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      A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

      research-article
      1 , * , 2 , 3 , 4 , 3 , 5 , 6 , 4 , 7 , 7 , 1 , 3 , 3 , 3 , 5 , 5 , 8 , 5 , 6 , 4 , 4 , 9 , 9 , 9 , 9 , 10 , 10 , 10 , 2 , 11 , 7 , 4 , 2 , *
      Science Advances
      American Association for the Advancement of Science

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          Abstract

          Cow genes dictate environmentally friendly microbiomes: a step towards reducing greenhouse gas emissions.

          Abstract

          A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.

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          Most cited references38

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            obitools: a unix-inspired software package for DNA metabarcoding.

            DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
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              Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii.

              Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species of Bifidobacterium are stimulated in vivo and whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive species Faecalibacterium prausnitzii exhibited a significant increase (10.3% for control period v. 14.5% during inulin intake, P=0.019). The composition of the genus Bifidobacterium was studied in four of the volunteers by clone library analysis. Between three and five Bifidobacterium spp. were found in each volunteer. Bifidobacterium adolescentis and Bifidobacterium longum were present in all volunteers, and Bifidobacterium pseudocatenulatum, Bifidobacterium animalis, Bifidobacterium bifidum and Bifidobacterium dentium were also detected. Real-time PCR was employed to quantify the four most prevalent Bifidobacterium spp., B. adolescentis, B. longum, B. pseudocatenulatum and B. bifidum, in ten volunteers carrying detectable levels of bifidobacteria. B. adolescentis showed the strongest response to inulin consumption, increasing from 0.89 to 3.9% of the total microbiota (P=0.001). B. bifidum was increased from 0.22 to 0.63% (P<0.001) for the five volunteers for whom this species was present.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                July 2019
                03 July 2019
                : 5
                : 7
                : eaav8391
                Affiliations
                [1 ]The Rowett Institute, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, UK.
                [2 ]Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel.
                [3 ]University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
                [4 ]Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland.
                [5 ]Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy.
                [6 ]Swedish University of Agricultural Sciences, Department of Agriculture for Northern Sweden, S-90 183 Umeå, Sweden.
                [7 ]Parco Tecnologico Padano, Via Einstein, 26900 Lodi, Italy.
                [8 ]Institute of Microbiology, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy.
                [9 ]Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic.
                [10 ]Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France.
                [11 ]Departments of Computer Science, Computational Medicine, Human Genetics, and Anesthesiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
                Author notes
                [* ]Corresponding author. Email: john.wallace@ 123456abdn.ac.uk (R.J.W.); imizrahi@ 123456bgu.ac.il (I.M.)
                [†]

                Joint first authors.

                [‡]

                Present address: Enterome Bioscience 94/96 Avenue Ledru-Rollin, 75011 Paris, France.

                [§]

                Present address: National Research Council, Institute of Biology and Biotechnology in Agriculture (CNR-IBBA), Via Bassini 15, 20133 Milan, Italy.

                [||]

                Present address: Department for Sustainable Food Process –DiSTAS, Università Cattolica del Sacro Cuore, Via E.Parmense 84, 29122 Piacenza, Italy.

                [¶]

                Present address: Agri-Food and Biosciences Institute, AFBI Large Park, Hillsborough BT26 6DR Co. Down, UK.

                [#]

                Present address: Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.

                [**]

                Joint last authors.

                [††]

                Deceased.

                Author information
                http://orcid.org/0000-0003-2691-1585
                http://orcid.org/0000-0001-5131-3398
                http://orcid.org/0000-0002-0752-9551
                http://orcid.org/0000-0002-5334-1015
                http://orcid.org/0000-0001-7855-7448
                http://orcid.org/0000-0002-4894-0662
                http://orcid.org/0000-0002-3901-2354
                http://orcid.org/0000-0002-8952-8826
                http://orcid.org/0000-0003-2692-6656
                http://orcid.org/0000-0003-4570-5138
                http://orcid.org/0000-0002-0617-6571
                http://orcid.org/0000-0003-1644-1911
                http://orcid.org/0000-0002-7811-5305
                http://orcid.org/0000-0003-1277-7821
                http://orcid.org/0000-0002-7480-842X
                http://orcid.org/0000-0001-9439-8168
                http://orcid.org/0000-0003-1907-3333
                http://orcid.org/0000-0002-8481-3038
                http://orcid.org/0000-0002-2428-2511
                http://orcid.org/0000-0001-7800-8609
                http://orcid.org/0000-0003-0021-9590
                http://orcid.org/0000-0002-3554-5954
                http://orcid.org/0000-0002-3675-3835
                http://orcid.org/0000-0001-5188-7957
                http://orcid.org/0000-0001-6636-8818
                Article
                aav8391
                10.1126/sciadv.aav8391
                6609165
                31281883
                48d4e4bf-e757-4d18-927e-1fedfa91e142
                Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 24 October 2018
                : 30 May 2019
                Funding
                Funded by: doi http://dx.doi.org/10.13039/100004431, European Commission Directorate-General for Research and Innovation;
                Award ID: 289319
                Funded by: doi http://dx.doi.org/10.13039/501100007601, Horizon 2020;
                Award ID: 640384
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Organismal Biology
                Organismal Biology
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                Sam Ardiente

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