Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 Page 3 of 17 Figure 1 Overview of this work. Assembly of the sequences resulted in 50 contigs and a total of 4,137,575 bp assembled. The entire genome is 4.1 Mb with 40% GC content, 4,417 coding sequences, and 81 RNAs. Bacillus sp. m3-13 was isolated from a desiccation lagoon in Cuatro Cienegas, Coahuila, Mexico within the same sampling of the previously described B. coahuilen- sis strain [16,26]. Using a 16S rRNA comparison, we determined that the B. horikoshii NBSL26 is the closest strain to Bacillus sp. m3-13 with 99% identity. Both B. coahuilensis and Bacillus sp. m3-13 live in the same oli- gotrophic environment, which includes low phosphorous levels (less than 0.3 μM), but they appear to have differ- ent strategies for dealing with the poor nutrient environ- ment. B. coahuilensis produces sulfolipids and replaces membrane phospholipids [16], In contrast, Bacillus sp. m3-13 has phn genes, which code for phosphonate ABC importers, permeases, and a phosphonate-lyase, and we hypothesize that the strain may use these genes to take up and assimilate phosphonates. Both strategies seem to be used by bacteria from the Cuatro Cienegas [27], as well as by marine bacteria [28,29]. Bacillus core genome phylogenetics To gain insight into the natural history of Bacillus based on the complete genome sequence, we performed a phy- logenetic reconstruction using all of the core genes. We chose at least one representative from each major divi- sion within the Bacillaceae family to maintain the meta- bolic cohesion behind the diverse ecological groups. The type of strains used for this analysis as well as their gen- eral genome features, habitats, accession numbers, isola- tion data, and outstanding phenotypes are summarized in Table 1. As noted in the literature, the total number of genes within a core-genome tends to diminish as more