{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T14:55:39Z","timestamp":1775055339809,"version":"3.50.1"},"reference-count":119,"publisher":"Oxford University Press (OUP)","issue":"1","funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/EBB-BIO\/119006\/2010"],"award-info":[{"award-number":["PTDC\/EBB-BIO\/119006\/2010"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PEst-OE\/EQB\/LA0004\/2011"],"award-info":[{"award-number":["PEst-OE\/EQB\/LA0004\/2011"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/29397\/06"],"award-info":[{"award-number":["SFRH\/BD\/29397\/06"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"DOI":"10.1093\/gbe\/evx270","type":"journal-article","created":{"date-parts":[[2017,12,19]],"date-time":"2017-12-19T15:15:34Z","timestamp":1513696534000},"page":"108-124","source":"Crossref","is-referenced-by-count":65,"title":["Genetic Competence Drives Genome Diversity in Bacillus subtilis"],"prefix":"10.1093","volume":"10","author":[{"given":"Patr\u00edcia H","family":"Brito","sequence":"first","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal"},{"name":"Nova Medical School, Faculdade de Ci\u00eancias M\u00e9dicas, Universidade Nova de Lisboa, Portugal"}]},{"given":"Bastien","family":"Chevreux","sequence":"additional","affiliation":[{"name":"DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA"}]},{"given":"Cl\u00e1udia R","family":"Serra","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Oeiras, Portugal"}]},{"given":"Ghislain","family":"Schyns","sequence":"additional","affiliation":[{"name":"DSM Nutritional Products, Ltd., 60 Westview street, Lexington MA, USA"}]},{"given":"Adriano O","family":"Henriques","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Oeiras, Portugal"}]},{"given":"Jos\u00e9 B","family":"Pereira-Leal","sequence":"additional","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal"},{"name":"Ophiomics\u2014Precision Medicine, Lisbon, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2017,12,20]]},"reference":[{"key":"key\n\t\t\t\t20180328133011_evx270-B1","doi-asserted-by":"crossref","first-page":"e1004636.","DOI":"10.1371\/journal.pgen.1004636","article-title":"Developmentally-regulated excision of the SP\u03b2 prophage reconstitutes a gene required for spore envelope maturation in Bacillus subtilis Viollier, PH, editor","volume":"10","author":"Abe","year":"2014","journal-title":"PLoS Genet"},{"issue":"7207","key":"key\n\t\t\t\t20180328133011_evx270-B2","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/nature07067","article-title":"Self-destructive cooperation mediated by phenotypic noise","volume":"454","author":"Ackermann","year":"2008","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180328133011_evx270-B3","author":"Agostinelli","year":"2013"},{"issue":"15","key":"key\n\t\t\t\t20180328133011_evx270-B4","doi-asserted-by":"crossref","first-page":"3922","DOI":"10.1128\/JB.00056-12","article-title":"Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars","volume":"194","author":"Ahmed","year":"2012","journal-title":"J Bacteriol"},{"issue":"1706","key":"key\n\t\t\t\t20180328133011_evx270-B5","doi-asserted-by":"crossref","first-page":"20150528.","DOI":"10.1098\/rstb.2015.0528","article-title":"Steady at the wheel: conservative sex and the benefits of bacterial transformation","volume":"371","author":"Ambur","year":"2016","journal-title":"Philos Trans R Soc B: Biol Sci"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B6","first-page":"39","article-title":"Natural transformation increases the rate of adaptation in the human pathogen Helicobacter pylori","volume":"62","author":"Baltrus","year":"2008","journal-title":"Evolution"},{"key":"key\n\t\t\t\t20180328133011_evx270-B7","doi-asserted-by":"crossref","first-page":"33.","DOI":"10.1186\/1471-2148-5-33","article-title":"Do orthologous gene phylogenies really support tree-thinking?","volume":"5","author":"Bapteste","year":"2005","journal-title":"BMC Evol Biol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B8","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1146\/annurev-phyto-081211-172936","article-title":"Interrelationships of food safety and plant pathology: the life cycle of human pathogens on plants","volume":"50","author":"Barak","year":"2012","journal-title":"Annu Rev Phytopathol"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B9","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1128\/AEM.71.2.968-978.2005","article-title":"Screening for bacillus isolates in the broiler gastrointestinal tract","volume":"71","author":"Barbosa","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"7269","key":"key\n\t\t\t\t20180328133011_evx270-B10","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nature08504","article-title":"Experimental evolution of bet hedging","volume":"462","author":"Beaumont","year":"2009","journal-title":"Nature"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B11","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1093\/oxfordjournals.molbev.a004050","article-title":"Evolution of microbial genomes: sequence acquisition and loss","volume":"19","author":"Berg","year":"2002","journal-title":"Mol Biol Evol"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B12","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1080\/03610918108812225","article-title":"The BIAS of the maximum likelihood estimators of the von mises-fisher concentration parameters","volume":"10","author":"Best","year":"1981","journal-title":"Commun Stat: Simul Comput"},{"issue":"Pt 7","key":"key\n\t\t\t\t20180328133011_evx270-B13","doi-asserted-by":"crossref","first-page":"2712","DOI":"10.1099\/ijs.0.048488-0","article-title":"Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus","volume":"63","author":"Bhandari","year":"2013","journal-title":"Int J Syst Evol Microbiol."