TY - STD TI - IPCC. In climate change 2007: mitigation of climate change: contribution of working group III to the fourth assessment report of the intergovernmental panel on climate change. In: Metz ORD B, Bosch PR, Dave R, Meyer LA, editors. Cambridge, United Kingdom and New York, NY, USA; 2007. ID - ref1 ER - TY - JOUR AU - Yusuf, R. O. AU - Noor, Z. Z. AU - Abba, A. H. AU - Hassan, M. A. A. AU - Din, M. F. M. PY - 2012 DA - 2012// TI - Renewable and sustainable energy reviews JO - Renew Sustain Energy Rev VL - 16 UR - https://doi.org/10.1016/j.rser.2012.04.008 DO - 10.1016/j.rser.2012.04.008 ID - Yusuf2012 ER - TY - CHAP AU - Zinder, S. H. ED - Ferry, J. G. PY - 1993 DA - 1993// TI - Physiological ecology of methanogens BT - Methanogenesis: ecology, physiology, biochemistry and genetics PB - Chapman and Hall CY - London UR - https://doi.org/10.1007/978-1-4615-2391-8_4 DO - 10.1007/978-1-4615-2391-8_4 ID - Zinder1993 ER - TY - JOUR AU - Hook, S. E. AU - Wright, A. -. D. G. AU - McBride, B. W. PY - 2010 DA - 2010// TI - Methanogens: methane producers of the rumen and mitigation strategies JO - Archaea VL - 2010 UR - https://doi.org/10.1155/2010/945785 DO - 10.1155/2010/945785 ID - Hook2010 ER - TY - JOUR AU - Lassey, K. R. AU - Ulyatt, M. J. AU - Martin, R. J. AU - Walker, C. F. AU - Shelton, I. D. PY - 1997 DA - 1997// TI - Methane emissions measured directly from grazing livestock in New Zealand JO - Atmos Environ VL - 31 UR - https://doi.org/10.1016/S1352-2310(97)00123-4 DO - 10.1016/S1352-2310(97)00123-4 ID - Lassey1997 ER - TY - JOUR AU - Pinares-Patiño, C. S. AU - Ebrahimi, S. H. AU - McEwan, J. C. AU - Dodds, K. G. AU - Clark, H. AU - Luo, D. PY - 2011 DA - 2011// TI - Is rumen retention time implicated in sheep differences in methane emission? JO - Proc New Zeal Soc Anim Prod VL - 71 ID - Pinares-Patiño2011 ER - TY - JOUR AU - Pinares-Patino, C. S. AU - McEwan, J. C. AU - Dodds, K. G. AU - Cardenas, E. A. AU - Hegarty, R. S. AU - Koolaard, J. P. PY - 2011 DA - 2011// TI - Repeatability of methane emissions from sheep JO - Anim Feed Sci Tech VL - 166–67 UR - https://doi.org/10.1016/j.anifeedsci.2011.04.068 DO - 10.1016/j.anifeedsci.2011.04.068 ID - Pinares-Patino2011 ER - TY - JOUR AU - Pinares-Patiño, C. S. AU - Hickey, S. M. AU - Young, E. A. AU - Dodds, K. G. AU - MacLean, S. AU - Molano, G. PY - 2013 DA - 2013// TI - Heritability estimates of methane emissions from sheep JO - Animal. VL - 7 UR - https://doi.org/10.1017/S1751731113000864 DO - 10.1017/S1751731113000864 ID - Pinares-Patiño2013 ER - TY - JOUR AU - Bain, W. E. AU - Bezuidenhout, L. AU - Jopson, N. B. AU - Pinares-Patino, C. AU - McEwan, J. C. PY - 2014 DA - 2014// TI - Rumen differences between sheep identified as being low or high methane emitters JO - Proc 10th World Cong Genet Appl Livest Prod. ID - Bain2014 ER - TY - JOUR AU - Goopy, J. P. AU - Donaldson, A. AU - Hegarty, R. AU - Vercoe, P. E. AU - Haynes, F. AU - Barnett, M. V. H. O. PY - 2014 DA - 2014// TI - Low-methane yield sheep have smaller rumens and shorter rumen retention time JO - Br J Nutr VL - 111 UR - https://doi.org/10.1017/S0007114513002936 DO - 10.1017/S0007114513002936 ID - Goopy2014 ER - TY - JOUR AU - Herd, R. M. AU - Arthur, P. F. AU - Donoghue, K. A. AU - Bird, S. H. AU - Bird-Gardiner, T. AU - Hegarty, R. S. PY - 2014 DA - 2014// TI - Measures of methane production and their phenotypic relationships with dry matter intake, growth, and body composition traits in beef cattle JO - J Anim Sci VL - 92 UR - https://doi.org/10.2527/jas.2014-8273 DO - 10.2527/jas.2014-8273 ID - Herd2014 ER - TY - JOUR AU - Robinson, D. L. AU - Goopy, J. P. AU - Hegarty, R. S. AU - Oddy, V. H. AU - Thompson, A. N. AU - Toovey, A. F. PY - 2014 DA - 2014// TI - Genetic and environmental variation in methane emissions of sheep at pasture JO - J Anim Sci VL - 92 UR - https://doi.org/10.2527/jas.2014-8042 DO - 10.2527/jas.2014-8042 ID - Robinson2014 ER - TY - JOUR AU - Robinson, D. L. AU - Goopy, J. P. AU - Donaldson, A. J. AU - Woodgate, R. T. AU - Oddy, V. H. AU - Hegarty, R. S. PY - 2014 DA - 2014// TI - Sire and liveweight affect feed intake and methane emissions of sheep confined in respiration chambers JO - Animal. VL - 8 UR - https://doi.org/10.1017/S1751731114001773 DO - 10.1017/S1751731114001773 ID - Robinson2014 ER - TY - JOUR AU - Pickering, N. K. AU - Chagunda, M. G. AU - Banos, G. AU - Mrode, R. AU - McEwan, J. C. AU - Wall, E. PY - 2015 DA - 2015// TI - Genetic parameters for predicted methane production and laser methane detector measurements JO - J Anim Sci VL - 93 UR - https://doi.org/10.2527/jas.2014-8302 DO - 10.2527/jas.2014-8302 ID - Pickering2015 ER - TY - JOUR AU - Orskov, E. R. AU - Ojwang, I. AU - Reid, G. W. PY - 1988 DA - 1988// TI - 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 JO - Anim Prod VL - 47 UR - https://doi.org/10.1017/S000335610003703X DO - 10.1017/S000335610003703X ID - Orskov1988 ER - TY - JOUR AU - Smuts, M. AU - Meissner, H. H. AU - Cronje, P. B. PY - 1995 DA - 1995// TI - Retention time of digesta in the rumen—its repeatability and relationship with wool production of merino rams JO - J Anim Sci VL - 73 UR - https://doi.org/10.2527/1995.731206x DO - 10.2527/1995.731206x ID - Smuts1995 ER - TY - JOUR AU - Benchaar, C. AU - Pomar, C. AU - Chiquette, J. PY - 2001 DA - 2001// TI - Evaluation of dietary strategies to reduce methane production in ruminants: a modelling approach JO - Can J Anim Sci. VL - 81 UR - https://doi.org/10.4141/A00-119 DO - 10.4141/A00-119 ID - Benchaar2001 ER - TY - JOUR AU - Pinares-Patino, C. S. AU - Ulyatt, M. J. AU - Lassey, K. R. AU - Barry, T. N. AU - Holmes, C. W. PY - 2003 DA - 2003// TI - Rumen function and digestion parameters associated with differences between sheep in methane emissions when fed chaffed lucerne hay JO - J Agric Sci. VL - 140 UR - https://doi.org/10.1017/S0021859603003046 DO - 10.1017/S0021859603003046 ID - Pinares-Patino2003 ER - TY - JOUR AU - Kittelmann, S. AU - Seedorf, H. AU - Walters, W. A. AU - Clemente, J. C. AU - Knight, R. AU - Gordon, J. I. PY - 2013 DA - 2013// TI - Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0047879 DO - 10.1371/journal.pone.0047879 ID - Kittelmann2013 ER - TY - JOUR AU - Shi, W. AU - Moon, C. D. AU - Leahy, S. C. AU - Kang, D. AU - Froula, J. AU - Kittelmann, S. PY - 2014 DA - 2014// TI - Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome JO - Gen Res. VL - 24 UR - https://doi.org/10.1101/gr.168245.113 DO - 10.1101/gr.168245.113 ID - Shi2014 ER - TY - JOUR AU - Kamke, J. AU - Kittelmann, S. AU - Soni, P. AU - Li, Y. AU - Tavendale, M. AU - Ganesh, S. PY - 2016 DA - 2016// TI - Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation JO - Microbiome. VL - 4 UR - https://doi.org/10.1186/s40168-016-0201-2 DO - 10.1186/s40168-016-0201-2 ID - Kamke2016 ER - TY - JOUR AU - Yu, Z. AU - Morrison, M. PY - 2004 DA - 2004// TI - Improved extraction of PCR-quality community DNA from digesta and fecal samples JO - BioTechn. VL - 36 ID - Yu2004 ER - TY - JOUR AU - Rosewarne, C. P. AU - Pope, P. B. AU - Denman, S. E. AU - McSweeney, C. S. AU - O’Cuiv, P. AU - Morrison, M. PY - 2011 DA - 2011// TI - High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut JO - Microb Ecol VL - 61 UR - https://doi.org/10.1007/s00248-010-9745-z DO - 10.1007/s00248-010-9745-z ID - Rosewarne2011 ER - TY - JOUR AU - Caporaso, J. C. AU - Kuczynski, J. AU - Stombaugh, J. AU - Bittinger, K. AU - Bushman, F. D. AU - Costello, E. K. PY - 2010 DA - 2010// TI - QIIME allows analysis of high-throughput community sequencing data JO - Nat Methods. ID - Caporaso2010 ER - TY - JOUR AU - McDonald, D. AU - Price, M. N. AU - Goodrich, J. AU - Nawrocki, E. P. AU - DeSantis, T. Z. AU - Probst, A. PY - 2012 DA - 2012// TI - An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.139 DO - 10.1038/ismej.2011.139 ID - McDonald2012 ER - TY - JOUR AU - Magoc, T. AU - Salzberg, S. L. PY - 2011 DA - 2011// TI - FLASH: fast length adjustment of short reads to improve genome assemblies JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr507 DO - 10.1093/bioinformatics/btr507 ID - Magoc2011 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - KEGG: Kyoto encyclopedia of genes and genomes JO - Nucl Acids Res. VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Edgar, R. C. PY - 2010 DA - 2010// TI - Search and clustering orders of magnitude faster than BLAST JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq461 DO - 10.1093/bioinformatics/btq461 ID - Edgar2010 ER - TY - JOUR AU - Subramanian, A. AU - Kuehn, H. AU - Gould, J. AU - Tamayo, P. AU - Mesirov, J. P. PY - 2007 DA - 2007// TI - GSEA-P: a desktop application for gene set enrichment analysis JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm369 DO - 10.1093/bioinformatics/btm369 ID - Subramanian2007 ER - TY - BOOK PY - 2013 DA - 2013// TI - R: a language and environment for statistical computing PB - R Foundation for Statistical Computing CY - Vienna ID - ref30 ER - TY - STD TI - Chung D, Chun H, Keleş S. Spls: sparse partial least squares (SPLS) regression and classification. R package; 2012. ID - ref31 ER - TY - JOUR AU - Markowitz, V. M. AU - Chen, I. M. AU - Chu, K. AU - Szeto, E. AU - Palaniappan, K. AU - Pillay, M. PY - 2014 DA - 2014// TI - IMG/M 4 version of the integrated metagenome comparative analysis system JO - Nucl Acids Res. VL - 42 UR - https://doi.org/10.1093/nar/gkt919 DO - 10.1093/nar/gkt919 ID - Markowitz2014 ER - TY - JOUR AU - Zhu, W. AU - Lomsadze, A. AU - Borodovsky, M. PY - 2010 DA - 2010// TI - Ab initio gene identification in metagenomic sequences JO - Nucl Acids Res. VL - 38 UR - https://doi.org/10.1093/nar/gkq275 DO - 10.1093/nar/gkq275 ID - Zhu2010 ER - TY - JOUR AU - Altschul, S. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 5 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Huson, D. H. AU - Mitra, S. AU - Ruscheweyh, H. J. AU - Weber, N. AU - Schuster, S. C. PY - 2011 DA - 2011// TI - Integrative analysis of environmental sequences using MEGAN4 JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.120618.111 DO - 10.1101/gr.120618.111 ID - Huson2011 ER - TY - JOUR AU - Eichinger, V. AU - Nussbaumer, T. AU - Platzer, A. AU - Jehl, M. -. A. AU - Arnold, R. AU - Rattei, T. PY - 2016 DA - 2016// TI - EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems JO - Nucl Acids Res. VL - 4 UR - https://doi.org/10.1093/nar/gkv1269 DO - 10.1093/nar/gkv1269 ID - Eichinger2016 ER - TY - JOUR AU - Kenters, N. AU - Henderson, G. AU - Jeyanathan, J. AU - Kittelmann, S. AU - Janssen, P. H. PY - 2011 DA - 2011// TI - Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium JO - J Microbiol Meth. VL - 84 UR - https://doi.org/10.1016/j.mimet.2010.10.011 DO - 10.1016/j.mimet.2010.10.011 ID - Kenters2011 ER - TY - JOUR AU - Joblin, K. N. AU - Naylor, G. E. AU - Williams, A. G. PY - 1990 DA - 1990// TI - Effect of Methanobrevibacter smithii on xylanolytic activity of anaerobic ruminal fungi JO - Appl Environ Microbiol VL - 56 ID - Joblin1990 ER - TY - JOUR AU - Galán, J. E. AU - Lara-Tejero, M. AU - Marlovits, T. C. AU - Wagner, S. PY - 2014 DA - 2014// TI - Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells JO - Annu Rev Microbiol VL - 68 UR - https://doi.org/10.1146/annurev-micro-092412-155725 DO - 10.1146/annurev-micro-092412-155725 ID - Galán2014 ER - TY - JOUR AU - Barker, J. AU - Brown, M. R. W. PY - 1994 DA - 1994// TI - Trojan horses of the microbial world: protozoa and the survival of bacterial pathogens in the environment JO - Microbiology VL - 140 UR - https://doi.org/10.1099/00221287-140-6-1253 DO - 10.1099/00221287-140-6-1253 ID - Barker1994 ER - TY - JOUR AU - Fauvart, M. AU - Michiels, J. PY - 2008 DA - 2008// TI - Rhizobial secreted proteins as determinants of host specificity in the rhizobium legume symbiosis JO - FEMS Microbiol Lett VL - 285 UR - https://doi.org/10.1111/j.1574-6968.2008.01254.x DO - 10.1111/j.1574-6968.2008.01254.x ID - Fauvart2008 ER - TY - JOUR AU - Bryant, M. P. AU - Small, N. PY - 1956 DA - 1956// TI - Characteristics of two new genera of anaerobic curved rods isolated from the rumen of cattle JO - J Bacteriol VL - 72 ID - Bryant1956 ER - TY - JOUR AU - Bryant, M. P. AU - Small, N. AU - Bouma, C. AU - Chu, H. PY - 1958 DA - 1958// TI - Bacteroides ruminicola n. sp. and Succinimonas amylolytica; the new genus and species; species of succinic acid-producing anaerobic bacteria of the bovine rumen JO - J Bacteriol VL - 76 ID - Bryant1958 ER - TY - JOUR AU - Campbell, L. L. AU - Postgate, J. R. PY - 1965 DA - 1965// TI - Classification of the spore-forming sulfate-reducing bacteria JO - Bacteriol Rev. VL - 29 ID - Campbell1965 ER - TY - JOUR AU - Petri, R. M. AU - Schwaiger, T. AU - Penner, G. B. AU - Beauchemin, K. A. AU - Forster, R. J. AU - McKinnon, J. J. PY - 2013 DA - 2013// TI - Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.03983-12 DO - 10.1128/AEM.03983-12 ID - Petri2013 ER - TY - JOUR AU - Mead, L. J. AU - Jones, G. A. PY - 1981 DA - 1981// TI - Isolation and presumptive identification of adherent epithelial bacteria (“epimural” bacteria) from the ovine rumen wall JO - Appl Environ Microbiol VL - 41 