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RA Gibbs, DM Muzny, GM Weinstock, DL Adelson, EE Eichler, L Elnitski, R Guigo, DL Hamernik, SM Kappes, HA Lewin, DJ Lynn, FW Nicholas, A Reymond, M Rijnkels, LC Skow, EM Zdobnov, L Schook, J Womack, T Alioto, SE Antonarakis, A Astashyn, CE Chapple, H-C Chen, J Chrast, F Camara, O Ermolaeva, CN Henrichsen, W Hlavina, Y Kapustin, B Kiryutin, P Kitts, F Kokocinski, M Landrum, D Maglott, K Pruitt, V Sapojnikov, SM Searle, V Solovyev, A Souvorov, C Ucla, C Wyss, JM Anzola, D Gerlach, E Elhaik, D Graur, JT Reese, RC Edgar, JC McEwan, GM Payne, JM Raison, T Junier, EV Kriventseva, E Eyras, M Plass, R Donthu, DM Larkin, J Reecy, MQ Yang, L Chen, Z Cheng, CG Chitko-McKown, GE Liu, LK Matukumalli, J Song, B Zhu, DG Bradley, FSL Brinkman, LPL Lau, MD Whiteside, A Walker, TT Wheeler, T Casey, JB German, DG Lemay, NJ Maqbool, AJ Molenaar, S Seo, P Stothard, CL Baldwin, R Baxter, CL Brinkmeyer-Langford, WC Brown, CP Childers, T Connelley, SA Ellis, K Fritz, EJ Glass, CTA Herzig, A Iivanainen, KK Lahmers, AK Bennett, CM Dickens, JGR Gilbert, DE Hagen, H Salih, J Aerts, AR Caetano, B Dalrymple, JF Garcia, CA Gill, SG Hiendleder, E Memili, D Spurlock, JL Williams, L Alexander, MJ Brownstein, L Guan, RA Holt, SJM Jones, MA Marra, R Moore, SS Moore, A Roberts, M Taniguchi, RC Waterman, J Chacko, MM Chandrabose, A Cree, MD Dao, HH Dinh, RA Gabisi, S Hines, J Hume, SN Jhangiani, V Joshi, CL Kovar, LR Lewis, Y-s Liu, J Lopez, MB Morgan, NB Nguyen, GO Okwuonu, SJ Ruiz, J Santibanez, RA Wright, C Buhay, Y Ding, S Dugan-Rocha, J Herdandez, M Holder, A Sabo, A Egan, J Goodell, K Wilczek-Boney, GR Fowler, ME Hitchens, RJ Lozado, C Moen, D Steffen, JT Warren, J Zhang, R Chiu, JE Schein, KJ Durbin, P Havlak, H Jiang, Y Liu, X Qin, Y Ren, Y Shen, H Song, SN Bell, C Davis, AJ Johnson, S Lee, LV Nazareth, BM Patel, L-L Pu, S Vattathil, Williams RL Jr, S Curry, C Hamilton, E Sodergren, DA Wheeler, W Barris, GL Bennett, A Eggen, RD Green, GP Harhay, M Hobbs, O Jann, JW Keele, MP Kent, S Lien, SD McKay, S McWilliam, A Ratnakumar, RD Schnabel, T Smith, WM Snelling, TS Sonstegard, RT Stone, Y Sugimoto, A Takasuga, JF Taylor, CP Van Tassell, MD MacNeil, ARR Abatepaulo, CA Abbey, V Ahola, IG Almeida, AF Amadio, E Anatriello, SM Bahadue, FH Biase, CR Boldt, JA Carroll, WA Carvalho, EP Cervelatti, E Chacko, JE Chapin, Y Cheng, J Choi, AJ Colley, TA de Campos, M De Donato, IKFdM Santos, CJF de Oliveira, H Deobald, E Devinoy, KE Donohue, P Dovc, A Eberlein, CJ Fitzsimmons, AM Franzin, GR Garcia, S Genini, CJ Gladney, JR Grant, ML Greaser, JA Green, DL Hadsell, HA Hakimov, R Halgren, JL Harrow, EA Hart, N Hastings, M Hernandez, Z-L Hu, A Ingham, T Iso-Touru, C Jamis, K Jensen, D Kapetis, T Kerr, SS Khalil, H Khatib, D Kolbehdari, CG Kumar, D Kumar, R Leach, JCM Lee, C Li, KM Logan, R Malinverni, E Marques, WF Martin, NF Martins, SR Maruyama, R Mazza, KL McLean, JF Medrano, BT Moreno, DD More, CT Muntean, HP Nandakumar, MFG Nogueira, I Olsaker, SD Pant, F Panzitta, RCP Pastor, MA Poli, N Poslusny, S Rachagani, S Ranganathan, A Razpet, PK Riggs, G Rincon, N Rodriguez-Osorio, SL Rodriguez-Zas, NE Romero, A Rosenwald, L Sando, SM Schmutz, L Shen, L Sherman, BR Southey, YS Lutzow, JV Sweedler, I Tammen, BPVL Telugu, JM Urbanski, YT Utsunomiya, CP Verschoor, AJ Waardenberg, Z Wang, R Ward, R Weikard, Welsh TH Jr, SN White, LG Wilming, KR Wunderlich, J Yang, F-Q Zhao 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522\u2013528.","DOI":"10.1126\/science.1169588"},{"key":"10.1017\/S1751731112000419_bib00147","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1126\/science.1183605","article-title":"A catalog of reference genomes from the human microbiome","volume":"328","year":"2010","journal-title":"Science"},{"key":"10.1017\/S1751731112000419_bib00148","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1111\/j.1365-2052.2010.02100.x","article-title":"The sheep genome reference sequence: a work in progress","volume":"41","author":"Archibald","year":"2010","journal-title":"Animal Genetics"},{"key":"10.1017\/S1751731112000419_bib00149","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.mib.2008.09.011","article-title":"A renaissance for the pioneering 16S rRNA