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Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

Rainer Roehe, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, Nest McKain, Dave W. Ross, Jimmy J. Hyslop, Anthony Waterhouse, Tom C. Freeman, Mick Watson, R. John Wallace, Tosso Leeb
2016 PLoS Genetics  
In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively  ...  Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency.  ...  Contributed reagents/materials/analysis tools: NM RJW MW. Wrote the paper: RR RJW RJD.  ... 
doi:10.1371/journal.pgen.1005846 pmid:26891056 pmcid:PMC4758630 fatcat:orhm6ty2uzhc3njlu3wsrof4xi

Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle

Joana Lima, Marc D. Auffret, Robert D. Stewart, Richard J. Dewhurst, Carol-Anne Duthie, Timothy J. Snelling, Alan W. Walker, Tom C. Freeman, Mick Watson, Rainer Roehe
2019 Frontiers in Genetics  
Consistent with this result, distinct clusters of a coabundance network were enriched with microbial genes identified to be related with feed conversion ratio and growth rate or daily feed intake and residual  ...  In the present research, the influence of the rumen microbiome on feed conversion efficiency, growth rate, and appetite of beef cattle was investigated using metagenomic data.  ...  Rumen Microbial Genes Associated With Feed Conversion Efficiency Traits The PLS analyses identified sets of 20 and 14 microbial genes whose relative abundances explained 63.4 and 65.4% of the variation  ... 
doi:10.3389/fgene.2019.00701 pmid:31440274 pmcid:PMC6694183 fatcat:ff7wctkhajgfvozwexn5vvsfxq

Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism

Robert J. Wallace, Timothy J. Snelling, Christine A. McCartney, Ilma Tapio, Francesco Strozzi
2017 Genetics Selection Evolution  
Metaproteomics describes the proteins present in the ecosystem, and is therefore arguably a better indication of microbial metabolism.  ...  Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments.  ...  Acknowledgements The Rowett Institute of Nutrition and Health is funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government.  ... 
doi:10.1186/s12711-017-0285-6 pmid:28093073 pmcid:PMC5240273 fatcat:r6bhgum4dbbfvolbadxkvfohdy

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets

Marc D. Auffret, Robert Stewart, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, Robert J. Wallace, Tom C. Freeman, Timothy J. Snelling, Mick Watson, Rainer Roehe
2018 Frontiers in Microbiology  
Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH 4 emissions by PLS analysis compared to phylogenetic parameters or functional genes.  ...  It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes.  ...  Correlation analysis of microbial gene abundance was used to construct networks, where nodes represent microbial genes and edges the correlation in their abundance.  ... 
doi:10.3389/fmicb.2017.02642 pmid:29375511 pmcid:PMC5767246 fatcat:es6746tqufa3vknfyg6ylofpri

Tiny but mighty: The role of the rumen microbes in livestock production

K M Cammack, K J Austin, W R Lamberson, G C Conant, H C Cunningham
2018 Journal of Animal Science  
Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency  ...  the rumen microbial composition to enhance long-term host health and performance.  ...  Additionally, functional analysis of microbes associated with feed conversion ratio uncovered 49 genes that explained 85.5% of the variation.  ... 
doi:10.1093/jas/skx053 pmid:29385535 pmcid:PMC6140983 fatcat:yovqjpoaufh2zhstuecszasd5y

Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine

Marina Martínez-Álvaro, Marc D. Auffret, Robert D. Stewart, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Barbara Shih, Tom C. Freeman, Mick Watson, Rainer Roehe
2020 Frontiers in Microbiology  
A network analysis including relative abundances of all ruminal microbial genera (archaea, bacteria, fungi, and protists) and their genes was performed to improve our understanding of how the interactions  ...  Our study provides insight into the interactions of the rumen microbial communities and their genes by uncovering functional niches affecting CH4, which will benefit the development of efficient CH4 mitigation  ...  Co-abundance Network Analysis The interactions among all microbial genes and genera (2,717 variables in total) were investigated from the rumen microbiome of the 63 animals in a co-abundance network analysis  ... 
doi:10.3389/fmicb.2020.00659 pmid:32362882 pmcid:PMC7181398 fatcat:uwj7lmmw4jhbnasvv2q6oadoja

Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission

I. Mizrahi, E. Jami
2018 Animal  
In this review, we focus on the natural variations in community composition, which are not the results of different management or feed but rather intrinsic features of animals.  ...  From the moment the feed is ingested, it enters a vast cascade in which specialized microorganisms degrade specific components of the feed turning them into molecules, which in turn are utilized as anabolic  ...  Acknowledgments The authors thank Tanita Wein and Matthew Metzger for their helpful comments and critical reading of the manuscript.  ... 
doi:10.1017/s1751731118001957 pmid:30139398 fatcat:wysoc3lqcrhlpbmwxgiddirnfe

