Table S1 List of analyzed species, strains and the GenBank accession number for 16S rRNA and rpoB
Species / Strain/isolate / Accession number / Reference16S rRNA / rpoB
Klebsiella pneumoniae / K2 / KT261771 / KU158386 / This study
Klebsiella pneumoniae / K6 / KT261772 / KU158387 / This study
Klebsiella pneumoniae / K7 / KT261773 / KU158388 / This study
Klebsiella pneumoniae / K9 / KT261774 / KU158389 / This study
Klebsiella pneumoniae / K10 / KT261775 / KU158390 / This study
Klebsiella pneumoniae / K12 / KT261776 / KU158391 / This study
Klebsiella pneumoniae / K13 / KT261777 / KU158392 / This study
Klebsiella pneumoniae / K15 / KT261778 / KU158393 / This study
Klebsiella pneumoniae / K17 / KT261779 / KU158394 / This study
Klebsiella pneumoniae / K18 / KT261780 / KU158395 / This study
Klebsiella pneumoniae / K21 / KT261781 / KU158396 / This study
Klebsiella pneumoniae / K22 / KT261782 / KU158397 / This study
Klebsiella pneumoniae / K23 / KT261783 / KU158398 / This study
Shigella sp. / K19 / KT970676 / KU158399 / This study
Enterobacter sp. / K24 / KT970677 / KU158400 / This study
Klebsiella pneumoniae / KCTC 2242 / - / NC_017540 / Shin et al. (2012)
Klebsiella pneumoniae subsp. ozaenae / NBRC 105683 / AB682259 / - / Nakagawa et al. (Unpublished)
Klebsiella pneumoniae subsp. ozaenae / HE19 / LN624808 / - / Vaz-Moreira et al. (Unpublished)
Klebsiella pneumoniae subsp. ozaenae / ATCC 11296 / - / AF129445 / Drancourt et al. (2001)
Klebsiella pneumoniae subsp. ozaenae / DSM 16358 / - / KJ499870 / Maldonado-Barragan et al. (Unpublished)
Klebsiella pneumoniae subsp. pneumoniae / NTUH-K2044 / NC_012731 / NC_012731 / Wu et al. (2009)
Klebsiella pneumoniae subsp. pneumoniae / HKUOPLC / NZ_CP012300 / NZ_CP012300 / Lu et al. (2015)
Klebsiella pneumoniae subsp. pneumoniae / HS11286 / - / NC_016845 / Liu et al. (2012)
Klebsiella pneumoniae subsp. rhinoscleromatis / NBRC 105682 / AB682258 / - / Nakagawa et al. (Unpublished)
Klebsiella pneumoniae subsp. rhinoscleromatis / HE17 / LN624806 / - / Vaz-Moreira et al. (Unpublished)
Klebsiella pneumoniae subsp. rhinoscleromatis / ATCC 13884 / - / AF129446 / Drancourt et al. (2001)
Klebsiella pneumoniae subsp. rhinoscleromatis / LMG 3184 / - / JX425352 / Brady et al. (2013)
Klebsiella granulomatis / K22-14 / EU333881 / - / Mayilrajand Saini (Unpublished)
Klebsiella granulomatis / NO data / - / AF218573 / Drancourt an Raoult (Unpublished)
Klebsiella michiganensis / RC10 / NZ_CP011077 / - / Xu et al. (Unpublished)
Klebsiella michiganensis / W14 / - / JQ269337 / Saha et al. (2013)
Klebsiella michiganensis / DSM 25444 / - / LN884275 / Li et al. (Unpublished)
Klebsiella oxytoca / HKOPL1 / NZ_CP004887 / - / Jiang et al. (2014)
Klebsiella oxytoca / KONIH1 / NZ_CP008788 / - / Conlan et al. (Unpublished)
Klebsiella oxytoca / ATCC 13182 / - / AY367363 / Rosenblueth et al. (2004)
Klebsiella oxytoca / NBRC 102593 / - / LN884236 / Gu (Unpublished)
Klebsiella singaporensis / LMG 23571 / - / DQ836221 / Stephan et al. (2007)
Klebsiella variicola / DX120E / NZ_CP009274 / NZ_CP009274 / Lin et al. (2015)
Klebsiella variicola / DSM 15968 / NZ_CP010523 / NZ_CP010523 / Chen et al. (2016)
