Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 Guanajuato 36500, México. 2Department of Biology, Wilfrid Laurier University, 75 University Ave. W. Waterloo, ON, N2L 3C5, Canada. 3Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CU, AP 70-275 Coyoacán 04510 México DF. 4Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Guanajuato, AP 629 Irapuato, Guanajuato 36500, México. Authors’ contributions LDA, GO, VS, and GM-H conceived and designed the study, LDA, GO, VS and LEE analyzed data, and LHE and GM-H contributed with reagents/materials/ analysis tools. LDA, GO, and GM-H wrote the paper. All authors read and approved the final manuscript. Competing interests The authors declare that they have no competing interests. Received: 29 December 2009 Accepted: 26 May 2010 Published: 26 May 2010 References 1. Ravel J, Fraser CM: Genomics at the genus scale. Trends Microbiol 2005, 13(3):95-97. 2. Earl AM, Losick R, Kolter R: Ecology and genomics of Bacillus subtilis. Trends Microbiol 2008, 16(6):269-275. 3. Merrill L, Dunbar J, Richardson J, Kuske CR: Composition of Bacillus Species in Aerosols from 11 U.S. Cities. Journal of Forensic Sciences 2006, 51(3):559-565. 4. Hugenholtz P: Exploring prokaryotic diversity in the genomic era. Genome Biol 2002, 3(2):REVIEWS0003. 5. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, et al: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009, 5(1):e1000344. 6. Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, et al: Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis. FEMS Microbiol Lett 2005, 250(2):175-184. 7. Priest FG, Barker M, Baillie LWJ, Holmes EC, Maiden MCJ: Population Structure and Evolution of the Bacillus cereus Group. J Bacteriol 2004, 186(23):7959-7970. 8. Helgason E, Tourasse NJ, Meisal R, Caugant DA, Kolsto A-B: Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group. Appl Environ Microbiol 2004, 70(1):191-201. 9. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, et al: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 2003, 423(6935):87-91. 10. Takami H, Takaki Y, Chee GJ, Nishi S, Shimamura S, Suzuki H, Matsui S, Uchiyama I: Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res 2004, 32(21):6292-6303. 11. Takami H, Takaki Y, Uchiyama I: Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 2002, 30(18):3927-3935. 12. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997, 390(6657):249-256. 13. Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, de Leon Lopez A, Xiang H, Gusti V, Clausen IG, et al: Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol 2004, 5(10):R77. 14. Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, et al: Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 2000, 28(21):4317-4331. 15. Siefert JL, Larios-Sanz M, Nakamura LK, Slepecky RA, Paul JH, Moore ER, Fox GE, Jurtshuk P Jr: Phylogeny of marine Bacillus isolates from the Gulf of Mexico. Curr Microbiol 2000, 41(2):84-88. Page 15 of 17 16. Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernandez G, Cruz A, Ramirez E, Putonti C, Jimenez B, Martinez E, et al: The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment. Proc Natl Acad Sci USA 2008, 105(15):5803-5808. 17. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 2005, 102(39):13950-13955. 18. Tettelin H, Riley D, Cattuto C, Medini D: Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 2008, 11(5):472-477. 19. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R: The microbial pan- genome. Curr Opin Genet Dev 2005, 15(6):589-594. 20. Uchiyama I: Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics 2008, 9:515. 21. Cortez D, Forterre P, Gribaldo S: A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biology 2009, 10(6): R65. 22. Harris JK, Kelley ST, Spiegelman GB, Pace NR: The genetic core of the universal ancestor. Genome Res 2003, 13(3):407-412. 23. Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, de Marsac NT, Wincker P, Dossat C, et al: Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol 2008, 9(5):R90. 24. Konstantinidis KT, Tiedje JM: Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007, 10(5):504-509. 25. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Peer Van de Y, Vandamme P, Thompson FL, et al: Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 2005, 3(9):733-739. 26. Cerritos R, Vinuesa P, Eguiarte LE, Herrera-Estrella L, Alcaraz-Peraza LD, Arvizu-Gomez JL, Olmedo G, Ramirez E, Siefert JL, Souza V: Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Cienegas Valley in Coahuila, Mexico. Int J Syst Evol Microbiol 2008, 58(Pt 4):919-923. 27. Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D: Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico. Environ Microbiol 2009, 11(1):16-34. 28. Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, Waterbury JB, Webb EA: Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature 2006, 439(7072):68-71. 29. Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblizek M, Lomas MW, Mincer TJ, Moore LR, Moutin T, et al: Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature 2009, 458(7234):69-72. 30. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC: The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008, , 36 Database: D475-479. 31. Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, et al: The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucl Acids Res 2004, 32(3):977-988. 32. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, et al: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003, 423(6935):81-86. 33. Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, et al: Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis. J Bacteriol 2006, 188(9):3382-3390. 34. Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, et al: The complete genome sequence of Bacillus anthracis Ames “Ancestor”. J Bacteriol 2009, 191(1):445-446. 35. Challacombe JF, Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, et al: The complete