},{"key":"key\n\t\t\t\t20180328133011_evx270-B14","doi-asserted-by":"crossref","first-page":"e1003825.","DOI":"10.1371\/journal.pgen.1003825","article-title":"Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability, Casades\u00fas, J, editor","volume":"9","author":"Bobay","year":"2013","journal-title":"PLoS Genet"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B15","doi-asserted-by":"crossref","first-page":"2173","DOI":"10.1093\/gbe\/evv135","article-title":"Gene loss dominates as a source of genetic variation within clonal pathogenic bacterial species","volume":"7","author":"Bolotin","year":"2015","journal-title":"Genome Biol Evol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B16","doi-asserted-by":"crossref","first-page":"35168.","DOI":"10.1038\/srep35168","article-title":"Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes","volume":"6","author":"Bolotin","year":"2016","journal-title":"Sci Rep"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B17","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1101\/gr.3024704","article-title":"Computing prokaryotic gene ubiquity: rescuing the core from extinction","volume":"14","author":"Charlebois","year":"2004","journal-title":"Genome Res"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B18","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.mib.2012.08.001","article-title":"Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?","volume":"15","author":"Charpentier","year":"2012","journal-title":"Curr Opin Microbiol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B19","author":"Chevreux","year":"1999"},{"key":"key\n\t\t\t\t20180328133011_evx270-B20","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1146\/annurev.micro.60.080805.142139","article-title":"Induction of competence regulons as a general response to stress in gram-positive Bacteria","volume":"60","author":"Claverys","year":"2006","journal-title":"Annu Rev Microbiol"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B21","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1128\/AEM.01988-09","article-title":"Ecology of speciation in the genus Bacillus","volume":"76","author":"Connor","year":"2010","journal-title":"Appl Environ Microbiol"},{"issue":"24","key":"key\n\t\t\t\t20180328133011_evx270-B22","doi-asserted-by":"crossref","first-page":"7696","DOI":"10.1128\/AEM.02411-13","article-title":"GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis","volume":"79","author":"Contreras-Moreira","year":"2013","journal-title":"Appl Environ Microbiol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B23","doi-asserted-by":"crossref","first-page":"210.","DOI":"10.1186\/1471-2148-10-210","article-title":"BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments","volume":"10","author":"Criscuolo","year":"2010","journal-title":"BMC Evol Biol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002394","article-title":"Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict","author":"Croucher","year":"2016","journal-title":"PLoS Biol"},{"issue":"15","key":"key\n\t\t\t\t20180328133011_evx270-B25","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1093\/bioinformatics\/btq315","article-title":"Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood","volume":"26","author":"Csuos","year":"2010","journal-title":"Bioinfo Appl Note"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B26","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1093\/molbev\/msp123","article-title":"Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model","volume":"26","author":"Csur\u00f6s","year":"2009","journal-title":"Mol Biol Evol"},{"issue":"6","key":"key\n\t\t\t\t20180328133011_evx270-B27","doi-asserted-by":"crossref","first-page":"e11147.","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS ONE"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B28","doi-asserted-by":"crossref","first-page":"772.","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nat Methods"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B29","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/btr088","article-title":"ProtTest 3: fast selection of best-fit models of protein evolution","volume":"27","author":"Darriba","year":"2011","journal-title":"Bioinformatics"},{"issue":"5634","key":"key\n\t\t\t\t20180328133011_evx270-B30","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1126\/science.1086568","article-title":"Phylogenetics and the cohesion of bacterial