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

Gemma Henderson, Faith Cox, Siva Ganesh, Arjan Jonker, Wayne Young, Peter H. Janssen, Leticia Abecia, Erika Angarita, Paula Aravena, Graciela Nora Arenas, Claudia Ariza, Graeme T. Attwood, Jose Mauricio Avila, Jorge Avila-Stagno, André Bannink, Rolando Barahona, Mariano Batistotti, Mads F. Bertelsen, Aya Brown-Kav, Andres M. CarvajalLaura Cersosimo, Alexandre Vieira Chaves, John Church, Nicholas Clipson, Mario A. Cobos-Peralta, Adrian L. Cookson, Silvio Cravero, Omar Cristobal Carballo, Katie Crosley, Gustavo Cruz, María Cerón Cucchi, Rodrigo De La Barra, Alexandre B. De Menezes, Edenio Detmann, Kasper Dieho, Jan Dijkstra, William L.S. Dos Reis, Mike E.R. Dugan, Seyed Hadi Ebrahimi, Emma Eythórsdóttir, Fabian Nde Fon, Martín Fraga, Francisco Franco, Chris Friedeman, Naoki Fukuma, Dragana Gagić, Isabelle Gangnat, Diego Javier Grilli, Le Luo Guan, Vahideh Heidarian Miri, Emma Hernandez-Sanabria, Alma Ximena Ibarra Gomez, Olubukola A. Isah, Suzanne Ishaq, Elie Jami, Juan Jelincic, Juha Kantanen, William J. Kelly, Seon Ho Kim, Athol Klieve, Yasuo Kobayashi, Satoshi Koike, Jan Kopecny, Torsten Nygaard Kristensen, Sophie Julie Krizsan, Hannah LaChance, Medora Lachman, William R. Lamberson, Suzanne Lambie, Jan Lassen, Sinead C. Leahy, Sang Suk Lee, Florian Leiber, Eva Lewis, Bo Lin, Raúl Lira, Peter Lund, Edgar Macipe, Lovelia L. Mamuad, Hilário Cuquetto Mantovani, Gisela Ariana Marcoppido, Cristian Márquez, Cécile Martin, Gonzalo Martinez, Maria Eugenia Martinez, Olga Lucía Mayorga, Tim A. McAllister, Chris McSweeney, Lorena Mestre, Elena Minnee, Makoto Mitsumori, Itzhak Mizrahi, Isabel Molina, Andreas Muenger, Camila Munoz, Bostjan Murovec, John Newbold, Victor Nsereko, Michael O'Donovan, Sunday Okunade, Brendan O'Neill, Sonia Ospina, Diane Ouwerkerk, Diana Parra, Luiz Gustavo Ribeiro Pereira, Cesar Pinares-Patino, Phil B. Pope, Morten Poulsen, Markus Rodehutscord, Tatiana Rodriguez, Kunihiko Saito, Francisco Sales, Catherine Sauer, Kevin Shingfield, Noriaki Shoji, Jiri Simunek, Zorica Stojanović-Radić, Blaz Stres, Xuezhao Sun, Jeffery Swartz, Zhi Liang Tan, Ilma Tapio, Tasia M. Taxis, Nigel Tomkins, Emilio Ungerfeld, Reza Valizadeh, Peter Van Adrichem, Jonathan Van Hamme, Woulter Van Hoven, Garry Waghorn, R. John Wallace, Min Wang, Sinéad M. Waters, Kate Keogh, Maren Witzig, Andre Denis G. Wright, Hidehisa Yamano, Tianhai Yan, David R. Yanez-Ruiz, Carl J. Yeoman, Ricardo Zambrano, Johanna Zeitz, Mi Zhou, Hua Wei Zhou, Cai Xia Zou, Pablo Zunino

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429 Scopus citations

Abstract

© 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.
Original languageAmerican English
JournalScientific Reports
DOIs
StatePublished - 9 Oct 2015

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