Table 2 Metagenomic community state types (mgCSTs) of the vaginal microbiome are dominated by different metagenomic subspecies

1

Lactobacillus crispatus 1

Lactobacillus crispatus 1

143

79

0.977

0.17

20

2

21

63

15

22

2

Lactobacillus crispatus 2

Lactobacillus crispatus 2

39

26

0.965

0.47

39

0

0

0

0

0

3

Lactobacillus crispatus 3

Lactobacillus crispatus 3

83

51

0.912

0.28

9

2

15

14

22

21

4

Lactobacillus crispatus 4

Lactobacillus crispatus 4

27

12

0.972

0.39

1

1

0

0

3

22

5

Lactobacillus crispatus 5

Lactobacillus crispatus 5

37

27

0.960

0.11

1

0

19

16

1

0

6

Lactobacillus crispatus 6

Lactobacillus crispatus 6

28

13

0.982

0.69

12

0

5

2

9

0

7

Lactobacillus gasseri 1

Lactobacillus gasseri 1

16

8

0.786

0.5

0

0

1

8

1

6

8

Lactobacillus gasseri 2

Lactobacillus gasseri 2

29

17

0.945

0.73

15

0

8

0

1

5

9

Lactobacillus gasseri 3

Lactobacillus gasseri 3

14

5

0.425

0.89

6

0

0

2

0

6

10

Lactobacillus iners 1

Lactobacillus iners 1

113

76

0.912

0.7

24

0

40

2

10

37

11

Lactobacillus iners 2

Lactobacillus iners 2

95

79

0.862

0.53

11

7

47

0

28

2

12

Lactobacillus iners 3

Lactobacillus iners 3

131

92

0.927

0.44

9

10

45

19

42

6

13

Lactobacillus iners 5

Lactobacillus iners 5

45

41

0.912

0.57

1

0

29

1

13

1

14

Lactobacillus iners 6

Lactobacillus iners 6

34

25

0.945

0.8

34

0

0

0

0

0

15

Lactobacillus jensenii 1

Lactobacillus jensenii 1

44

28

0.888

0.77

8

1

3

10

18

4

16

Lactobacillus jensenii 2

Lactobacillus jensenii 2

67

39

0.859

0.71

8

0

15

15

13

16

17

"Ca. Lachnocurva vaginae" 1

"Ca. Lachnocurva vaginae" 1

58

57

0.552

1.48

3

0

51

1

3

0

18

"Ca. Lachnocurva vaginae" 2

"Ca. Lachnocurva vaginae" 2

28

27

0.574

1.57

0

0

27

0

1

0

19

"Ca. Lachnocurva vaginae" 3

"Ca. Lachnocurva vaginae" 3

43

36

0.574

1.91

7

0

27

0

9

0

20

Gardnerella vaginalis 1

Gardnerella vaginalis 1

250

171

0.799

1.62

90

2

98

2

38

20

21

Gardnerella vaginalis 1

Gardnerella vaginalis 1

37

21

0.542

1.97

37

0

0

0

0

0

22

Gardnerella vaginalis 2

Prevotella amnii 4

202

159

0.607

1.79

30

0

91

3

67

11

23

Gardnerella vaginalis 3

Gardnerella vaginalis 3

53

42

0.862

0.88

18

5

15

2

5

8

24

Gardnerella vaginalis 4

Gardnerella vaginalis 4

145

106

0.959

1.21

44

0

64

6

24

7

25

Gardnerella vaginalis 5

Gardnerella vaginalis 5

34

17

0.983

0.83

11

1

9

6

2

5

26

Bifidobacterium breve

Bifidobacterium breve

16

11

0.750

0.9

5

0

1

0

8

2

27

Bifidobacterium dentium

Enterococcus faecalis 3

87

76

0.750

1.78

23

13

22

2

9

18