Citrobacter freundii / CAV1741 / NZ_CP011657 / NZ_CP011657 / Sheppard et al. (Unpublished)
Citrobacter koseri / ATCC BAA-895 / NC_009792 / NC_009792 / McClelland et al. (Unpublished)
Enterobacter ludwigii / EN-119 / AJ853891 / - / Gu et al. (2014)
Enterobacter ludwigii / LMG 23768 / - / JX425244 / Brady et al. (2013)
Enterobacter aerogenes / KCTC 2190 / NC_015663 / NC_015663 / Shin et al. (2012a)
Enterobacter aerogenes / CAV1320 / NZ_CP011574 / NZ_CP011574 / Sheppard et al. (Unpublished)
Enterobacter asburiae / L1 / NZ_CP007546 / NZ_CP007546 / Lau et al. (2013)
Enterobacter cancerogenus / LMG 2693 / Z96078 / - / Gu et al. (2014)
Enterobacter cancerogenus / ATCC 33241 / - / AJ566943 / Hoffmann et al. (2003)
Enterobacter cloacae subsp. cloacae / ATCC 13047 / NC_014121 / NC_014121 / Ren et al. (2010)
Enterobacter cloacae subsp. dissolvens / SDM / NC_018079 / NC_018079 / Xu et al. (2012)
Enterobacter hormaechei / CIP 103441 / AJ508302 / - / Gu et al. (2014)
Enterobacter hormaechei / ATCC 49162 / - / AJ543724 / Hoffmann et al. (2003)
Enterobacter mori / LMG 25706 / EU721605 / - / Gu et al. (2014)
Enterobacter mori / LMG 25706 / - / JX425251 / Brady et al. (2013)
Enterobacter soli / LF7 / GU814270 / - / Gu et al. (2014)
Enterobacter soli / LMG 26282 / - / JX425254 / Brady et al. (2013)
Escherichia albertii / KF1 / NZ_CP007025 / NZ_CP007025 / Fiedoruk et al. (2014)
Escherichia Coli / KO11 / NC_016902 / - / Lucas et al. (Unpublished)
Escherichia Coli / CFSAN029787 / NZ_CP011416 / - / Strain et al. (Unpublished)
Escherichia Coli / ATCC 8739 / - / NC_010468 / Copeland et al. (Unpublished)
Escherichia fergusonii / ATCC 35469 / NC_011740 / NC_011740 / Genoscope (Unpublished)
Escherichia hermannii / CIP 103176 / JN175345 / - / Yarza (Unpublished)
Escherichiavulneris / ATCC 33821 / NR_119109 / - / Cilia et al. (1996)
Serratia ficaria / JCM 1241 / AB004745 / - / Boye et al. (2003)
Serratia marcescen / ATCC 13880 / M59160 / - / Boye et al. (2003)
Serratia marcescens / SM39 / - / NZ_AP013063 / Iguchi et al. (2014)
Shigella boydii / Sb227 / NC_007613 / - / Yang et al. (2005)
Shigella boydii / ATCC 9210 / - / CP011511 / Jeong and Lee (Unpublished)
Shigella dysenteriae / Sd197 / NC_007606 / - / Yang et al. (2005)
Shigella dysenteriae / Sd1617 / - / CP006736 / Vongsawan et al. (2015)
Shigella flexneri / 2002017 / NC_017328 / NC_017328 / Ye et al. (2010)
Shigella sonnei / 53G / NC_016822 / NC_016822 / Aslett (Unpublished)
Yersinia enterocolitica / 2516-87 / NC_CP009838 / NC_CP009838 / Johnson et al. (2015)
References
Boye K. Hansen DS (2003) Sequencing of 16S rDNA of Klebsiella: taxonomic relations within the genus and to other Enterobacteriaceae. Int J Med Microbiol 292:495–503
Brady C, Cleenwerck I, Venter S et al (2013) Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 36:309–319
Chen M, Li Y, Li S et al (2016) Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae. J Basic Microbiol 56:78–84
Cilia V, Lafay B, Christen R (1996) Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13:451–461