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
2015 Scientific Reports  
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.  ...  The following funding sources allowed Global Rumen Census collaborators to supply samples and metadata, listed with the primary contact(s) for each funding source: Agencia Nacional de Investigación  ... 
doi:10.1038/srep14567 pmid:26449758 pmcid:PMC4598811 fatcat:xc6jj2yxhfcrngtjvv7aqwknca

Erratum: Erratum: 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
2016 Scientific Reports  
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.  ...  The following funding sources allowed Global Rumen Census collaborators to supply samples and metadata, listed with the primary contact(s) for each funding source: Agencia Nacional de Investigación  ... 
doi:10.1038/srep19175 pmid:26789699 pmcid:PMC4726308 fatcat:s5ofpnocufakfoadyz2a6cfrca

Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review

Gunasekaran Rajeswari, Samuel Jacob, Anuj Kumar Chandel, Vinod Kumar
2021 Microbial Cell Factories  
This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding  ...  A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB)  ...  Vinod Kumar and Dr. Anuj Kumar Chandel for their valuable contribution in framing the manuscript.  ... 
doi:10.1186/s12934-021-01597-0 pmid:34044834 fatcat:rci4au7dqrdptesbobmmqgdiru

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, Milka Popova, Rafael Muñoz-Tamayo, Evelyne Forano, Sinead M. Waters, Matthias Hess, Ilma Tapio, Hauke Smidt (+25 others)
2018 Frontiers in Microbiology  
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.  ...  In terms of metataxonomics, microbial correlations to feed efficiency and/or methane production in ruminants, using rRNA genes or the Methyl coenzyme M reductase (mcrA) gene in methanogens are difficult  ... 
doi:10.3389/fmicb.2018.02161 pmid:30319557 pmcid:PMC6167468 fatcat:az36f22n3ffq3l32irxzduf6cu

New aspects and strategies for methane mitigation from ruminants

Sanjay Kumar, Prasanta Kumar Choudhury, Maria Dolores Carro, Gareth Wyn Griffith, Sumit Singh Dagar, Monica Puniya, Serena Calabro, Sreenivas Rao Ravella, Tejpal Dhewa, Ramesh Chandra Upadhyay, Sunil Kumar Sirohi, Shivlal Singh Kundu (+2 others)
2013 Applied Microbiology and Biotechnology  
Chemogenomics will help in finding target enzymes and 35 proteins, which will further assist in the screening of natural as well chemical inhibitors. 36 The construction of a methanogenic gene catalogue  ...  This will lead to understand the microbiome function, its relation 38 with the host and feeds, and therefore, will form the basis of practically viable and eco-39 friendly methane mitigation approaches  ...  of 597 diet type and feed efficiency status on rumen microbial populations in sheep.  ... 
doi:10.1007/s00253-013-5365-0 pmid:24247990 fatcat:w37gdptcuvbmpcs53w5kkmfpje

Rumen metaproteomics: closer to linking rumen microbial function to animal productivity traits

Thea Os Andersen, Benoit J. Kunath, Live H. Hagen, Magnus Ø. Arntzen, Phillip B. Pope
2020 Methods  
accurate reconstruction of active microbial populations in the rumen.  ...  The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi.  ...  ACKNOWLEDGEMENTS 634 We are grateful for support from The Research Council of Norway (Project no. 250479), the 635  ... 
doi:10.1016/j.ymeth.2020.07.011 pmid:32758682 fatcat:yimq4kqz6reutprbf4ampujfzu

The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle

Marc D. Auffret, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Tom C. Freeman, Robert Stewart, Mick Watson, Rainer Roehe
2017 Microbiome  
Roehe, R 2017, 'The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle' Microbiome, vol 5, no. 1.  ...  Availability of data and materials These data can be downloaded from the European Nucleotide Archive under accession PRJEB10338 and PRJEB21624.  ...  Irene Cabeza Luna, Andrew Southwell, Asier Zaragoza, Laura Nicoll, Lesley Deans, and Claire Broadbent for the excellent technical support.  ... 
doi:10.1186/s40168-017-0378-z pmid:29228991 pmcid:PMC5725880 fatcat:ngrcqa2xjrbxrodqbcmccjjkmi

Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle

Marc D. Auffret, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Tom C. Freeman, Robert Stewart, Mick Watson, Rainer Roehe
2019 Microbiome  
Following publication of the original article [1], the authors reported an error in the Additional file 1.  ...  Availability of data and materials These data can be downloaded from the European Nucleotide Archive under accession PRJEB10338 and PRJEB21624.  ...  Irene Cabeza Luna, Andrew Southwell, Asier Zaragoza, Laura Nicoll, Lesley Deans, and Claire Broadbent for the excellent technical support.  ... 
doi:10.1186/s40168-019-0764-9 pmid:31739805 pmcid:PMC6862725 fatcat:lbk22bjrrjfydmqebrfrxjdidy
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