosis - metabolism; Dysbiosis - microbiology; Firmicutes - genetics; Firmicutes - metabolism; Gastrointestinal diseases; Gastrointestinal Microbiome - genetics; Genes; Gut microbiota; Humans; IBD; Inflammatory Bowel Diseases - metabolism; Inflammatory Bowel Diseases - microbiology; Life Sciences; Medical research; Metabolomics; Metagenomics; Microarrays; Microbial Genetics and Genomics; Microbiota (Symbiotic organisms); Plant Genetics and Genomics; Prokaryote microbial genomics; Proteomics; Research Article; Secondary bile acids; Gut microbiota; Metagenomics; Metabolomics; And bile salt biotransformation genes; IBD; Secondary bile acids; Bioinformatics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-5899-3

Background In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to secondary bile acids have been known to be involved in the immune regulation of human physiology. Several 16S amplicon-based studies with inflammatory bowel disease (IBD) subjects were found to have an association with the level of fecal bile acids. However, a detailed investigation of all the bile salt biotransformation genes in the gut microbiome of healthy and IBD subjects has not been performed. Results Here, we report a comprehensive analysis of the bile salt biotransformation genes and their distribution at the phyla level. Based on the analysis of shotgun metagenomes, we found that the IBD subjects harbored a significantly lower abundance of these genes compared to the healthy controls. Majority of these genes originated from Firmicutes in comparison to other phyla. From metabolomics data, we found that the IBD subjects were measured with a significantly low level of secondary bile acids and high levels of primary bile acids compared to that of the healthy controls. Conclusions Our bioinformatics-driven approach of identifying bile salt biotransformation genes predicts the bile salt biotransformation potential in the gut microbiota of IBD subjects. The functional level of dysbiosis likely contributes to the variation in the bile acid pool. This study sets the stage to envisage potential solutions to modulate the gut microbiome with the objective to restore the bile acid pool in the gut.