Reisinger A, Clark H. How much do direct livestock emissions actually contribute to global warming? Glob Change Biol. 2018;24:1749–61.
Article
Google Scholar
Wollenberg E, Richards M, Smith P, Havlik P, Obersteiner M, Tubiello F, et al. Reducing emissions from agriculture to meet the 2 °C target. Glob Change Biol. 2016;22:3859–64.
Article
Google Scholar
Seedorf H, Kittelmann S, Janssen PH. Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle. Appl Environ Microbiol. 2015;81:986–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vantcheva ZM, Prodhan K, Hemken RW. Rumen methanol in vivo and in vitro. J Dairy Sci. 1970;53:1511–4.
Article
CAS
PubMed
Google Scholar
Martinez-Fernandez G, Duval S, Kindermann M, Schirra HJ, Denman SE, McSweeney CS. 3-NOP vs. halogenated compound: Methane production, ruminal fermentation and microbial community response in forage fed cattle. Front Microbiol. 2018;9:1582.
Article
PubMed
PubMed Central
Google Scholar
Chung D, Pattathil S, Biswal AK, Hahn MG, Mohnen D, Westpheling J. Deletion of a gene cluster encoding pectin degrading enzymes in Caldicellulosiruptor bescii reveals an important role for pectin in plant biomass recalcitrance. Biotechnol Biofuels. 2014;7:147.
Article
CAS
PubMed
PubMed Central
Google Scholar
Silley P. A note on the pectinolytic enzymes of Lachnospira multiparus. J Appl Bacteriol. 1985;58:145–50.
Article
CAS
Google Scholar
Silley P. The production and properties of a crude pectin lyase from Lachnospira multiparus. Lett Appl Microbiol. 1986;2:29–31.
Article
CAS
Google Scholar
Bryant MP, Barrentine BF, Sykes JF, Robinson IM, Shawver CV, Williams LW. Predominant bacteria in the rumen of cattle on bloat-provoking ladino clover pasture. J Dairy Sci. 1960;43:1435–44.
Article
Google Scholar
Duskova D, Marounek M. Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rumen bacterium Lachnospira multiparus. Lett Appl Microbiol. 2001;33:159–63.
Article
CAS
PubMed
Google Scholar
Rode LM, Sharak-Genther BR, Bryant MP. Syntrophic association of methanol and CO2-H2-utilising species of Eubacterium limosum and pectin-fermenting Lachnospira multiparus during growth in a pectin medium. Appl Environ Microbiol. 1981;42:20–2.
CAS
PubMed
PubMed Central
Google Scholar
Henderson G, Cox F, Ganesh S, Jonker J, Young W. Global Rumen Census Collaborators, et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep. 2015;5:14567.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dawson RMC, Hemington NL. Digestion of grass lipids and pigments in the sheep rumen. Brit J Nutr. 1974;32:327–40.
Article
CAS
PubMed
Google Scholar
Ametaj BN, Zebeli Q, Saleem F, Psychogios NG, Lewis M, Dunn SM, et al. Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows. Metabolomics. 2010;6:583–94.
Article
CAS
Google Scholar
Bovine Rumen Metabolome Database; http://www.rumendb.ca. Accessed 29 June 2018.
Broad TE, Dawson RM. Role of choline in the nutrition of the rumen protozoon Entodinium caudatum. J Gen Microbiol. 1976;92:391–7.
Article
CAS
PubMed
Google Scholar
Neill AR, Grime DW, Dawson RM. Conversion of choline methyl groups through trimethylamine into methane in the rumen. Biochem J. 1978;170:529–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morgavi DP, Rathahao-Paris E, Popova M, Boccard J, Nielsen KF, Boudra H. Rumen microbial communities influence metabolic phenotypes in lambs. Front Microbiol. 2015. https://doi.org/10.3389/fmicb.2015.01060.
Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, et al. Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell. 2015;163:1585–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown JM, Hazen SL. Microbial modulation of cardiovascular disease. Nat Rev Microbiol. 2018;16:171–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472:57–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Craciun S, Balskus EP. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc Natl Acad Sci U S A. 2012;109:21307–12.
Article
PubMed
PubMed Central
Google Scholar
Martínez-del Campo A, Bodeaa S, Hamera HA, Marksa JA, Haiserb HJ, Turnbaugh PJ, et al. Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria. MBio. 2015;6:e00042–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Romano KA, Vivas EI, Amador-Noguez D, Rey FE. Intestinal microbiota composition modulates choline bioavailability. MBio. 2015;6:e02481–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rath S, Heidrich B, Pieper DH, Vital M. Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Microbiome. 2017;5:54.
