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Sci Adv. 2019 Jul 3;5(7):eaav8391. doi: 10.1126/sciadv.aav8391. eCollection 2019 Jul.

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

Author information

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.

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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