Skip to main content

The Human Gut Mobile Metagenome: A Metazoan Perspective

  • Living reference work entry
  • First Online:
Encyclopedia of Metagenomics

Definitions

Metazoan: Multicellular eukaryotic organisms containing fully differentiated tissues, including humans and other animals.

Hologenome and Holobiont: The hologenome associated with a particular metazoan organism (such as humans or other animals) can be defined as the collective genetic material of the eukaryotic host organism plus that of all its associated mutualistic microbial symbiotes. The host species plus attendant microbes is referred to as the holobiont.

Coevolution: Reciprocal evolutionary changes in two or more interacting species (e.g., human host and resident microbes) driven by natural selection.

Microbiome: Can be generally defined as the collection of microorganisms that populate a given habitat. For host-associated microbiomes (such as the human microbiome), this may be further defined as the total community of commensal, mutualistic, and pathogenic microbes that normally constitute long-term residents at various body sites.

Metagenome: The collective genomes...

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

Access this chapter

Institutional subscriptions

References

  • Anderson MT, Seifert HS. Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen. MBio. 2011;2(1):e00005–e00011.

    Article  PubMed Central  PubMed  Google Scholar 

  • Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–20.

    Article  PubMed  Google Scholar 

  • Brucker RM, Bordenstein SR. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science. 2013;341(6146):667–9.

    Article  CAS  PubMed  Google Scholar 

  • Caporaso JG, Knight R, Kelley ST. Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PLoS ONE. 2011;6:e16900.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cummings JH, Antoine JM, Azpiroz F, Bourdet-Sicard R, Brandtzaeg P, Calder PC, et al. PASSCLAIM1 – gut health and immunity. Eur J Nutr. 2004;43 Suppl 2:118–73.

    Google Scholar 

  • Denarie J, Boistard P, Cassedelbart F, Atherly AG, Berry JO, Russell P. Indigenous plasmids of Rhizobium. Int Rev Cytol. 1981;13(Suppl):225–46.

    CAS  Google Scholar 

  • Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811–8.

    Article  CAS  PubMed  Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Relman DA, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–8.

    Article  PubMed Central  PubMed  Google Scholar 

  • Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol. 2007;9(5):1101–11.

    Article  CAS  PubMed  Google Scholar 

  • Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003;361:512–9.

    Article  PubMed  Google Scholar 

  • Hehemann J-K, Correc G, Barbeyon T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010;464:908–12.

    Article  CAS  PubMed  Google Scholar 

  • Jones BV. The human gut mobile metagenome: a metazoan perspective. Gut Microbes. 2010;1(6):417–33.

    Article  Google Scholar 

  • Jones BV. The human gut mobile metagenome. In: Nelson K, Highlander S, editors. The encyclopedia of metagenomics, volume III: human metagenomics. Springer; (in press). ISBN 978-1-4614-4674-3.

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods. 2007b;4:55–61.

    Article  CAS  PubMed  Google Scholar 

  • Jones BV, Begley M, Hill C, Gahan CGM, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci USA. 2008;105:13580–5.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jones BV, Sun F, Marchesi JR. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC Genomics. 2010;11:46.

    Article  PubMed Central  PubMed  Google Scholar 

  • Jones BV, Gahan CGM. Metagenomic analysis of bile salt hydrolases in the human gut microbiome. In: Nelson K, Highlander S, editors. The encyclopedia of metagenomics, volume III: human metagenomics. Springer; (in press) ISBN 978-1-4614-4674-3.

    Google Scholar 

  • Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. Insights into the bovine rumen plasmidome. Proc Nat Acad Sci USA. 2012;109:5452–7.

    Article  CAS  PubMed Central  Google Scholar 

  • Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, 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 

  • Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–48.

    Article  CAS  PubMed  Google Scholar 

  • Licht TN, Wilcks A. Conjugative gene transfer in the gastrointestinal environment. Adv Appl Microbiol. 2006;58:77–95.

    Article  CAS  PubMed  Google Scholar 

  • Lombardo P. Access to mutualistic endosymbiotic microbes: an underappreciated benefit of group living. Behav Ecol Sociobiol. 2008;62:479–97.

    Article  Google Scholar 

  • Louis P, McCrae SI, Charrier C, Flint HJ. Organization of butyrate synthetic genes in human colonic bacteria: phylogenetic conservation and horizontal gene transfer. FEMS Microbiol Lett. 2007;269:240–7.

