Effects of Sampling Techniques and Sites on Rumen Microbiome and Fermentation Parameters in Hanwoo Steers |
Song, Jaeyong
(Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration)
Choi, Hyuck (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Jeong, Jin Young (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Lee, Seul (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Lee, Hyun Jung (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Baek, Youlchang (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Ji, Sang Yun (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) Kim, Minseok (Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration) |
1 | Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. DOI |
2 | Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 - Approximately maximum-likihood trees for large alignments. PLoS One 5: e9490. DOI |
3 | Erwin ES, Marco GJ, Emery EM. 1961. Volatile fatty acid analyses of blood and rumen fluid by gas chromatography. J. Dairy Sci. 44: 1768-1771. DOI |
4 | Benson AK, Kelly SA, Legge R, Ma FR, Low SJ, Kim J, et al. 2010. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. P. Natl. Acad. Sci. USA 107: 18933-18938. DOI |
5 | Kim M, Morrison M, Yu Z. 2011. Status of the phy logenetic diversity census of ruminal microbiomes. FEMS Microbiol. Ecol. 76: 49-63. DOI |
6 | Laflin SL, Gnad DP. 2008. Rumen cannulation: procedure and use of a cannulated bovine. Vet. Clin. North Am. Food Anim. Pract. 24: 335-340. |
7 | Lodge-Ivey SL, Browne-Silva J, Horvath MB. 2009. Technical note: bacterial diversity and fermentation end products in rumen fluid samples collected via oral lavage or rumen cannula. J. Anim. Sci. 87: 2333-2337. DOI |
8 | Terre M, Castells L, Fabregas F, Bach A. 2013. Short communication: comparison of pH, volatile fatty acids, and microbiome of rumen samples from preweaned calves obtained via cannula or stomach tube. J. Dairy Sci. 96: 5290-5294. DOI |
9 | Ramos-Morales E, Arco-Perez A, Martin-Garcia AI, Yanez-Ruiz DR, Frutos P, Hervas G. 2014. Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats. Anim. Feed Sci. Technol. 198: 57-66. DOI |
10 | Paz HA, Anderson CL, Muller MJ, Kononoff PJ, Fernando SC. 2016. Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method. Front. Microbiol. 7: 1206. |
11 | Yu Z, Morrison M. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36: 808-812. DOI |
12 | Shen JS, Chai Z, Song LJ, Liu JX, Wu YM. 2012. Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows. J. Dairy Sci. 95: 5978-5984. DOI |
13 | Geishauser T, Gitzel A. 1996. A comparison of rumen fluid sampled by oro-ruminal probe versus rumen fistula. Small Ruminant Res. 21: 63-69. DOI |
14 | Duffield T, Plaizier JC, Fairfield A, Bagg R, Vessie G, Dick P, et al. 2004. Comparison of techniques for measurement of rumen pH in lactating dairy cows. J. Dairy Sci. 87: 59-66. DOI |
15 | Herlemann DP, Labrenz M, Jurgens K, Bertilsson S, Waniek JJ, Andersson AF. 2011. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5: 1571-1579. DOI |
16 | Magoc M, Salzberg S. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957-2963. DOI |
17 | Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7: 335-336. DOI |
18 | Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21: 494-504. DOI |
19 | DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. 2006. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72: 5069-5072. DOI |