PMID- 25517115
OWN - NLM
STAT- MEDLINE
DCOM- 20160112
LR  - 20181113
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 9
IP  - 12
DP  - 2014
TI  - Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and 
      type 2 diabetes metagenomes.
PG  - e115175
LID - 10.1371/journal.pone.0115175 [doi]
LID - e115175
AB  - 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.
FAU - Labbe, Alain
AU  - Labbe A
AD  - Micropharma Limited, Montreal, Quebec, Canada.
FAU - Ganopolsky, Jorge G
AU  - Ganopolsky JG
AD  - Micropharma Limited, Montreal, Quebec, Canada.
FAU - Martoni, Christopher J
AU  - Martoni CJ
AD  - Micropharma Limited, Montreal, Quebec, Canada.
FAU - Prakash, Satya
AU  - Prakash S
AD  - Biomedical Technology and Cell Therapy Research Laboratory, Department of 
      Biomedical Engineering, Faculty of Medicine, Montreal, Quebec, Canada; 
      Micropharma Limited, Montreal, Quebec, Canada.
FAU - Jones, Mitchell L
AU  - Jones ML
AD  - Biomedical Technology and Cell Therapy Research Laboratory, Department of 
      Biomedical Engineering, Faculty of Medicine, Montreal, Quebec, Canada; 
      Micropharma Limited, Montreal, Quebec, Canada.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20141217
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Bile Acids and Salts)
RN  - EC 1.1.- (Hydroxysteroid Dehydrogenases)
RN  - EC 1.1.1.159 (7 alpha-hydroxysteroid dehydrogenase)
RN  - EC 3.5.- (Amidohydrolases)
RN  - EC 3.5.1.24 (choloylglycine hydrolase)
SB  - IM
MH  - Amidohydrolases/genetics
MH  - Animals
MH  - Bacteria/enzymology
MH  - Bile Acids and Salts/*metabolism
MH  - Colitis, Ulcerative/*enzymology/genetics/microbiology
MH  - Crohn Disease/*enzymology/genetics/microbiology
MH  - Databases, Factual
MH  - Diabetes Mellitus, Type 2/*enzymology/genetics/microbiology
MH  - Feces/enzymology/microbiology
MH  - Gastrointestinal Tract/*enzymology/microbiology
MH  - Genes, Bacterial/*genetics
MH  - Humans
MH  - Hydroxysteroid Dehydrogenases/genetics
MH  - *Metagenome
MH  - Metagenomics
MH  - Mice
MH  - Microbiota
MH  - Phylogeny
PMC - PMC4269443
COIS- Competing Interests: Micropharma Limited funded this research. MLJ and SP are 
      co-founders and shareholders of Micropharma. MLJ, CJM, JGG and AL are employed by 
      and CJM is a shareholder of Micropharma. AL, JGG and MLJ designed the research. 
      AL collected and analyzed the data. AL, JGG, CJM and MLJ prepared the manuscript 
      for publication. Micropharma Limited holds no editorial restriction over the work 
      published and the authors' association with it does not alter their adherence to 
      PLOS ONE policies on sharing data and materials.
EDAT- 2014/12/18 06:00
MHDA- 2016/01/13 06:00
PMCR- 2014/12/17
CRDT- 2014/12/18 06:00
PHST- 2014/05/29 00:00 [received]
PHST- 2014/11/19 00:00 [accepted]
PHST- 2014/12/18 06:00 [entrez]
PHST- 2014/12/18 06:00 [pubmed]
PHST- 2016/01/13 06:00 [medline]
PHST- 2014/12/17 00:00 [pmc-release]
AID - PONE-D-14-24012 [pii]
AID - 10.1371/journal.pone.0115175 [doi]
PST - epublish
SO  - PLoS One. 2014 Dec 17;9(12):e115175. doi: 10.1371/journal.pone.0115175. 
      eCollection 2014.