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,...
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References
Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–80.
Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.
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.
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.
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.
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.
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.
Li LL, McCorkle SR, Monchy S, et al. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels. 2009;2:10.
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.
Peterson J, Garges S, Giovanni M, et al. The NIH human microbiome project. Genome Res. 2009;19(12):2317–23.
Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
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.
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.
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.
Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7.
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.
Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009;5(8):e1000465.
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Ye, Y. (2015). Metabolic and Species Diversity Analysis for Metagenomics. In: Highlander, S.K., Rodriguez-Valera, F., White, B.A. (eds) Encyclopedia of Metagenomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7475-4_88
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DOI: https://doi.org/10.1007/978-1-4899-7475-4_88
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