Table 2

Sampling depth and biodiversity found by amplicon 454 pyrosequencing V1V2 and V6 regions from eight culture negative female urine samples

Sample

Combined sequence pool

F1

F2

F3

F4

F5

F6

F7

F8

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6

V1V2

V6


Sampling depth

Total reads

78346

74067

14579

18362

12629

6565

4305

17474

9877

5005

12645

6586

8216

5692

7861

6986

8234

7397

Length

cutoff1

48861

45382

8479

8039

8416

4752

2721

13066

6253

3467

10116

5074

4428

3047

3967

3495

4481

4442

Denoised 2

48860

45136

8479

7977

8416

4703

2721

13064

6253

3461

10116

5057

4427

3031

3967

3432

4481

4411

Cleaned 3

48452

44760

8476

7969

8353

4682

2720

13060

6242

3459

10109

5053

4361

2988

3711

3138

4480

4411

Unique OTUs

1354

2069

61

376

456

328

22

115

116

102

95

81

523

134

322

581

163

538

OTUs4 3%

1209

1435

52

240

411

254

20

81

101

85

73

63

504

116

300

499

130

338

OTUs4 6%

1092

1072

50

178

379

210

19

61

92

73

62

51

472

101

270

436

116

244

Phyla5 (11)

10

8

4

4

6

3

1

3

4

4

3

3

3

4

8

7

4

4

Genera5 (45)

35

28

8

8

15

10

1

8

10

5

6

4

4

4

19

17

9

8

Diversity indices

Chao16 (3%)

1211

2469

64.75

456.36

412.62

410.33

24.5

128.83

104

195.5

86.04

108.76

504.11

130.6

324.6

1121.43

250.12

835.02

Chao1 LCI95

1209

2286

56.13

371.05

411.36

353.85

20.97

102.95

101.7

136.49

77.88

82.43

504

122.1

313.14

953.17

195.84

670.9

Caho1 HCI95

1216

2690

91.27

597.21

418.2

498.76

40.69

185.2

112.75

322.11

107.8

170.8

506.28

148.39

346.03

1352.03

349.14

1080.04

Shannon index7 (3%)

2.99

3.05

0.52

1.96

1.99

1.62

0.23

0.49

1.44

1.44

0.33

0.44

3.01

1.32

3.76

4.07

2.06

3.31

Normalized Shannon index (3%) 8

0.52

1.96

1.86

1.63

0.23

0.50

1.42

1.44

0.34

0.45

2.89

1.35

3.72

4.07

2.06

3.31


1Length cutoff at minimum 218 nt for V1V2 reads and 235 nt for V6 reads.

2Total number of sequences after processing the dataset through the PyroNoise program developed by Quince et al., 2009 [34].

3The number of reads per dataset after removal of sequences that could be from the same source as those in the contamination control dataset.

4OTUs: Operational Taxonomic Units at 3% or 6% nucleotide difference.

5Number of phyla and genera are based on taxonomic classification by MEGAN V3.4 [36,37], with the total number of phyla and genera detected in parenthesis.

6Chao1 is an estimator of the minimum richness and is based on the number of rare OTUs (singletons and doublets) within a sample.

7The Shannon index combines estimates of richness (total number of OTUs) and evenness (relative abundance).

8The Shannon index after normalization of the number of sequences (as described in Methods).

Siddiqui et al. BMC Microbiology 2011 11:244   doi:10.1186/1471-2180-11-244

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