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Table 1. Genomes used in this study

From: Veillonella, Firmicutes: Microbes disguised as Gram negatives

Phylum Name of organism and strain Strain designation Type strain? NCBI Taxon ID NCBI Project ID
Acidobacteria Acidobacterium capsulatum ATCC 51196 Yes 240015 28085
Acidobacteria Korebacter versatiles Ellin 345   204669 15771
Acidobacteria Solibacter usitatus Ellin6076   234267 12638
Actinobacteria Bifidobacterium bifidum 317B No 1681 42863
Actinobacteria Catenulispora acidiphila ID139908, DSM 44928 Yes 479433 21085
Actinobacteria Corynebacterium pseudotuberculosis C231 No 681645 40875
Actinobacteria Segniliparus rugosus ATCC BAA-974 Yes 679197 40685
Actinobacteria Streptomyces bingchenggensis BCW-1 Name not validly published 749414 46847
Actinobacteria Tropheryma whipplei Twist Yes 203267 95
Aquificae Persephonella marina EX-H1 Yes 123214 12526
Aquificae Sulfurihydrogenibium sp. YO3AOP1 No type strain available 436114 18889
Aquificae Thermocrinis albus HI 11/12, DSM 14484 Yes 638303 37275
Bacteroidetes Bacteroides thetaiotaomicron VPI-5482 Yes 226186 399
Bacteroidetes Candidatus Sulcia muelleri DMIN   641892 37785
Bacteroidetes Chitinophaga pinensis UQM 2034, DSM 2588 Yes 485918 27951
Bacteroidetes Paludibacter propionicigenes WB4, DSM 17365 Yes 694427 42009
Chlamydiae Protochlamydia amoebophila UWE25 Yes 264201 10700
Chlamydiae Chlamydia trachomatis E/Sweden2 No 634464 43167
Chlamydiae Chlamydophila pneumoniae AR39 No 115711 247
Chlamydiae Waddlia chondrophila WSU 86-1044 Yes 716544 43761
Chlorobi Chlorobium chlorochromatii CaD3 Name not validly published 340177 13921
Chlorobi Chlorobium tepidum TLS Yes 194439 302
Chloroflexi Chloroflexus aggregans DSM 9485 Yes 326427 16708
Chloroflexi Dehalococcoides sp BAV1 No 216389 15770
Chloroflexi Herpetosiphon aurantiacus ATCC 23779 Yes 316274 16523
Chloroflexi Roseiflexus sp. RS-1 No type strain available 357808 16190
Cyanobacteria Anabaena variabilis 3 ATCC 2941 No 240292 10642
Cyanobacteria Cyanothece sp. PCC 7822 No 497965 28535
Cyanobacteria Prochlorococcus marinus MIT9301 No 167546 15746
Cyanobacteria Synechocystis sp. PCC6803 No 1148 60
Deferribacteres Calditerrivibrio nitroreducens Yu37-1, DSM 19672 Yes 768670 49523
Deferribacteres Deferribacter desulfuricans SSM1, DSM 14783 Yes 197162 37285
Deferribacteres Denitrovibrio acetiphilus N2460, DSM 12809 Yes 522772 29431
Deinococcus-Thermus Oceanithermus profundus 506, DSM 14977 Yes 670487 40223
Deinococcus-Thermus Thermus thermophilus HB8 Yes 300852 13202
Deinococcus-Thermus Truepera radiovictrix RQ-24, DSM 17093 Yes 649638 38371
Dictyoglomi Dictyoglomus turgidum DSM 6724 Yes 515635 29175
Elusimicrobia Elusimicrobium minutum Pei 191 Yes 445932 19701
Fibrobacteres Fibrobacter succinogenes S85 Yes 59374 32617
Firmicutes Acetohalobium arabaticum Z-7288, DSM 5501 Yes 574087 32769
Firmicutes Acidaminococcus fermentans VR4, DSM 20731 Yes 591001 33685
Firmicutes Acidaminococcus sp. D21 No type strain available 563191 34117
Firmicutes Alkaliphilus oremlandii OhILAs Yes 350688 16083
Firmicutes Bacillus subtilis subsp. subtilis 168 Yes 224308 76
Firmicutes Clostridium botulinum F Langeland No 441772 19519
Firmicutes Clostridium cellulolyticum H10 Yes 394503 17419