genomes","volume":"301","author":"Daubin","year":"2003","journal-title":"Science"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B31","doi-asserted-by":"crossref","first-page":"2070","DOI":"10.1128\/JB.00129-11","article-title":"Complete genome sequence of Bacillus subtilis BSn5, an endophytic bacterium of Amorphophallus konjac with antimicrobial activity for the plant pathogen Erwinia carotovora subsp. carotovora","volume":"193","author":"Deng","year":"2011","journal-title":"J Bacteriol"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B32","doi-asserted-by":"crossref","first-page":"M5","DOI":"10.1016\/S0962-8924(99)01664-5","article-title":"Lateral genomics","volume":"9","author":"Doolittle","year":"1999","journal-title":"Trends Cell Biol"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B33","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1073\/pnas.0610699104","article-title":"Pattern pluralism and the tree of life hypothesis","volume":"104","author":"Doolittle","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B34","doi-asserted-by":"crossref","first-page":"116.","DOI":"10.1186\/gb-2006-7-9-116","article-title":"Genomics and the bacterial species problem","volume":"7","author":"Doolittle","year":"2006","journal-title":"Genome Biol"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B35","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1128\/JB.01343-06","article-title":"Bacillus subtilis genome diversity","volume":"189","author":"Earl","year":"2007","journal-title":"J Bacteriol"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B36","doi-asserted-by":"crossref","first-page":"3475","DOI":"10.1111\/j.1558-5646.2011.01402.x","article-title":"Competence increases survival during stress in Streptococcus pneumoniae","volume":"65","author":"Engelmoer","year":"2011","journal-title":"Evolution"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B37","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1007\/s10886-013-0319-7","article-title":"Ecological and mechanistic insights into the direct and indirect antimicrobial properties of Bacillus subtilis lipopeptides on plant pathogens","volume":"39","author":"Falardeau","year":"2013","journal-title":"J Chem Ecol"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B38","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1128\/JB.01351-10","article-title":"Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b, isolated from the Indian Ocean","volume":"193","author":"Fan","year":"2011","journal-title":"J Bacteriol"},{"issue":"21","key":"key\n\t\t\t\t20180328133011_evx270-B39","doi-asserted-by":"crossref","first-page":"6288","DOI":"10.1128\/JB.183.21.6288-6293.2001","article-title":"DNA as a nutrient: novel role for bacterial competence gene homologs","volume":"183","author":"Finkel","year":"2001","journal-title":"J Bacteriol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B40","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.meegid.2004.03.004","article-title":"Which species concept for pathogenic bacteria? An E-debate","volume":"5","author":"Godreuil","year":"2005","journal-title":"Infect Genet Evol"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B41","doi-asserted-by":"crossref","first-page":"2226","DOI":"10.1093\/oxfordjournals.molbev.a004046","article-title":"Prokaryotic evolution in light of gene transfer","volume":"19","author":"Gogarten","year":"2002","journal-title":"Mol Biol Evol"},{"issue":"Pt 1","key":"key\n\t\t\t\t20180328133011_evx270-B42","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA\u2013DNA hybridization values and their relationship to whole-genome sequence similarities","volume":"57","author":"Goris","year":"2007","journal-title":"Int J Syst Evol Microbiol."},{"issue":"4393","key":"key\n\t\t\t\t20180328133011_evx270-B43","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1126\/science.107592","article-title":"Gene exchange and natural selection cause Bacillus subtilis to evolve in soil culture","volume":"204","author":"Graham","year":"1979","journal-title":"Science"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B44","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1111\/mmi.13040","article-title":"ComGA\u2013RelA interaction and persistence in the Bacillus subtilis K-state","volume":"97","author":"Hahn","year":"2015","journal-title":"Mol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B45","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1046\/j.1365-2958.2001.02363.x","article-title":"A ComGA-dependent checkpoint limits growth during the escape from competence","volume":"40","author":"Haijema","year":"2001","journal-title":"Mol Microbiol"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B46","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/0167-7799(92)90233-L","article-title":"Bacillus subtilis and its relatives: molecular biological and industrial workhorses","volume":"10","author":"Harwood","year":"1992","journal-title":"Trends