Bacterial phylogeny based on 16S and 23S rRNA sequence analysis

Abstract

Molecular phylogeny increasingly supports the understanding of organismal relationships and provides the basis for the classification of microorganisms according to their natural affiliations. Comparative sequence analysis of ribosomal RNAs or the corresponding genes currently is the most widely used approach for the reconstruction of microbial phylogeny. The highly and less conserved primary and higher order structure elements of rRNAs document the history of microbial evolution and are informative for definite phylogenetic levels. An optimal alignment of the primary structures and a careful data selection are prerequisites for reliable phylogenetic conclusions. rRNA based phylogenetic trees can be reconstructed and the significance of their topologies evaluated by applying distance, maximum parsimony and maximum likelihood methods of phylogeny inference in comparison, and by fortuitous or directed resampling of the data set. Phylogenetic trees based on almost equivalent data sets of bacterial 23S and 16S rRNAs are in good agreement and their overall topologies are supported by alternative phylogenetic markers such as elongation factors and ATPase subunits. Besides their phylogenetic information content, the differently conserved primary structure regions of rRNAs provide target sites for specific hybridization probes which have been proven to be powerful tools for the identification of microbes on the basis of their phylogenetic relationships.

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

“…The 97% sequence similarity used as a criterion for assigning 16S rDNA sequences to individual phylotypes and to assign phylotypes to known species is based on the empirical observation that bacteria sharing less than 97.5% sequence similarity unlikely will be identified as different species in the phylophenetic species concept (42 sequences only, because of the inherent structure of conserved and variable regions of the rRNA molecule. Therefore, and because correct phylogenetic relationships of sequences without any close relatives can be determined only from full 16S rDNA sequences (15,22), the phylogenetic analysis presented in this paper was based on the near-full-length sequences. It is important to note that our estimate of 375 phylotypes found in the pig GI tract is not conclusive but varies according to the conditions set for the analysis.…”

The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.

“…The most important factor in this selection is to choose molecules that are found ubiquitously in the living world, and SSU rRNA, large-subunit (LSU) rRNA (De Rijk et al, 1995;Ludwig et al, 1998), elongation factor EF-Tu/a (Ludwig et al, 1998), RNA polymerases (Klenk & Zillig, 1994), F 1 F 0 ATPase b-subunit (Ludwig et al, 1993(Ludwig et al, , 1998Ludwig & Schleifer, 1994), RecA protein (Wetmur et al, 1994;Eisen, 1995;Karlin et al, 1995) and Hsp60 heat-shock protein (Viale et al, 1994;Gupta, 1998) have, for this reason, proved to be good molecules for the phylogenetic inference of prokaryote taxonomy. SSU rRNA gene sequences have advantages over the other molecules.…”

Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes)

“…Various proteinencoding genes have been used to make phylogenetic inferences (Toth et al, 1994;Falah & Gupta, 1997;Gupta, 1998;Teichmann & Mitchison, 1999;Bébéar et al, 2000;Wolf et al, 2004). However, because 16S rRNA gene sequence analysis has provided satisfactory resolution across the entire prokaryotic spectrum (Ludwig et al, 1998), it will probably retain its primacy in the taxonomy of prokaryotes (Ludwig & Schleifer, 1994. At the time of preparation of this document, at least ten mollicute genomes have been sequenced (Fraser et al, 1995;Himmelreich et al, 1996;Glass et al, 2000;Chambaud et al, 2001;Sasaki et al, 2002;Papazisi et al, 2003;Jaffe et al, 2004;Minion et al, 2004;Oshima et al, 2004;Westberg et al, 2004), and many more are approaching complete annotation.…”