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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