Firmicutes Clostridium difficile 630 (epidemic type X) No 272563 78
Firmicutes Desulfotomaculum reducens MI-1 Name not validly published 349161 13424
Firmicutes Dialister invisus DSM 15470 Yes 592028 33143
Firmicutes Dialister micraerophilus Oral Taxon 843 DSM 19965 Yes 888062 53029
Firmicutes Dialister micraerophilus UPII-345-E No 910314 59521
Firmicutes Enterococcus faecalis V583 No 226185 70
Firmicutes Eubacterium cylindroides T2-87 No 717960 45917
Firmicutes Eubacterium rectale A1-86, DSM 17629 No 39491 39159
Firmicutes Exiguobacterium sibiricum 255-15 Yes 262543 10649
Firmicutes Geobacillus kaustophilus HTA426 Yes 235909 13233
Firmicutes Lactococcus lactis cremoris MG1363 No 416870 18797
Firmicutes Lysinibacillus sphaericus C3-41 No 444177 19619
Firmicutes Megamonas hypermegale ART12/1 No 158847 39163
Firmicutes Megasphaera genomosp. type 1 28L No type strain available 699218 42553
Firmicutes Megasphaera micronuciformis F0359 No 706434 43125
Firmicutes Mitsuokella multacida A 405-1, DSM 20544 Yes 500635 28653
Firmicutes Paenibacillus sp. JDR-2 No 324057 20399
Firmicutes Phascolarctobacterium sp. YIT 12067 No 626939 48505
Firmicutes Selenomonas artemidis F0399 No 749551 47277
Firmicutes Selenomonas flueggei ATCC 43531 Yes 638302 37273
Firmicutes Selenomonas noxia ATCC 43541 Yes 585503 34641
Firmicutes Selenomonas sp. Oral Taxon 137 F0430 No type strain available 879310 52055
Firmicutes Selenomonas sp. Oral Taxon 149 67H29BP No type strain available 864563 50535
Firmicutes Selenomonas sputigena DSM 20758 Yes 546271 51247
Firmicutes Staphylococcus aureus aureus ED98 No 681288 39547
Firmicutes Streptococcus pneumoniae TIGR4 No 170187 277
Firmicutes Thermoanaerobacter sp. X514 Name not validly published 399726 16394
Firmicutes Thermosinus carboxydivorans Nor1 Yes 401526 17587
Firmicutes Turicibacter sp. PC909 702450 42765 No   
Firmicutes Veillonella atypica ACS-049-V-Sch6 No 866776 51075
Firmicutes Veillonella atypica ACS-134-V-Col7a No 866778 51079
Firmicutes Veillonella dispar ATCC 17748 Yes 546273 30491
Firmicutes Veillonella parvula ATCC 17745 No 686660 41557
Firmicutes Veillonella parvula Te3, DSM 2008 Yes 479436 21091
Firmicutes Veillonella sp. 3 1 44 Name not validly published 457416 41975
Firmicutes Veillonella sp. 6 1 27 Name not validly published 450749 41977
Firmicutes Veillonella sp. Oral Taxon 158 F0412 Name not validly published 879309 52053
Fusobacteria Fusobacterium nucleatum nucleatum ATCC 25586 Yes 190304 295
Fusobacteria Ilyobacter polytropus CuHBu1, DSM 2926 Yes 572544 32577
Fusobacteria Leptotrichia buccalis C-1013-b, DSM 1135 Yes 523794 29445
Fusobacteria Sebaldella termitidis NCTC 11300 Yes 526218 29539
Fusobacteria Streptobacillus moniliformis 9901, DSM 12112 Yes 519441 29309
Planctomycetes Pirellula staleyi DSM 6068 Yes 530564 29845
Planctomycetes Planctomyces limnophilus Mu 290, DSM 3776 Yes 521674 29411
Proteobacteria Acinetobacter baumannii SDF No 509170 13001
Proteobacteria Alkalilimnicola ehrlichii MLHE-1 Yes 187272 15763
Proteobacteria Arcobacter nitrofigilis DSM 7299 Yes 572480 32593
Proteobacteria Burkholderia xenovorans (fungorum) LB400 Yes 266265 254
Proteobacteria Campylobacter jejuni doylei 269.97 No 360109 17163
