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

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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?’

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          Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

          Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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            Rebuilding community ecology from functional traits.

            There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.
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              Microbial biogeography: putting microorganisms on the map.

              We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.
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                Author and article information

                Journal
                FEMS Microbiol Rev
                FEMS Microbiol. Rev
                fmr
                Fems Microbiology Reviews
                BlackWell Publishing Ltd (Oxford, UK )
                0168-6445
                1574-6976
                January 2014
                28 August 2013
                : 38
                : 1
                : 90-118
                Affiliations
                [1 ]Department of Biology, Dalhousie University Halifax, NS, Canada
                [2 ]Faculty of Computer Science, Dalhousie University Halifax, NS, Canada
                [3 ]Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, NS, Canada
                [4 ]Faculty of Graduate Studies, Dalhousie University Halifax, NS, Canada
                Author notes
                Correspondence: Robert G. Beiko, Faculty of Computer Science, Dalhousie University, 6050 University Avenue, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2., Tel.: +1 902 494 8043; fax: +1 902 492 1517; e-mail: beiko@ 123456cs.dal.ca
                Article
                10.1111/1574-6976.12035
                4298764
                23909933
                5def2172-4acb-444a-93da-799ada5b8b54
                © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 April 2013
                : 02 July 2013
                : 04 August 2013
                Categories
                Review Articles

                Microbiology & Virology
                microbial communities,metagenomics,genome evolution,trait-based ecology,black queen hypothesis,public goods hypothesis

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