Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis

Gene

Volumn 493, Issue 1, 2012, Pages 13-17

  Chaudhary, Prem Prashant ^a,b   Sirohi, Sunil Kumar ^a   Saxena, Jyoti ^c  

^a NATIONAL DAIRY RESEARCH INSTITUTE   (India)

^b BANASTHALI UNIVERSITY   (India)

^c BT Kumaon Institute of Technology   (India)

Author keywords

Buffalo; Diversity; India; Methanogens; Phylogenetic analysis; Riboprinting

Indexed keywords

GENOMIC DNA; RIBOSOME DNA;

AMPLIFIED RIBOSOMAL DNA RESTRICTION ANALYSIS; ARTICLE; BUBALUS BUBALIS; BUFFALO; DNA ISOLATION; GENE LIBRARY; GENETIC VARIABILITY; MALE; METHANOBACTERIALES; METHANOBREVIBACTER; METHANOCOCCALES; METHANOGEN; METHANOMICROBIALES; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RUMINANT STOMACH; SEQUENCE ANALYSIS;

ANIMALS; BUFFALOES; EVOLUTION, MOLECULAR; MALE; METHANE; PHYLOGENY; RIBOTYPING; RNA, RIBOSOMAL, 16S; RUMEN;

BUBALUS; BUBALUS BUBALIS; METHANOBACTERIALES; METHANOBREVIBACTER; METHANOBREVIBACTER GOTTSCHALKII; METHANOCOCCALES; METHANOMICROBIALES; METHANOMICROBIUM MOBILE; MICROMESISTIUS POUTASSOU;

EID: 84655163822     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.11.041     Document Type: Article

References (30)

1. Chaudhary P.P., Sirohi S.K. Dominance of Methanomicrobium phylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis). Lett. Appl. Microbiol. 2009, 49:274-277.
2. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
3. Finlay B.J., Esteban G., Clarke K.J., Williams A.G., Embley T.M., Hirt R.P. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol. Lett. 1994, 117:157-161.
4. Jarvis G.N., Strömpl C., Burgess D.M., Skillman L.C., Moore E.R.B., Joblin K.N. Isolation and identification of ruminal methanogens from grazing cattle. Curr. Microbiol. 2000, 40:327-332.
5. Karr E.A., Ng J.M., Belchik S.M., Sattley W.M., Madigan M.T., Achenbach L.A. Biodiversity of methanogenic and other archaea in the permanently frozen Lake Fryxell, Antarctica. Appl. Environ. Microbiol. 2006, 72:1663-1666.
6. Kocherginskaya S.A., Aminov R.I., White B.A. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 2001, 7:119-134.
7. 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.
8. Lloyd D.J., Ralphs L., Durrant A.G., Williams A.G., Amann R. Studies of the bacterial endosymbionts of "anaerobic protozoa" using fluorescently-labelled rRNA-targeted oligonucleotide probes. Biochem. Soc. Trans. 1994, 22:323S.
9. Lloyd D., Williams A.G., Amann R. Intracellular prokaryotes in rumen ciliate protozoa - detection by confocal laser-scanning microscopy after in-situ hybridization with fluorescent 16S ribosomal-RNA probes. Eur. J. Protist. 1996, 32:523-531.
10. Madden T.L., Tatusov R.L., Zhang J. Applications of network BLAST server. Methods in Enzymology 1996, 131-141. Academic Press. F.D. Russell (Ed.).
11. Marc F Whitford R.M.T.a.R.J.F. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol. 2001, 5.
12. Ramšak A., Peterka M., Tajima K., Martin J.C., Wood J., Johnston M.E.A., et al. Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol. Ecol. 2000, 33:69-79.
13. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
14. Singh K.M., Tripathi A.K., Pandya P.R., Parnerkar S., Rank D.N., Kothari R.K., et al. Methanogen diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis. Res. Vet. Sci. 2011, Apr 18. [Electronic publication ahead of print]. doi:10.1016/j.rvsc.2011.03.022.
15. Steinfeld H., Gerber P., Wassenaar T. Livestock's long shadow: environmental issues and options 2006, http://www.virtualcentre.org/en/library/key_pub/longshad/A0701E00.pdf.
16. Tajima K., Aminov R.I., Nagamine T., Ogata K., Nakamura M., Matsui H., et al. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 1999, 29:159-169.
17. Tajima K., Arai S., Ogata K., Nagamine T., Matsui H., Nakamura M., et al. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 2000, 6:273-284.
18. Tajima K., Nagamine T., Matsui H., Nakamura M., Aminov R.I. 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 Microbiol. Lett. 2001, 200:67-72.
19. Tamura K.N.M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:11030-11035.
20. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
21. Tokura M., Chagan I., Ushida K., Kojima Y. Phylogenetic study of methanogens associated with rumen ciliates. Curr. Microbiol. 1999, 39:123-128.
22. Tokura M., Tajima K., Ushida K. Isolation of Methanobrevibacter sp. as a ciliate-associated ruminal methanogen. J. Gen. Appl. Microbiol. 1999, 45:43-47.
23. Whitby C., Earl J., Lanyon C., Gray S., Robinson J., Meadows J., et al. The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLP. J. Appl. Microbiol. 2004, 97:973-984.
24. Whitford M.F., Forster R.J., Beard C.E., Gong J., Teather R.M. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 1998, 4:153-163.
25. Wolin M.J., Miller T.L., Stewart C.S. Microbe-microbe interactions. The Rumen Microbial Ecosystem 1997, 467-491. Blackie Academic and Professional, New York. P.N. Hobson, C.S. Stewart (Eds.).
26. Wright A.-D.G., Pimm C. Improved strategy for presumptive identification of methanogens using 16S riboprinting. J. Microbiol. Methods 2003, 55:337-349.
27. Wright A.-D.G., Auckland C.H., Lynn D.H. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl. Environ. Microbiol. 2007, 73:4206-4210.
28. Wright A.D., Ma X., Obispo N.E. Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microb. Ecol. 2008, 56:390-394.
29. Yanagita K., Kamagata Y., Kawaharasaki M., Suzuki T., Nakamura Y., Minato H. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile By fluorescence in situ hybridization. Biosci. Biotechnol. Biochem. 2000, 64:1737-1742.
30. Yu Y., Breitbart M., McNairnie P., Rohwer F. FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 2006, 7:57.