Biotechnol"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B47","doi-asserted-by":"crossref","first-page":"2192","DOI":"10.1073\/pnas.96.5.2192","article-title":"Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage","volume":"96","author":"Hendrix","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"issue":"22","key":"key\n\t\t\t\t20180328133011_evx270-B48","doi-asserted-by":"crossref","first-page":"8186","DOI":"10.1128\/JB.00690-07","article-title":"Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome","volume":"189","author":"Hiller","year":"2007","journal-title":"J Bacteriol"},{"issue":"6","key":"key\n\t\t\t\t20180328133011_evx270-B49","doi-asserted-by":"crossref","first-page":"R103","DOI":"10.1186\/gb-2007-8-6-r103","article-title":"Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains","volume":"8","author":"Hogg","year":"2007","journal-title":"Genome Biol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B50","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.femsre.2004.12.001","article-title":"The use of bacterial spore formers as probiotics","volume":"29","author":"Hong","year":"2005","journal-title":"FEMS Microbiol Rev"},{"key":"key\n\t\t\t\t20180328133011_evx270-B51","doi-asserted-by":"crossref","first-page":"16048.","DOI":"10.1038\/nmicrobiol.2016.48","article-title":"A new view of the tree of life","volume":"1","author":"Hug","year":"2016","journal-title":"Nat Microbiol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B52","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1534\/genetics.108.099523","article-title":"Episodic selection and the maintenance of competence and natural transformation in Bacillus subtilis","volume":"181","author":"Johnsen","year":"2009","journal-title":"Genetics"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B53","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/nrmicro3199","article-title":"Bacterial transformation: distribution, shared mechanisms and divergent control","volume":"12","author":"Johnston","year":"2014","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-13-577","article-title":"Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverseEscherichia coli genomes","volume":"13","author":"Kaas","year":"2012","journal-title":"BMC Genomics"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B55","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software Version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"12","key":"key\n\t\t\t\t20180328133011_evx270-B56","doi-asserted-by":"crossref","first-page":"e231","DOI":"10.1371\/journal.pgen.0030231","article-title":"Patterns and implications of gene gain and loss in the evolution of prochlorococcus","volume":"3","author":"Kettler","year":"2007","journal-title":"PLoS Genet"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B57","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1046\/j.1365-2958.1997.3501715.x","article-title":"Dynamic bacterial genome organization","volume":"24","author":"Kolst\u00f8","year":"1997","journal-title":"Mol Microbiol"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B58","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"issue":"21","key":"key\n\t\t\t\t20180328133011_evx270-B59","doi-asserted-by":"crossref","first-page":"6688","DOI":"10.1093\/nar\/gkn668","article-title":"Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world","volume":"36","author":"Koonin","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180328133011_evx270-B60","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1099\/13500872-142-8-2031","article-title":"The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous","volume":"142","author":"Krogh","year":"1996","journal-title":"Microbiology"},{"issue":"18","key":"key\n\t\t\t\t20180328133011_evx270-B61","doi-asserted-by":"crossref","first-page":"6463","DOI":"10.1128\/AEM.00448-11","article-title":"Phylogenetic analysis of Bacillus subtilis strains applicable to Natto (fermented soybean) production","volume":"77","author":"Kubo","year":"2011","journal-title":"Appl Environ Microbiol"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B62","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1101\/gr.1092603","article-title":"The balance of driving forces during genome evolution in Prokaryotes","volume":"13","author":"Kunin","year":"2003","journal-title":"Genome Res"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B63","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1111\/j.1574-6976.2008.00140.x","article-title":"The fate of new bacterial genes","volume":"33","author":"Kuo","year":"2009","journal-title":"FEMS Microbiol Rev"},{"issue":"5743","key":"key\n\t\t\t\t20180328133011_evx270-B64","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1126\/science.1114383","article-title":"Phenotypic diversity, population growth, and information in fluctuating environments","volume":"309","author":"Kussell","year":"2005","journal-title":"Science"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B65","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1099\/00221287-148-3-815","article-title":"Comparison of ribitol and glycerol teichoic acid genes in Bacillus subtilis W23 and 168: identical function, similar divergent organization, but different regulation","volume":"148","author":"Lazarevic","year":"2002","journal-title":"Microbiology (Reading, Engl)"},{"issue":"0","key":"key\n\t\t\t\t20180328133011_evx270-B66","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1093\/gbe\/evq048","article-title":"Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept","volume":"2","author":"Lef\u00e9bure","year":"2010","journal-title":"Genome Biol Evol"},{"issue":"6","key":"key\n\t\t\t\t20180328133011_evx270-B67","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.mib.2008.09.020","article-title":"Stochastic switching to competence","volume":"11","author":"Leisner","year":"2008","journal-title":"Curr Opin Microbiol"},{"issue":"5","key":"key\n\t\t\t\t20180328133011_evx270-B68","doi-asserted-by":"crossref","first-page":"e130.","DOI":"10.1371\/journal.pbio.0030130","article-title":"Evolutionary origins of genomic repertoires in bacteria","volume":"3","author":"Lerat","year":"2005","journal-title":"PLoS Biol"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B69","doi-asserted-by":"crossref","first-page":"2458","DOI":"10.1093\/gbe\/evv160","article-title":"Found and lost: the fates of horizontally acquired genes in arthropod-symbiotic spiroplasma","volume":"7","author":"Lo","year":"2015","journal-title":"Genome Biol Evol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B70","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1111\/j.1574-6976.2008.00148.x","article-title":"Generation of multiple cell types in Bacillus subtilis","volume":"33","author":"Lopez","year":"2009","journal-title":"FEMS Microbiol Rev"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B71","doi-asserted-by":"crossref","first-page":"e00373-13.","DOI":"10.1128\/mBio.00373-13","article-title":"Evolution of divergent life history strategies in marine alphaproteobacteria","volume":"4","author":"Luo","year":"2013","journal-title":"MBio"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B72","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1111\/j.1365-2958.2005.04592.x","article-title":"Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop","volume":"56","author":"Maamar","year":"2005","journal-title":"Mol Microbiol"},{"issue":"42","key":"key\n\t\t\t\t20180328133011_evx270-B73","doi-asserted-by":"crossref","first-page":"15611","DOI":"10.1073\/pnas.0607117103","article-title":"Comparative genomics of the lactic acid bacteria","volume":"103","author":"Makarova","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B74","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1038\/ismej.2016.22","article-title":"Beyond the black queen hypothesis","volume":"10","author":"Mas","year":"2016","journal-title":"ISME J."},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B75","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nrmicro2670","article-title":"Extreme genome reduction in symbiotic bacteria","volume":"10","author":"McCutcheon","year":"2011","journal-title":"Nat Rev Microbiol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B76","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1093\/gbe\/evt038","article-title":"The evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome","volume":"5","author":"McNally","year":"2013","journal-title":"Genome Biol Evol"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B77","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1128\/JB.01293-13","article-title":"Natural competence and the evolution of DNA uptake specificity","volume":"196","author":"Mell","year":"2014","journal-title":"J Bacteriol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B78","doi-asserted-by":"crossref","first-page":"411.","DOI":"10.3389\/fmicb.2014.00411","article-title":"Plant innate immunity against human bacterial pathogens","volume":"5","author":"Melotto","year":"2014","journal-title":"Front Microbiol"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B79","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1111\/j.1469-185X.2010.00151.x","article-title":"Rickettsial evolution in the light of comparative genomics","volume":"86","author":"Merhej","year":"2011","journal-title":"Biol Rev Camb Philos Soc"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B80","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1073\/pnas.93.7.2873","article-title":"Accelerated evolution and Muller's rachet in endosymbiotic bacteria","volume":"93","author":"Moran","year":"1996","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B81","doi-asserted-by":"crossref","first-page":"e00036-12.","DOI":"10.1128\/mBio.00036-12","article-title":"The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss","volume":"3","author":"Morris","year":"2012","journal-title":"MBio"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B82","doi-asserted-by":"crossref","first-page":"e02057-15.","DOI":"10.1128\/mBio.02057-15","article-title":"Defying Muller's Ratchet: ancient heritable endobacteria escape extinction through retention of recombination and genome plasticity","volume":"7","author":"Naito","year":"2016","journal-title":"MBio"},{"issue":"6784","key":"key\n\t\t\t\t20180328133011_evx270-B83","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/35012500","article-title":"Lateral gene transfer and the nature of bacterial