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Open Access Highly Accessed Research article

Comparison of 16S rRNA gene sequences of genus Methanobrevibacter

Abhijit S Dighe1, Kamlesh Jangid1, José M González2, Vyankatesh J Pidiyar1, Milind S Patole1, Dilip R Ranade3 and Yogesh S Shouche1*

Author Affiliations

1 Molecular Biology Unit, National Centre for Cell Science, Pune – 411007, India

2 Departamento de Microbiología y Biología Celular, Facultad de Farmacia, Universidad de La Laguna, 38206 La Laguna – Tenerife, Spain

3 Division of microbial sciences, Agharkar Research Institute, Pune – 411004, India

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BMC Microbiology 2004, 4:20  doi:10.1186/1471-2180-4-20

Published: 5 May 2004

Abstract

Background

The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter.

Results

The phylogenetic analysis of the genus based on 786 bp aligned region from fifty-four representative sequences of the 120 available sequences for the genus revealed seven multi-member groups namely, Ruminantium, Smithii, Woesei, Curvatus, Arboriphilicus, Filiformis, and the Termite gut symbionts along with three separate lineages represented by Mbr. wolinii, Mbr. acididurans, and termite gut flagellate symbiont LHD12. The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequences used for the tree was found to be 0.913 indicating the high degree of goodness of fit of the tree topology. A significant relationship was found between the 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) for the genus with the correlation coefficient (r) for logD and logS, and for [ln(-lnD) and ln(-lnS)] being 0.73 and 0.796 respectively. Our analysis revealed that for this genus, when S = 0.984, D would be <70% at least 99% of the times, and with 70% D as the species "cutoff", any 16S rRNA gene sequence showing <98% sequence similarity can be considered as a separate species. In addition, we deduced group specific signature positions that have remained conserved in evolution of the genus.

Conclusions

A very significant relationship between D and S was found to exist for the genus Methanobrevibacter, implying that it is possible to predict D from S with a known precision for the genus. We propose to include the termite gut flagellate symbiont LHD12, the methanogenic endosymbionts of the ciliate Nyctotherus ovalis, and rat feces isolate RT reported earlier, as separate species of the genus Methanobrevibacter.