Skip to main content
SpringerLink
Log in

Metabolic and Species Diversity Analysis for Metagenomics

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

Definition

Metagenome is the entire collection of genetic material of a microbial community.

Species diversity of a community is defined as the number of species in the community, and in metagenomics, it is often estimated using the number of operational taxonomic units (OTUs).

Functional diversity of a microbial community refers to the variety of functions and biological processes encoded by its metagenome.

Introduction

Microbial communities are the major resources for genetic and metabolic diversity. Metagenomics, the direct analysis of DNA from environmental samples, has been applied to studies of microbial communities in various environments, including soil, ocean water, and human bodies, and has shown the impact of microbial organisms on almost every aspect of life on Earth. Some microbial communities have rather simple structures; for example, a biofilm from the acid mine drainage (AMD) was shown to contain merely several species (Tyson et al. 2004). Others are more complex,...

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

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–80.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Curtis TP, Sloan WT. Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol. 2004;7(3):221–6.

    Article  PubMed  Google Scholar 

  • Gilbert JA, Field D, Swift P, et al. The taxonomic and functional diversity of microbes at a temperate coastal site: a ‘multi-omic’ study of seasonal and diel temporal variation. PLoS ONE. 2010;5(11):e15545.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Grzymski JJ, Riesenfeld CS, Williams TJ, et al. A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters. ISME J. 2012;6:1901.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hess M, Sczyrba A, Egan R, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463–7.

    Article  CAS  PubMed  Google Scholar 

  • Kalyuzhnaya MG, Lapidus A, Ivanova N, et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008;26(9):1029–34.

    Article  CAS  PubMed  Google Scholar 

  • Li LL, McCorkle SR, Monchy S, et al. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels. 2009;2:10.

    Article  PubMed Central  PubMed  Google Scholar 

  • Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55(2):205–11.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Peterson J, Garges S, Giovanni M, et al. The NIH human microbiome project. Genome Res. 2009;19(12):2317–23.

    Article  PubMed Central  PubMed  Google Scholar 

  • Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Shah N, Tang H, Doak TG, et al. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. 2011; 165–76.

    Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37–43.

    Article  CAS  PubMed  Google Scholar 

  • Warnecke F, Luginbuhl P, Ivanova N, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560–5.

    Article  CAS  PubMed  Google Scholar 

  • Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ye Y. Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. Proc IEEE Int Conf Bioinforma Biomed. 2011;2010:153–7.

    Google Scholar 

  • Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009;5(8):e1000465.

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Informatics and Computing, Indiana University, 301G Lindley Hall, Bloomington, IN, 47408, USA

    Yuzhen Ye

Authors
  1. Yuzhen Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuzhen Ye .

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

© 2012 Springer Science+Business Media New York

About this entry

Cite this entry

Ye, Y. (2012). Metabolic and Species Diversity Analysis for Metagenomics. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_88-4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_88-4

  • 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