Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Shi, Weibing; Moon, Christina D.; Leahy, Sinead C.; Kang, Dongwan; Froula, Jeff; Kittelmann, Sandra; Fan, Christina; Deutsch, Samuel; Gagic, Dragana; Seedorf, Henning; Kelly, William J.; Atua, Renee; Sang, Carrie; Soni, Priya; Li, Dong; Pinares-Patiño, Cesar S.; McEwan, John C.; Janssen, Peter H.; Chen, Feng; Visel, Axel; Wang, Zhong; Attwood, Graeme T.; Rubin, Edward M.

doi:10.1101/gr.168245.113

Title: Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Journal Article · Fri Jun 06 00:00:00 EDT 2014 · Genome Research

DOI:https://doi.org/10.1101/gr.168245.113· OSTI ID:1625629

^[1]; Moon, Christina D. ^[2]; Leahy, Sinead C. ^[2]; Kang, Dongwan ^[1]; Froula, Jeff ^[1]; Kittelmann, Sandra ^[2]; Fan, Christina ^[1]; Deutsch, Samuel ^[1]; Gagic, Dragana ^[2]; Seedorf, Henning ^[2]; Kelly, William J. ^[2]; Atua, Renee ^[2]; Sang, Carrie ^[2]; Soni, Priya ^[2]; Li, Dong ^[2]; Pinares-Patiño, Cesar S. ^[2]; McEwan, John C. ^[2]; Janssen, Peter H. ^[2]; Chen, Feng ^[1]; Visel, Axel ^[3] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
AgResearch Limited, Palmerston (New Zealand). Grasslands Research Centre
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division; Univ. of California, Merced, CA (United States). School of Natural Sciences

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.

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Research Organization:: Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625629

Journal Information:: Genome Research, Vol. 24, Issue 9; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

References (53)