ID - Mead1981 ER - TY - JOUR AU - Bryant, M. P. PY - 1959 DA - 1959// TI - Bacterial species of the rumen JO - Bacteriol Rev. VL - 23 ID - Bryant1959 ER - TY - JOUR AU - Bryant, M. P. PY - 1970 DA - 1970// TI - Normal flora-rumen bacteria JO - Am J Clin Nutr VL - 23 ID - Bryant1970 ER - TY - JOUR AU - Henderson, G. AU - Cox, F. AU - Ganesh, S. AU - Jonker, A. AU - Young, W. AU - Collaborators, G. l. o. b. a. l. R. u. m. e. n. C. e. n. s. u. s. PY - 2015 DA - 2015// TI - Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range JO - Sci Rep. VL - 5 UR - https://doi.org/10.1038/srep14567 DO - 10.1038/srep14567 ID - Henderson2015 ER - TY - JOUR AU - Southern, P. M. PY - 1975 DA - 1975// TI - Bacteremia due to Succinivibrio dextrinosolvens. Report of a case JO - Am J Clin Pathol VL - 64 UR - https://doi.org/10.1093/ajcp/64.4.540 DO - 10.1093/ajcp/64.4.540 ID - Southern1975 ER - TY - JOUR AU - Porschen, R. K. AU - Chan, P. PY - 1977 DA - 1977// TI - Anaerobic vibrio-like organisms cultured from blood: Desulfovibrio desulfuricans and Succinivibrio species JO - J Clin Microbiol VL - 5 ID - Porschen1977 ER - TY - JOUR AU - Dean, P. PY - 2011 DA - 2011// TI - Functional domains and motifs of bacterial type III effector proteins and their roles in infection JO - FEMS Microbiol Rev VL - 35 UR - https://doi.org/10.1111/j.1574-6976.2011.00271.x DO - 10.1111/j.1574-6976.2011.00271.x ID - Dean2011 ER - TY - JOUR AU - Wallace, R. J. AU - Rooke, J. A. AU - McKain, N. AU - Duthie, C. -. A. AU - Hyslop, J. J. AU - Ross, D. W. PY - 2015 DA - 2015// TI - The rumen microbial metagenome associated with high methane production in cattle JO - BMC Genom. VL - 16 UR - https://doi.org/10.1186/s12864-015-2032-0 DO - 10.1186/s12864-015-2032-0 ID - Wallace2015 ER - TY - JOUR AU - McCabe, M. S. AU - Cormican, P. AU - Keogh, K. AU - O’Connor, A. AU - O’Hara, E. AU - Palladino, R. A. PY - 2015 DA - 2015// TI - Illumina MiSeq phylogenetic amplicon sequencing shows a large reduction of an uncharacterised Succinivibrionaceae and an increase of the Methanobrevibacter gottschalkii clade in feed restricted cattle JO - PLoS ONE VL - 10 UR - https://doi.org/10.1371/journal.pone.0133234 DO - 10.1371/journal.pone.0133234 ID - McCabe2015 ER - TY - STD TI - Jeyanathan J. Investigation of rumen methanogens in New Zealand livestock. PhD Thesis. New Zealand: Massey University; 2010. ID - ref55 ER - TY - JOUR AU - Pol, A. AU - Demeyer, D. I. PY - 1988 DA - 1988// TI - Fermentation of methanol in the sheep rumen JO - Appl Environ Microbiol VL - 54 ID - Pol1988 ER - TY - JOUR AU - Paul, K. AU - Nonoh, J. O. AU - Mikulski, L. AU - Brune, A. PY - 2012 DA - 2012// TI - “Methanoplasmatales”, Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens JO - Appl Environ Microbiol VL - 78 UR - https://doi.org/10.1128/AEM.02193-12 DO - 10.1128/AEM.02193-12 ID - Paul2012 ER - TY - JOUR AU - Pope, P. B. AU - Denman, S. E. AU - Jones, M. AU - Tringe, S. G. AU - Barry, K. AU - Malfatti, S. A. PY - 2010 DA - 2010// TI - Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.1005297107 DO - 10.1073/pnas.1005297107 ID - Pope2010 ER - TY - JOUR AU - Miller, T. L. AU - Lin, C. PY - 2002 DA - 2002// TI - Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov JO - Int J Syst Evol Microbiol VL - 52 ID - Miller2002 ER -