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    Interactions in the microbiome: communities of organisms and communities of genes

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    BoonMeehan_Communities_FEMS_2013.pdf (572.4Kb)
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    Publication date
    2014-01-01
    Author
    Boon, E.
    Meehan, Conor J.
    Whidden, C.
    Wong, D. H.-J.
    Langille, M.G.I.
    Beiko, R.G.
    Keyword
    Microbial communities
    Metagenomics
    Genome evolution
    Trait-based ecology
    Black Queen hypothesis
    Public Goods hypothesis
    Rights
    (c) 2014 John Wiley & Sons. This is an Open Access article distributed under the Creative Commons CC-BY-NC-ND licence (http://creativecommons.org/licenses/by-nc-nd/3.0/)
    Peer-Reviewed
    Yes
    
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    Abstract
    A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term ‘community’ is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to the mechanistically driven question of ‘How will they respond?’
    URI
    http://hdl.handle.net/10454/17259
    Version
    Published version
    Citation
    Boon E, Meehan CJ, Whidden C et al (2014) Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiology Reviews. 38(1): 90-118.
    Link to publisher’s version
    https://doi.org/10.1111/1574-6976.12035
    Type
    Article
    Collections
    Life Sciences Publications

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