Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks (Bos grunniens)

Molecular Biology Reports

Volumn 37, Issue 1, 2010, Pages 553-562

  Yang, L Y ^a   Chen, J ^a   Cheng, X L ^b   Xi, D M ^a   Yang, S L ^a   Deng, W D ^a   Mao, H M ^a  

^a YUNNAN AGRICULTURAL UNIVERSITY   (China)

^b Bio Resource Institute of Diqing District Science and Technology Bureau   (China)

Author keywords

16S rRNA gene; Phylogenetic analysis; Rumen bacteria; Yaks

Indexed keywords

RNA 16S;

ANIMAL EXPERIMENT; ARTICLE; BACTEROIDES; BUTYRIVIBRIO FIBRISOLVENS; CYTOPHAGA; DIET; FEEDING; FLEXIBACTER; GENE LIBRARY; GENE SEQUENCE; MALE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREVOTELLA RUMINICOLA; PROTEOBACTERIA; PSEUDOBUTYRIVIBRIO RUMINIS; RUMEN MICROORGANISM; RUMINANT STOMACH; RUMINOCOCCUS FLAVEFACIENS; SELENOMONAS RUMINANTIUM; SUCCINICLASTICUM RUMINIS; YAK;

ANIMALS; BACTERIA; BASE COMPOSITION; BASE SEQUENCE; BIODIVERSITY; CLONE CELLS; DIET; PHYLOGENY; RNA, RIBOSOMAL, 16S; RUMEN; SEQUENCE HOMOLOGY, NUCLEIC ACID;

BACTERIA (MICROORGANISMS); BACTEROIDETES; BOS; BOS GRUNNIENS; BUTYRIVIBRIO FIBRISOLVENS; MEDICAGO SATIVA; PREVOTELLA RUMINICOLA; PROTEOBACTERIA; PSEUDOBUTYRIVIBRIO RUMINIS; RUMINOCOCCUS FLAVEFACIENS; SELENOMONAS RUMINANTIUM; SUCCINICLASTICUM RUMINIS;

EID: 77749319192     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9794-x     Document Type: Article

References (44)