Contribution of Transcriptomics to Systems-Level Understanding of Methanogenic Archaea Browne, Patrick D.; Cadillo-Quiroz, Hinsby Archaea, Vol. 2013 https://doi.org/10.1155/2013/586369	journal	January 2013
Strategies to reduce methane emissions from farmed ruminants grazing on pasture Buddle, Bryce M.; Denis, Michel; Attwood, Graeme T. The Veterinary Journal, Vol. 188, Issue 1 https://doi.org/10.1016/j.tvjl.2010.02.019	journal	April 2011
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle Carberry, Ciara A.; Kenny, David A.; Han, Sukkyan Applied and Environmental Microbiology, Vol. 78, Issue 14 https://doi.org/10.1128/AEM.07759-11	journal	May 2012
Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type Carberry, CIara A.; Waters, Sinead M.; Kenny, David A. Applied and Environmental Microbiology, Vol. 80, Issue 2 https://doi.org/10.1128/AEM.03131-13	journal	November 2013
Structural Insight into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, Cedervall, Peder E.; Dey, Mishtu; Pearson, Arwen R. Biochemistry, Vol. 49, Issue 35 https://doi.org/10.1021/bi100458d	journal	September 2010
Methane emissions from sheep pasture, measured with an open-path eddy covariance system Dengel, Sigrid; Levy, Peter E.; Grace, John Global Change Biology, Vol. 17, Issue 12 https://doi.org/10.1111/j.1365-2486.2011.02466.x	journal	July 2011
Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane: Monitoring of rumen methanogenic Archaea Denman, Stuart E.; Tomkins, Nigel W.; McSweeney, Christopher S. FEMS Microbiology Ecology, Vol. 62, Issue 3 https://doi.org/10.1111/j.1574-6941.2007.00394.x	journal	December 2007
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
Comparative Proteomic Analysis of Methanothermobacter themautotrophicus ΔH in Pure Culture and in Co-Culture with a Butyrate-Oxidizing Bacterium Enoki, Miho; Shinzato, Naoya; Sato, Hiroaki PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0024309	journal	August 2011
When should we expect microbial phenotypic traits to predict microbial abundances? Fox, Jeremy W. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00268	journal	January 2012
The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis Fricke, W. F.; Seedorf, H.; Henne, A. Journal of Bacteriology, Vol. 188, Issue 2 https://doi.org/10.1128/JB.188.2.642-658.2006	journal	December 2005
Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide Glass, Jennifer B.; Orphan, Victoria J. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00061	journal	January 2012
Low-methane yield sheep have smaller rumens and shorter rumen retention time Goopy, John P.; Donaldson, Alastair; Hegarty, Roger British Journal of Nutrition, Vol. 111, Issue 4 https://doi.org/10.1017/S0007114513002936	journal	October 2013
Methane Emissions from Dairy Cows Measured Using the Sulfur Hexafluoride (SF6) Tracer and Chamber Techniques Grainger, C.; Clarke, T.; McGinn, S. M. Journal of Dairy Science, Vol. 90, Issue 6 https://doi.org/10.3168/jds.2006-697	journal	June 2007
Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency Guan, Le Luo; Nkrumah, Joshua D.; Basarab, John A. FEMS Microbiology Letters, Vol. 288, Issue 1 https://doi.org/10.1111/j.1574-6968.2008.01343.x	journal	November 2008
Identification of Methyl Coenzyme M Reductase A (mcrA) Genes Associated with Methane-Oxidizing Archaea Hallam, S. J.; Girguis, P. R.; Preston, C. M. Applied and Environmental Microbiology, Vol. 69, Issue 9 https://doi.org/10.1128/AEM.69.9.5483-5491.2003	journal	September 2003
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins Hansen, E. E.; Lozupone, C. A.; Rey, F. E. Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1 https://doi.org/10.1073/pnas.1000071108	journal	February 2011
