This paper communicates the results of three major analyses, with the first two involving protein content comparisons at the genus level, and the third involving

BMS202 chemical structure comparisons at the species level. In the first analysis, we quantify and analyze the number of proteins (i.e. orthologues) found in all members of a given bacterial genus (its “”core proteome”"), the number of proteins found in one genus, but in none of the other genera used in this study (its “”unique proteome”"), and the number of proteins found in only a single isolate of a genus (“”singlets”"). The second analysis examines the relationship between protein content similarity and 16S rRNA gene percent identity in pairs of bacterial isolates from the same genus. Finally, the third analysis examines several bacterial species to determine whether their proteomes are more cohesive than randomly-selected sets of isolates from the same genus. For the third analysis, we use an operational definition of “”cohesion”". Specifically, we say that a bacterial species is proteomically cohesive if it satisfies two criteria: first, that its core proteome is larger than those of randomly-selected groups of isolates from the same Temozolomide purchase genus; and second, that it contains more proteins

unique to all members of that species than there are proteins unique to randomly-selected groups of isolates from the same genus. Results and Discussion Proteomes used Sixteen genera met the Tau-protein kinase requirements outlined in the Methods section, comprising a total of 211 isolates from 106 species. Table 1 shows the number of isolates and species used for each genus, while additional file 1 provides more detailed information about each individual isolate (i.e. genus, species, strain/isolate identity, proteome size, and genome size). Table 1 Bacteria used in this study Genus N I N S Bacillus 16 10 Brucella 8 5 Burkholderia 19 10 Clostridium 19 10 Lactobacillus 15 12 Mycobacterium 14 11 Neisseria 6 2 Pseudomonas 15 7 Rhizobium 4 2 Rickettsia

11 9 Shigella 7 4 Staphylococcus 18 4 Streptococcus 31 9 Vibrio 8 5 Xanthomonas 8 3 Yersinia 12 3 For each bacterial genus used in this study, the number of isolates used (N I ), as well as the number of species (N S ), is indicated. Orthologue detection To detect orthologues, we used a variation on the reciprocal BLAST hits (RBH) method. Specifically, for two proteins to be declared orthologues, they had to be each other’s best BLAST hit, and both BLAST hits had to attain E-values less than a defined threshold. The Methods section describes an analytical method for choosing this E-value threshold, as well as an empirical technique for estimating the selleck chemicals degree to which the chosen E-value threshold will affect our analyses. In this section, we apply those techniques to choose an appropriate E-value threshold for the comparisons done in this study.