Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2014, Article ID 483574, 10 pages
http://dx.doi.org/10.1155/2014/483574
Research Article

Comparative Analysis of the Methanogen Diversity in Horse and Pony by Using mcrA Gene and Archaeal 16S rRNA Gene Clone Libraries

1Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-Cho, Tsu, Mie 514-8507, Japan
2Livestock Breeding and Veterinary Department, Yangon Diagnostic Laboratory, Yangon 11121, Myanmar

Received 24 May 2013; Revised 15 October 2013; Accepted 21 October 2013; Published 30 January 2014

Academic Editor: Stefan Spring

Copyright © 2014 Khin-Ohnmar Lwin and Hiroki Matsui. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. S. Stewart, “Microorganisms in hindgut fermentors,” in GastroIntestInal Microbiology, I. Mackie, B. A. White, and R. E. Issacson, Eds., vol. 2, pp. 162–171, Chapman and Hall, New York, NY, USA, 1996. View at Google Scholar
  2. K. Daly, C. S. Stewart, H. J. Flint, and S. P. Shirazi-Beechey, “Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes,” FEMS Microbiology Ecology, vol. 38, no. 2-3, pp. 141–151, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. B. E. Moore and B. A. Dehority, “Effects of diet and hindgut defaunation on diet digestibility and microbial concentrations in the cecum and colon of the horse,” Journal of Animal Science, vol. 71, no. 12, pp. 3350–3358, 1993. View at Google Scholar · View at Scopus
  4. C. Lin and D. A. Stahl, “Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations,” Applied and Environmental Microbiology, vol. 61, no. 4, pp. 1348–1351, 1995. View at Google Scholar · View at Scopus
  5. H. Yamano, S. Koike, Y. Kobayashi, and H. Hata, “Phylogenetic analysis of hindgut microbiota in Hokkaido native horses compared to light horses,” Animal Science Journal, vol. 79, no. 2, pp. 234–242, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. P. M. Hastie, K. Mitchell, and J.-A. M. D. Murray, “Semi-quantitative analysis of Ruminococcus flavefaciens, Fibrobacter succinogenes and Streptococcus bovis in the equine large intestine using real-time polymerase chain reaction,” British Journal of Nutrition, vol. 100, no. 3, pp. 561–568, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. S. Koike, Y. Shingu, H. Inaba et al., “Fecal bacteria in Hokkaido native horses as characterized by microscopic enumeration and competitive polymerase chain reaction assays,” Journal of Equine Science, vol. 11, no. 2, pp. 45–50, 2000. View at Google Scholar · View at Scopus
  8. V. Julliand, A. de Vaux, L. Millet, and G. Fonty, “Identification of Ruminococcus flavefaciens as the predominant cellulolytic bacterial species of the equine cecum,” Applied and Environmental Microbiology, vol. 65, no. 8, pp. 3738–3741, 1999. View at Google Scholar · View at Scopus
  9. Y. Kobayashi, S. Koike, M. Miyaji, H. Hata, and K. Tanaka, “Hindgut microbes, fermentation and their seasonal variations in Hokkaido native horses compared to light horses,” Ecological Research, vol. 21, no. 2, pp. 285–291, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. C. Lin and T. L. Miller, “Phylogenetic analysis of Methanobrevibacter isolated from feces of humans and other animals,” Archives of Microbiology, vol. 169, no. 5, pp. 397–403, 1998. View at Publisher · View at Google Scholar · View at Scopus
  11. A.-D. G. Wright, A. J. Williams, B. Winder, C. T. Christophersen, S. L. Rodgers, and K. D. Smith, “Molecular diversity of rumen methanogens from sheep in Western Australia,” Applied and Environmental Microbiology, vol. 70, no. 3, pp. 1263–1270, 2004. View at Publisher · View at Google Scholar · View at Scopus
  12. E. C. Shin, B. R. Choi, W. J. Lim et al., “Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence,” Anaerobe, vol. 10, no. 6, pp. 313–319, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. E. E. King, R. P. Smith, B. St-Pierre, and A.-D. G. Wright, “Differences in the rumen methanogen populations of lactating Jersey and holstein dairy cows under the same diet regimen,” Applied and Environmental Microbiology, vol. 77, no. 16, pp. 5682–5687, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. H. Y. Tan, C. C. Sieo, C. M. Lee, N. Abdullah, J. B. Liang, and Y. W. Ho, “Diversity of bovine rumen methanogens in vitro in the presence of condensed tannins, as determined by sequence analysis of 16S rRNA gene library,” Journal of Microbiology, vol. 49, no. 3, pp. 492–498, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Tajima, T. Nagamine, H. Matsui, M. Nakamura, and R. I. Aminov, “Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens,” FEMS Microbiology Letters, vol. 200, no. 1, pp. 67–72, 2001. View at Publisher · View at Google Scholar · View at Scopus
  16. K. Yanagita, Y. Kamagata, M. Kawaharasaki, T. Suzuki, Y. Nakamura, and H. Minato, “Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization,” Bioscience, Biotechnology and Biochemistry, vol. 64, no. 8, pp. 1737–1742, 2000. View at Google Scholar · View at Scopus
  17. K. O. Lwin, M. Kondo, T. Ban-Tokuda et al., “Ruminal fermentation and microbial ecology of buffaloes and cattle fed the same diet,” Animal Science Journal, vol. 83, no. 12, pp. 767–776, 2012. View at Publisher · View at Google Scholar
