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bacilliformis in response to environmental cues","volume":"34","author":"SA Coleman","year":"2003","journal-title":"Microb Pathog"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1128\/jb.175.1.12-18.1993","article-title":"Thin, aggregative fimbriae mediate binding of Salmonella enteritidis to fibronectin","volume":"175","author":"SK Collinson","year":"1993","journal-title":"J Bacteriol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1128\/IAI.69.4.2659-2665.2001","article-title":"Curli Fibers Mediate Internalization of Escherichia coli by Eukaryotic Cells","volume":"69","author":"U Gophna","year":"2001","journal-title":"Infect Immun"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1111\/j.1462-2920.2008.01824.x","article-title":"Synergistic role of curli and cellulose in cell adherence and biofilm formation of attaching and effacing Escherichia coli and identification of Fis as a negative regulator of curli","volume":"11","author":"Z Salda\u00f1a","year":"2009","journal-title":"Environ Microbiol"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrmicro1636","article-title":"The tad locus: postcards from the widespread colonization island","volume":"5","author":"M Tomich","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"ref94","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.VMBF-0012-2015","article-title":"Bacterial Secretion Systems\u2014An overview","volume":"4","author":"ER Green","year":"2016","journal-title":"Microbiol Spectr"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1128\/MMBR.05017-11","article-title":"Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria","volume":"76","author":"D B\u00fcttner","year":"2012","journal-title":"Microbiol Mol Biol Rev MMBR"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2180-9-S1-S2","article-title":"Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology","volume":"9","author":"T-T Tseng","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"6488","DOI":"10.1128\/JB.187.18.6488-6498.2005","article-title":"Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition","volume":"187","author":"V Joardar","year":"2005","journal-title":"J Bacteriol"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"2858","DOI":"10.1128\/JB.01757-07","article-title":"Naturally Occurring Nonpathogenic Isolates of the Plant Pathogen Pseudomonas syringae Lack a Type III Secretion System and Effector Gene Orthologues","volume":"190","author":"TJ Mohr","year":"2008","journal-title":"J Bacteriol"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1038\/ismej.2011.202","article-title":"Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic","volume":"6","author":"M Demba Diallo","year":"2012","journal-title":"ISME J"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1094\/MPMI-22-9-1069","article-title":"The Majority of the Type III Effector Inventory of Pseudomonas syringae pv. tomato DC3000 Can Suppress Plant Immunity","volume":"22","author":"M Guo","year":"2009","journal-title":"Mol Plant-Microbe Interact MPMI"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.chom.2015.05.007","article-title":"Pseudomonas syringae pv. tomato DC3000 Type III Secretion Effector Polymutants Reveal an Interplay between HopAD1 and AvrPtoB","volume":"17","author":"H-L Wei","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"13497","DOI":"10.1073\/pnas.0605443103","article-title":"The Salmonella effector protein PipB2 is a linker for kinesin-1","volume":"103","author":"T Henry","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1146\/annurev.biochem.73.011303.073626","article-title":"ATP-binding cassette transporters in bacteria","volume":"73","author":"AL Davidson","year":"2004","journal-title":"Annu Rev Biochem"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"3160","DOI":"10.1073\/pnas.0308653100","article-title":"Trends between gene content and genome size in prokaryotic species with larger genomes","volume":"101","author":"KT Konstantinidis","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1016\/j.resmic.2004.12.002","article-title":"An association between ATP binding cassette systems, genome sizes and lifestyles of bacteria","volume":"156","author":"DN Harland","year":"2005","journal-title":"Res Microbiol"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tibs.2009.05.002","article-title":"CRISPR-based adaptive and heritable immunity in prokaryotes","volume":"34","author":"J van der Oost","year":"2009","journal-title":"Trends Biochem Sci"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"4360","DOI":"10.1093\/nar\/gkt157","article-title":"Comparative genomics of defense systems in archaea and bacteria","volume":"41","author":"KS Makarova","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"10613","DOI":"10.1038\/ncomms10613","article-title":"Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems","volume":"7","author":"D Burstein","year":"2016","journal-title":"Nat Commun"},{"key":"ref109","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2016.01751","article-title":"An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes","volume":"7","author":"H Horn","year":"2016","journal-title":"Front Microbiol"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"2481","DOI":"10.1111\/1462-2920.13161","article-title":"The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur","volume":"18","author":"R-M Tian","year":"2016","journal-title":"Environ Microbiol"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/nrmicro2577","article-title":"Evolution and classification of the CRISPR-Cas systems","volume":"9","author":"K S Makarova","year":"2011","journal-title":"Nat Rev Microbiol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro884","article-title":"Genomic islands in pathogenic and environmental microorganisms","volume":"2","author":"U Dobrindt","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"e62","DOI":"10.1371\/journal.pgen.0010062","article-title":"Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands","volume":"1","author":"WWL Hsiao","year":"2005","journal-title":"PLOS Genet"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1101\/gr.341802","article-title":"Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast","volume":"12","author":"FSL Brinkman","year":"2002","journal-title":"Genome Res"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00239-004-0311-5","article-title":"A comparative categorization of protein function encoded in bacterial or archeal genomic islands","volume":"62","author":"R Merkl","year":"2006","journal-title":"J Mol Evol"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"3801","DOI":"10.1073\/pnas.96.7.3801","article-title":"Horizontal gene transfer among genomes: the complexity hypothesis","volume":"96","author":"R Jain","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"e33759","DOI":"10.1371\/journal.pone.0033759","article-title":"High-density transcriptional initiation signals underline genomic islands in bacteria","volume":"7","author":"Q Huang","year":"2012","journal-title":"PloS One"},{"key":"ref118","first-page":"255","article-title":"Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803","volume":"21","author":"M Kopf","year":"2014","journal-title":"DNA Res Int J Rapid Publ Rep Genes Genomes"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1111\/j.1574-6976.2010.00231.x","article-title":"RTX proteins: a highly diverse family secreted by a common mechanism","volume":"34","author":"I Linhartov\u00e1","year":"2010","journal-title":"Fems Microbiol Rev"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1038\/ismej.2009.45","article-title":"The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation","volume":"3","author":"MA Allen","year":"2009","journal-title":"ISME J"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"e3252","DOI":"10.1371\/journal.pone.0003252","article-title":"Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment","volume":"3","author":"T Thomas","year":"2008","journal-title":"PloS One"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/S0966-842X(03)00103-3","article-title":"Transcription regulation and environmental adaptation in bacteria","volume":"11","author":"I Cases","year":"2003","journal-title":"Trends Microbiol"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"R65","DOI":"10.1186\/gb-2009-10-6-r65","article-title":"A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes","volume":"10","author":"D Cortez","year":"2009","journal-title":"Genome Biol"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"e8094","DOI":"10.1371\/journal.pone.0008094","article-title":"The Association of Virulence Factors with Genomic Islands","volume":"4","author":"SJH Sui","year":"2009","journal-title":"PLOS ONE"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1093\/embo-reports\/kve097","article-title":"Ecological 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