Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
Gemma Henderson(AgResearch), Faith Cox(AgResearch), Siva Ganesh(AgResearch), Arjan Jonker(AgResearch), Wayne Young(AgResearch), Global Rumen Census Collaborators(Consejo Superior de Investigaciones Científicas), Leticia Abecia(Consejo Superior de Investigaciones Científicas), Erika Angarita(University of Concepción), Paula Aravena(Universidad Nacional de Cuyo), Graciela Nora Arenas(Universidad Nacional de Cuyo), Claudia Ariza(AgResearch), Graeme T. Attwood(University of Cundinamarca), Jose Mauricio Avila(University of Concepción), Jorge Ávila–Stagno(University of Concepción), A. Bannink(Universidad Nacional de Colombia), Rolando Barahona Rosales(Universidad Nacional de Colombia), Mariano Batistotti(Copenhagen Zoo), Mads F. Bertelsen(Copenhagen Zoo), Aya Brown-Kav(Agricultural Research Organization), A. Carvajal(University of Vermont), Laura Cersosimo(University of Vermont), Alex V. Chaves(The University of Sydney), John S. Church(University College Dublin), Nicholas Clipson(University College Dublin), Mario A. Cobos-Peralta(AgResearch), Adrian L. Cookson(AgResearch), Silvio Cravero(Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias), Omar Cristobal-Carballo(University of Aberdeen), Katie Crosley(University of Aberdeen), G. D. Cruz(National Institute of Industrial Technology), María Esperanza Cerón‐Cucchi(National Institute of Industrial Technology), Rodrigo de la Barra(University College Dublin), Alexandre B. de Menezes(University College Dublin), Edênio Detmann(Universidade Federal de Viçosa), K. Dieho(Wageningen University & Research), J. Dijkstra(Universidade Federal de Viçosa), William Lima Santiago dos Reis(Agriculture and Agri-Food Canada), M. E. R. Dugan(Agriculture and Agri-Food Canada), Seyed Hadi Ebrahimi(Agricultural University of Iceland), Emma Eythórsdóttir(Agricultural University of Iceland), Fabian Nde Fon(University of Zululand), Martín Fraga(National University of San Marcos), Francisco Franco(National University of San Marcos), Chris Friedeman(Hokkaido University), Naoki Fukuma(Hokkaido University), Dragana Gagić(ETH Zurich), Isabelle D.M. Gangnat(Universidad Nacional de Cuyo), Diego Grilli(University of Alberta), Le Luo Guan(University of Alberta), Vahideh Heidarian Miri(University of Alberta), Emma Hernandez‐Sanabria(University of Alberta), Alma Ximena Ibarra Gomez(Federal University of Agriculture), O. A. Isah(University of Vermont), Suzanne L. Ishaq(University of Vermont), Elie Jami(Agricultural Research Organization), Juan Jelincic(Natural Resources Institute Finland), Juha Kantanen(University of Eastern Finland), William J. Kelly(Sunchon National University), Seon‐Ho Kim(The University of Queensland), Athol V. Klieve(The University of Queensland), Yasuo Kobayashi(Hokkaido University), Satoshi Koike(Hokkaido University), J Kopečný(Czech Academy of Sciences, Institute of Animal Physiology and Genetics), Torsten Nygaard Kristensen(Swedish University of Agricultural Sciences), S.J. Krizsan(University of Vermont), Hannah Lachance(University of Vermont), Medora Lachman(Montana State University), W. R. Lamberson(AgResearch), Suzanne C. Lambie(Aarhus University), Jan Lassen(Aarhus University), Sinead C. Leahy(Sunchon National University), Sang-Suk Lee(Sunchon National University), Florian Leiber(University College Dublin), E. Lewis(University College Dublin), Bo Lin(Instituto de Investigaciones Agropecuarias), Raúl Lira(Aarhus University), Peter Lund(Aarhus University), Edgar Macipe(Sunchon National University), Lovelia L. Mamuad(Universidade Federal de Viçosa), Hilário Cuquetto Mantovani(Universidade