Skip to main content
SpringerLink
Log in
Book cover

Encyclopedia of Metagenomics pp 1–13Cite as

Metagenomic Analysis of Bile Salt Hydrolases in the Human Gut Microbiome

  • Living reference work entry
  • First Online:

Definitions

Metagenome/metagenomics: The collective genomes of all members of a particular microbial community may be referred to as the metagenome (or a genome of many). Metagenomics refers to methods which seek to understand the composition, development, and function of microbial ecosystems through analysis of the community metagenome.

Function-driven metagenomics: A metagenomic approach in which emphasis is placed on the recovery of genes encoding a defined function of interest, through assays based on heterologous gene expression. Typically metagenomic DNA is used to generate genetic libraries in a surrogate host species that may be easily manipulated in the laboratory. Each clone in the library (analogous to books in a conventional library) represents a fragment of metagenomic DNA from a member of the microbial community under study. Libraries are then subsequently screened to identify clones encoding and expressing activities of interest.

Large-insert library/genetic library:...

This is a preview of subscription content, log in via an institution.

References

  • Begley M et al. The interaction between bacteria and bile. FEMS Microbiol Rev. 2005a;29:625–91.

    Article  CAS  PubMed  Google Scholar 

  • Begley M et al. Contribution of three bile-associated loci, bsh, pva, and btlB, to gastrointestinal persistence and bile tolerance of Listeria monocytogenes. Infect Immun. 2005b;73:894–904.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Begley M et al. Bile salt hydrolase activity in probiotics. Appl Environ Microbiol. 2006;72:1729–38.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bernstein H et al. Bile acids as carcinogens in human gastrointestinal cancers. Mutat Res. 2005;589:47–65.

    Article  CAS  PubMed  Google Scholar 

  • Dashkevicz MP, Feighner SD. Development of a differential medium for bile salt hydrolase-active Lactobacillus spp. Appl Environ Microbiol. 1989;55:11–6.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Debruyne PR et al. Mutat Res. 2001;480–81:359–69.

    Article  Google Scholar 

  • Duboc H et al. Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut. 2013;62:531–9.

    Article  CAS  PubMed  Google Scholar 

  • Gadaleta RM et al. Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease. Gut. 2011;60:463–72.

    Article  CAS  PubMed  Google Scholar 

  • Gill SR et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–85.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hill MJ. Bile flow and colon cancer. Mutat Res. 1990;238:313–20.

    Article  CAS  PubMed  Google Scholar 

  • Hofmann AF, Eckmann L. How bile acids confer gut mucosal protection against bacteria. Proc Natl Acad Sci U S A. 2006;103:4333–4.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Houten SM et al. Endocrine functions of bile acids. EMBO J. 2006;25:1419–25.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Inagaki T et al. Regulation of antibacterial defense in the small intestine by the nuclear bile acid receptor. Proc Natl Acad Sci U S A. 2006;103:3920–5.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jones BV. Bacterial bile acid modification and potential pharmaceutical applications. J Appl Ther Res. 2011;8:94–100.

    CAS  Google Scholar 

  • Jones BV, Marchesi JR. Accessing the mobile metagenome of the human gut microbiota. Mol Biosyst. 2007;3:749–58.

    Article  CAS  PubMed  Google Scholar 

  • Jones BV et al. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A. 2008;105:13580–5.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim GB et al. Cloning and characterization of the bile salt hydrolase genes (bsh) from Bifidobacterium bifidum strains. Appl Environ Microbiol. 2004;70:5603–12.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kumar RS et al. Structural and functional analysis of a conjugated bile salt hydrolase from Bifidobacterium longum reveals an evolutionary relationship with penicillin V acylase. J Biol Chem. 2006;281:32516–25.

    Article  CAS  PubMed  Google Scholar 

  • Kurokawa K et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14:169–81.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lambert JM et al. Functional analysis of four bile salt hydrolase and penicillin acylase family members in Lactobacillus plantarum WCFS1. Appl Environ Microbiol. 2008a;74:4719–26.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lambert JM et al. Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria. Microbiology. 2008b;154:2492–500.

    Article  CAS  PubMed  Google Scholar 

  • Ley RE et al. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–48.

    Article  CAS  PubMed  Google Scholar 

  • Lodola A et al. A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS ONE. 2012;7:e32397. doi:10.1371/journal.pone.0032397.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Manichanh C et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Maran RRM et al. Farnesoid X receptor deficiency in mice leads to increased intestinal epithelial cell proliferation and tumor development. J Pharmacol Exp Ther. 2009;328:469–77.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Modica S et al. Nuclear bile acid receptor FXR protects against intestinal tumorigenesis. Cancer Res. 2008;68:9589–94.

    Article  CAS  PubMed  Google Scholar 

  • O’Keefe SJD. Nutrition and colonic health: the critical role of the microbiota. Curr Opin Gastroenterol. 2008;24:51–8.

    Article  PubMed  Google Scholar 

  • Ogilvie LA, Jones BV. Dysbiosis modulates capacity for bile acid metabolism in the gut microbiomes of patients with IBD: a mechanism or marker for disease? Gut. 2012. doi:10.1136/gutjnl-2012-302137.

    PubMed Central  PubMed  Google Scholar 

  • Ogilvie LA et al. Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. Bioeng Bugs. 2012;3:1–19.

    Article  Google Scholar 

  • Qin J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ridlon JM et al. Bile salt biotransformations by human intestinal bacteria. J Lipid Res. 2006;47:241–59.

    Article  CAS  PubMed  Google Scholar 

  • Rossocha M et al. Conjugated bile acid hydrolase is a tetrameric N-terminal thiol hydrolase with specific recognition of its cholyl but not of its tauryl product. Biochemistry. 2005;44:5739–48.

    Article  CAS  PubMed  Google Scholar 

  • Suresh CG et al. Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members. Nat Struct Biol. 1999;6:414–6.

    Article  CAS  PubMed  Google Scholar 

  • Thomas C et al. Targeting bile-acid signalling for metabolic diseases. Nat Rev Drug Discov. 2008;7:678–93.

    Article  CAS  PubMed  Google Scholar 

  • Watanabe M et al. Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation. Nature. 2006;439:484–9.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centre Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Lewes Road, Brighton, East Sussex, UK, BN2 4GJ

    B. V. Jones

  2. Department of Microbiology, School of Pharmacy & Alimentary Pharmabiotic Centre, University College Cork, Room 431 Food Science Building, Cork, Ireland

    C. G. M. Gahan

Authors
  1. B. V. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. G. M. Gahan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to B. V. Jones .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Jones, B.V., Gahan, C.G.M. (2013). Metagenomic Analysis of Bile Salt Hydrolases in the Human Gut Microbiome. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_777-1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_777-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics

Search

Navigation