Bacterial phylogeny based on comparative sequence analysis (review)

Abstract

Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

“…Sequences (500-600 bp) of selected clones for 16S rRNA genes, pmoA, mmoX and coxL were obtained using the University of Warwick Central Molecular Biology Services Laboratory. Sequences from the NCBI database that were closely related to clone sequences and excised DGGE sequences in this study were identified by ARB (Ludwig et al, 1998) and Basic Local Alignment Search Tool (Altschul et al, 1990). Partial sequences of 16S rRNA were imported into an ARB database (Ludwig et al, 1998) and pre-aligned against the closest relative and alignments were manually checked for consistency and valid secondary structure.…”

“…Sequences from the NCBI database that were closely related to clone sequences and excised DGGE sequences in this study were identified by ARB (Ludwig et al, 1998) and Basic Local Alignment Search Tool (Altschul et al, 1990). Partial sequences of 16S rRNA were imported into an ARB database (Ludwig et al, 1998) and pre-aligned against the closest relative and alignments were manually checked for consistency and valid secondary structure. The dendrogram was derived using maximum likelihood (Axml in ARB) based on alignment columns corresponding to Escherichia coli positions 166-625.…”

Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils

“…3), tentatively named 'Solibacter usitatus' (http://jgi.doe.gov), with sequence similarities of only 81.7-82.6 %. Although the phylogenetic definition of a genus has been a matter of debate (Wayne et al, 1987), a value of 95 % 16S rRNA gene sequence similarity has previously been suggested to delineate different prokaryotic genera (Ludwig et al, 1998). Furthermore, bootstrap support for the separate cluster encompassing strains Jbg-1 T and Wbg-1 T and three additional sequences was high ( Fig.…”

Fluorescent in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples

“…Oligonucleotide probes were designed with the ARB software package (Ludwig et al, 1998), and rRNA sequences were obtained in an aligned form from the Ribosomal Database Project (RDP) (Maidak et al, 1997) supplemented with newly deposited rRNA sequences from GenBank. Fluorescein-labelled oligonucleotides against selected specific target sequences of E. faecalis and E. faecium were synthesized commercially (Eurogentec) and tested for specificity against the set of reference organisms listed in Table 1. All strains were cultured in the appropriate fluid medium until exponential phase; this medium was diluted 1 : 50 in PBS (8 g NaCl l À1 , 0 .…”