Cattle selected for lower residual feed intake have reduced daily methane production1,2 Hegarty, R. S.; Goopy, J. P.; Herd, R. M. Journal of Animal Science, Vol. 85, Issue 6 https://doi.org/10.2527/jas.2006-236	journal	June 2007
Impact of Feed Efficiency and Diet on Adaptive Variations in the Bacterial Community in the Rumen Fluid of Cattle Hernandez-Sanabria, Emma; Goonewardene, Laksiri A.; Wang, Zhiquan Applied and Environmental Microbiology, Vol. 78, Issue 4 https://doi.org/10.1128/AEM.05114-11	journal	February 2012
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen Hess, M.; Sczyrba, A.; Egan, R. Science, Vol. 331, Issue 6016 https://doi.org/10.1126/science.1200387	journal	January 2011
Methanogens: Methane Producers of the Rumen and Mitigation Strategies Hook, Sarah E.; Wright, André-Denis G.; McBride, Brian W. Archaea, Vol. 2010 https://doi.org/10.1155/2010/945785	journal	January 2010
Influence of hydrogen on rumen methane formation and fermentation balances through microbial growth kinetics and fermentation thermodynamics Janssen, Peter H. Animal Feed Science and Technology, Vol. 160, Issue 1-2 https://doi.org/10.1016/j.anifeedsci.2010.07.002	journal	August 2010
Structure of the Archaeal Community of the Rumen Janssen, P. H.; Kirs, M. Applied and Environmental Microbiology, Vol. 74, Issue 12 https://doi.org/10.1128/AEM.02812-07	journal	April 2008
Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets: Rumen methanogen community Jeyanathan, Jeyamalar; Kirs, Marek; Ronimus, Ron S. FEMS Microbiology Ecology, Vol. 76, Issue 2 https://doi.org/10.1111/j.1574-6941.2011.01056.x	journal	February 2011
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
Increased methane emissions from an invasive wetland plant under elevated carbon dioxide levels Kao-Kniffin, Jenny; Freyre, Dominique S.; Balser, Teri C. Applied Soil Ecology, Vol. 48, Issue 3 https://doi.org/10.1016/j.apsoil.2011.04.008	journal	July 2011
Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities Kittelmann, Sandra; Seedorf, Henning; Walters, William A. PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0047879	journal	February 2013
The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions Leahy, Sinead C.; Kelly, William J.; Altermann, Eric PLoS ONE, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pone.0008926	journal	January 2010
Sarsaponin Effects on Ruminal Fermentation and Microbes, Methane Production, Digestibility and Blood Metabolites in Steers Lila, Zeenat Ara; Mohammed, Nazimuddin; Kanda, Shuhei Asian-Australasian Journal of Animal Sciences, Vol. 18, Issue 12 https://doi.org/10.5713/ajas.2005.1746	journal	December 2005
Methane-suppressing effect of myristic acid in sheep as affected by dietary calcium and forage proportion Machmüller, Andrea; Soliva, Carla R.; Kreuzer, Michael British Journal of Nutrition, Vol. 90, Issue 3 https://doi.org/10.1079/BJN2003932	journal	September 2003
FLASH: fast length adjustment of short reads to improve genome assemblies Magoc, T.; Salzberg, S. L. Bioinformatics, Vol. 27, Issue 21 https://doi.org/10.1093/bioinformatics/btr507	journal	September 2011
Effects of propyl propane thiosulfinate on nutrient utilization, ruminal fermentation, microbial population and methane emissions in goats Martínez-Fernández, G.; Abecia, L.; Ramos-Morales, E. Animal Feed Science and Technology, Vol. 191 https://doi.org/10.1016/j.anifeedsci.2014.01.008	journal	May 2014
Hydrogen regulation of growth, growth yields, and methane gene transcription in Methanobacterium thermoautotrophicum deltaH. Morgan, R. M.; Pihl, T. D.; Nölling, J. Journal of bacteriology, Vol. 179, Issue 3 https://doi.org/10.1128/jb.179.3.889-898.1997	journal	January 1997
Microbial ecosystem and methanogenesis in ruminants Morgavi, D. P.; Forano, E.; Martin, C. animal, Vol. 4, Issue 7 https://doi.org/10.1017/S1751731110000546	journal	April 2010
