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Front. Microbiol. | doi: 10.3389/fmicb.2018.02161

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future

  • 1Queen's University Belfast, United Kingdom
  • 2Ben-Gurion University of the Negev, Israel
  • 3Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
  • 4INRA Centre Auvergne Rhône Alpes, France
  • 5INRA UMR Mia-Paris, France
  • 6Teagasc Food Research Centre (Dublin), Ireland
  • 7University of California, Davis, United States
  • 8Natural Resources Institute Finland (Luke), Finland
  • 9Wageningen University & Research, Netherlands
  • 10Swedish University of Agricultural Sciences, Sweden
  • 11Estación Experimental del Zaidín (EEZ), Spain
  • 12University of Alberta, Canada
  • 13Lethbridge Research Center, Agriculture and Agri-Food Canada, Canada
  • 14Scotland's Rural College, United Kingdom
  • 15Rowett Institute, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
  • 16Roslin Institute, University of Edinburgh, United Kingdom
  • 17University of Wisconsin-Madison, United States
  • 18Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, United Kingdom
  • 19Universidade Estadual de Maringá, Brazil
  • 20Universidade Federal de Viçosa, Brazil
  • 21AgResearch (New Zealand), New Zealand
  • 22Robert Gordon University, United Kingdom
  • 23Agri Food and Biosciences Institute, United Kingdom
  • 24Corporación Colombiana de Investigación Agropecuaria (CORPOICA), Colombia

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that is inedible for humans, whilst providing metabolic energy to the host and producing methane. Consequently, ruminants produce meat and milk, which are rich in high quality protein, vitamins and minerals and therefore contribute to food security. As world population is predicted to reach approximately 9.7 billion by 2050, ruminant production has to increase to satisfy global protein demand, despite limited land availability, whilst ensuring environmental impact is minimised. These goals can be met by deepening our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in ‘omic’ data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent ‘omics’ approaches continue to revolutionise our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Keywords: Rumen, microbiome, host, Diet, production, Methane, omics, metataxonomics, Metagenomics, metatranscriptomics, Metaproteomics, Metabolomics

Received: 31 May 2018; Accepted: 23 Aug 2018.

Edited by:

Zhongtang Yu, The Ohio State University, United States

Reviewed by:

Shengguo Zhao, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China
Suzanne L. Ishaq, University of Oregon, United States  

Copyright: © 2018 Huws, Creevey, Oyama, Mizrahi, Denman, Popova, Munoz-tamayo, Forano, Waters, Hess, Tapio, Smidt, Krizsan, Yanez-Ruiz, Belanche, Guan, Gruninger, McAllister, Newbold, Roehe, Dewhurst, Snelling, Watson, Suen, Hart, Kingston-Smith, Scollan, Do Prado, Pilau, Mantovani, Attwood, Edwards, McEwan, Morrison, Mayorga, Elliott and Morgavi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Sharon A. Huws, HUWS., Queen's University Belfast, Belfast, Belfast, BT9 7PL, United Kingdom, S.Huws@qub.ac.uk