Drancourt M, Bollet C, Carta A et al (2001) Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol 51:925–932
Fiedoruk K, Daniluk T, Swiecicka I et al (2014) First completeg enome sequence of Escherichia albertii strain KF1, a new potential human enteric pathogen. Genome Announc 2:e00004–14
Gu CT, Li CY, Yang LJ et al (2014) Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov." Int J Syst Evol Microbiol 64:2650–2656
Hoffmann H, Roggenkamp A (2003) Population genetics of the nomenspecies Enterobacter cloacae. Appl Environ Microbiol 69:5306–5318
Iguchi A, Nagaya Y, Pradel E et al (2014) Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. Genome Biol Evol 6:2096–2110
Jiang J, Tun HM, Mauroo NF et al (2014) Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces. BMC Res Notes 7:827
Johnson SL, Daligault HE, Davenport KW et al (2015) Thirty-two complete genome assemblies of nine Yersinia species, including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica. Genome Announc 3:e00148-15
Lau YY, Sulaiman J, Chen JW et al (2013) Quorum sensing activity of Enterobacter asburiae isolated from lettuce leaves. Sensors (Basel) 13:14189–14199
Lin L, Wei C, Chen M et al (2015) Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E. Stand Genomic Sci 10:22.
Liu P, Li P, Jiang X et al (2012) Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol 194:1841–1842
Lu MG, Jiang J, Liu L et al (2015) Complete genome sequence of Klebsiella pneumoniae strain HKUOPLC, a cellulose-degrading bacterium isolated from giant panda feces. Genome Announc 3:e01318–15
Ren Y, Ren Y, Zhou Z et al (2010) Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047. J Bacteriol 192:2463–2464
Rosenblueth M, Martinez L, Silva J et al (2004) Klebsiella variicola, a novel species with clinical and plant-associated isolates. Syst Appl Microbiol 27:27–35
Saha R, Farrance CE, Verghese B et al (2013) Klebsiella michiganensis sp. nov., a new bacterium isolated from a tooth brush holder. Curr Microbiol 66:72–78
Shin SH, Kim S, Kim JY et al (2012) Complete genome sequence of the 2, 3-butanediol-producing Klebsiella pneumoniae strain KCTC 2242. J Bacteriol 194:2736–2737
Shin SH, Kim S, Kim JY et al (2012a) Complete genome sequence of Enterobacter aerogenes KCTC 2190. J Bacteriol 194:2373–2374
Stephan R, Van Trappen S, Cleenwerck I et al (2007) Enterobacter turicensis sp. nov. and Enterobacter helveticus sp. nov., isolated from fruit powder. Int J Syst Evol Microbiol 57:820–826
Vongsawan AA, Kapatral V, Vaisvil B et al (2015) The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis. FEMS Microbiol Lett 362. doi: 10.1093/femsle/fnv011
Wu K-M, Li L-H, Yan J-J et al (2009) Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 191:4492–4501
Xu Y, Wang A, Tao F et al (2012) Genome sequence of Enterobacter cloacae subsp. dissolvens SDM, an efficient biomass-utilizing producer of platform chemical 2,3-butanediol. J Bacteriol 194:897-898
Yang F, Yang J, Zhang X et al (2005) Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 33:6445–6458
Ye C, Lan R, Xia S et al (2010) Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri. J Clin Microbiol 48:419–426