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

Huws, Sharon A.; Creevey, Christopher J.; Oyama, Linda B.; Mizrahi, Itzhak; Denman, Stuart E.; Popova, Milka; Mu�oz-Tamayo, Rafael; Forano, Evelyne; Waters, Sinead M.; Hess, Matthias; Tapio, Ilma; Smidt, Hauke; Krizsan, Sophie J.; Y��ez-Ruiz, David R.; Belanche, Alejandro; Guan, Leluo; Gruninger, Robert J.; McAllister, Tim A.; Newbold, C. Jamie; Roehe, Rainer; Dewhurst, Richard J.; Snelling, Tim J.; Watson, Mick; Suen, Garret; Hart, Elizabeth H.; Kingston-Smith, Alison H.; Scollan, Nigel D.; do Prado, Rodolpho M.; Pilau, Eduardo J.; Mantovani, Hilario C.; Attwood, Graeme T.; Edwards, Joan E.; McEwan, Neil R.; Morrisson, Steven; Mayorga, Olga L.; Elliott, Christopher; Morgavi, Diego P.

doi:10.3389/fmicb.2018.02161

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

Huws, Sharon A.; Creevey, Christopher J.; Oyama, Linda B.; Mizrahi, Itzhak; Denman, Stuart E.; Popova, Milka; Mu�oz-Tamayo, Rafael; Forano, Evelyne; Waters, Sinead M.; Hess, Matthias; Tapio, Ilma; Smidt, Hauke; Krizsan, Sophie J.; Y��ez-Ruiz, David R.; Belanche, Alejandro; Guan, Leluo; Gruninger, Robert J.; McAllister, Tim A.; Newbold, C. Jamie; Roehe, Rainer; Dewhurst, Richard J.; Snelling, Tim J.; Watson, Mick; Suen, Garret; Hart, Elizabeth H.; Kingston-Smith, Alison H.; Scollan, Nigel D.; do Prado, Rodolpho M.; Pilau, Eduardo J.; Mantovani, Hilario C.; Attwood, Graeme T.; Edwards, Joan E.; McEwan, Neil R.; Morrisson, Steven; Mayorga, Olga L.; Elliott, Christopher; Morgavi, Diego P.

Authors

Sharon A. Huws

Christopher J. Creevey

Linda B. Oyama

Itzhak Mizrahi

Stuart E. Denman

Milka Popova

Rafael Mu�oz-Tamayo

Evelyne Forano

Sinead M. Waters

Matthias Hess

Ilma Tapio

Hauke Smidt

Sophie J. Krizsan

David R. Y��ez-Ruiz

Alejandro Belanche

Leluo Guan

Robert J. Gruninger

Tim A. McAllister

C. Jamie Newbold

Rainer Roehe

Richard J. Dewhurst

Tim J. Snelling

Mick Watson

Garret Suen

Elizabeth H. Hart

Alison H. Kingston-Smith

Nigel D. Scollan

Rodolpho M. do Prado

Eduardo J. Pilau

Hilario C. Mantovani

Graeme T. Attwood

Joan E. Edwards

Neil R. McEwan

Steven Morrisson

Olga L. Mayorga

Christopher Elliott

Diego P. Morgavi

Abstract

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 cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, 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 the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on 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 revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Citation

HUWS, S.A., CREEVEY, C.J., OYAMA, L.B., MIZRAHI, I., DENMAN, S.E., POPOVA, M., MUÑOZ-TAMAYO, R., FORANO, E., WATERS, S.M., HESS, M., TAPIO, I., SMIDT, H., KRIZSAN, S.J., YÁÑEZ-RUIZ, D.R., BELANCHE, A., GUAN, L., GRUNINGER. R.J., MCALLISTER, T.A., NEWBOLD, C.J., ROEHE. R., DEWHURST, R.J., SNELLING, T.J., WATSON, M., SUEN, G., HART, E.H., KINGSTON-SMITH, A.H., SCOLLAN, N.D., DO PRADO, R.M., PILAU, E.J., MANTOVANI, H.C., ATTWOOD, G.T., EDWARDS, J.E., MCEWAN, N.R., MORRISSON, S., MAYORGA, O.L., ELLIOTT, C. and MORGAVI, D.P. 2018. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future. Frontiers in microbiology [online], 9, Article 2161. Available from: https://doi.org/10.3389/fmicb.2018.02161

Journal Article Type	Article
Acceptance Date	Aug 23, 2018
Online Publication Date	Sep 25, 2018
Publication Date	Sep 25, 2018
Deposit Date	Sep 25, 2018
Publicly Available Date	Sep 25, 2018
Journal	Frontiers in microbiology
Print ISSN	1664-302X
Electronic ISSN	1664-302X
Publisher	Frontiers Media
Peer Reviewed	Peer Reviewed
Volume	9
Article Number	2161
DOI	https://doi.org/10.3389/fmicb.2018.02161
Keywords	Rumen; Microbiome; Host; Diet Production; Methane; Omics; Metataxonomics; Metagenomics; Metatranscriptomics; Metaproteomics; Metabolomics
Public URL	http://hdl.handle.net/10059/3147
Contract Date	Sep 25, 2018