Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

Phylogenetic Analysis of 16S rDNA Sequences Manifest Rumen Bacterial Diversity in Gayals (Bos frontalis) Fed Fresh Bamboo Leaves and Twigs (Sinarumdinaria)

  • Deng, Weidong (Yunnan Provincial Laboratory of Animal Nutrition and Feed Science Yunnan Agricultural University) ;
  • Wanapat, Metha (Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University) ;
  • Ma, Songcheng (Faculty of Animal Science, Yunnan Agricultural University) ;
  • Chen, Jing (Faculty of Animal Science, Yunnan Agricultural University) ;
  • Xi, Dongmei (Faculty of Animal Science, Yunnan Agricultural University) ;
  • He, Tianbao (Nujiang District Animal Science and Veterinary Bureau) ;
  • Yang, Zhifang (Nujiang District Animal Science and Veterinary Bureau) ;
  • Mao, Huaming (Yunnan Provincial Laboratory of Animal Nutrition and Feed Science Yunnan Agricultural University)
  • Received : 2006.10.30
  • Accepted : 2007.04.10
  • Published : 2007.07.01
Download PDF
⟨ Previous Next ⟩

Abstract

Six male Gayal (Bos frontalis), approximately two years of age and with a mean live weight of $203{\pm}17$ kg ($mean{\pm}standard\;deviation$), were housed indoors in metabolism cages and fed bamboo (Sinarundinaria) leaves and twigs. After an adjustment period of 24 days of feeding the diet, samples of rumen liquor were obtained for analyses of bacteria in the liquor. The diversity of rumen bacteria was investigated by constructing a 16S rDNA clone library. A total of 147 clones, comprising nearly full length sequences (with a mean length of 1.5 kb) were sequenced and submitted to an on-line similarity search and phylogenetic analysis. Using the criterion of 97% or greater similarity with the sequences of known bacteria, 17 clones were identified as Ruminococcus albus, Butyrivibrio fibrosolvens, Quinella ovalis, Clostridium symbiosium, Succiniclasticum ruminis, Selenomonas ruminantium and Allisonella histaminiformans, respectively. A further 22 clones shared similarity ranging from 90-97% with known bacteria but the similarity in sequences for the remaining 109 clones was less than 90% of those of known bacteria. Using a phylogenetic analysis it was found that the majority of the clones identified (57.1%) were located in the low G+C subdivision, with most of the remainder (42.2% of clones) located in the Cytophage-Flexibacter-Bacteroides (CFB) phylum and one clone (0.7%) was identified as a Spirochaete. It was apparent that Gayal have a large and diverse range of bacteria in the rumen liquor which differ from those of cattle and other ruminants. This may explain the greater live weights of Gayal, compared to cattle, grazing in the harsh natural environments in which Gayal are located naturally.

