TY - JOUR AU - Tian, H. AU - Lu, C. AU - Ciais, P. AU - Michalak, A. M. AU - Canadell, J. G. AU - Saikawa, E. PY - 2016 DA - 2016// TI - The terrestrial biosphere as a net source of greenhouse gases to the atmosphere JO - Nature. VL - 531 UR - https://doi.org/10.1038/nature16946 DO - 10.1038/nature16946 ID - Tian2016 ER - TY - JOUR AU - Huang, J. AU - Yu, H. AU - Dai, A. AU - Wei, Y. AU - Kang, L. PY - 2017 DA - 2017// TI - Drylands face potential threat under 2 °c global warming target JO - Nat Clim Chang VL - 7 UR - https://doi.org/10.1038/nclimate3275 DO - 10.1038/nclimate3275 ID - Huang2017 ER - TY - JOUR AU - Kirschke, S. AU - Bousquet, P. AU - Ciais, P. AU - Saunois, M. AU - Canadell, J. G. AU - Dlugokencky, E. J. PY - 2013 DA - 2013// TI - Three decades of global methane sources and sinks JO - Nat Geosci VL - 6 UR - https://doi.org/10.1038/ngeo1955 DO - 10.1038/ngeo1955 ID - Kirschke2013 ER - TY - JOUR AU - Nisbet, E. G. AU - Dlugokencky, E. J. AU - Bousquet, P. PY - 2014 DA - 2014// TI - Methane on the rise - again JO - Science. VL - 343 UR - https://doi.org/10.1126/science.1247828 DO - 10.1126/science.1247828 ID - Nisbet2014 ER - TY - JOUR AU - Huws, S. A. AU - Creevey, C. J. AU - Oyama, L. B. AU - Mizrahi, I. AU - Denman, S. E. AU - Popova, M. PY - 2018 DA - 2018// TI - Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future JO - Front Microbiol VL - 9 UR - https://doi.org/10.3389/fmicb.2018.02161 DO - 10.3389/fmicb.2018.02161 ID - Huws2018 ER - TY - JOUR AU - Wollenberg, E. AU - Richards, M. AU - Smith, P. AU - Havlík, P. AU - Obersteiner, M. AU - Tubiello, F. N. PY - 2016 DA - 2016// TI - Reducing emissions from agriculture to meet the 2 °C target JO - Glob Chang Biol VL - 22 UR - https://doi.org/10.1111/gcb.13340 DO - 10.1111/gcb.13340 ID - Wollenberg2016 ER - TY - STD TI - Hook SE, Wright ADG, McBride BW. Methanogens: methane producers of the rumen and mitigation strategies. Archaea. 2010;2010. ID - ref7 ER - TY - JOUR AU - Matthews, C. AU - Crispie, F. AU - Lewis, E. AU - Reid, M. AU - O’Toole, P. W. AU - Cotter, P. D. PY - 2019 DA - 2019// TI - The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency JO - Gut Microbes VL - 10 UR - https://doi.org/10.1080/19490976.2018.1505176 DO - 10.1080/19490976.2018.1505176 ID - Matthews2019 ER - TY - JOUR AU - Thauer, R. K. AU - Kaster, A. K. AU - Seedorf, H. AU - Buckel, W. AU - Hedderich, R. PY - 2008 DA - 2008// TI - Methanogenic archaea: ecologically relevant differences in energy conservation JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1931 DO - 10.1038/nrmicro1931 ID - Thauer2008 ER - TY - JOUR AU - Lan, W. AU - Yang, C. PY - 2019 DA - 2019// TI - Ruminal methane production: associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation JO - Sci Total Environ VL - 654 UR - https://doi.org/10.1016/j.scitotenv.2018.11.180 DO - 10.1016/j.scitotenv.2018.11.180 ID - Lan2019 ER - TY - STD TI - Söllinger A, Tveit AT, Poulsen M, Noel SJ, Bengtsson M, Bernhardt J, et al. Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation. mSystems. 2018;3. ID - ref11 ER - TY - STD TI - Tapio I, Snelling TJ, Strozzi F, Wallace RJ. The ruminal microbiome associated with methane emissions from ruminant livestock. J Animal Sci Biotechnology. 2017;8. ID - ref12 ER - TY - STD TI - John Wallace R, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, et al. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv. 2019;5. ID - ref13 ER - TY - STD TI - Li F, Li C, Chen Y, Liu J, Zhang C, Irving B, et al. Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome. 2019;7. ID - ref14 ER - TY - JOUR AU - Difford, G. F. AU - Plichta, D. R. AU - Løvendahl, P. AU - Lassen, J. AU - Noel, S. J. AU - Højberg, O. PY - 2018 DA - 2018// TI - Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows JO - PLoS Genet VL - 14 UR - https://doi.org/10.1371/journal.pgen.1007580 DO - 10.1371/journal.pgen.1007580 ID - Difford2018 ER - TY - JOUR AU - Singh, K. M. AU - Reddy, B. AU - Patel, A. K. AU - Panchasara, H. AU - Parmar, N. AU - Patel, A. B. PY - 2014 DA - 2014// TI - Metagenomic analysis of buffalo rumen microbiome: effect of roughage diet on dormancy and sporulation genes JO - Meta Gene VL - 2 UR - https://doi.org/10.1016/j.mgene.2014.01.005 DO - 10.1016/j.mgene.2014.01.005 ID - Singh2014 ER - TY - JOUR AU - Kala, A. AU - Kamra, D. N. AU - Kumar, A. AU - Agarwal, N. AU - Chaudhary, L. C. AU - Joshi, C. G. PY - 2017 DA - 2017// TI - Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0172051 DO - 10.1371/journal.pone.0172051 ID - Kala2017 ER - TY - JOUR AU - Zou, C. AU - Gu, Q. AU - Zhou, X. AU - Zhongsheng, X. AU - Muhammad, W. I. AU - Tang, Q. PY - 2019 DA - 2019// TI - Ruminal microbiota composition associated with ruminal fermentation parameters and milk yield in lactating buffalo in Guangxi, China—A preliminary study JO - J Anim Physiol Anim Nutr (Berl) VL - 103 UR - https://doi.org/10.1111/jpn.13154 DO - 10.1111/jpn.13154 ID - Zou2019 ER - TY - JOUR AU - Wood, D. E. AU - Lu, J. AU - Langmead, B. PY - 2019 DA - 2019// TI - Improved metagenomic analysis with kraken 2 JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1891-0 DO - 10.1186/s13059-019-1891-0 ID - Wood2019 ER - TY - STD TI - Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2019. https://doi.org/10.1093/bioinformatics/btz848. ID - ref20 ER - TY - STD TI - Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12. ID - ref21 ER - TY - JOUR AU - Franzosa, E. A. AU - McIver, L. J. AU - Rahnavard, G. AU - Thompson, L. R. AU - Schirmer, M. AU - Weingart, G. PY - 2018 DA - 2018// TI - Species-level functional profiling of metagenomes and metatranscriptomes JO - Nat Methods VL - 15 UR - https://doi.org/10.1038/s41592-018-0176-y DO - 10.1038/s41592-018-0176-y ID - Franzosa2018 ER - TY - STD TI - Jovel J, Patterson J, Wang W, Hotte N, O’Keefe S, Mitchel T, et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front Microbiol. 2016;7. ID - ref23 ER - TY - STD TI - Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;2019. ID - ref24 ER - TY - JOUR AU - Stewart, R. D. AU - Auffret, M. D. AU - Snelling, T. J. AU - Roehe, R. AU - Watson, M. PY - 2019 DA - 2019// TI - MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs) JO - Bioinformatics. VL - 35 UR - https://doi.org/10.1093/bioinformatics/bty905 DO - 10.1093/bioinformatics/bty905 ID - Stewart2019 ER - TY - JOUR AU - Suzek, B. E. AU - Wang, Y. AU - Huang, H. AU - McGarvey, P. B. AU - Wu, C. H. PY - 2015 DA - 2015// TI - UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches JO - Bioinformatics. VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu739 DO - 10.1093/bioinformatics/btu739 ID - Suzek2015 ER - TY - JOUR AU - Seshadri, R. AU - Leahy, S. C. AU - Attwood, G. T. AU - Teh, K. H. AU - Lambie, S. C. AU - Cookson, A. L. PY - 2018 DA - 2018// TI - Cultivation and sequencing of rumen microbiome members from the Hungate1000 collection JO - Nat Biotechnol VL - 36 UR - https://doi.org/10.1038/nbt.4110 DO - 10.1038/nbt.4110 ID - Seshadri2018 ER - TY - JOUR AU - Singh, K. M. AU - Ahir, V. B. AU - Tripathi, A. K. AU - Ramani, U. V. AU - Sajnani, M. AU - Koringa, P. G. PY - 2012 DA - 2012// TI - Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study JO - Mol Biol Rep VL - 39 UR - https://doi.org/10.1007/s11033-011-1278-0 DO - 10.1007/s11033-011-1278-0 ID - Singh2012 ER - TY - JOUR AU - Stewart, R. D. AU - Auffret, M. D. AU - Warr, A. AU - Walker, A. W. AU - Roehe, R. AU - Watson, M. PY - 2019 DA - 2019// TI - Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery JO - Nat Biotechnol VL - 37 UR - https://doi.org/10.1038/s41587-019-0202-3 DO - 10.1038/s41587-019-0202-3 ID - Stewart2019 ER - TY - STD TI - Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun. 2018;9. ID - ref30 ER - TY - STD TI - Matsui H;, Ogata K, Tajima K, Nakamura M, Nagamine T, Aminov R, et al. Phenotypic characterization of polysaccharidases produced by four Prevotella type strains. Curr Microbiol 2020;41:45. ID - ref31 ER - TY - STD TI - Stevenson DM, Weimer PJ. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol 2007;75:165–174. ID - ref32 ER - TY - STD TI - Fondevila M, Dehority BA. Interactions between Fibrobacter succinogenes, Prevotella ruminicola, and Ruminococcus flavefaciens in the digestion of cellulose from forages. J Anim Sci 1996;74:678–684. ID - ref33 ER - TY - JOUR AU - Flint, H. J. AU - Bayer, E. A. AU - Rincon, M. T. AU - Lamed, R. AU - White, B. A. PY - 2008 DA - 2008// TI - Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1817 DO - 10.1038/nrmicro1817 ID - Flint2008 ER - TY - STD TI - Vaidya JD, van den Bogert B, Edwards JE, Boekhorst J, van Gastelen S, Saccenti E, et al. The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows. Front Microbiol. 2018;9. ID - ref35 ER - TY - JOUR AU - Deusch, S. AU - Camarinha-Silva, A. AU - Conrad, J. AU - Beifuss, U. AU - Rodehutscord, M. AU - Seifert, J. PY - 2017 DA - 2017// TI - A structural and functional elucidation of the rumen microbiome influenced by various diets and microenvironments JO - Front Microbiol VL - 8 UR - https://doi.org/10.3389/fmicb.2017.01605 DO - 10.3389/fmicb.2017.01605 ID - Deusch2017 ER - TY - STD TI - Avguštin G, Wallace RJ, Flint HJ. Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola. Int J Syst Bacteriol 1997;47:284–288. ID - ref37 ER - TY - STD TI - Wallnöfer P, Baldwin RL. Pathway of propionate formation in Bacteroides ruminicola. J Bacteriol 1967;93:504–505. http://www.ncbi.nlm.nih.gov/pubmed/6020420. Accessed 12 Feb 2020. UR - http://www.ncbi.nlm.nih.gov/pubmed/6020420 ID - ref38 ER - TY - JOUR AU - Nevel, C. J. AU - Henderickx, H. K. AU - Demeyer, D. I. AU - Martin, J. PY - 1969 DA - 1969// TI - Effect of chloral hydrate on methane and propionic acid in the rumen JO - Appl Microbiol VL - 17 UR - https://doi.org/10.1128/AEM.17.5.695-700.1969 DO - 10.1128/AEM.17.5.695-700.1969 ID - Nevel1969 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Seemann, T. PY - 2014 DA - 2014// TI - Prokka: rapid prokaryotic genome annotation JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu153 DO - 10.1093/bioinformatics/btu153 ID - Seemann2014 ER - TY - JOUR AU - Steinegger, M. AU - Mirdita, M. AU - Söding, J. PY - 2019 DA - 2019// TI - Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold JO - Nat Methods VL - 16 UR - https://doi.org/10.1038/s41592-019-0437-4 DO - 10.1038/s41592-019-0437-4 ID - Steinegger2019 ER - TY - STD TI - Steinegger M, Söding J. Clustering huge protein sequence sets in linear time. Nat Commun. 2018;9. ID - ref43 ER - TY - JOUR AU - Buchfink, B. AU - Xie, C. AU - Huson, D. H. PY - 2014 DA - 2014// TI - Fast and sensitive protein alignment using DIAMOND JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3176 DO - 10.1038/nmeth.3176 ID - Buchfink2014 ER -