Accession CDS ACPC00000000 4294 (WGS semi-finished) NZ_ABFU00000000 3642 (WGS semi-finished) NC_000964 4408 4326 6248 5569 3736 5610 5641 5590 6010 3733 4349 5973 5090 3913 GC% 40 38 43.5 43.7 38 35.4 35.7 35.3 35.4 35.4 35.4 52.1 44.8 35.4 35.4 41.3 NC_002570 NC_003909 NC_003997 NC_004193 NC_004722 NC_005945 NC_005957 NC_006274 NC_006510 NC_006582 NC_007530 NC_008600 NC_009848 NC_006270 4371 46.2 NC_010184 6133 35.4 Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 Table 1 Species, accession numbers, and general features of Bacillus sp. used in this work [30] Strains Bacillus sp. m3-13 Bacillusc oahuilensis m4-4 Bacillus subtilis subsp. subtilis str. 168 Bacillus halodurans C-125 Bacillus cereus ATCC 10987 Bacillus anthracis str. Ames Oceanobacillus iheyensis HTE831 Bacillus cereus ATCC 14579 Bacillus anthracis str. Sterne Bacillus thuringiensis serovar konkukian str. 97-27 Bacillus licheniformis ATCC 14580 Bacillus cereus E33L Geobacillus kaustophilus HTA426 Bacillus clausii KSM- K16 Bacillus anthracis str. ‘Ames Ancestor’ Bacillus thuringiensis str. Al Hakam Bacillus pumilus SAFR- 032 Bacillus weihenstephanensis KBAB4 Bacillus sp. NRRLB14911 Habitat Fresh water Fresh water Soil Soil, Fresh water Dairy isolate, Soil Soil Marine Soil Soil Host, Soil Soil Soil Deep sea, Marine Soil Soil Host, Soil Soil Soil Phenotype Alkalophile Pathogen Non-Pathogen Alkalophile Pathogen Non-Pathogen Pathogen Pathogen, Subtilisin production, Amylase production Pathogen Alkalitolerant, Probiotic, Protease production Pathogen Biomass degrader, Pathogen, Radiation resistant Non-Pathogen Page 4 of 17 Reference This work [16] [12] [14] [31] [32] [11] [9] [33] [13] [33] [10] [34] [35] [36] [15] Unpublished Unpublished Unpublished NZ_AAOX00000000 5869 (WGS semi-finished) 45.7 Marine 10 meters depth in the Gulf of Mexico genomes from related strains are incorporated into the analysis [5,17,23]. B. coahuilensis has the smallest gen- ome reported for a Bacillus and thus is a good reference to address the number of genes shared between all of the representatives of Bacillus. A full matrix of Recipro- cal Blast Hits (RBH) was constructed for the identifica- tion of the 814 orthologous genes shared by all 20 species analyzed and was defined as the core genome. The average gene content for Bacillus was 4,973 ± 923 genes and thus the core genome reflected only a fifth of the total content of an average genome. In contrast, after clustering homologous protein families, an esti- mated pan-genome size of 155,747 genes was obtained. All pan-genome genes were grouped into 19,043 families and reflect the large repertoire of genes within this cos- mopolitan group. We reconstructed a Maximum Likelihood (ML) phylo- geny using concatenated alignments of the 814 trans- lated core genes across the 20 species (Additional file 1), resulting in a 308,782 amino-acid length alignment (Fig- ure 2A). The phylogeny created clusters of the following major groups: B. clausii-halodurans, B. subtilis- Isolation environment Chihuahuan desert lagoon in Cuatro Cienegas, Coahuila, Mexico in 2005 Chihuahuan desert lagoon in Cuatro Cienegas, Coahuila, Mexico in 2005 X-ray irradiated strain in Marburg in 1947 1977 Cheese spoilage in Canada Deep sea mud at 1050 m depth from the Iheya ridge near Okinawa Japan in 1998 Severe human tissue necrosis Swab of a zebra carcass in Ethosha National Park in Namibia in 1996 Pathogen Severe human tissue necrosis Spacecraft Assembly Facility at NASA Jet Propulsion Laboratory