Keywords

References

  1. Amann, R. I., W. Ludwig and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
  2. An, D., X. Dong and 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. https://doi.org/10.1016/j.anaerobe.2005.02.001
  3. AOAC. 1990. Official Methods of Analysis. 15th edn. Association of Official Analytical Chemists, Arlington, Virginia.
  4. Birnboim, H. C. and J. Doly. 1979. A rapid alkaline extraction procedure for recombinant plasmid DNA. Nucl. Acids Res. 7:1513-1523. https://doi.org/10.1093/nar/7.6.1513
  5. Cheng, P. 1984. Livestock Breeds of China. Animal Production and Health. Paper 46 (E, F, S). Publication by FAO, Rome.
  6. Deng, W. D., L. P. Wang, S. C. Ma, B. Jin, T. B. He, Z. F. Yang, H. M. Mao and M. Wanapat. 2007. Comparison of Gayal (Bos frontalis) and Yunnan Yellow Cattle (Bos taurus): rumen function, digestibilities and nitrogen balance during feeding of pelleted lucerne (Medicago sativum). Asian-Aust. J. Anim. Sci. 20:900-907. https://doi.org/10.5713/ajas.2007.900
  7. Edwards, J. E., N. R. McEwan, A. J. Travis and R. J. Wallace. 2004. 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek. 86:263-281. https://doi.org/10.1023/B:ANTO.0000047942.69033.24
  8. Farrelly, V., F. A. Rainey and 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.
  9. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evol. 39:783-791. https://doi.org/10.2307/2408678
  10. Garner, M. R., J. F. Flint and J. B. Russell. 2002. Allisonella histaminiformans gen. nov., sp. nov. a novel bacterium that produces histamine, utilizes histidine as its sole energy source, and could play a role in bovine and equine laminitis. Syst. Appl. Microbiol. 25:498-506. https://doi.org/10.1078/07232020260517625
  11. Giasuddin, M. and M. R. Islam. 2003. Physical feature, physicalogical character and behavior study of gayal (Bos frontalis). Asian-Aust. J. Anim. Sci. 16:1599-1603. https://doi.org/10.5713/ajas.2003.1599
  12. Giasuddin, M., K. S. Huque and J. Alam. 2003. Reproductive potentials of gayal (Bos frontalis) under semi-intensive management. Asian-Aust. J. Anim. Sci. 16:331-334. https://doi.org/10.5713/ajas.2003.331
  13. Goering, H. K. and P. J. Van Soest. 1970. Forage Fiber Analysis (Apparatus, Reagent, Procedures and Some Application): Agric. Handbook No. 379. ARS, USDA, Washington, D. C.
  14. Hungate, R. E. 1966. The Rumen and Its Microbes. Academic Press, New York.
  15. Khampa, S., M. Wanapat, C. Wachirapakorn, N. Nontaso and M. Wattiaux. 2006a. Effects of urea level and sodium dl-malate in concentrate containing high cassava chip on ruminal fermentation efficiency, microbial protein synthesis in lactating dairy cows raised under tropical condition. Asian-Aust. J. Anim. Sci. 19:837-844. https://doi.org/10.5713/ajas.2006.837
  16. Khampa, S., M. Wanapat, C. Wachirapakorn, N. Nontaso, M. A. Wattiaux and P. Rowlison. 2006b. Effect of levels of sodium dl-malate supplementation on ruminal fermentation efficiency of concentrates containing high levels of cassava chip in dairy steers. Asian-Aust. J. Anim. Sci. 19:368-375. https://doi.org/10.5713/ajas.2006.368
  17. Kobayashi, Y. 2006. Inclusion of novel bacteria in rumen microbiology: Need for basic and applied science. Anim. Sci. J. 77:375-385. https://doi.org/10.1111/j.1740-0929.2006.00362.x
  18. Kocherginskaya, S. A., R. I. Aminov and B. A. 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. https://doi.org/10.1006/anae.2001.0378
  19. Koike, S., J. Pan, Y. Kobayashi and K. Tanaka. 2003a. Kinetics of in sacco fiber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR. J. Dairy Sci. 86:1429-1435. https://doi.org/10.3168/jds.S0022-0302(03)73726-6
  20. Koike, S., S. Yoshitani, Y. Kobayashi and K. Tanaka. 2003b. Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol. Lett. 229:23-30. https://doi.org/10.1016/S0378-1097(03)00760-2
  21. Krause, D. O. and J. B. Russell. 1996. How many ruminal bacteria are there? J. Dairy Sci. 79:1467-1475. https://doi.org/10.3168/jds.S0022-0302(96)76506-2
  22. Krause, D. O., S. E. Denman, R. I. Mackie, M. Morrison, A. L. Rae, G. T. Attwood and C. S. McSweeney. 2003. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol. Rev. 27:663-693. https://doi.org/10.1016/S0168-6445(03)00072-X
  23. Krumholz, L. R., M. P. Bryant, W. J. Brulla, J. L. Vicini, J. H. Clark and D. A. Stahl. 1993. Proposal of Quinella ovalis gen. nov., sp. nov., Based on phylogenetic analysis. Int. J. Syst. Bacteriol. 43:293-296. https://doi.org/10.1099/00207713-43-2-293
  24. Latham, M. J., J. E. Storry and M. E. Sharpe. 1972. Effect of low-roughage diets on the microflora and lipid metabolism in the rumen. Appl. Microbiol. 24:871-877.
  25. Lila, Z. A., N. Mohammed, S. Kanda, M. Kurihara and H. Itabashi. 2005. Sarsaponin effects on ruminal fermentation and microbes, methane production, digestibility and blood metabolites in steers. Asian-Aust. J. Anim. Sci. 18:1746-1751. https://doi.org/10.5713/ajas.2005.1746
  26. Madden, T. L., R. L. Tatusov and J. Zhang. 1996. Application of network BLAST server. Meth. Enzymol. 266:131-141. https://doi.org/10.1016/S0076-6879(96)66011-X
  27. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. P. Jr, P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucl. Acids Res. 29:173-174. https://doi.org/10.1093/nar/29.1.173
  28. Mao, H. M., W. D. Deng and J. K. Wen. 2005. The biology characteristics of gayal (Bos frontalis) and potential exploitation and utilization. J. Yunnan Agri. Univ. 20:258-261 (in Chinese, with English abstract).