innovation","volume":"405","author":"Ochman","year":"2000","journal-title":"Nature"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B84","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1099\/00207713-37-1-69","article-title":"Bacillus amyloliquefaciens sp. nov., nom. rev","volume":"37","author":"Priest","year":"1987","journal-title":"Int J Syst Bacteriol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B85","doi-asserted-by":"crossref","first-page":"66.","DOI":"10.1186\/s12915-014-0066-4","article-title":"Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes","volume":"12","author":"Puigb\u00f2","year":"2014","journal-title":"BMC Biol"},{"issue":"6","key":"key\n\t\t\t\t20180328133011_evx270-B86","doi-asserted-by":"crossref","first-page":"59.","DOI":"10.1186\/jbiol159","article-title":"Search for a \u2018Tree of Life\u2019 in the thicket of the phylogenetic forest","volume":"8","author":"Puigb\u00f2","year":"2009","journal-title":"J Biol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B87","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1093\/gbe\/evu048","article-title":"Phylogenomics and the dynamic genome evolution of the genus Streptococcus","volume":"6","author":"Richards","year":"2014","journal-title":"Genome Biol Evol"},{"issue":"45","key":"key\n\t\t\t\t20180328133011_evx270-B88","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B89","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.jtbi.2005.08.037","article-title":"Comparisons of dN\/dS are time dependent for closely related bacterial genomes","volume":"239","author":"Rocha","year":"2006","journal-title":"J Theor Biol"},{"issue":"10","key":"key\n\t\t\t\t20180328133011_evx270-B90","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1099\/ijs.0.009126-0","article-title":"Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov","volume":"59","author":"Rooney","year":"2009","journal-title":"Int J Syst Evol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B91","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1139\/w03-076","article-title":"Developments in the use of Bacillus species for industrial production","volume":"50","author":"Schallmey","year":"2004","journal-title":"Can J Microbiol"},{"issue":"11","key":"key\n\t\t\t\t20180328133011_evx270-B92","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1094\/PHYTO.2004.94.11.1267","article-title":"Formulation of Bacillus spp. for biological control of plant diseases","volume":"94","author":"Schisler","year":"2004","journal-title":"Phytopathology"},{"issue":"14","key":"key\n\t\t\t\t20180328133011_evx270-B93","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"41","key":"key\n\t\t\t\t20180328133011_evx270-B94","doi-asserted-by":"crossref","first-page":"11399","DOI":"10.1073\/pnas.1614083113","article-title":"Theory of prokaryotic genome evolution","volume":"113","author":"Sela","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"issue":"23","key":"key\n\t\t\t\t20180328133011_evx270-B95","doi-asserted-by":"crossref","first-page":"4184","DOI":"10.1128\/JB.01993-14","article-title":"Sporulation during growth in a gut isolate of Bacillus subtilis","volume":"196","author":"Serra","year":"2014","journal-title":"J Bacteriol"},{"issue":"48","key":"key\n\t\t\t\t20180328133011_evx270-B96","doi-asserted-by":"crossref","first-page":"19107","DOI":"10.1073\/pnas.1103630108","article-title":"Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus","volume":"108","author":"Shank","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"key\n\t\t\t\t20180328133011_evx270-B97","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1111\/j.1365-2958.2005.04488.x","article-title":"Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development","volume":"56","author":"Smits","year":"2005","journal-title":"Mol Microbiol"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B98","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1101\/gr.176501","article-title":"Genomes in flux: the evolution of archaeal and proteobacterial gene content","volume":"12","author":"Snel","year":"2002","journal-title":"Genome Res"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B99","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"4890","key":"key\n\t\t\t\t20180328133011_evx270-B100","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1126\/science.2536191","article-title":"Chromosomal rearrangement generating a composite gene for a developmental transcription factor","volume":"243","author":"Stragier","year":"1989","journal-title":"Science"},{"issue":"28","key":"key\n\t\t\t\t20180328133011_evx270-B101","doi-asserted-by":"crossref","first-page":"11463","DOI":"10.1073\/pnas.1304246110","article-title":"Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean","volume":"110","author":"Swan","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"key\n\t\t\t\t20180328133011_evx270-B102","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1128\/JB.188.7.2692-2700.2006","article-title":"The intestinal life cycle of Bacillus subtilis and close relatives","volume":"188","author":"Tam","year":"2006","journal-title":"J Bacteriol"},{"issue":"4","key":"key\n\t\t\t\t20180328133011_evx270-B103","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1128\/IAI.01255-13","article-title":"Gut adhesive Bacillus subtilis spores as a platform for mucosal delivery of antigens","volume":"82","author":"Tavares Batista","year":"2014","journal-title":"Infect Immun"},{"issue":"39","key":"key\n\t\t\t\t20180328133011_evx270-B104","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial \u2018pan-genome\u2019","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B105","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1023\/A:1018513530268","article-title":"ADE-4: a multivariate analysis and graphical display software","volume":"7","author":"Thioulouse","year":"1997","journal-title":"Stat Comput."