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Addressing Global Ruminant Agricultural Challenges Through Understanding The Rumen Microbiome: Past, Present, And Future

S. Huws, C. Creevey, L. Oyama, I. Mizrahi, S. Denman, M. Popova, Rafael Muñoz-Tamayo, E. Forano, S. Waters, M. Hess, I. Tapio, H. Smidt, S. Krizsan, D. Yáñez-Ruiz, A. Belanche, Le-luo Guan, R. Gruninger, T. McAllister, C. J. Newbold, R. Roehe, R. Dewhurst, Tim J. Snelling, M. Watson, Garret Suen, E. H. Hart, A. Kingston-Smith, Nigel D. Scollan, R. M. do Prado, E. Pilau, H. C. Mantovani, G. Attwood, J. Edwards, N. R. McEwan, Steven Morrisson, O. Mayorga, C. Elliott, D. Morgavi
Published 2018 · Medicine, Biology
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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.
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10.1017/s1751731119003252
Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host.
Charles Jamie Newbold (2020)
10.1038/s41467-020-15652-8
Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics
Ori Furman (2020)
10.7488/DS/2470
The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
Mick Watson (2018)
10.7287/PEERJ.PREPRINTS.27831V1
A mechanistic overview of ruminal fibre digestion.
Adrian E. Naas (2019)
Effect of olive oil and hydrogenated vegetable oil supplementation on rumen bacterial composition in dairy cows
Nathaly. Cancino Padilla (2019)
10.1101/2020.06.08.140780
Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria
Leeann Klassen (2020)
10.1101/489443
The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
Robert D. Stewart (2018)
10.1017/s1751731119003100
Review: Fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation.
K A Beauchemin (2020)
10.3389/fmicb.2020.00244
Changes in the Solid-, Liquid-, and Epithelium-Associated Bacterial Communities in the Rumen of Hu Lambs in Response to Dietary Urea Supplementation
Zhi-peng Li (2020)
10.1007/978-3-030-21309-1_2
Gut/Rumen Microbiome—A Livestock and Industrial Perspective
Birbal Singh (2019)
10.1111/jbg.12427
Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows
Y. Ramayo-Caldas (2019)
10.1101/421024
Open prediction of polysaccharide utilisation loci (PUL) in 5414 public Bacteroidetes genomes using PULpy
Rob D. Stewart (2018)
10.1186/s40168-020-00818-9
Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts
Alba García Cortés (2020)
Identification and Genomic Characterization of Candidate Starch and Lactate Utilizing Bacteria from the Rumen of Beef Cattle
Venkata Vinay Kumar Bandarupalli (2020)
10.3389/fmicb.2020.00450
Rumen Virus Populations: Technological Advances Enhancing Current Understanding
Rosalind A. Gilbert (2020)
10.1002/fes3.209
A route to decreasing N pollution from livestock: Use of Festulolium hybrids improves efficiency of N flows in rumen simulation fermenters
Stephen D. Kamau (2020)
10.3390/microorganisms8060877
An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli
Panagiotis Sapountzis (2020)
10.1038/s41467-019-13118-0
Characterization of antibiotic resistance genes in the species of the rumen microbiota
Yasmin Neves Vieira Sabino (2019)
10.1038/s41598-020-58401-z
Dietary supplemental plant oils reduce methanogenesis from anaerobic microbial fermentation in the rumen
J. E. Vargas (2020)
A modelling odyssey in the tree of life
Rafael Muñoz-Tamayo (2019)
10.1038/s41587-019-0202-3
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
Robert D. Stewart (2019)
10.1016/j.psj.2019.12.019
Poultry processing and the application of microbiome mapping.
Kristina Marie Feye (2020)
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