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Table 2 Phylogenetic annotation of identified T-RFs

From: PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

eTRFa(bp)

dTRFa(bp)

dTRF shiftedb(bp)

Countsc(−)

Relative contribution to T-RFd(%)

Phylogenetic affiliatione

Reference OTUf

Reference GenBank accession numberg

SW mapping scoreh(−)

Normalized SW mapping scorei(−)

Aerobic granular sludge biofilms from wastewater treatment reactors

n.a. (32)j

39

34

550

70.6

F: Xanthomonadaceae

4015

GQ396926

386

0.960

(276)

(35.0)

(G: Thermomonas)

(4045)

(EU834762)

(452)

(0.983)

(128)

(16.0)

(G: Pseudoxanthomonas)

(4035)

(EU834761)

(385)

(0.955)

   

112

14.3

O: Flavobacteriales

1151

AY468464

434

1.000

   

46

5.9

F: Rhodobacteraceae

2718

AY212706

448

1.000

   

37

4.8

S: Rhodocyclus tenuis

3160

AB200295

363

0.917

   

18

2.3

O: Sphingobacteriales

1229

GU454872

394

0.990

   

5

0.6

C: Gammaproteobacteria

3370

AY098896

403

0.906

   

4

0.5

O: Rhizobiales

2549

EU429497

360

0.981

   

4

0.5

O: Myxococcales

3246

DQ228369

302

0.765

   

1

0.1

O: Bacteroidales

991

EU104248

180

0.636

194

198

193

10

90.9

G: Acidovorax

3011

AJ864847

384

1.000

   

1

9.1

F: Xanthomonadaceae

4035

EF027004

303

0.819

214

219

214

769

99.6

S: Rhodocyclus tenuis

3160

AB200295

371

0.949

   

1

0.1

G: Methyloversatilis

3158

DQ066958

368

0.958

   

1

0.1

G: Dechloromonas

3156

DQ413103

321

0.988

   

1

0.1

G: Nitrosomonas

3136

EU937892

278

0.753

220

225

220

50

92.6

O: Rhizobiales

2580

NR025302

  

(31)

(57.0)

(G: Aminobacter)

   

2

3.7

S: Rhodocyclus tenuis

3160

AB200295

206

0.703

   

1

1.9

F: Hyphomonadaceae

2656

AF236001

229

0.636

   

1

1.9

P: Firmicutes

2235

DQ413080

284

1.000

216

221

216

10

34.5

S: Rhodocyclus tenuis

3160

AF502230

296

0.773

   

8

27.6

G: Nitrosomonas

3136

GU183579

364

0.948

   

6

20.7

C: Anaerolineae

1317

EU104216

202

0.598

   

3

10.3

G: Methyloversatilis

3158

CU922545

360

0.909

   

1

3.4

G: Aminobacter

2580

L20802

281

0.829

   

1

3.4

G: Dechloromonas

3156

DQ413103

273

0.898

223

228

223

44

 

F: Intrasporangiaceae

418

AF255629

  
 

(G: Tetrasphaera)

  
   

15

24.6

F: Hyphomonadaceae

2656

AF236001

298

0.674

   

1

1.6

F: Microbacteriaceae

441

GQ009478

228

0.544

   

1

1.6

O: Acidimicrobiales

268

GQ009478

153

0.447

239

243

238

275

98.9

C: Gammaproteobacteria

3370

EU529737

446

0.982

   

2

0.7

G: Leptospira

4092

AB476706

350

0.926

   

1

0.4

P: Armatimonadetes

975

EU332819

275

0.846

249

253

249

9

100.0

S: Rhodocyclus tenuis

3160

AB200295

228

0.752

255

258

253

7

100.0

O: Sphingobacteriales

1171

FJ793188

355

0.989

260

263

258

16

94.1

G: Nitrospira

2360

GQ487996

389

0.982

   

1

5.9

O: Sphingobacteriales

1171

FJ536916

251

0.640

260

264

259

38

97.4

O: Sphingobacteriales

1170

EU104185

267

0.706

   

