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

SA Huws, C Creevey, LB Oyama, I Mizrahi, SE Denman, M Popova, R Munoz-tamayo, E Forano, SM Waters, M Hess, I Tapio, H Smidt, S Krizsan, DR Yanez-Ruiz, A Belanche, LL Guan, RJ Gruninger, T McAllister, J Newbold, R RoeheRJ Dewhurst, TJ Snelling, M Watson, G Suen, E Hart, A Kingston-Smith, N Scollan, RM Do Prado, E Pilau, HC Mantovani, GT Attwood, JE Edwards, N McEwan, S Morrison, O Mayorga, C Elliott, DP Morgavi

Research output: Contribution to journalReview article

13 Citations (Scopus)
2 Downloads (Pure)

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 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.
Original languageEnglish
Pages (from-to)21-61
Number of pages33
JournalFrontiers in Microbiology
Volume9
Early online date25 Sep 2018
DOIs
Publication statusFirst published - 25 Sep 2018

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ruminants
rumen
livestock
microorganisms
animal breeding
Archaea
microbiome
food security
bacteriophages
methane
Protozoa
vitamins
biomarkers
environmental impact
mathematical models
proteins
meat
minerals
phenotype
milk

Bibliographical note

1030565
1030571

Keywords

  • Diet
  • Host
  • Metabolomics
  • Metagenomics
  • Metaproteomics
  • Metataxonomics
  • Metatranscriptomics
  • Methane
  • Microbiome
  • Omics
  • Production
  • Rumen

Cite this

Huws, SA ; Creevey, C ; Oyama, LB ; Mizrahi, I ; Denman, SE ; Popova, M ; Munoz-tamayo, R ; Forano, E ; Waters, SM ; Hess, M ; Tapio, I ; Smidt, H ; Krizsan, S ; Yanez-Ruiz, DR ; Belanche, A ; Guan, LL ; Gruninger, RJ ; McAllister, T ; Newbold, J ; Roehe, R ; Dewhurst, RJ ; Snelling, TJ ; Watson, M ; Suen, G ; Hart, E ; Kingston-Smith, A ; Scollan, N ; Do Prado, RM ; Pilau, E ; Mantovani, HC ; Attwood, GT ; Edwards, JE ; McEwan, N ; Morrison, S ; Mayorga, O ; Elliott, C ; Morgavi, DP. / Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future. In: Frontiers in Microbiology. 2018 ; Vol. 9. pp. 21-61.
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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 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.",
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Huws, SA, Creevey, C, Oyama, LB, Mizrahi, I, Denman, SE, Popova, M, Munoz-tamayo, R, Forano, E, Waters, SM, Hess, M, Tapio, I, Smidt, H, Krizsan, S, Yanez-Ruiz, DR, Belanche, A, Guan, LL, Gruninger, RJ, McAllister, T, Newbold, J, Roehe, R, Dewhurst, RJ, Snelling, TJ, Watson, M, Suen, G, Hart, E, Kingston-Smith, A, Scollan, N, Do Prado, RM, Pilau, E, Mantovani, HC, Attwood, GT, Edwards, JE, McEwan, N, Morrison, S, Mayorga, O, Elliott, C & Morgavi, DP 2018, 'Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future', Frontiers in Microbiology, vol. 9, pp. 21-61. https://doi.org/10.3389/fmicb.2018.02161

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future. / Huws, SA; Creevey, C; Oyama, LB; Mizrahi, I; Denman, SE; Popova, M; Munoz-tamayo, R; Forano, E; Waters, SM; Hess, M; Tapio, I; Smidt, H; Krizsan, S; Yanez-Ruiz, DR; Belanche, A; Guan, LL; Gruninger, RJ; McAllister, T; Newbold, J; Roehe, R; Dewhurst, RJ; Snelling, TJ; Watson, M; Suen, G; Hart, E; Kingston-Smith, A; Scollan, N; Do Prado, RM; Pilau, E; Mantovani, HC; Attwood, GT; Edwards, JE; McEwan, N; Morrison, S; Mayorga, O; Elliott, C; Morgavi, DP.

In: Frontiers in Microbiology, Vol. 9, 25.09.2018, p. 21-61.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future

AU - Huws, SA

AU - Creevey, C

AU - Oyama, LB

AU - Mizrahi, I

AU - Denman, SE

AU - Popova, M

AU - Munoz-tamayo, R

AU - Forano, E

AU - Waters, SM

AU - Hess, M

AU - Tapio, I

AU - Smidt, H

AU - Krizsan, S

AU - Yanez-Ruiz, DR

AU - Belanche, A

AU - Guan, LL

AU - Gruninger, RJ

AU - McAllister, T

AU - Newbold, J

AU - Roehe, R

AU - Dewhurst, RJ

AU - Snelling, TJ

AU - Watson, M

AU - Suen, G

AU - Hart, E

AU - Kingston-Smith, A

AU - Scollan, N

AU - Do Prado, RM

AU - Pilau, E

AU - Mantovani, HC

AU - Attwood, GT

AU - Edwards, JE

AU - McEwan, N

AU - Morrison, S

AU - Mayorga, O

AU - Elliott, C

AU - Morgavi, DP

N1 - 1030565 1030571

PY - 2018/9/25

Y1 - 2018/9/25

N2 - 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.

AB - 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.

KW - Diet

KW - Host

KW - Metabolomics

KW - Metagenomics

KW - Metaproteomics

KW - Metataxonomics

KW - Metatranscriptomics

KW - Methane

KW - Microbiome

KW - Omics

KW - Production

KW - Rumen

U2 - 10.3389/fmicb.2018.02161

DO - 10.3389/fmicb.2018.02161

M3 - Review article

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VL - 9

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EP - 61

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

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