gene","volume":"11","author":"Tringe","year":"2008","journal-title":"Current Opinion in Microbiology"},{"key":"10.1017\/S1751731112000419_bib00150","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"10.1017\/S1751731112000419_bib00151","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1126\/science.1133420","article-title":"Quantitative phylogenetic assessment of microbial communities in diverse environments","volume":"315","author":"von Mering","year":"2007","journal-title":"Science"},{"key":"10.1017\/S1751731112000419_bib00152","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1017\/S1751731108001687","article-title":"Gut microbiology - broad genetic diversity, yet specific metabolic niches","volume":"2","author":"Wallace","year":"2008","journal-title":"Animal"},{"key":"10.1017\/S1751731112000419_bib00153","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.micres.2008.12.002","article-title":"Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches","volume":"164","author":"Wang","year":"2009","journal-title":"Microbiological Research"},{"key":"10.1017\/S1751731112000419_bib00154","doi-asserted-by":"crossref","first-page":"U560","DOI":"10.1038\/nature06269","article-title":"Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite","volume":"450","author":"Warnecke","year":"2007","journal-title":"Nature"},{"key":"10.1017\/S1751731112000419_bib00155","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/ismej.2010.180","article-title":"Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics","volume":"5","author":"Weber","year":"2011","journal-title":"ISME Journal"},{"key":"10.1017\/S1751731112000419_bib00156","doi-asserted-by":"crossref","first-page":"3114","DOI":"10.2527\/1998.76123114x","article-title":"Manipulating ruminal fermentation: a microbial ecological perspective","volume":"76","author":"Weimer","year":"1998","journal-title":"Journal of Animal Science"},{"key":"10.1017\/S1751731112000419_bib00157","series-title":"Enzymatic degradation of insoluble carbohydrates","first-page":"291","article-title":"Cellulose degradation by ruminal microbes: physiological and hydrolytic diversity among ruminal cellulolytic bacteria","author":"Weimer","year":"1995"},{"key":"10.1017\/S1751731112000419_bib00158","doi-asserted-by":"crossref","first-page":"5323","DOI":"10.1016\/j.biortech.2009.04.075","article-title":"Lessons from the cow: what the ruminant animal can teach us about consolidated bioprocessing of cellulosic biomass","volume":"100","author":"Weimer","year":"2009","journal-title":"Bioresource Technology"},{"key":"10.1017\/S1751731112000419_bib00159","doi-asserted-by":"crossref","first-page":"646","DOI":"10.3168\/jds.2007-0693","article-title":"Effect of feeding Propionibacteria on milk production by early lactation dairy cows","volume":"91","author":"Weiss","year":"2008","journal-title":"Journal of Dairy Science"},{"key":"10.1017\/S1751731112000419_bib00160","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.anaerobe.2009.07.002","article-title":"ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle","volume":"16","author":"Welkie","year":"2010","journal-title":"Anaerobe"},{"key":"10.1017\/S1751731112000419_bib00161","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1006\/anae.1998.0155","article-title":"Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes","volume":"4","author":"Whitford","year":"1998","journal-title":"Anaerobe"},{"key":"10.1017\/S1751731112000419_bib00162","series-title":"The Rumen Protozoa","author":"Williams","year":"1992"},{"key":"10.1017\/S1751731112000419_bib00163","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.mib.2011.04.004","article-title":"Microbial diversity of cellulose hydrolysis","volume":"14","author":"Wilson","year":"2011","journal-title":"Current Opinion in Microbiology"},{"key":"10.1017\/S1751731112000419_bib00164","series-title":"The rumen microbial ecosystem","first-page":"467","article-title":"Microbe-microbe interactions","author":"Wolin","year":"1997"},{"key":"10.1017\/S1751731112000419_bib00165","doi-asserted-by":"crossref","first-page":"803","DOI":"10.2174\/092986610791190381","article-title":"Cloning and characterization of an exo-xylogucanase from rumenal microbial metagenome","volume":"17","author":"Wong","year":"2010","journal-title":"Protein