Federal de Viçosa), Gisela Marcoppido(National Institute of Industrial Technology), Cristian Márquez(Instituto de Investigaciones Agropecuarias), Cécile Martin(Université Claude Bernard Lyon 1), G. Martı́nez(Consejo Superior de Investigaciones Científicas), María Eugenia Martínez(Instituto de Investigaciones Agropecuarias), Olga Lucía Mayorga(Agriculture and Agri-Food Canada), Tim A. McAllister(Commonwealth Scientific and Industrial Research Organisation), Christopher S. McSweeney(Commonwealth Scientific and Industrial Research Organisation), Lorena Mestre(Colombian Corporation for Agricultural Research - AGROSAVIA), Elena Minnée(Institute of Livestock and Grassland Science), Makoto Mitsumori(Agricultural Research Organization), Itzhak Mizrahi(Universidad Nacional de Colombia), Isabel Molina(Universidad Nacional de Colombia), A. Muenger(Instituto de Investigaciones Agropecuarias), Camila Muñoz(University of Ljubljana), Boštjan Murovec(University of Ljubljana), J.R. Newbold(Cargill (Netherlands)), Victor Nsereko(University College Dublin), M. O’Donovan(Forestry Research Institute of Nigeria), Sunday Adewale Okunade(University College Dublin), H B O'Neill(Colombian Corporation for Agricultural Research - AGROSAVIA), Sonia Ospina(Colombian Corporation for Agricultural Research - AGROSAVIA), D. Ouwerkerk(University of Cundinamarca), Diana C. Parra(Brazilian Agricultural Research Corporation), Luiz Gustavo Ribeiro Pereira(Brazilian Agricultural Research Corporation), C.S. Pinares-Patiño(AgResearch), Phillip B. Pope(Aarhus University), Morten Poulsen(University of Hohenheim), M. Rodehutscord(University of Hohenheim), Tatiana Rodríguez(Colombian Corporation for Agricultural Research - AGROSAVIA), Kunihiko Saito(Instituto de Investigaciones Agropecuarias), Francisco Sales(Aarhus University), Catherine Sauer(Aarhus University), K.J. Shingfield(Natural Resources Institute Finland), Noriaki Shoji(Czech Academy of Sciences, Institute of Animal Physiology and Genetics), Jiřı́ Šimůnek(University of Nis), Zorica Stojanović‐Radić(University of Nis), Blaž Stres(University of Ljubljana), Xuezhao Sun(Montana State University), Jeffery Swartz(Chinese Academy of Sciences), Zhi Liang Tan(Chinese Academy of Sciences), Ilma Tapio(Natural Resources Institute Finland), Tasia M. Taxis(Commonwealth Scientific and Industrial Research Organisation), Nigel Tomkins(Commonwealth Scientific and Industrial Research Organisation), Emilio M. Ungerfeld(Instituto de Investigaciones Agropecuarias), Řeža Valizadeh(Cargill (Netherlands)), Peter van Adrichem(Thompson Rivers University), Jonathan D. Van Hamme(University of Vermont), Woulter Van Hoven(University of Vermont), G. C. Waghorn(University of Aberdeen), R. J. Wallace(University of Aberdeen), Min Wang(Teagasc - The Irish Agriculture and Food Development Authority), Sinéad M. Waters(Teagasc - The Irish Agriculture and Food Development Authority), Kate Keogh(University of Hohenheim), Maren Witzig(University of Hohenheim), André‐Denis G. Wright(University of Vermont), Hidehisa Yamano(Hokkaido University), T. Yan(Consejo Superior de Investigaciones Científicas), David R. Yáñez-Ruíz(Consejo Superior de Investigaciones Científicas), Carl J. Yeoman(Montana State University), Ricardo Xavier Cárdenas Zambrano(ETH Zurich), Johanna O. Zeitz(University of Alberta), Mi Zhou(University of Alberta), Hua Zhou(Chinese Academy of Sciences), Cai Xia Zou(Guangxi Buffalo Research Institute), Pablo Zunino(AgResearch), Peter H. Janssen(AgResearch)
Cited by 1,711Open Access
Abstract
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.
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