},{"issue":"1","key":"key\n\t\t\t\t20180328133011_evx270-B106","doi-asserted-by":"crossref","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","article-title":"Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths","volume":"5","author":"Touchon","year":"2009","journal-title":"PLoS Genet"},{"key":"key\n\t\t\t\t20180328133011_evx270-B107","doi-asserted-by":"crossref","first-page":"3250.","DOI":"10.1038\/srep03250","article-title":"The fungus-growing termite Macrotermes natalensis harbors bacillaene-producing Bacillus sp. that inhibit potentially antagonistic fungi","volume":"3","author":"Um","year":"2013","journal-title":"Sci Rep"},{"key":"key\n\t\t\t\t20180328133011_evx270-B108","doi-asserted-by":"crossref","first-page":"e1002141.","DOI":"10.1371\/journal.pbio.1002141","article-title":"From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate, Laub, MT, editor","volume":"13","author":"van Gestel","year":"2015","journal-title":"PLoS Biol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B109","first-page":"e1000059","article-title":"The emergence and fate of horizontally acquired genes in Escherichia coli","author":"van Passel","year":"2008"},{"key":"key\n\t\t\t\t20180328133011_evx270-B110","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1146\/annurev.micro.62.081307.163002","article-title":"Bistability, epigenetics, and bet-hedging in bacteria","volume":"62","author":"Veening","year":"2008","journal-title":"Annu Rev Microbiol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B111","doi-asserted-by":"crossref","first-page":"45","DOI":"10.3389\/fmicb.2014.00791","article-title":"Interactions of Salmonella with animals and plants","volume":"5","author":"Wiedemann","year":"2015","journal-title":"Front Microbiol"},{"issue":"2","key":"key\n\t\t\t\t20180328133011_evx270-B112","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.jtbi.2004.11.020","article-title":"Diversity in times of adversity: probabilistic strategies in microbial survival games","volume":"234","author":"Wolf","year":"2005","journal-title":"J Theor Biol"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B113","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1002\/bies.201300037","article-title":"Genome reduction as the dominant mode of evolution","volume":"35","author":"Wolf","year":"2013","journal-title":"BioEssays"},{"key":"key\n\t\t\t\t20180328133011_evx270-B114","doi-asserted-by":"crossref","first-page":"46.","DOI":"10.1186\/1745-6150-7-46","article-title":"Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer","volume":"7","author":"Wolf","year":"2012","journal-title":"Biol Direct"},{"issue":"8","key":"key\n\t\t\t\t20180328133011_evx270-B115","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrmicro2382","article-title":"Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow","volume":"8","author":"Wozniak","year":"2010","journal-title":"Nat Rev Microbiol"},{"key":"key\n\t\t\t\t20180328133011_evx270-B116","first-page":"1","article-title":"A versatile nano display platform from bacterial spore coat proteins","volume":"6","author":"Wu","year":"2015","journal-title":"Nat Commun"},{"issue":"9","key":"key\n\t\t\t\t20180328133011_evx270-B117","doi-asserted-by":"crossref","first-page":"e1001108.","DOI":"10.1371\/journal.pgen.1001108","article-title":"Optimal strategy for competence differentiation in Bacteria","volume":"6","author":"Wylie","year":"2010","journal-title":"PLoS Genet"},{"key":"key\n\t\t\t\t20180328133011_evx270-B118","doi-asserted-by":"crossref","first-page":"3110.","DOI":"10.3389\/fmicb.2016.00888","article-title":"Fitness trade-offs in competence differentiation of Bacillus subtilis","volume":"7","author":"Y\u00fcksel","year":"2016","journal-title":"Front Microbiol"},{"issue":"Web Server issue","key":"key\n\t\t\t\t20180328133011_evx270-B119","doi-asserted-by":"crossref","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: a fast phage search tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/10\/1\/108\/23601849\/evx270.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T14:33:26Z","timestamp":1522247606000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/10\/1\/108\/4767717"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12,20]]},"references-count":119,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12,20]]},"published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evx270","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1]]},"published":{"date-parts":[[2017,12,20]]}}}