  18. L. C. Skillman, A. F. Toovey, A. J. Williams, and A.-D. G. Wright, “Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet,” Applied and Environmental Microbiology, vol. 72, no. 1, pp. 200–206, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. M. Regensbogenova, N. R. McEwan, P. Javorsky et al., “A re-appraisal of the diversity of the methanogens associated with the rumen ciliates,” FEMS Microbiology Letters, vol. 238, no. 2, pp. 307–313, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. M. Tokura, I. Chagan, K. Ushida, and Y. Kojima, “Phylogenetic study of methanogens associated with rumen ciliates,” Current Microbiology, vol. 39, no. 3, pp. 123–128, 1999. View at Publisher · View at Google Scholar · View at Scopus
  21. M. F. Whitford, R. M. Teather, and R. J. Forster, “Phylogenetic analysis of methanogens from the bovine rumen,” BMC Microbiology, vol. 1, article 5, 2001. View at Google Scholar · View at Scopus
  22. R. Sharp, C. J. Ziemer, M. D. Stern, and D. A. Stahl, “Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system,” FEMS Microbiology Ecology, vol. 26, no. 1, pp. 71–78, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. S. E. Denman, N. W. Tomkins, and C. S. McSweeney, “Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane,” FEMS Microbiology Ecology, vol. 62, no. 3, pp. 313–322, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. Y. Ozutsumi, K. Tajima, A. Takenaka, and H. Itabashi, “The mcrA gene and 16S rRNA gene in the phylogenetic analysis of methanogens in the rumen of faunated and unfaunated cattle,” Animal Science Journal, vol. 83, no. 11, pp. 727–734, 2012. View at Publisher · View at Google Scholar · View at Scopus
  25. K. Paul, J. O. Nonoh, L. Mikulski, and A. Brune, “Methanoplasmatales, thermoplasmatales-related archaea in termite guts and other environments, are the seventh oder of methanogens,” Applied and Environmental Microbiology, vol. 78, no. 23, pp. 8245–8253, 2012. View at Publisher · View at Google Scholar
  26. B. A. Dehority and C. G. Orpin, “Development of, and natural fluctuations in, rumen microbial populations,” in The Rumen Microbial Ecosystem, P. N. Hobson, Ed., pp. 151–183, Elsevier Applied Science, London, UK, 1988. View at Google Scholar
  27. H. Sato and J. Nakajima, “Fecal ammonia, urea, volatile fatty acid and lactate levels in dairy cows and their pathophysiological significance during diarrhea,” Animal Science Journal, vol. 76, no. 6, pp. 595–599, 2005. View at Publisher · View at Google Scholar · View at Scopus
  28. K. O. Lwin, M. Hayakawa, T. Ban-Tokuda, and H. Matsui, “Real-time PCR assays for monitoring anaerobic fungal biomass and population size in the rumen,” Current Microbiology, vol. 62, no. 4, pp. 1147–1151, 2011. View at Publisher · View at Google Scholar · View at Scopus
  29. S. E. Denman and C. S. McSweeney, “Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen,” FEMS Microbiology Ecology, vol. 58, no. 3, pp. 572–582, 2006. View at Publisher · View at Google Scholar · View at Scopus
  30. A.-D. G. Wright and C. Pimm, “Improved strategy for presumptive identification of methanogens using 16S riboprinting,” Journal of Microbiological Methods, vol. 55, no. 2, pp. 337–349, 2003. View at Publisher · View at Google Scholar · View at Scopus
  31. P. E. Luton, J. M. Wayne, R. J. Sharp, and P. W. Riley, “The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill,” Microbiology, vol. 148, no. 11, pp. 3521–3530, 2002. View at Google Scholar · View at Scopus
  32. H. Matsui, T. Ban-Tokuda, and M. Wakita, “Detection of fiber-digesting bacteria in the ceca of ostrich using specific primer sets,” Current Microbiology, vol. 60, no. 2, pp. 112–116, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  34. J. R. Cole, B. Chai, T. L. Marsh et al., “The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy,” Nucleic Acids Research, vol. 31, no. 1, pp. 442–443, 2003. View at Publisher · View at Google Scholar · View at Scopus
  35. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  36. N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, no. 4, pp. 406–425, 1987. View at Google Scholar · View at Scopus
  37. P. D. Schloss and J. Handelsman, “Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness,” Applied and Environmental Microbiology, vol. 71, no. 3, pp. 1501–1506, 2005. View at Publisher · View at Google Scholar · View at Scopus
  38. A. E. Magurran, Ecological Diversity and Its Measurement, Princeton University Press, Princeton, NJ, USA, 1988.
  39. P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. P. N. Evans, L. A. Hinds, L. I. Sly, C. S. McSweeney, M. Morrison, and A.-D. G. Wright, “Community composition and density of Methanogens in the foregut of the Tammar wallaby (Macropus eugenii),” Applied and Environmental Microbiology, vol. 75, no. 8, pp. 2598–2602, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. T. L. Miller and M. J. Wolin, “Methanogens in human and animal intestinal tracts,” Systematic and Applied Microbiology, vol. 7, no. 2-3, pp. 223–229, 1986. View at Publisher · View at Google Scholar
  42. B. B. Jensen, “Methanogenesis in monogastric animals,” Environmental Monitoring and Assessment, vol. 42, no. 1-2, pp. 99–112, 1996. View at Publisher · View at Google Scholar · View at Scopus
  43. B. Morvan, F. Bonnemoy, G. Fonty, and P. Gouet, “Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals,” Current Microbiology, vol. 32, no. 3, pp. 129–133, 1996. View at Google Scholar · View at Scopus
  44. P. P. Chaudhary, S. K. Sirohi, and J. Saxena, “Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis,” Gene, vol. 493, no. 1, pp. 13–17, 2012. View at Publisher · View at Google Scholar · View at Scopus