Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 R E S E A R C H A R T I C L E Open Access Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics Luis David Alcaraz1, Gabriel Moreno-Hagelsieb2, Luis E Eguiarte3, Valeria Souza3, Luis Herrera-Estrella1,4, Gabriela Olmedo1* Abstract Background: The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus. Results: Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches. Conclusions: The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches. Background Bacillus is one of the best characterized bacterial genera. Since the late 19th century, the long history of Bacilli research has included classical microbiology, biochemis- try, and more modern genomic and proteomic approaches. Bacillus is defined as a Gram-positive, rod- shaped bacterium that can be aerobic or facultative anaerobic [1] and produces highly resistant dormant * Correspondence: golmedo@ira.cinvestav.mx 1Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Guanajuato, AP 629 Irapuato, Guanajuato 36500, México endospores in response to nutritional or environmental stresses [2]. Bacilli are ubiquitous bacteria that exploit a wide variety of organic and inorganic substrates as nutrient sources [1]. However, spore dispersal by air and water [3] may lead to false conclusions about the ecological significance of recovered bacillus isolates, since it is not clear if the robust presence of the bacteria is due to the resistant nature of the dispersed spores or due rather to a large adaptive capacity that would allow the bacteria to be found in an active, vegetative state in diverse environments [2]. This study of the Bacillus © 2010 Alcaraz et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.