  29. Mondal, M., A. Dhali, C. Rajkhowa and B. K. Prakash. 2004. Secretion patterns of growth hormone in growing captive mithuns (Bos frontalis). Zool. Sci. 21:1125-1129. https://doi.org/10.2108/zsj.21.1125
  30. Nelson, K. E., S. H. Zinder, I. Hance, P. Burr, D. Odongo, D. Wasawo, A. Odenyo and 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. https://doi.org/10.1046/j.1462-2920.2003.00526.x
  31. Ozutsumi, Y., K. Tajima, A. Takenaka and H. Itabashi. 2005. The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries. Biosci. Biotechnol. Biochem. 69:499-506. https://doi.org/10.1271/bbb.69.499
  32. Paster, B. J., F. E. Dewhirst, W. G. Weisburg, G. J. Fraser, L. A. Tordoff, R. B. Hespell, T. B. Stanton, L. Zablen and C. R. Woese. 1991. Phylogenetic analysis of the spirochetes. J. Bacteriol. 173:6101-6109. https://doi.org/10.1128/jb.173.19.6101-6109.1991
  33. Rajkhowa, S., D. K. Sarma and C. Rajkhowa. 2006. Seroprevalence of toxoplasma gondii antibodies in captive mithuns (Bos frontalis) from India. Vet. Parasitol. 135:369-374. https://doi.org/10.1016/j.vetpar.2005.10.007
  34. Regensbogenova, M., N. R. McEwan, P. Javorsky, S. Kisidayova, T. Michalowski, C. J. Newbold, J. H. P. Hackstein and P. Pristas. 2004. A re-appraisal of the diversity of the methanogens associated with the rumen ciliates. FEMS Microbiol. Lett. 238:307-313. https://doi.org/10.1111/j.1574-6968.2004.tb09771.x
  35. Reysenbach, A. L., L. J. Giver, G. S. Wickham and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
  36. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  37. Shin, E. C., B. R. Choi, W. J. Lim, S. Y. Hong, C. L. An, K. M. Cho, Y. K. Kim, J. M. An, J. M. Kang, S. S. Lee, H. Kim and H. D. Yun. 2004a. Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe. 10:313-319. https://doi.org/10.1016/j.anaerobe.2004.08.002
  38. Shin, E. C., K. M. Cho, W. J. Lim, S. Y. Hong, C. L. An, E. J. Kim, Y. K. Kim, B. R. Choi, J. M. An, J. M. Kang, H. Kim and H. D. Yun. 2004b. Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences. J. Appl. Microbiol. 97:378-383. https://doi.org/10.1111/j.1365-2672.2004.02304.x
  39. Srinivas, B. and U. Krishnamoorthy. 2005. Influence of diet induced changes in rumen microbial characteristics on gas production kinetics of straw substrates in vitro. Asian-Aust. J. Anim. Sci. 18:990-996. https://doi.org/10.5713/ajas.2005.990
  40. Stackebrandt, E. and B. M. 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. https://doi.org/10.1099/00207713-44-4-846
  41. Stahl, D. A., B. Flesher, H. R. Mansfield and L. Montgomery. 1988. Use of phylogenetically-based hybridization probes for studies of rumen microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
  42. Stewart, C. S., H. J. Flint and M. P. Bryant. 1997. The rumen bacteria. In: The Rumen Microbial Ecosystem. 2nd ED. (Ed. P. N. Hobson and C. S. Stewart). Chapman and Hall, New York, pp. 10-72.
  43. Suzuki, M. T. and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
  44. Sylvester, J. T., S. K. R. Karnati, Z. Yu, M. Morrison and J. L. Firkins. 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J. Nutr. 134:3378-3384. https://doi.org/10.1093/jn/134.12.3378
  45. Tajima, K., R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui and Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29:159-169. https://doi.org/10.1111/j.1574-6941.1999.tb00607.x
  46. Tajima, K., S. Arai, K. Ogata, T. Nagamine, H. Matsui, M. Nakamura, R. I. Aminov and Y. Benno. 2000. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe. 6:273-284. https://doi.org/10.1006/anae.2000.0353
  47. Tajima, K., R. I. Aminov, T. Nagamine, H. Matsui, M. Nakamura and Y. Benno. 2001. Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl. Environ. Microbiol. 67:2766-2774. https://doi.org/10.1128/AEM.67.6.2766-2774.2001
  48. Thompson, J. D., D. G. Higgins and T. J. 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. https://doi.org/10.1093/nar/22.22.4673
  49. Yuangklang, C., M. Wanapat and C. Wachirapakorn. 2005. Effects of pelleted sugarcane tops on voluntary feed intake, digestibility and rumen fermentation in beef cattle. Asian-Aust. J. Anim. Sci. 18:22-26. https://doi.org/10.5713/ajas.2005.22
  50. Van Soest, P. J. 1994. Nutritional Ecology of the Ruminant. 2nd ED. Cornell University Press, Ithaca, New York.
  51. Von Wintzingerode, F., U. B. Goebel and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229. https://doi.org/10.1111/j.1574-6976.1997.tb00351.x
  52. White, B. A., I. K. O. Cann, S. A. Kocherginskaya, R. I. Amino, L. A. Thill, R. I. Mackie and R. Onodera. 1999. Molecular analysis of archaea, bacteria and eucarya communities in the rumen-review. Asian-Aust. J. Anim. Sci. 12:129-138. https://doi.org/10.5713/ajas.1999.129
  53. Whitford, M. F., R. J. Forster, C. E. Beard, J. Gong and R. M. Teather. 1998. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe. 4:153-163. https://doi.org/10.1006/anae.1998.0155
  54. Xi, D. M., M. Wanapat, W. D. Deng, T. B. He, Z. F. Yang and H. M. Mao. 2007. Comparison of Gayal (Bos frontalis) and Yunnan Yellow Cattle (Bos taurus): in vitro dry matter digestibility and gas production for a range of forages. Asian-Aust. J. Anim. Sci. In press.
  55. Zoetendal, E. G., A. L. Akkermans and W. M. 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.

