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Table 4 Estimated mean primer set values from the AA48.48 and the corresponding significant 454 GS FLX Titanium sequencing results

From: The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity

Primer set

Estimated mean percentages relative to total bacteria

P-values

S-

S+

L-

L+

S+/ S-

L+/ L-

Domain Bacteria B 1

24.96

20.32

25.13

25.46

0.003

0.857

[22.39;27.73]

[16.83;24.32]

[22.26;28.27]

[23.23;27.84]

  Genus Streptococcus

0.0061

0.0061

  Species S. alactolyticus

0.0099

0.0134

Phylum Firmicutes

36.08

27.59

30.59

17.79

0.649

0.278

[17.64;65.91]

[7.50;72.58]

[13.64;59.56]

[9.79;29.83]

  Genus Streptococcus

0.0242

0.0102

  Unclassified

0.0462

0.0176

Class Bacilli

14.01

15.92

8.30

12.04

0.473

0.52

[4.85;32.09]

[2.22;57.40]

[2.50;20.64]

[4.99;24.63]

  Genus Streptococcus

0.0287

0.0061

  Unclassified

0.1516

0.029

Genus Enterococcus

0.036

0.39

0.04

0.11

0.208

0.34

[0.0038;0.14]

[0.0049;2.51]

[0.0032;0.18]

[0.018;0.39]

  Genus Enterococcus

0.0424

0.9273

Genus Streptococcus

4.04

1.00

5.10

0.56

0.0003

0.00002

[1.84;7.73]

[0.24;2.83]

[2.10;10.46]

[0.29;0.98]

  Genus Streptococcus

0.0061

0.0121

  Species S. alactolyticus

0.0467

0.0121

Genus Lactobacillus

33.97

53.70

33.27

27.55

0.643

0.846

[12.03;76.74]

[7.82;190.09]

[10.27;81.52]

[11.62;55.67]

Family Clostridium cluster I

0.65

0.17

0.32

0.079

0.231

0.139

[0.16;1.81]

[0.012;0.76]

[0.064;0.97]

[0.025;0.19]

  Genus Clostridium

0.0171

0.2558

Species C lostridium perfringens

3.03

2.82

2.33

0.63

0.81

0.219

[0.62;9.24]

[0.14;14.31]

[0.38;7.86]

[0.17;1.66]

Family Clostridium cluster XIV

0.89

16.84

10.82

5.02

0.818

0.672

[0.098;3.53]

[0.22;106.79]

[0.86;47.63]

[0.82;16.95]

Phylum Bacteroidetes and Genus Bacteroides

2.25

76.17

22.05

5.10

0.924

0.567

[0.082;12.19]

[0.091;505.28]

[0.48;130.66]

[0.34;23.65]

  Species Bacteroides uniformis (generated from the primer set Genus Bacteroides)

0.0447

0.0985

Phylum Actinobacteria

0.32

3.92

1.02

0.32

0.034

0.068

[0.13;0.68]

[0.70;12.70]

[0.35;2.32]

[0.15;0.61]

  Genus Actinomyces

1

0.0363

  Species Actinomyces hyovaginalis

0.1042

0.0179

  Species Bifidobacterium pseudolongum

1

0.0368

  Unclassified

0.072

0.0104

Family Bifidobacteriaceae

0.0064

0.011

0.0063

0.012

0.399

0.24

[0.0026;0.013]

[0.0022;0.036]

[0.0023;0.014]

[0.0056;0.022]

  Species Bifidobacterium pseudolongum

1

0.0424

Phylum Fusobacteria

1.59

32.60

6.28

9.71

0.413

0.604

[0.18;6.17]

[0.48;203.87]

[0.54;27.06]

[1.66;32.13]

Class β- and γ-proteobacteria; Family Enterobacteriaceae and Species Escherichia coli

2.96

0.54

0.61

3.17

0.6

0.029

[0.83;7.69]

[0.049;2.28]

[0.14;1.72]

[1.10;7.25]

  Family Enterobacteriaceae (generated from the primer set Family Enterobacteriaceae)

0.0424

1

  Species Escherichia fergusonii (generated from the primer set Family Enterobacteriaceae)

0.0368

0.7758

  Genus Shigella (generated from the primer set Family Enterobacteriaceae)

0.0462

0.9244

  Species Shigella flexneri (generated from the primer set Family Enterobacteriaceae)

0.0413

0.5626

Phylum Spirochaetes

0.0059

0.010

0.0091

0.0056

0.73

0.081

[0.004;0.0085]

[0.005;0.019]

[0.0058;0.014]

[0.004;0.0076]

  Genus Streptococcus

0.0169

0.0127

  Unclassified

0.0191

0.0694

  1. 1Domain Bacteria B is expressed in percentage relative to the final number of thermal cycles run, 35.
  2. Primer set values from the AA48.48 are expressed as percentages relative to total bacteria, and beneath (indented) are listed the significant 454-sequencing results for the respective primer sets. Numbers in bold indicate significant p-values. L: Large intestine, S: small intestine, +: with diarrhoea, –: without diarrhoea. [95% lower level; 95% upper level].
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BMC Genomics

ISSN: 1471-2164

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