Proteobacteria Candidatus Pelagibacter ubique SAR11 HTCC1062 Name not validly published 335992 13989
Proteobacteria Candidatus Zinderia insecticola CARI Name not validly published 871271 51243
Proteobacteria Cellvibrio japonicus Ueda107 Yes 498211 28329
Proteobacteria Cupriavidus taiwanensis LMG19424 Yes 164546 15733
Proteobacteria Escherichia coli K-12, MG1655 No 511145 225
Proteobacteria Geobacter uraniireducens Rf4 Yes 351605 15768
Proteobacteria Hahella chejuensis KCTC 2396 Yes 349521 16064
Proteobacteria Haliangium ochraceum SMP-2, DSM 14365 Yes 502025 28711
Proteobacteria Helicobacter pylori 908 No 869727 50869
Proteobacteria Lawsonia intracellularis PHE/MN1-00 No 363253 183
Proteobacteria Magnetococcus sp. MC-1 Name not validly published 156889 262
Proteobacteria Methylobacterium nodulans ORS2060 Yes 460265 20477
Proteobacteria Neisseria meningitidis Z2491 No 122587 252
Proteobacteria Neorickettsia sennetsu Miyayama Yes 222891 357
Proteobacteria Nitrosomonas eutropha C91 (C71) Yes 335283 13913
Proteobacteria Photorhabdus luminescens laumondii TT01 Yes 243265 9605
Proteobacteria Polynucleobacter necessarius STIR1 No 452638 19991
Proteobacteria Pseudomonas aeruginosa LESB58 No 557722 31101
Proteobacteria Pseudomonas fluorescens SBW25 No 216595 31229
Proteobacteria Pseudomonas stutzeri A1501 No 379731 16817
Proteobacteria Salmonella enterica enterica PT4 P125109 No 550537 30687
Proteobacteria Shewanella oneidensis MR-1 Yes 211586 335
Proteobacteria Sorangium cellulosum So ce56 No 448385 28111
Proteobacteria Stigmatella aurantiaca DW4/3-1 No 378806 52561
Proteobacteria Sulfurospirillum deleyianum 5175, DSM 6946 No 525898 29529
Proteobacteria Vibrio cholerae O395 No 345073 32853
Spirochaetes Borrelia turicatae 91E135 Yes 314724 13597
Spirochaetes Brachyspira murdochii 56-150, DSM 12563 Yes 526224 29543
Spirochaetes Leptospira interrogans lai 56601 No 189518 293
Synergistetes Thermanaerovibrio acidaminovorans Su883, DSM 6589 Yes 525903 29531
Tenericutes Acholeplasma laidlawii PG-8A No 441768 19259
Tenericutes Candidatus Phytoplasma asteris yellows witches’-broom AY-WB 322098 Name not validly published 13478  
Tenericutes Candidatus Phytoplasma mali AT Name not validly published 37692 25335
Tenericutes Mycoplasma genitalium G37 Yes 243273 97
Tenericutes Mycoplasma pneumoniae FH No 722438 49525
Tenericutes Ureaplasma parvum sv 3, ATCC 27815 No 505682 19087
Thermotogae Fervidobacterium nodosum Rt17-B1 Yes 381764 16719
Thermotogae Kosmotoga olearia TBF 19.5.1 Yes 521045 29419
Thermotogae Petrotoga mobilis SJ95 Yes 403833 17679
Thermotogae Thermotoga naphthophila RKU-10 Yes 590168 33663
Verrucomicrobia Akkermansia muciniphila ATCC BAA-835 Yes 349741 20089
Verrucomicrobia Opitutus terrae   Yes PB90-1 452637
Crenarchaeota Sulfolobus solfataricus P2   273057 108
Crenarchaeota Thermosphaera aggregans M11TL, DSM 11486 Yes 633148 36571
Euryarchaeota Halogeometricum borinquense PR3, DSM 11551 Yes 469382 20743
Euryarchaeota Methanocella sp. RC-I Name not validly published 351160 19641
Euryarchaeota Methanothermus fervidus V24S, DSM 2088 Yes 523846 33689
Korarchaeota Candidatus Korarchaeum cryptofilum OPF8 Name not validly published 374847 16525
Nanoarchaeota Nanoarchaeum equitans Kin4-M Name not validly published 228908 9599