Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 assembly of Bacillus sp. NRRL-B14911 [15]. A core gen- ome is a dynamic entity, since the incorporation of new genomes into the database will reduce the total number of genes within core genomes. How does core data com- pare with experimental data, such as the essential genes of B. subtilis [76]?. In this study, we found that the core genome for the sequenced Bacillus includes 61 of the 79 essential genes of B. subtilis. Another approach, using synteny [20] rather than RBH, defined 761 genes of the core genome. That particular study used several definitions of a core-genome and only considered com- plete genomes in the analysis. Our approach defined 814 genes and therefore obtained 54 more genes than the synteny approach. The use of a synteny strategy to identify a core genome would clearly miss rearranged orthologs and would also be limited if it were applied to WGS assemblies. Thus, working with orthologs as RBH may be a better approach. Pan-genomes at genus level are only beginning to be described, and the number of gene families in these is expected to grow as more genomes are included. This approach however is highly valuable to reveal niche spe- cific genes, to guide future studies linking genes to ecol- ogy, and even for selecting new genomes to sequence that could balance and enrich our knowledge of the Bacillus genus. The genetic features that explain meta- bolic diversity and that are part of the pan-genome and the non-core genes (known also as dispensable or “accessory” genes) are missing from the usual rRNA and MLST analysis. Genes involved in niche adaptation are amongst the dispensable genes and the whole pan-gen- ome. Several of these genes are mobilized by means of HGT, such as genomic islands or individual elements involved in pathogenicity, as is the case for the B. cereus group [77], responses to environmental stresses like phosphorous deprivation found for B. coahuilensis [16]. In addition to core genome phylogenetics and the deter- mination of ecological and geographical features, we suggest taking into account gene functions, such as COG comparative distributions, in order to describe species clusters and compare the phylogenetic profile with the functional profile. These data will aid in the analysis of the concordance or incongruence between them. The existence of model organisms, such as B. subtilis str. 168, has been crucial for inferring homologous gene functions through all bacteria using physiological, genetic, and molecular biology approaches. The power and unequivocal value of the model organism in tackling biological mysteries is clear, but recent work on the intra-specific diversity of this model organism [78] has led us to recognize the great genomic variation that exists. These findings suggest that strain-specific genes are at the base of broad adaptations of B. subtilis to the Page 13 of 17 terrestrial and aquatic environments from where it has been isolated. The B. subtilis str. 168 genome was sequenced in early 1997, but concerns regarding the effects of domestication of the strain in the laboratory and the subsequent genomic changes, as well as reeva- luation of the quality of the original sequence, led to the re-sequencing of str. 168 [79]. Interestingly, other strains within the subtilis species show differences in the con- servancy of genes. This is true even within the so-called essential genes, sporulation and competence genes, which are a central part of Bacillus biology. Therefore, the variability of gene content in the sporulation and essential genes amongst other representatives of the genus comes as no surprise. Although spore formation is central to the definition of Bacilli, it is clear that variability in the sensing of stress conditions, spore resistance, and germination is the result of specific niche constrains. Use of comparative genomics, ecological and evolu- tionary facts, and the lowering costs of genomic sequen- cing are together aiding in the understanding of microbial diversity. Our next steps must focus on ana- lyzing the temporal and spatial patterns of genes present or absent using high throughput genetic expression in order to understand the roles of microbes in their envir- onments. Science is moving into a paradigm shift in the study of bacteria from single individuals to populations with the boost from metagenomic approaches. The chal- lenges of unveiling comprehensive relationships between the environment, genes, and evolution of the bacterial species remain ahead. Conclusions We have determined and defined a set of 814 genes that make up the core genome of Bacillus. From the core genome, we have reconstructed a robust phylogeny of the group using GSS index data, which use the total number of pairwise shared genes to resolve phylogenetic relationships within the group. Both the core genome and GSS phylogenies describe a new group of aquatic Bacilli that have similar habitats. To understand the biology of each group of Bacillus as defined by the respective phylogenies, we have described functional roles of their genes as well as differences between the core and pan-genomes. Our results show that a total of 53 genes comprise the sporulation and competence core genome. In addition, we have highlighted the differences in gene set conservancy across all Bacillus species that have been previously defined for B. subtilis. Our work will be a valuable resource for understanding the evolu- tionary and functional relationships within the Bacillus genus. The core genome defined here may also be used as a list of genetic markers for future population genet- ics studies. The lack of conservancy in non-subtilis