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      Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

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          Abstract

          Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity.

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          Most cited references 57

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          QIIME allows analysis of high-throughput community sequencing data.

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            Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

            A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
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              Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

              DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
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                Author and article information

                Journal
                Ecol Lett
                Ecol. Lett
                ele
                Ecology Letters
                BlackWell Publishing Ltd (Oxford, UK )
                1461-023X
                1461-0248
                August 2014
                22 May 2014
                : 17
                : 8
                : 979-987
                Affiliations
                [1 ]Howard Hughes Medical Institute and Section of Integrative Biology, University of Texas at Austin Austin, TX, 78712, USA
                [2 ]Section of Integrative Biology, University of Texas at Austin Austin, TX, 78712, USA
                [3 ]Program Man-Society-Environment, University of Basel Vesalgasse 1, Basel, CH-4051, Switzerland
                [4 ]Department of Ecology and Genetics, Uppsala University Norbyvägen 18D, Uppsala, SE-752 36, Sweden
                [5 ]Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, 80309-0216, USA
                [6 ]Howard Hughes Medical Institute and Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, CO, 80309-0215, USA
                [7 ]Department of Biological Sciences, Northern Arizona University Flagstaff, AZ, 86011, USA
                [8 ]Institute for Genomics and Systems Biology, Argonne National Laboratory Argonne, IL, 60439, USA
                Author notes
                *Correspondence: E-mail: danbolnick@ 123456austin.utexas.edu

                Editor, David Post

                Article
                10.1111/ele.12301
                4084827
                24847735
                © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

                This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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