1. D An X Dong Z Dong 2005 Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses Anaerobe 11 207 215 10.1016/j.anaerobe.2005.02.001 1:CAS:528: DC%2BD2MXkt1Ggu7s%3D 16701570 (Pubitemid 40724527)
2. Sasaki M (1994) Yak: Hardy multi-purpose animal of Asia highland. Pages 1-5 in proceedings of 1st international congress Yak, Lanzhou, China. Supplement of Journal of Gansu Agricultural University, Lanzhou, China
3. Wiener G, Han JL, Long RJ (2003) Origins, domestication and distribution of yak, and production characteristics of yak, 2nd edn. Regional Office for Asia and the Pacific of the Food and Agriculture Organization of the United Nations, Bangkok, Thailand Pages 2, 136-137 in The Yak
4. Van Soest PJ (1994) Nutritional ecology of the ruminant, 2nd edn. Cornell University Press, Ithaca, New York
5. DO Krause JB Russell 1996 How many ruminal bacteria are there? J Dairy Sci 79 1467 1475 1:CAS:528:DyaK28Xlslelsbg%3D 8880472
6. DO Krause SE Denman RI Mackie M Morrison AL Rae GT Attwood CS McSweeney 2003 Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics FEMS Microbiol Rev 27 663 693 10.1016/S0168-6445(03)00072- X 1:CAS:528:DC%2BD3sXpt1ekur8%3D 14638418 (Pubitemid 37456863)
7. EC Shin KM Cho WJ Lim SY Hong CL An EJ Kim YK Kim BR Choi JM An JM Kang H Kim HD Yun 2004 Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences J Appl Microbiol 97 378 383 10.1111/j.1365-2672. 2004.02304.x 1:CAS:528:DC%2BD2cXnt1Klu7Y%3D 15239705 (Pubitemid 38998670)
8. EG Zoetendal AL Akkermans WM Devos 1998 Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria Appl Environ Microbiol 64 3854 3859 1:CAS:528:DyaK1cXms1entLY%3D 9758810
9. S Koike J Pan Y Kobayashi K Tanaka 2003 Kinetics of in sacco fiber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR J Dairy Sci 86 1429 1435 1:CAS:528:DC%2BD3sXjtVajtbo%3D 12741567
10. DA Stahl B Flesher HR Mansfield L Montgomery 1988 Use of phylogenetically-based hybridization probes for studies of rumen microbial ecology Appl Environ Microbiol 54 1079 1084 1:CAS:528:DyaL1cXktlGitr4%3D 3389805
11. JT Sylvester SKR Karnati Z Yu M Morrison JL Firkins 2004 Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR J Nutr 134 3378 3384 1:CAS:528:DC%2BD2cXhtVyitbbF 15570040
12. SA Kocherginskaya RI Aminov BA White 2001 Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches Anaerobe 7 119 134 10.1006/anae.2001.0378 1:CAS:528:DC%2BD3MXotFSrt7k%3D (Pubitemid 32928200)
13. M Regensbogenova NR McEwan P Javorsky S Kisidayova T Michalowski CJ Newbold JHP Hackstein P Pristas 2004 A re-appraisal of the diversity of the methanogens associated with the rumen ciliates FEMS Microbiol Lett 238 307 313 10.1111/j.1574-6968.2004.tb09771.x 1:CAS:528:DC%2BD2cXnsFGmsb4%3D 15358415
14. EC Shin BR Choi WJ Lim SY Hong CL An KM Cho YK Kim JM An JM Kang SS Lee H Kim HD Yun 2004 Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence Anaerobe 10 313 319 10.1016/j.anaerobe. 2004.08.002 1:CAS:528:DC%2BD2cXpsl2hsb8%3D 16701533 (Pubitemid 39535395)
15. WD Deng DM Xi HM Mao M Wanapat 2008 The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review Mol Biol Rep 35 265 274 10.1007/s11033-007-9079-1 1:CAS:528:DC%2BD1cXmtVWrsbo%3D 17484038 (Pubitemid 351713258)
16. CS McSweeney SE Denman ADG Wright Z Yu 2007 Application of recent DNA/RNA-based techniques in rumen ecology Asian-Aust J Anim Sci 20 283 294 1:CAS:528:DC%2BD2sXhsVOksb0%3D
17. BA White IKO Cann SA Kocherginskaya RI Amino LA Thill RI Mackie R Onodera 1999 Molecular analysis of archaea, bacteria and eucarya communities in the rumen-review Asian-Aust J Anim Sci 12 129 138
18. Goering HK, Van Soest PJ (1970) Forage fiber analysis (apparatus, reagent, procedures and some application): agric. Handbook no. 379. ARS, USDA, Washington
19. AOAC (1990) Official methods of analysis, 15th edn. Association of Official Analytical Chemists, Arlington, Virginia
20. WD Deng M Wanapat SC Ma J Chen DM Xi TB He ZF Yang HM Mao 2007 Phylogenetic analysis of 16S rDNA sequences manifest rumen bacterial diversity in Gayals (Bos frontalis) fed fresh bamboo leaves and twigs (Sinarumdinaria) Asian-Aust J Anim Sci 20 1057 1066 1:CAS:528:DC%2BD2sXhtVWqtrfF
21. HC Birnboim J Doly 1979 A rapid alkaline extraction procedure for recombinant plasmid DNA Nucl Acids Res 7 1513 1523 10.1093/nar/7.6.1513 1:CAS:528:DyaL3cXlsVKrtQ%3D%3D 388356
