J Microbiol Methods 2003, 55:337–349.PubMedCrossRef 28. Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95–98. 29. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389–3402.PubMedCrossRef 30. Ashelford KE, Chuzhanova OSI-906 in vivo NA, Fry JC, Jones AJ, Weightman AJ: At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies.

Appl Environ Microbiol 2005, 71:7724–7736.PubMedCrossRef 31. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, VanHorn DJ, Weber CF: Introducing mothur: open-source, platform-independent, community-supported software for describing

and comparing microbial communities. Appl Environ Microbiol 2009,75(23):7537–7541.PubMedCrossRef 32. Shannon CE, Weaver W: The mathematical theory of communication Urbana. University of Illinois Press; 1949. 33. Thompson JD, Higgins DG, Gibson Nirogacestat TJ, Gibson TJ: CLUSTAL W: improving the Selleckchem ISRIB sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673–4680.PubMedCrossRef 34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Dapagliflozin Evolutionary Genetics Analysis using Maximum Likelihood,

Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011, 28:2731–2739.PubMedCrossRef 35. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987,4(4):406–425.PubMed 36. Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985,39(4):783–791.CrossRef 37. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980,16(2):111–120.PubMedCrossRef Competing interests The authors declare that they have no competing interests. Authors’ contributions XDH sampled rumen contents from animals, performed DNA extractions, PCR amplification of methanogen 16S rRNA genes, clone library construction, data analysis, and drafted the manuscript. HYT contributed to all of the lab works and drafted the manuscript. RL conceived the study, sampled rumen contents from animals and drafted the manuscript. JBL contributed to the design of the study and drafted the manuscript; ADW performed data analysis, and drafted the manuscript. All authors read and approved the final manuscript.”
“Background Plant cells are permanently monitoring their immediate environment to identify attacking pathogens and subsequently initiate defense.