Relationships of feedlot feed efficiency, performance, and feeding behavior with metabolic rate, methane production, and energy partitioning in beef cattle1 Nkrumah, J. D.; Okine, E. K.; Mathison, G. W. Journal of Animal Science, Vol. 84, Issue 1 https://doi.org/10.2527/2006.841145x	journal	January 2006
A study on consistency of differences between cows in rumen outflow rate of fibrous particles and other substrates and consequences for digestibility and intake of roughages Ørskov, E. R.; Ojwang, I.; Reid, G. W. Animal Science, Vol. 47, Issue 1 https://doi.org/10.1017/S000335610003703X	journal	August 1988
“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens Paul, Kristina; Nonoh, James O.; Mikulski, Lena Applied and Environmental Microbiology, Vol. 78, Issue 23 https://doi.org/10.1128/AEM.02193-12	journal	September 2012
Repeatability of methane emissions from sheep Pinares-Patiño, C. S.; McEwan, J. C.; Dodds, K. G. Animal Feed Science and Technology, Vol. 166-167 https://doi.org/10.1016/j.anifeedsci.2011.04.068	journal	June 2011
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores Pope, P. B.; Denman, S. E.; Jones, M. Proceedings of the National Academy of Sciences, Vol. 107, Issue 33 https://doi.org/10.1073/pnas.1005297107	journal	July 2010
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen Poulsen, Morten; Schwab, Clarissa; Borg Jensen, Bent Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2432	journal	February 2013
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
Methanogenesis: genes, genomes, and who's on first? Reeve, J. N.; Nölling, J.; Morgan, R. M. Journal of Bacteriology, Vol. 179, Issue 19 https://doi.org/10.1128/jb.179.19.5975-5986.1997	journal	October 1997
High-Yield and Phylogenetically Robust Methods of DNA Recovery for Analysis of Microbial Biofilms Adherent to Plant Biomass in the Herbivore Gut Rosewarne, Carly P.; Pope, Phillip B.; Denman, Stuart E. Microbial Ecology, Vol. 61, Issue 2 https://doi.org/10.1007/s00248-010-9745-z	journal	September 2010
Retention time of digesta in the rumen: its repeatability and relationship with wool production of Merino rams. Smuts, M.; Meissner, H. H.; Cronjé, P. B. Journal of Animal Science, Vol. 73, Issue 1 https://doi.org/10.2527/1995.731206x	journal	January 1995
Functional responses of methanogenic archaea to syntrophic growth Walker, Christopher B.; Redding-Johanson, Alyssa M.; Baidoo, Edward E. The ISME Journal, Vol. 6, Issue 11 https://doi.org/10.1038/ismej.2012.60	journal	June 2012
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite Warnecke, Falk; Luginbühl, Peter; Ivanova, Natalia Nature, Vol. 450, Issue 7169 https://doi.org/10.1038/nature06269	journal	November 2007
Improved extraction of PCR-quality community DNA from digesta and fecal samples Yu, Zhongtang; Morrison, Mark BioTechniques, Vol. 36, Issue 5 https://doi.org/10.2144/04365ST04	journal	May 2004
Methane emission by sectors: A comprehensive review of emission sources and mitigation methods Yusuf, Rafiu O.; Noor, Zainura Z.; Abba, Ahmad H. Renewable and Sustainable Energy Reviews, Vol. 16, Issue 7 https://doi.org/10.1016/j.rser.2012.04.008	journal	September 2012
Assessment of the Microbial Ecology of Ruminal Methanogens in Cattle with Different Feed Efficiencies Zhou, Mi; Hernandez-Sanabria, Emma; Guan, Le Luo Applied and Environmental Microbiology, Vol. 75, Issue 20 https://doi.org/10.1128/AEM.02815-08	journal	October 2009
Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions, as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis Zhou, Mi; Hernandez-Sanabria, Emma; Guan, Le Luo Applied and Environmental Microbiology, Vol. 76, Issue 12 https://doi.org/10.1128/AEM.00010-10	journal	June 2010
Physiological Ecology of Methanogens Zinder, Stephen H. Methanogenesis https://doi.org/10.1007/978-1-4615-2391-8_4	book	January 1993

