Metagenomic analysis of bile salt biotransformation in the human gut microbiome
Journal article, 2019

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.

and bile salt biotransformation genes

gut microbiota

ibd

bioinformatics

metagenomics

metabolomics

secondary bile acids

Author

Promi Das

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Simonas Marcisauskas

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Boyang Ji

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Technical University of Denmark (DTU)

BMC Genomics

1471-2164 (ISSN)

Vol. 20 1 517

Subject Categories

Evolutionary Biology

Bioinformatics and Systems Biology

Genetics

DOI

10.1186/s12864-019-5899-3

PubMed

31234773

More information

Latest update

2/15/2021