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Background  The  Bacteroidetes  and  Chlorobi  species constitute two main groups of the  Bacteria  that are closely related in phylogenetic trees. The  Bacteroidetes  species are widely distributed and include many important periodontal pathogens. In contrast, all  Chlorobi  are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.    Results  Systematic blast searches were performed on each open reading frame in the genomes of  Porphyromonas gingivalis  W83,  Bacteroides fragilis  YCH46,  B. thetaiotaomicron  VPI-5482,  Gramella forsetii KT0803, Chlorobium luteolum  (formerly  Pelodictyon luteolum ) DSM 273 and  Chlorobaculum tepidum  (formerly  Chlorobium tepidum ) TLS to search for proteins that are uniquely present in either all or certain subgroups of  Bacteroidetes  and  Chlorobi . These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced  Bacteroidetes  and  Chlorobi  genomes, respectively; 52 and 38 proteins that are limited to species from the  Bacteroidales  and  Flavobacteriales  orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the  Bacteroides  genus. Additionally, 6 proteins that are uniquely shared by species from the  Bacteroidetes  and  Chlorobi  phyla (one of them also present in the  Fibrobacteres ) have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the  Chlorobi  species and a 3 aa deletion in ClpB chaperone that is mainly found in various  Bacteroidales, Flavobacteriales  and  Flexebacteraceae , but generally not found in the homologs from other organisms. Phylogenetic analyses of the  Bacteroidetes  and  Chlorobi  species is also reported based on concatenated sequences for 12 conserved proteins by different methods including the character compatibility (or clique) approach. The placement of  Salinibacter ruber  with other  Bacteroidetes  species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.    Conclusion  The molecular signatures described here provide novel tools for identifying and circumscribing species from the  Bacteroidetes  and  Chlorobi  phyla as well as some of their main groups in clear terms. These results also provide strong evidence that species from these two phyla (and also possibly  Fibrobacteres ) are specifically related to each other and they form a single superphylum. Functional studies on these proteins and indels should aid in the discovery of novel biochemical and physiological characteristics that are unique to these groups of bacteria.

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species