Table 1 The relative representation of individual phyla (in% of total microbiota) prior to, during and after the antibiotic therapy

Day

0

0

2

2

0

2

2

14

14

16

16

phyllum

Str

Tet

Str

Tet

Str/Tet

Str

Tet

Str

Tet

Str

Tet

Bacteria. other

0.02

0.02

0.02

0.02

0.02

0.01

ND

0.09

0.46

ND

ND

Actinobacteria

7.21

4.09

0.38

0.09

1.67

8.7

0.01

0.35

1.76

0.24

0.11

Bacteroidetes

13.04

3.56

0.07

0.02

6.61

0.57

ND

2.48

11.3

0.04

ND

Cyanobacteria

0.01

ND

0.02

0.01

ND

ND

ND

ND

ND

ND

ND

Deferribacteres

ND

ND

ND

ND

0.02

ND

ND

ND

0.23

ND

ND

Firmicutes

61.83

86.60

45.07

27.81

89.88

90.3

99.88

89.84

82.94

99.22

99.8

Fusobacteria

ND

ND

ND

ND

0.77

0.12

ND

6.81

0.24

0.4

ND

Chloroflexi

ND

ND

0.003

ND

ND

ND

ND

ND

ND

ND

ND

Lentisphaerae

ND

ND

ND

ND

0.003

ND

ND

ND

ND

ND

ND

Proteobacteria

17.80

5.33

54.41

72.04

0.9

0.16

0.08

0.28

2.2

0.03

0.04

Spirochaetes

ND

ND

ND

ND

0.001

ND

ND

ND

ND

ND

ND

Synergistetes

ND

ND

ND

ND

0.1

0.07

ND

0.11

0.82

ND

ND

Tenericutes

ND

ND

ND

ND

0.001

ND

ND

ND

ND

ND

ND

TM7

0.09

0.39

0.01

ND

0.01

0.02

ND

0.01

ND

0.01

ND

OTU*

590

709

172

273

2222

433

182

896

1028

236

228

Chao1

1106

932

488

263

4592

709

263

1675

1860

490

364

OTU 14,446

478

528

131

182

869

433

164

541

799

211

165

Chao1 14,446

769

887

209

240

1791

709

290

1043

1510

422

357

Evenness

0.615

0.57

0.3

0.24

0.37

0.47

0.2

0.39

0.45

0.22

0.28

Shannon index

4.03

3.68

1.71

1.26

2.87

2.85

1.03

2.65

3.12

1.25

1.53

Total n. of reads

22,885

29,269

32,010

25,031

76,785

14,446

19,834

37,707

22,615

17,808

27,703