Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 important differences in this category, since the fine tuning of gene expression reflects the far and wide dis- tribution of metabolic diversity in Bacillus. We also expected an underrepresentation of genes in COG T (signal transduction; core = 0.03/average = 0.04) and COG V (defense mechanisms; core = 0.01/average = 0.02) in the core, since the different environments where Bacillus activity takes place vary dramatically among species. Therefore, the mechanisms for sensing and responding to stimuli within each niche are not expected to be conserved but to be a part of the acces- sory genes. In contrast, the composition of COGs in the pan-genome shows similarity to that of the B. cereus- anthracis-thuringiensis group. This simply reflects the large redundancy of this group within the overall num- ber of gene families (19,043 families) in the pan-genome. B. cereus, B. thuringiensis, B. anthracis, and B. weihen- stephanensis are described as members of a single spe- cies or taxon, the B. cereus group [43,44], and have the largest number of sequenced members as well as the largest genomes among known Bacillus (5,716 ± 354 coding genes). Therefore, it is remarkable that category G (carbohydrate transport and metabolism; B. cereus = 0.05/average = 0.07) is underrepresented compared to all other groups, while all other groups have similar amounts of genes from this category. This finding reflects a specialization in the metabolism of carbohy- drates when compared to other groups. It is well docu- mented that B. cereus has considerably less genes for the degradation of carbohydrates compared to B. subtilis [9], and this observation contradicts the hypothesis that the ancestor of B. cereus was a soil bacterium. The B. cereus group lacks the metabolic potential for the uptake and assimilation of plant-derived carbohydrates that exists in soil bacteria, such as B. subtilis, limiting the number of polysaccharides that are degraded by this group to glycogen, starch, chitin and chitosan [9]. The pathogenic Bacillius are included in the B. cereus group, and similar to the pan-genome, there is a clear predomi- nance of genes in COG category V (involved in defense mechanisms; B. cereus = 0.03/average = 0.02), compared to a lower basal average for all of the Bacillus groups and the core genome. As expected, the largest repertoire of antibiotic resistance genes is present in the B. cereus group. This group is actively suffering selective pressure for these traits, a feature that is not observed in any of the other groups [33,45,46]. Restriction endonucleases, ABC-type transporters for the detoxification of cells, cation/multidrug efflux pumps, and enzymes involved in antibiotic resistance are all found within the COG V category. However, most pathogenic traits of these strains are encoded in plasmids and mobile elements. Examples of this are the Cry toxins of B. thuringiensis, the anthrax toxin and capsule genes of B. anthracis Page 8 of 17 located on the pX01 and pX02 plasmids, and the emetic toxin of B. cereus located on the pX01-like plasmid (this feature has been used for phenotypic differentiation of the closely related strains). However, it has recently been shown that there can be multiple plasmid transfers among the B. cereus group strains [44], thereby compro- mising the main genetic and phenotypic differences within the cereus-thuringiensis-anthracis group. Two interesting features appear when comparing the B. coahuilensis-m313-NRRLB14911 group to the other groups. First, this group contains the largest proportion of genes in category T (signal transduction; B. coahui- lensis’ group = 0.05/average = 0.04). These genes are thought to have been acquired through HGT, most likely from a Cyanobateria, in a similar manner as the sensory rhodopsin from B. coahuilensis [16]. The three members of this group were isolated from shallow waters exposed to high radiation and oligotrophic condi- tions. Two of them were isolated from a desiccation lagoon and the Bacillus sp. NRRLB14911 strain was iso- lated from the Gulf of Mexico at a depth of 10 m. These environments may require the strains to be responsive to sudden changes in conditions [15,16,26], and thus environmental sensing through signal trans- duction genes may be of greater importance than for other groups of Bacillus. This is a particularly noticeable feature of B. coahuilensis, a strain with a genome that seems to have undergone extensive size reduction [16]. The second interesting feature is that with exception to the O. iheyensis group, the B. coahuilensis-m313- NRRLB14911 group has fewer genes from category K (transcription factors; B. coahuilensis group = 0.08/aver- age = 0.09) than all other groups. This group shares phenotypic traits, such as pigmentation, and are subject to a similar osmotic pressure due to salinity. This group also shows an underrepresentation of genes in category C (energy production and conversion; B. coahuilensis group = 0.05/average = 0.06), P (transport and metabo- lism of inorganic ions; B. coahuilensis group = 0.05/ average = 0.06), and E (amino acid metabolism genes; B. coahuilensis group = 0.09/average = 0.1). All of these categories are involved in several of the early stages of amino acid synthesis. Several auxotrophies as well as specialization within these strains have been shown, par- ticularly for B. coahuilensis [16]. This group exhibits the largest genome size variation with a range between 3.3 and 5 Mb. Despite the differences in the number of cod- ing genes, the largest genome (that of NRRLB14911) does not bias the result of the COG T nor does it show an increase in transcription related genes. Finally, a lar- ger than average gene content in the COG J category (translation, ribosome structure; B. coahuilensis group = 0.05/average = 0.06) is noticed in the group, which is congruent with the fact that they have an increase in