The models used (setting mixed model) for generating

the final 50% majority rule trees were estimated by the program itself. The Bayesian inference of phylogenies was initiated from a random starting tree and four chains were run simultaneously for 1 000 000 generations; trees were sampled every 100 generations. Kinase Inhibitor Library purchase The first 25% of trees generated were discarded (“burn-in”) and the remaining trees were used to compute the posterior probability values. Phylogenetic trees were constructed for RpoD, 16S rDNA and all the key genes associated with the EryA genes. Phylogenetic trees were plotted with the TreeView program [29] using MEGA5 and/or MrBayes tree Z-IETD-FMK in vitro outfiles. Final trees were annotated using Adobe Illustrator. Results Phylogenetic distribution of putative erythritol loci Based on homology to eryA from Sinorhizobium meliloti and Rhizobium leguminosarum we have compiled a data set of 19 different putative erythritol loci from 19 different proteobacteria (Table  1).

Previous studies suggested that erythritol loci may be restricted to the alpha-proteobacteria [20]. While a majority of the erythritol loci we identified followed this scheme, CP-690550 cell line surprisingly we identified putative erythritol catabolic loci in Verminephrobacter eiseniae (a beta-proteobacterium) and Escherichia fergusonii (a gamma-proteobacterium). Erythritol loci are not widely distributed through the alpha-proteobacteria. A majority of the loci we identified were within the order Rhizobiales. Outside of the Rhizobiales we also identified erythritol loci in Acidiphilium species and Roseobacter species. Within the Rhizobiales, erythritol loci were notably absent from a large number of bacterial species such as Rhizobium etli, Agrobacterium tumefaciens and Bradyrhizobium japonicum that are closely related to other species that we have identified that contain erythritol loci. We also note that Sinomenine erythritol loci appear to be plasmid

localized only in S. fredii and R. leguminosarum. In all other cases the loci appear to be found on chromosomes. Table 1 Bacterial genomes used in this study containing erythritol loci Genome Accession number Reference/ Affiliation Sinorhizobium meliloti 1021 AL591688.1 [17] Sinorhizobium medicae WSM419 CP000738.1 [30] Sinorhizobium fredii NGR234 CP000874.1 [31] Mesorhizobium opportunism WSM2075 CP002279.1 US DOE Joint Genome Institute Mesorhizobium loti MAFF303099 BA000012.4 [32] Mesorhizobium ciceri bv. biserrulae WSM1271 CP002447.1 US DOE Joint Genome Institute Bradyrhizobium sp. BTAi1 CP000494.1 [33] Bradyrhizobium sp. ORS278 CU234118.1 [33] Agrobacterium radiobacter K84 CP000629.1 [34] Ochrobactrum anthropi ATCC 49188 CP000759.1 [35] Brucella suis 1330 CP002998.1 [36] Brucella melitensis 16M AE008918.1 [37] Acidiphilium multivorum AIU301 AP012035.1 NITE Bioresource Information Center Acidiphilium cryptum JF-5 CP000697.1 US DOE Joint Genome Institute Roseobacter denitrificans Och114 CP000362.