22. BL Maidak JR Cole TG Lilburn Jr CTP Saxman PR Farris RJ Farris GM Garrity GJ Olsen TM Schmidt JM Tiedje 2001 The RDP-II (ribosomal database project) Nucl Acids Res 29 173 174 10.1093/nar/29.1.173 1:CAS:528:DC%2BD3MXjtlWmsr0%3D 11125082
23. TL Madden RL Tatusov J Zhang 1996 Application of network BLAST server Meth Enzymol 266 131 141 10.1016/S0076-6879(96)66011-X 1:CAS:528: DyaK28Xltl2nsLk%3D 8743682 (Pubitemid 26165865)
24. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucl Acids Res 22 4673 4680 10.1093/nar/22.22.4673 1:CAS:528:DyaK2MXitlSgu74%3D 7984417
25. E Stackebrandt BM Goebel 1994 Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology Int J Syst Bacteriol 44 846 847 1:CAS:528:DyaK2MXitFCnsb4%3D
26. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425 1:STN:280: DyaL1c7ovFSjsA%3D%3D 3447015
27. J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791 10.2307/2408678
28. BJ Paster FE Dewhirst WG Weisburg GJ Fraser LA Tordoff RB Hespell TB Stanton L Zablen CR Woese 1991 Phylogenetic analysis of the spirochetes J Bacteriol 173 6101 6109 1:CAS:528:DyaK3MXmslGmt78%3D 1917844
29. IL Good 1953 The population frequencies of species and the estimation of population parameters Biometrika 40 237 264
30. JB Hughes JJ Hellman TH Ricketts BJ Bohannan 2001 Counting the uncountable: statistical approaches to estimating microbial diversity Appl Environ Microbiol 67 4399 4406 10.1128/AEM.67.10.4399-4406.2001 1:CAS:528:DC%2BD3MXns1Wisro%3D 11571135 (Pubitemid 33646064)
31. K Tajima RI Aminov T Nagamine K Ogata M Nakamura H Matsui Y Benno 1999 Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries FEMS Microbiol Ecol 29 159 169 10.1111/j.1574-6941.1999.tb00607.x 1:CAS:528:DyaK1MXksVygt78%3D
32. JE Edwards NR McEwan AJ Travis RJ Wallace 2004 16S rDNA library-based analysis of ruminal bacterial diversity Antonie Van Leeuwenhoek 86 263 281 10.1023/B:ANTO.0000047942.69033.24 1:CAS:528:DC%2BD2cXps1aisLo%3D (Pubitemid 39517705)
33. RI Mackie RI Aminov W Hu AV Klieve D Ouwerkerk MA Sundset Y Kamagata 2003 Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches Appl Environ Microbiol 69 6808 6815 10.1128/AEM.69.11.6808-6815.2003 1:CAS:528: DC%2BD3sXptVyktbo%3D 14602644 (Pubitemid 37420221)
34. R Villemur M Lanthier R Beaudet F Lépine 2006 The Desulfitobacterium genus FEMS Microbiol Rev 30 706 733 10.1111/j.1574-6976.2006. 00029.x 1:CAS:528:DC%2BD28XpslaisLg%3D 16911041 (Pubitemid 44199347)
35. Stewart CS, Flint HJ, Bryant MP (1997) The rumen bacteria. In: Hobson PN, Stewart CS (eds) The rumen microbial ecosystem, 2nd edn. Chapman and Hall, New York, pp 10-72
36. KE Nelson SH Zinder I Hance P Burr D Odongo D Wasawo A Odenyo R Bishop 2003 Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche Environ Microbiol 5 1212 1220 10.1046/j.1462-2920.2003.00526.x 14641599 (Pubitemid 37417791)
37. MF Whitford RJ Forster CE Beard J Gong RM Teather 1998 Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes Anaerobe 4 153 163 10.1006/anae.1998.0155 1:CAS:528:DyaK1cXlsFeisbw%3D 16887636 (Pubitemid 28391036)
38. S Koike S Yoshitani Y Kobayashi K Tanaka 2003 Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria FEMS Microbiol Lett 229 23 30 10.1016/S0378-1097(03)00760-2 1:CAS:528:DC%2BD3sXptlOqs78%3D 14659538 (Pubitemid 37504999)
39. Y Kobayashi 2006 Inclusion of novel bacteria in rumen microbiology: need for basic and applied science Anim Sci J 77 375 385 10.1111/j.1740-0929.2006. 00362.x 1:CAS:528:DC%2BD28XhtVegs77L (Pubitemid 44134184)
40. F Von Wintzingerode UB Gobel E Stackebrandt 1997 Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol Rev 21 213 229 10.1111/j.1574-6976.1997.tb00351.x
41. AL Reysenbach LJ Giver GS Wickham NR Pace 1992 Differential amplification of rRNA genes by polymerase chain reaction Appl Environ Microbiol 58 3417 3418 1:CAS:528:DyaK38XmsVKhs7k%3D 1280061
42. K Tajima RI Aminov T Nagamine H Matsui M Nakamura Y Benno 2001 Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR Appl Environ Microbiol 67 2766 2774 10.1128/AEM.67.6.2766-2774. 2001 1:CAS:528:DC%2BD3MXkt1CitLs%3D 11375193 (Pubitemid 33639756)
43. V Farrelly FA Rainey E Stackebrandt 1995 Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species Appl Environ Microbiol 61 2798 2801 1:CAS:528: DyaK2MXms1GrsLc%3D 7618894
44. MT Suzuki SJ Giovannoni 1996 Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR Appl Environ Microbiol 62 625 630 1:CAS:528:DyaK28XovVCrug%3D%3D 8593063