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Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size Hoedt, Emily C.; Parks, Donovan H.; Volmer, James G. The ISME Journal, Vol. 12, Issue 12 https://doi.org/10.1038/s41396-018-0225-7	journal	August 2018
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future Huws, Sharon A.; Creevey, Christopher J.; Oyama, Linda B. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02161	journal	September 2018
Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake Noel, Samantha J.; Olijhoek, Dana W.; Mclean, Farran Animals, Vol. 9, Issue 8 https://doi.org/10.3390/ani9080498	journal	July 2019
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance Xue, Ming-Yuan; Sun, Hui-Zeng; Wu, Xue-Hui Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00819-8	journal	May 2020
Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria Hart, E. H.; Creevey, C. J.; Hitch, T. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28827-7	journal	July 2018
Genetic parameters of plasma and ruminal volatile fatty acids in sheep fed alfalfa pellets and genetic correlations with enteric methane emissions1 Jonker, Arjan; Hickey, Sharon M.; McEwan, John C. Journal of Animal Science, Vol. 97, Issue 7 https://doi.org/10.1093/jas/skz162	journal	June 2019
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies Noecker, Cecilia; Chiu, Hsuan-Chao; McNally, Colin P. mSystems, Vol. 4, Issue 6 https://doi.org/10.1128/msystems.00579-19	journal	December 2019
Supplementation of Pelleted Hazel (Corylus avellana) Leaves Decreases Methane and Urinary Nitrogen Emissions by Sheep at Unchanged Forage Intake S., Wang,; Melissa, Terranova,; Michael, Kreuzer, ETH Zurich https://doi.org/10.3929/ethz-b-000254685	text	January 2018
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha mSystems, Vol. 1, Issue 1 https://doi.org/10.1128/msystems.00013-15	journal	December 2015
Shifts of Hydrogen Metabolism From Methanogenesis to Propionate Production in Response to Replacement of Forage Fiber With Non-forage Fiber Sources in Diets in vitro Wang, Kun; Nan, Xuemei; Chu, Kangkang Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02764	journal	November 2018
Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen van Lingen, Henk J.; Edwards, Joan E.; Vaidya, Jueeli D. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00425	journal	March 2017
Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure Danielsson, Rebecca; Dicksved, Johan; Sun, Li Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00226	journal	February 2017
Cow responses and evolution of the rumen bacterial and methanogen community following a complete rumen content transfer De Mulder, T.; Vandaele, L.; Peiren, N. The Journal of Agricultural Science, Vol. 156, Issue 8 https://doi.org/10.1017/s0021859618001053	journal	October 2018
Comparative Genomic Analysis of Members of the Genera Methanosphaera and Methanobrevibacter Reveals Distinct Clades with Specific Potential Metabolic Functions Poehlein, Anja; Schneider, Dominik; Soh, Melissa Archaea, Vol. 2018 https://doi.org/10.1155/2018/7609847	journal	August 2018
Metatranscriptomics reveals mycoviral populations in the ovine rumen Hitch, Thomas C. A.; Edwards, Joan E.; Gilbert, Rosalind A. FEMS Microbiology Letters, Vol. 366, Issue 13 https://doi.org/10.1093/femsle/fnz161	journal	July 2019
Gut Microbiota of Wild and Captive Alpine Musk Deer (Moschus chrysogaster) Sun, Yewen; Sun, Yujiao; Shi, Zhihui Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03156	journal	January 2020
Can rumen bacteria communicate to each other? Won, Mi-Young; Oyama, Linda B.; Courtney, Stephen J. Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00796-y	journal	February 2020
Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets Auffret, Marc D.; Stewart, Robert; Dewhurst, Richard J. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02642	journal	January 2018
Diverse hydrogen production and consumption pathways influence methane production in ruminants Greening, Chris; Geier, Renae; Wang, Cecilia The ISME Journal, Vol. 13, Issue 10 https://doi.org/10.1038/s41396-019-0464-2	journal	June 2019
Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production Mi, Lan; Yang, Bin; Hu, Xialu Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00575	journal	March 2018
Ammonia determines transcriptional profile of microorganisms in anaerobic digestion Zhang, Nan; Peng, Huijuan; Li, Yong Brazilian Journal of Microbiology, Vol. 49, Issue 4 https://doi.org/10.1016/j.bjm.2018.04.008	journal	October 2018
Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats Wang, Zuo; Elekwachi, Chijioke O.; Jiao, Jinzhen Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-00500-5	journal	March 2017
Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome Ghanbari Maman, Leila; Palizban, Fahimeh; Fallah Atanaki, Fereshteh Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-61942-y	journal	March 2020
Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling McRae, Km; Schultz, M.; Mackintosh, Cg New Zealand Veterinary Journal, Vol. 64, Issue 3 https://doi.org/10.1080/00480169.2015.1121845	journal	January 2016
Evolution and Diversity of the Ras Superfamily of Small GTPases in Prokaryotes Wuichet, Kristin; Søgaard-Andersen, Lotte Genome Biology and Evolution, Vol. 7, Issue 1 https://doi.org/10.1093/gbe/evu264	journal	December 2014
Draft Genome Sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501, and Methanobrevibacter oralis DSM7256 Poehlein, Anja; Seedorf, Henning Genome Announcements, Vol. 4, Issue 3 https://doi.org/10.1128/genomea.00617-16	journal	June 2016
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 Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne PLOS Genetics, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pgen.1005846	journal	February 2016
Lower Methane Emissions from Yak Compared with Cattle in Rusitec Fermenters Mi, Jiandui; Zhou, Jianwei; Huang, Xiaodan PLOS ONE, Vol. 12, Issue 1 https://doi.org/10.1371/journal.pone.0170044	journal	January 2017
Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period Zhu, Zhigang; Noel, Samantha Joan; Difford, Gareth Frank PLOS ONE, Vol. 12, Issue 11 https://doi.org/10.1371/journal.pone.0187858	journal	November 2017
Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes Xiang, Ruidong; McNally, Jody; Bond, Jude Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00330	journal	August 2018
Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations Weimer, Paul J. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00296	journal	April 2015
Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock Yang, Chengjian; Rooke, John A.; Cabeza, Irene Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00132	journal	February 2016
Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur Neves, Andre L. A.; Li, Fuyong; Ghoshal, Bibaswan Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02445	journal	December 2017
The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing Wirth, Roland; Kádár, Gyula; Kakuk, Balázs Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02285	journal	September 2018
Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation Kaur, Parwinder; Appels, Rudi; Bayer, Philipp E. Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01463	journal	September 2017

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