Comparison of proteomic similarity with 16S rRNA gene similarity Phylogenetic studies currently use 16S rRNA gene sequence comparisons as the standard method for the taxonomic classification of prokaryotes. Two isolates are typically

described as being of the same species if their 16S rRNA genes are more than 97% identical, and of the same genus if their 16S rRNA genes are more than 95% identical [34], although our data (see Table 2) suggest CP673451 that the lower limit for a genus is closer to 90% (and Clostridium and Lactobacillus represent exceptions even to this boundary, as some pairs of isolates in these genera have identities well below 90%). However, analogous thresholds for proteomic similarity–if they exist–are currently unknown. Captisol Additionally, while other studies have reported a relationship between genomic similarity and identity of the 16S rRNA gene, no statistical correlation has been reported (a substantial review of this topic is given by Rosello-Mora and Amann [35]). We therefore sought to investigate the relationship between protein content similarity and 16S rRNA gene similarity in pairs of isolates from the same genus. In doing so, we used two different measures of proteomic similarity: “”shared proteins”" (the number of proteins found in the proteomes of both isolates–in other words, the number of orthologues), and “”average unique proteins”" (the average

of the number of proteins found in isolate A but not isolate B, and the number of proteins found in isolate B but not isolate A). For a given genus, both of these proteomic similarity measures were plotted against the 16S rRNA gene percent identity for all pairs of isolates, and linear regression was used to describe the nature of the relationship (slope and R 2 value) between these variables. As described in the Methods section, only pairs of isolates Amisulpride whose 16S rRNA genes were less than 99.5% identical were included in this analysis. As a result, no slope and R 2 values could be determined for Brucella and Xanthomonas, as no pairs of isolates within these genera had

16S rRNA gene percent identities less than this cutoff. Table 2 contains the results of these analyses. Table 2 Results of comparison between protein content similarity and 16S rRNA gene percent identity Genus 16S range Shared proteins Average unique proteins     Range Slope R 2 Range Slope R 2 Bacillus 90.4-100% 1741-5204 231 0.83* 248-3000 -176 0.69* Brucella 99.9-100% JPH203 purchase 2495-3060 NDa ND 154-454 NDa ND Burkholderia 93.8-100% 2861-6337 192 0.26* 337-4554 -394 0.67* Clostridium 80.3-100% 917-3333 38 0.47* 141-2987 -60 0.36* Lactobacillus 85.8-100% 720-2348 42 0.49* 235-1595 -46 0.19* Mycobacterium 91.3-100% 1258-4327 99 0.13* 87-2994 -151 0.47* Neisseria 98.4-100% 1470-1794 -263 0.19 206-753 305 0.03 Pseudomonas 93.1-100% 2368-5339 68 0.06* 383-2847 -129 0.37* Rhizobium 98.