and Peptide Letters"},{"key":"10.1017\/S1751731112000419_bib00166","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1007\/s00253-009-2364-2","article-title":"A novel xyloglucan-specific endo-\u00df-1,4-glucanase: biochemical properties and inhibition studies","volume":"86","author":"Wong","year":"2010","journal-title":"Applied Microbiology and Biotechnology"},{"key":"10.1017\/S1751731112000419_bib00167","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1007\/s00253-008-1504-4","article-title":"Cloning and characterization of a novel exo-a-1,5-L-arabinanase gene and the enzyme","volume":"79","author":"Wong","year":"2008","journal-title":"Applied Microbiology and Biotechnology"},{"key":"10.1017\/S1751731112000419_bib00168","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.2174\/092986609789839313","article-title":"Functional cloning and expression of a novel endo-a-1,5-L-arabinanase from a metagenomic library","volume":"16","author":"Wong","year":"2009","journal-title":"Protein and Peptide Letters"},{"key":"10.1017\/S1751731112000419_bib00169","unstructured":"World Bank 2008. Rising Food and Fuel Prices: Addressing the Risks to Future Generations. Retrieved September 1, 2009, from http:\/\/siteresources.worldbank.org\/DEVCOMMEXT\/Resources\/Food-Fuel.pdf"},{"key":"10.1017\/S1751731112000419_bib00170","doi-asserted-by":"crossref","first-page":"10452","DOI":"10.1073\/pnas.1734063100","article-title":"Inaugural article: honor thy symbionts","volume":"100","author":"Xu","year":"2003","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1017\/S1751731112000419_bib00171","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1071\/EA07237","article-title":"Diet composition at weaning affects the rumen microbial population and methane emissions by lambs","volume":"48","author":"Yanez-Ruiz","year":"2008","journal-title":"Australian Journal of Experimental Agriculture"},{"key":"10.1017\/S1751731112000419_bib00172","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1111\/j.1574-6941.2010.00852.x","article-title":"The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs","volume":"72","author":"Y\u00e1\u00f1ez-Ruiz","year":"2010","journal-title":"FEMS Microbiology Ecology"},{"key":"10.1017\/S1751731112000419_bib00173","doi-asserted-by":"crossref","first-page":"6701","DOI":"10.1128\/AEM.00361-10","article-title":"Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library","volume":"76","author":"Zhao","year":"2010","journal-title":"Applied and Environmental Microbiology"},{"key":"10.1017\/S1751731112000419_bib00174","doi-asserted-by":"crossref","first-page":"3776","DOI":"10.1128\/AEM.00010-10","article-title":"Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis","volume":"76","author":"Zhou","year":"2010","journal-title":"Applied and Environmental Microbiology"},{"key":"10.1017\/S1751731112000419_bib00175","first-page":"213","article-title":"Construction and analysis of rumen bacterial artificial chromosome library from a dairy cow rumen microflora","volume":"47","author":"Zhu","year":"2007","journal-title":"Wei Sheng Wu Xue Bao (Acta Microbiologica Sinica)"}],"container-title":["Animal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1751731112000419?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1751731112000419?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S1751731112000419","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T23:19:18Z","timestamp":1761693558000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1751731112000419"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"references-count":176,"alternative-id":["S1751731112000419"],"URL":"https:\/\/doi.org\/10.1017\/s1751731112000419","relation":{},"ISSN":["1751-7311"],"issn-type":[{"value":"1751-7311","type":"print"}],"subject":[],"published":{"date-parts":[[2013]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Rumen microbial (meta)genomics and its application to ruminant production","name":"articletitle","label":"Article Title"},{"value":"Animal","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1017\/S1751731112000419","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2012 The Animal Consortium. 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