References
- Flint HJ, Bayer EA, Rincon MT, Lamed R, White BW. Polysaccharide utilization by gut bacteria: Potential for new insights from genomic analysis. Nat Rev Microbiol 2008;6:121-31. https://doi.org/10.1038/nrmicro1817
- Jami E, Israel A, Kotser A, Mizrahi I. Exploring the bovine rumen bacterial community from birth to adulthood. ISME J 2013;7:1069-79. https://doi.org/10.1038/ismej.2013.2
- Bekele AZ, Koike S, Kobayashi Y. Genetic diversity and diet specificity of ruminal prevotella revealed by 16s rrna gene-based analysis. FEMS Microbiol Lett 2010;305:49-57. https://doi.org/10.1111/j.1574-6968.2010.01911.x
- Pitta D, Pinchak W, Dowd S, et al. Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture. Anaerobe 2014;30:11-7. https://doi.org/10.1016/j.anaerobe.2014.07.008
- Menezes AB, Lewis E, O'Donovan M, et al. Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiol Ecol 2011;78:256-65. https://doi.org/10.1111/j.1574-6941.2011.01151.x
- Wanapat M, Cherdthong A. Use of real-time pcr technique in studying rumen cellulolytic bacteria population as affected by level of roughage in swamp buffalo. Curr Microbiol 2009;58:294-9. https://doi.org/10.1007/s00284-008-9322-6
- Huang XD, Tan HY, Long R, Liang JB, Wright ADG. Comparison of methanogen diversity of yak (bos grunniens) and cattle (bos taurus) from the qinghai-tibetan plateau, china. BMC Microbiol 2012;12:1. https://doi.org/10.1186/1471-2180-12-1
- Sun Y, Mao S, Zhu W. Rumen chemical and bacterial changes during stepwise adaptation to a high-concentrate diet in goats. Animal 2010;4:210-7. https://doi.org/10.1017/S175173110999111X
- Mohammadzadeh H, Yanez-Ruiz DR, Martinez-Fernandez G, Abecia L. Molecular comparative assessment of the microbial ecosystem in rumen and faeces of goats fed alfalfa hay alone or combined with oats. Anaerobe 2014;29:52-8. https://doi.org/10.1016/j.anaerobe.2013.11.012
- Highlander SK. High throughput sequencing methods for microbiome profiling: Application to food animal systems. Anim Health Res Rev 2012;13:40-53. https://doi.org/10.1017/S1466252312000126
- Caporaso JG, Lauber CL, Walters WA, et al. Global patterns of 16s rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci 2011;108:4516-22. https://doi.org/10.1073/pnas.1000080107
- Walters WA, Caporaso JG, Lauber CL, et al. Primerprospector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics 2011;27:1159-61. https://doi.org/10.1093/bioinformatics/btr087
- Caporaso JG, Lauber CL, Walters WA et al. Ultra-high-throughput microbial community analysis on the illumina hiseq and miseq platforms. ISME J 2012;6:1621-4. https://doi.org/10.1038/ismej.2012.8
- Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. Uchime improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194-200. https://doi.org/10.1093/bioinformatics/btr381
- Caporaso JG, Bittinger K, Bushman FD, et al. Pynast: A flexible tool for aligning sequences to a template alignment. Bioinformatics 2010;26:266-267. https://doi.org/10.1093/bioinformatics/btp636
- Caporaso JG, Kuczynski J, Stombaugh J, et al. Qiime allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-6. https://doi.org/10.1038/nmeth.f.303
- Benson AK, Kelly SA, Legge R, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci USA 2010;107:18933-8. https://doi.org/10.1073/pnas.1007028107
- Hong PY, Wheeler E, Cann IK, Mackie RI. 2011. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the galapagos islands using 16s rRNA-based pyrosequencing. ISME J 5:1461-70. https://doi.org/10.1038/ismej.2011.33
- Shanks OC, Kelty CA, Archibeque S, et al. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 2011;77:2992-3001. https://doi.org/10.1128/AEM.02988-10
- Jami E, Mizrahi I. Similarity of the ruminal bacteria across individual lactating cows. Anaerobe 2012;18:338-43. https://doi.org/10.1016/j.anaerobe.2012.04.003
- Doerner KC, White, BA. Assessment of the endo-1, 4-beta-glucanase components of ruminococcus flavefaciens fd-1. Appl Environ Microbiol 1990;56:1844-50.
- Shinkai T, Ueki T, Koike S, Kobayashi Y. Determination of bacteria constituting ruminal fibrolytic consortia developed on orchard grass hay stem. J Anim Sci 2014;85:254-61. https://doi.org/10.1111/asj.12145
- Huws SA, Lee MR, Muetzel SM, et al. Forage type and fish oil cause shifts in rumen bacterial diversity. FEMS Microbiol Ecol 2010;73:396-407.
- Lin HH, Yin LJ, Jiang ST. Cloning, expression, and purification of Pseudomonas aeruginosa keratinase in Escherichia coli AD494 (DE3) plyss expression system. J Agric Food Chem 2009;57:3506-11. https://doi.org/10.1021/jf803752j
- Huo W, Zhu W, Mao S. Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats. J Microbiol Biotechn 2014;30:669-80. https://doi.org/10.1007/s11274-013-1489-8
- Koike S, Yoshitani S, Kobayashi Y, Tanaka K. Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol Lett 2003;229:23-30. https://doi.org/10.1016/S0378-1097(03)00760-2
- Huws SA, Kim EJ, Lee MR, et al. As yet uncultured bacteria phylogenetically classified as Prevotella, Lachnospiraceae incertae sedis and unclassified Bacteroidales, Clostridiales, and Ruminococcaceae may play a predominant role in ruminal biohydrogenation. Environ Microbiol 2011;13:1500-12. https://doi.org/10.1111/j.1462-2920.2011.02452.x
- Taguchi H, Koike S, Kobayashi Y, Cann IK, Karita S. Partial characterization of structure and function of a xylanase gene from the rumen hemicellulolytic bacterium Eubacterium ruminantium. J Anim Sci 2004;75:325-32. https://doi.org/10.1111/j.1740-0929.2004.00193.x
- Tajima K, Aminov R, Nagamine T, et al. Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl Environ Microbiol 2001;67:2766-74. https://doi.org/10.1128/AEM.67.6.2766-2774.2001
Cited by
- Changes in the ruminal fermentation and bacterial community structure by a sudden change to a high-concentrate diet in Korean domestic ruminants vol.32, pp.1, 2019, https://doi.org/10.5713/ajas.18.0262
- Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits vol.7, pp.None, 2017, https://doi.org/10.7717/peerj.7910
- Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau vol.65, pp.12, 2017, https://doi.org/10.1139/cjm-2019-0154
- Comparative Analysis of Soil Microbiome Profiles in the Companion Planting of White Clover and Orchard Grass Using 16S rRNA Gene Sequencing Data vol.11, pp.None, 2017, https://doi.org/10.3389/fpls.2020.538311
- Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing vol.8, pp.None, 2017, https://doi.org/10.7717/peerj.10184
- Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats vol.10, pp.11, 2017, https://doi.org/10.3390/ani10111951
- Lignocelluloytic activities and composition of bacterial community in the camel rumen vol.7, pp.3, 2017, https://doi.org/10.3934/microbiol.2021022
- The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi vol.9, pp.1, 2021, https://doi.org/10.3390/microorganisms9010157
- Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts vol.9, pp.None, 2021, https://doi.org/10.7717/peerj.12447
- Ruminal microbiota-host interaction and its effect on nutrient metabolism vol.7, pp.1, 2017, https://doi.org/10.1016/j.aninu.2020.12.001