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Beyond the Venn diagram: the hunt for a core microbiome.
Environ Microbiol. 2012 Jan; 14(1):4-12
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28 Oct 2011
Review / Commentary
DOI: 10.3410/f.13357270.14726644
This is an excellent short review about different ways to define and detect core microbiomes. I think focus on persistence and connectivity is going to be very important in metagenome studies. When focusing on persistence, one takes into account the fact that microbial assemblages vary over time, while...Continue reading
This is an excellent short review about different ways to define and detect core microbiomes. I think focus on persistence and connectivity is going to be very important in metagenome studies. When focusing on persistence, one takes into account the fact that microbial assemblages vary over time, while with connectivity one will try to include information about interactions between the operational taxonomic units (OTUs) in the microbiomes.
The review also includes a discussion about caveats associated with the different types of microbiome definitions, as well as a nice table with the terms often used when discussing microbiomes, their definitions and references.
The review also includes a discussion about caveats associated with the different types of microbiome definitions, as well as a nice table with the terms often used when discussing microbiomes, their definitions and references.
Disclosures
None declared
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Nesbo C: F1000Prime Recommendation of [Shade A and Handelsman J, Environ Microbiol 2012, 14(1):4-12]. In F1000Prime, 28 Oct 2011; DOI: 10.3410/f.13357270.14726644. F1000Prime.com/13357270#eval14726644
F1000Prime Recommendations, Dissents and Comments for [Shade A and Handelsman J, Environ Microbiol 2012, 14(1):4-12]. In F1000Prime, 25 May 2013; F1000Prime.com/13357270
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Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems.
© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
DOI: 10.1111/j.1462-2920.2011.02585.x
PMID: 22004523
