Metagenomic analysis of bile salt biotransformation in the human gut microbiome

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 wit...

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Published inBMC genomics Vol. 20; no. 1; pp. 517 - 12
Main Authors Das, Promi, Marcišauskas, Simonas, Ji, Boyang, Nielsen, Jens
Format Journal Article
LanguageEnglish
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
Online AccessGet full text
ISSN1471-2164
1471-2164
DOI10.1186/s12864-019-5899-3

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Abstract 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.
AbstractList 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.BACKGROUNDIn 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.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.RESULTSHere, 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.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.CONCLUSIONSOur 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.
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. 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. 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.
Abstract 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.
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. Keywords: Secondary bile acids, Gut microbiota, IBD, Bioinformatics, Metagenomics, Metabolomics, And bile salt biotransformation genes
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. 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. 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.
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.
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.
ArticleNumber 517
Audience Academic
Author Nielsen, Jens
Ji, Boyang
Marcišauskas, Simonas
Das, Promi
Author_xml – sequence: 1
  givenname: Promi
  surname: Das
  fullname: Das, Promi
  organization: Department of Biology and Biological Engineering, Chalmers University of Technology
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  surname: Marcišauskas
  fullname: Marcišauskas, Simonas
  organization: Department of Biology and Biological Engineering, Chalmers University of Technology
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  givenname: Boyang
  surname: Ji
  fullname: Ji, Boyang
  organization: Department of Biology and Biological Engineering, Chalmers University of Technology
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  givenname: Jens
  orcidid: 0000-0002-9955-6003
  surname: Nielsen
  fullname: Nielsen, Jens
  email: nielsenj@chalmers.se
  organization: Department of Biology and Biological Engineering, Chalmers University of Technology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31234773$$D View this record in MEDLINE/PubMed
https://research.chalmers.se/publication/511693$$DView record from Swedish Publication Index
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Issue 1
Keywords Gut microbiota
Metagenomics
Metabolomics
And bile salt biotransformation genes
IBD
Secondary bile acids
Bioinformatics
Language English
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PublicationTitle BMC genomics
PublicationTitleAbbrev BMC Genomics
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SSID ssj0017825
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Snippet Background In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of...
In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to...
Background In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of...
Background: In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of...
Abstract Background In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation...
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SubjectTerms 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
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Title Metagenomic analysis of bile salt biotransformation in the human gut microbiome
URI https://link.springer.com/article/10.1186/s12864-019-5899-3
https://www.ncbi.nlm.nih.gov/pubmed/31234773
https://www.proquest.com/docview/2246906836
https://pubmed.ncbi.nlm.nih.gov/PMC6591925
https://research.chalmers.se/publication/511693
https://doaj.org/article/33b245080bea4aaea91ccc1218a809cb
Volume 20
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