Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes.

Alain Labbé,Satya Prakash,Christopher J Martoni,Mitchell L Jones,Jorge G Ganopolsky,Simon Patrick Hogan

doi:10.1371/journal.pone.0115175

Abstract

We performed an analysis to determine the importance of bile acid modification genes in the gut microbiome of inflammatory bowel disease and type 2 diabetic patients. We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh), 7 alpha-dehydroxylase gene (adh) and 7-alpha hydroxysteroid dehydrogenase gene (hsdh) in fecal bacteria in diseased populations of Crohn's disease (CD), Ulcerative Colitis (UC) and Type 2 diabetes mellitus (T2DM). Phylum level abundance analysis showed a significant reduction in Firmicute-derived bsh in UC and T2DM patients but not in CD patients, relative to healthy controls. Reduction of adh and hsdh genes was also seen in UC and T2DM patients, while an increase was observed in the CD population as compared to healthy controls. A further analysis of the bsh genes showed significant differences in the correlations of certain Firmicutes families with disease or healthy populations. From this observation we proceeded to analyse BSH protein sequences and identified BSH proteins clusters representing the most abundant strains in our analysis of Firmicute bsh genes. The abundance of the bsh genes corresponding to one of these protein clusters was significantly reduced in all disease states relative to healthy controls. This cluster includes bsh genes derived from Lachospiraceae, Clostridiaceae, Erysipelotrichaceae and Ruminococcaceae families. This metagenomic analysis provides evidence of the importance of bile acid modifying enzymes in health and disease. It further highlights the importance of identifying gene and protein clusters, as the same gene may be associated with health or disease, depending on the strains expressing the enzyme, and differences in the enzymes themselves.

Highlights

The gut microbiome is important for multiple metabolic functions, including the absorption and production of nutrients and the development of the immune system
We used a sequential BLAST methodology to extract homologous sequences from short reads and quantified the number of hits to the bile salt hydrolase genes from a library including all annotated bile salt hydrolases from NCBI Protein database
As we are first selecting hits corresponding to a specific protein (BSH, hydroxysteroid dehydrogenase (HSDH) or action of bacterial dehydroxylase (ADH)), our analysis is similar to that used by platforms such as CloVR-Metagenomics[22], providing functional assignment by aligning to a protein database and taxonomy information by matching the open reading frames to a bacterial genome database

Summary

Introduction

The gut microbiome is important for multiple metabolic functions, including the absorption and production of nutrients and the development of the immune system. Metagenomics is the study of the total microbial genomic DNA isolated from an environmental sample, and when applied to human fecal samples provides a catalogue of all microbial genes present in the gut. Examining changes to this profile of genes is likely to yield meaningful contrast between health and disease and provide mechanistic information on the role of certain microbial genes in host metabolism [1,2,3,4]. The action of bacterial dehydroxylase (ADH) and dehydrogenase (HSDH) activities on deconjugates in the GI leads to the production of BAs with altered capacity to enter cells, transmit signals and reenter the enterohepatic circulation [5, 6]

Methods

Results

Conclusion