Article
PubMed
PubMed Central
Google Scholar
Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, et al. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res. 2014;24:1517–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. Assembly of 913 microbial genomes from metagenomics sequencing of the cow rumen. Nat Commun. 2018. https://doi.org/10.1038/s41467-018-03317-6.
Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 collection. Nat Biotechnol. 2018;36:359–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microb Biotechnol. 2014;7:467–79.
Article
PubMed
PubMed Central
Google Scholar
Terrapon N, Lombard V, Drula E, Lapébie P, Al-Masaudi S, Gilbert HJ, et al. PULDB: the expanded database of polysaccharide utilization loci. Nucleic Acids Res. 2018;46(D1):D677–83.
Article
CAS
PubMed
Google Scholar
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337:1661–5.
Article
CAS
PubMed
Google Scholar
Abbott DW, Hrynuik S, Boraston AB. Identification and characterization of a novel periplasmic polygalacturonic acid binding protein from Yersinia enterolitica. J Mol Biol. 2007;367:1023–33.
Article
CAS
PubMed
Google Scholar
Caro-Quintero A, Ritalahti KM, Cusick KD, Löffler FE, Konstantinidis KT. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. MBio. 2012;15:e00025–12.
Google Scholar
Fricke W, Seedorf H, Henne A, Krüer M, Liesegang H, Hedderich R, et al. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol. 2006;188:642–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME J. 2018;12:2942–53.
Article
PubMed
PubMed Central
Google Scholar
Hoedt EC, Cuív PÓ, Evans PN, Smith WJ, McSweeney CS, Denman SE, et al. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J. 2016;10:2376–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leahy SC, Kelly WJ, Li D, Li Y, Altermann E, Lambie SC, et al. The complete genome sequence of Methanobrevibacter sp. AbM4. Stand Genomic Sci. 2013;8:215–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee J-H, Rhee M-S, Kumar S, Lee G-H, Chang D-H, Kim D-S, et al. Genome sequence of Methanobrevibacter sp. strain JH1, isolated from rumen of Korean native cattle. Genome Announc. 2013. https://doi.org/10.1128/genomeA.00002-13.
Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, et al. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One. 2010. https://doi.org/10.1371/journal.pone.0008926.
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol. 2008;6:579–91.
Article
CAS
PubMed
Google Scholar
Kabel MA, Yeoman CJ, Han Y, Dodd D, Abbas CA, de Bont JA, Morrison M, Cann IK, Mackie RI. Biochemical characterization and relative expression levels of multiple carbohydrate esterases of the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate. Appl Environ Microbiol. 2011;77:5671–81. https://doi.org/10.1128/AEM.05321-11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Joblin KN, Naylor GE. The ruminal mycoplasmas: a review. J Appl Anim Res. 2002;21:161–79.
Article
Google Scholar
Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, et al. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One. 2009. https://doi.org/10.1371/journal.pone.0006650.
Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, et al. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One. 2011. https://doi.org/10.1371/journal.pone.0018814.
Weimar MR, Cheung J, Dey D, McSweeney C, Morrison M, Kobayashi Y, et al. Development of multiwell-plate methods using pure cultures of methanogens to identify new inhibitors for suppressing ruminant methane emissions. Appl Environ Microbiol. 2017;83:e00396–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eddy SR. Accelerated profile HMM searches. PLOS Comp Biol. 2011;7:e1002195.
Article
CAS
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25(7):1307–20.
Article
CAS
PubMed
Google Scholar
Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, Ganesh S, Janssen PH, Shi W, Froula J, Rubin EM, Attwood GT. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome. 2016;4:56.
Article
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G. Durbin R, and 1000 genome project data processing subgroup, the sequence alignment/map (SAM) format and SAMtools. Bioinfo. 2009;25:2078–9.
Article
CAS
Google Scholar
Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen PH. Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Meth. 2011;84:52–60.
Article
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Article
CAS
PubMed
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 2015. https://doi.org/10.7717/peerj.1165.
Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, et al. Toward a standard in structural genome annotation for prokaryotes. Stand Genomic Sci. 2015;10:45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In: Deng M, Jiang R, Sun F, Zhang X, editors. Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821. Berlin: Springer; 2013. p. 158–70.
Google Scholar
Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, et al. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci. 2016;11:17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen I-M A, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017;45:D1:D507–16.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.
CAS
PubMed
Google Scholar
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolut. 1985;39:783–91.
Article
Google Scholar
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comp Appl Biosci. 1992;8:275–82.
CAS
PubMed
Google Scholar