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Comparison of 16S rRNA gene sequences of genus Methanobrevibacter.

Dighe AS, Jangid K, González JM, Pidiyar VJ, Patole MS, Ranade DR, Shouche YS - BMC Microbiol. (2004)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Biology Unit, National Centre for Cell Science, Pune-411007, India. abhijitdighe@hotmail.com

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.

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Alignment of sequences showing differences in the 16S rRNA gene sequence of endosymbiont of Nyctotherus ovalis strain NO Sequence for strain NO is shown in bold letters. The positions with differences in the 16S rRNA gene sequence of strain NO with other members are shown in bold-italics. See text for GenBank Accession numbers against the strain names used above. "*" indicates conserved positions amongst the sequences used.
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Figure 3: Alignment of sequences showing differences in the 16S rRNA gene sequence of endosymbiont of Nyctotherus ovalis strain NO Sequence for strain NO is shown in bold letters. The positions with differences in the 16S rRNA gene sequence of strain NO with other members are shown in bold-italics. See text for GenBank Accession numbers against the strain names used above. "*" indicates conserved positions amongst the sequences used.

Mentions: We aligned the 16S rRNA gene sequence of the strain NO (AJ132639) along with other members of the Arboriphilicus and Filiformis group (U41095, U82322, AB009827, AB026925, and AB065294), representative species of the genus Methanobrevibacter (U55233, U55240, U62533 and RDP-Mbb.rumina.), Msp. stadtmanae (M59139) and that of E. coli (J01859, Fig. 3). It was clearly seen that there was an insertion of one additional triplet 'AAG' at E. coli position 934. Similarly, there was an insertion of a single base 'A' at E. coli position 1032. Furthermore, there was a deletion of one base each at E. coli positions 970, 995 and 999. As a result of these insertions and deletions, the strain formed a separate branch in the tree. Hence placement of methanogenic endosymbionts of Nyctotherus in the genus Methanobrevibacter needs to be reconsidered and it should be regarded as a separate species of the genus.


Comparison of 16S rRNA gene sequences of genus Methanobrevibacter.

Dighe AS, Jangid K, González JM, Pidiyar VJ, Patole MS, Ranade DR, Shouche YS - BMC Microbiol. (2004)

Alignment of sequences showing differences in the 16S rRNA gene sequence of endosymbiont of Nyctotherus ovalis strain NO Sequence for strain NO is shown in bold letters. The positions with differences in the 16S rRNA gene sequence of strain NO with other members are shown in bold-italics. See text for GenBank Accession numbers against the strain names used above. "*" indicates conserved positions amongst the sequences used.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC415545&req=5

Figure 3: Alignment of sequences showing differences in the 16S rRNA gene sequence of endosymbiont of Nyctotherus ovalis strain NO Sequence for strain NO is shown in bold letters. The positions with differences in the 16S rRNA gene sequence of strain NO with other members are shown in bold-italics. See text for GenBank Accession numbers against the strain names used above. "*" indicates conserved positions amongst the sequences used.
Mentions: We aligned the 16S rRNA gene sequence of the strain NO (AJ132639) along with other members of the Arboriphilicus and Filiformis group (U41095, U82322, AB009827, AB026925, and AB065294), representative species of the genus Methanobrevibacter (U55233, U55240, U62533 and RDP-Mbb.rumina.), Msp. stadtmanae (M59139) and that of E. coli (J01859, Fig. 3). It was clearly seen that there was an insertion of one additional triplet 'AAG' at E. coli position 934. Similarly, there was an insertion of a single base 'A' at E. coli position 1032. Furthermore, there was a deletion of one base each at E. coli positions 970, 995 and 999. As a result of these insertions and deletions, the strain formed a separate branch in the tree. Hence placement of methanogenic endosymbionts of Nyctotherus in the genus Methanobrevibacter needs to be reconsidered and it should be regarded as a separate species of the genus.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Biology Unit, National Centre for Cell Science, Pune-411007, India. abhijitdighe@hotmail.com

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.

Show MeSH
Related in: MedlinePlus