Cited by

  1. Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks (Bos grunniens) vol.37, pp.1, 2010, https://doi.org/10.1007/s11033-009-9794-x
  2. Phylogenetic analysis of the fecal flora of the wild pygmy loris vol.72, pp.8, 2010, https://doi.org/10.1002/ajp.20826
  3. Dominant bacterial communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens) and Yunnan Yellow Cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis vol.38, pp.8, 2011, https://doi.org/10.1007/s11033-010-0627-8
  4. Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis vol.39, pp.5, 2012, https://doi.org/10.1007/s11033-011-1375-0
  5. The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review vol.35, pp.2, 2008, https://doi.org/10.1007/s11033-007-9079-1
  6. Comparison of Gayal (Bos frontalis) and Yunnan Yellow Cattle (Bos taurus): In vitro Dry Matter Digestibility and Gas Production for a Range of Forages vol.20, pp.8, 2007, https://doi.org/10.5713/ajas.2007.1208
  7. Assessment of rumen microbial diversity of buffalo raised under typical feeding condition using Illumina Sequencing technique vol.247, pp.None, 2007, https://doi.org/10.1088/1755-1315/247/1/012064
  8. The use illumina sequencing technique in studying rumen bacteria diversity of Bali cattle given a feed comprised of elephant grass and rice straw vol.492, pp.None, 2007, https://doi.org/10.1088/1755-1315/492/1/012019