Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

© 2015 Macmillan Publishers Limited. Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
We thank Ron Ronimus, Paul Newton, and Christina Moon for reading and commenting on the manuscript. We thank all who provided assistance that allowed Global Rumen Census collaborators to supply samples and metadata (Supplemental Text 1). AgResearch was funded by the New Zealand Government as part of its support for the Global Research Alliance on Agricultural Greenhouse Gases. The following funding sources allowed Global Rumen Census collaborators to supply samples and metadata, listed with the primary contact(s) for each funding source: Agencia Nacional de Investigación e Innovación, Martín Fraga; Alberta Livestock and Meat Agency, Canada, Tim A. McAllister; Area de Ciencia y Técnica, Universidad Juan A Maza (Resolución Proy. N° 508/2012), Diego Javier Grilli; Canada British Columbia Ranching Task Force Funding Initiative, John Church; CNPq, Hilário Cuquetto Mantovani, Luiz Gustavo Ribeiro Pereira; FAPEMIG, Hilário Cuquetto Mantovani; FAPEMIG, PECUS RumenGases, Luiz Gustavo Ribeiro Pereira; Cooperative Research Program for Agriculture Science & Technology Development (project number PJ010906), Rural Development Administration, Republic of Korea, Sang-Suk Lee; Dutch Dairy Board & Product Board Animal Feed, André Bannink, Kasper Dieho, Jan Dijkstra; Ferdowsi University of Mashhad, Vahideh Heidarian Miri; Finnish Ministry of Agriculture and Forestry, Ilma Tapio; Instituto Nacional de Tecnología Agropecuaria, Argentina (Project PNBIO1431044), Silvio Cravero, María Cerón Cucchi; Irish Department of Agriculture, Fisheries and Food, Alexandre B. De Menezes; Meat & Livestock Australia; and Department of Agriculture, Fisheries & Forestry (Australian Government), Chris McSweeney; Ministerio de Agricultura y desarrollo sostenible (Colombia), Olga Lucía Mayorga; Montana Agricultural Experiment Station project (MONB00113), Carl Yeoman; Multistate project W-3177 Enhancing the competitiveness of US beef (MONB00195), Carl Yeoman; NSW Stud Merino Breeders’ Association, Alexandre Vieira Chaves; Queensland Enteric Methane Hub, Diane Ouwerkerk; RuminOmics, Jan Kopecny, Ilma Tapio; Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government and the Technology Strategy Board, UK, R. John Wallace; Science Foundation Ireland (09/RFP/GEN2447), Sinead Waters; Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación, Mario A. Cobos-Peralta; Slovenian Research Agency (project number J1-6732 and P4-0097), Blaz Stres; Strategic Priority Research Program, Climate Change: Carbon Budget and Relevant Issues (Grant No.XDA05020700), ZhiLiang Tan; The European Research Commission Starting Grant Fellowship (336355—MicroDE), Phil B. Pope; The Independent Danish Research Council (project number 4002-00036), Torsten Nygaard Kristensen; and The Independent Danish Research Council (Technology and Production, project number 11-105913), Jan Lassen. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.