    Article  CAS  PubMed  Google Scholar 

  • Luzopone CA, Hamady M, Cantral BL, Coutinho PM, Henrissat B, Gordon JI, et al. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci USA. 2008;105:15076–81.

    Article  Google Scholar 

  • Martinez E, Romero D, Palacios R. The Rhizobium genome. Crit Rev Plant Sci. 1990;9:59–93.

    Article  CAS  Google Scholar 

  • McIntyre A, Gibson PR, Young GP. Butyrate production from dietary fiber and protection against large bowel cancer in a rat model. Gut. 1993;34:386–91.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • McNiel NI. The contribution of the large intestine to energy supplies in man. Am J Clin Nutr. 1984;39:338–42.

    Google Scholar 

  • Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 2013;499(7457):219–22.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EP. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol. 2009;19(20):1683–91.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299–304.

    Article  CAS  PubMed  Google Scholar 

  • Ogilvie LA, Overall ADJ, Jones BV. The human-microbiome coevolutionary continuum. In: Ogilvie LA, Hirsch P, editors. Microbial ecological theory: current perspectives. UK: Caister Academic Press; 2012a. p. 25–42. ISBN 190-8-2300-96.

    Google Scholar 

  • Ogilvie LA, Firouzmand S, Jones BV. Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. Bioeng Bugs. 2012b;3(1):1–19.

    Article  Google Scholar 

  • Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, et al. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage ɸB124-14. PLoS ONE. 2012c;7(4):e35053.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, et al. Genome signature-based dissection of metagenomic datasets to extract subliminal viral sequences. Nature Commun 2013;4:2420.

    Article  Google Scholar 

  • Oliver KM, Degnan PH, Hunter MS, Moran NA. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science. 2009;325:992–4.

    Article  CAS  PubMed  Google Scholar 

  • Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett. 2002;217:133–9.

    Article  CAS  PubMed  Google Scholar 

  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rankin DJ, Rocha EP, Brown SP. What traits are carried on mobile genetic elements, and why? Heredity. 2011;106:1–10.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, Rosenberg E. The coral probiotic hypothesis. Environ Microbiol. 2006;8(12):2068–73.

    Article  CAS  PubMed  Google Scholar 

  • Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466:334–8.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Riley DR, Sieber KB, Robinson KM, White JR, Ganesan A, Nourbakhsh S, Dunning-Hotopp JC. Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PLoS Comput Biol. 2013;9(6):e1003107.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007;5(5):355–62.

    Article  CAS  PubMed  Google Scholar 

  • Rosenberg E, Sharon G, Zilber-Rosenberg I. The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework. Environ Microbiol. 2009;11(12):2959–62.

    Article  PubMed  Google Scholar 

  • Sharon G, Segal D, Ringo JM, Hefetz A, Zilber-Rosenberg I, Rosenberg E. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci USA. 2010;107(46):20051–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Smalla K, Osburne AM, Wellington EMH. Isolation and characterisation of plasmids from bacteria. In: Thomas CA, editor. The horizontal gene pool, bacterial plasmids and gene spread. Amsterdam: Harwood Academic Publishers; 2000. p. 207–48. ISBN 90-5702-462-4.

    Google Scholar 

  • Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011;480(7376):241–4.

    Article  CAS  PubMed  Google Scholar 

  • Top EM, Moenne-Loccoz Y, Pembroke T, Thomas CM. Phenotypic traits conferred by plasmids. In: Thomas CM, editor. The horizontal gene pool, bacterial plasmids and gene spread. Amsterdam: Harwood Academic Publishers; 2000. p. 249–85. ISBN 90-5702-462-4.

    Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–83.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wilks M. Bacteria and early human development. Early Hum Dev. 2007;83:165–70.

    Article  PubMed  Google Scholar 

  • Xu J, Mahowals MA, Ley RE, Lozupone CA, Hamady M, Martens EC, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 2007;5(7):e156.

    Article  PubMed Central  PubMed  Google Scholar 

  • Zaneveld JR, Lozupone C, Gordon JI, Knight R. Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res. 2010;38:3869–79.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008;32:723–35.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Brian V Jones .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Ogilvie, L.A., Jones, B.V. (2013). The Human Gut Mobile Metagenome: A Metazoan Perspective. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_782-1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_782-1

  • 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