1

2.6

G: Nitrospira

2360

GQ487996

319

0.788

297

302

297

26

100.0

G: Herpetosiphon

1359

NC009972

339

0.867

307

311

306

38

97.4

P: Armatimonadetes

975

CU921283

218

0.472

   

1

2.6

O: Sphingobacteriales

1171

EU104210

196

0.525

321

323

318

17

100.0

G: Cytophaga

1208

EU104191

367

0.968

393

397

392

33

100.0

G: Bdellovibrio

3173

CU466777

262

0.663

Groundwater samples from chloroethene-contaminated aquifers

63

69

64

93

85.3

F: Methylococcaceae

3686

AB354618

432

0.915

   

14

12.8

F: Crenotrichaceae

3681

GU454947

290

0.816

   

1

0.9

F: Ectothiorhodospiraceae

3510

AM902494

168

0.542

   

1

0.9

P: candidate phylum OP3

2388

GQ356152

187

0.488

165

168

163

143

100.0

G: Dehalococcoides

1368

EF059529

448

0.953

190

193

191

12

54.6

F: Desulfobulbaceae

3177

AJ389624

379

0.945

   

4

13.6

F: Sphingomonadaceae

2880

AY785128

263

0.555

   

2

9.1

F: Erythrobacteraceae

2872

DQ811848

343

0.771

   

2

9.1

C: Alphaproteobacteria

2451

AY921822

337

0.926

   

1

4.6

F: Rhodospirillaceae

2793

AY625147

294

0.679

   

1

4.6

F: Rhodobiaceae

2641

AB374390

328

0.877

198

201

196

140

98.6

G: Desulfovibrio

3215

FJ810587

473

1.000

   

2

1.4

F: Comamonadaceae

3039

FN428768

311

0.814

210

214

209

233

98.3

F: Dehalococcoidaceae

1367

EU679418

262

0.665

   

2

0.8

O: Burkhorderiales

3009

AM777991

367

0.927

   

1

0.4

F: Spirochaetaceae

4130

EU073764

295

0.848

   

1

0.4

P: candidate phylum TM7

4379

DQ404736

277

0.723

216

221

216

1010

90.9

F: Gallionellaceae

3080

EU802012

353

0.869

   

94

8.5

G: Rhodoferax

3050

DQ628925

369

0.920

   

3

0.3

G: Methylotenera

3093

AY212692

291

0.744

   

1

0.1

G: Methyloversatilis

3158

GQ340363

296

0.765

   

1

0.1

F: Clostridiaceae

2005

AJ863357

338

0.833

   

1

0.1

C: Anaerolineae

1315

AB179693

229

0.511

   

1

0.1

C: Actinobacteria

949

EU644115

372

0.907

243

247

243

389

99.7

F: Dehalococcoidaceae

1367

EU679418

255

0.631

   

1

0.3

F: Anaerolinaceae

1321

AB447642

253

0.806

  1. a Experimental (eT-RF) and digital T-RFs (dT-RF).
  2. b Digital T-RF obtained after having shifted the digital dataset with the most probable average cross-correlation lag.
  3. c Number of reads of the target phylotype that contribute to the T-RF.
  4. d Diverse bacterial affiliates can contribute to the same T-RF.
  5. e Phylogenetic affiliation of the T-RF (K: kingdom, P: phylum, C: class, O: order, F: family, G: genus, S: species). Only the last identified phylogenetic branch is presented here.
  6. f Reference operational taxonomic unit (OTU) from the Greengenes public database related with the best SW mapping score. In the Greengenes taxonomy, OTU refer to terminal levels at which sequences are classified.
  7. g GenBank accession numbers provided by Greengenes for reference sequences.
  8. h Best SW mapping score obtained. SW scores consider nucleotide positions and gaps. The highest SW mapping score that can be obtained for a read is the length of the read itself.
  9. i SW mapping score normalized by the read length, as an estimation of the percentage of identity.
  10. j After having observed the presence of the dT-RF 34 bp, we returned to the raw eT-RFLP data and found an important eT-RF at 32 bp. However, Rossi et al. [8] considered that T-RFs below 50 bp are inconsistent and lacks of precision in sizing. This peak was therefore initially not taken into account in the original eT-RFLP profiles.