Table 2 Relative abundance of dominant phyla and families in faecal microbiota of infants at 3–4 months, according to birth scenarios and pet exposure

Vaginal, IAP−

171 (45.6%)

32 (8.5%)

172 (45.9%)

Actinobacteria

6.7 (2.4–16.1)

4.3 (1.3–13.2)

7.2 (1.8–18.9)

0.29

0.84

  Bifidobacteriaceae

5.4 (1.3–14.6)

5.2 (0.3–14.8)

4.9 (0.99–13.6)

0.96

0.96

Bacteroidetes

38.6 (2.0–6.9)

37.7 (2.5–73.9)

35.2 (0.87–67.0)

0.71

0.88

  Bacteroidaceae

18.1 (0.09–58.4)

1.28 (0.07–35.84)

7.6 (0.07–54.32)

0.41

0.88

  Porphyromonadaceae

0.01 (0.00–0.13)

0.01 (0.00–0.60)

0.01 (0.00–0.15)

0.92

0.95

Firmicutes

17.3 (5.5–32.3)

22.9 (10.1–40.3)

16.2 (7.9–32.3)

0.44

0.88

  Streptococcaceae

0.65 (0.21–1.8)

1.1 (0.23–2.8)

0.57 (0.18–1.9)

0.59

0.88

  Clostridiaceae

0.33 (0.02–2.1)

0.35 (0.09–1.8)

0.45 (0.06–2.9)

0.52

0.88

  Lachnospiraceae

2.6 (0.03–9.4)

4.7 (0.16–12.3)

2.2 (0.04–10.4)

0.59

0.88

  Rumminococcaceae

0.09 (0.00–1.10)

0.62 (0.00–2.5)

0.05 (0.00–1.7)

0.55

0.88

  Vellionellaceae

4.4 (0.48–17.2)

9.7 (3.4–17.7)

6.2 (1.2–20.3)

0.17

0.72

Proteobacteria

17.6 (9.7–37.4)

7.2 (2.0–28.6)**

15.5 (7.6–35.4)

0.005

0.07

  Enterobacteriaceae

17.0 (6.5–37.8)

12.0 (3.9–47.0)

14.7 (4.8–37.7)

0.61

0.88

Verrucomicrobia

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.36

0.88

  Verrucomicrobiaceae

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.00 (0.00–0.02)*

0.05

0.45

F/B ratio

0.47 (0.1–6.2)

0.58 (0.15–12.6)

0.57 (0.15–23.3)

0.67

0.88

F/P ratio

0.91 (0.29–2.3)

2.5 (0.77–11.6)***

1.0 (0.39–3.4)

0.003

0.05

E/B ratio

0.84 (0.15–353.7)

21.0 (0.12–333.7)

1.3 (0.12–487.6)

0.92

0.95

Vaginal, IAP+

75 (42.6%)

14 (8.0%)

87 (49.4%)

Actinobacteria

2.1 (0.24–10.9)

2.7 (0.52–4.4)

4.0 (0.56–17.8)

0.18

0.72

  Bifidobacteriaceae

6.9 (1.3–20.3)

3.7 (1.7–10.9)

3.6 (1.4–14.5)

0.69

0.88

Bacteroidetes

2.8 (0.07–61.3)

33.7 (0.05–66.9)

21.3 (0.05–69.9)

0.9

0.95

  Bacteroidaceae

9.5 (0.08–43.2)

27.6 (0.04–66.5)

35.2 (0.65–65.0)**

0.01

0.12

  Porphyromonadaceae

0.01 (0.00–0.28)

0.00 (0.00–0.14)

0.01 (0.00–0.29)

0.52

0.88

Firmicutes

20.7 (8.2–53.4)

21.1 (5.3–57.9)

17.1 (7.4–46.7)

0.89

0.95

  Streptococcaceae

1.0 (0.38–4.1)

0.27 (0.1–0.62)**

0.43 (0.2–0.97)***

<0.001

0.03

  Clostridiaceae

0.49 (0.02–2.7)

0.36 (0.1–5.1)

0.29 (0.03–2.0)

0.73

0.88

  Lachnospiraceae

1.8 (0.07–10.1)

1.6 (0.03–4.3)

2.4 (0.09–11.4)

0.54

0.88

  Rumminococcaceae

0.33 (0.01–1.6)

0.03 (0.00–3.1)

0.12 (0.00–1.2)

0.76

0.88

  Vellionellaceae

6.7 (0.7–18.3)

2.6 (0.41–34.4)

3.0 (0.56–11.1)

0.32

0.85

Proteobacteria

22.9 (11.3-42.5)

26.7 (10.9–52.1)

15.3 (4.5–40.1)

0.06

0.48

  Enterobacteriaceae

19.7 (7.2–40.5)

19.2 (6.5–47.2)

13.7 (5.0–33.0)

0.38

0.88

Verrucomicrobia

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.7

0.88

  Verrucomicrobiaceae

0.00 (0.00–0.01)

0.00 (0.00–0.00)

0.00 (0.00–0.01)

0.74

0.88

F/B ratio

10.3 (0.21–494.0)

0.49 (0.1–1333.3)

1.8 (0.15–819.4)

0.96

0.96

F/P ratio

0.88 (0.31–2.5)

1.0 (0.14–3.1)

1.4 (0.54–3.6)

0.14

0.63

E/B ratio

1.7 (0.23–460.4)

2.5 (0.16–1307.1)

0.43 (0.1–64.3)**

0.02

0.21

Caesarean, scheduled

42 (48.3%)

4 (4.6%)

41 (47.1%)

Actinobacteria

5.3 (0.89–23.2)

4.7 (0.58–20.9)

9.1 (2.4–17.1)

0.63

0.88

  Bifidobacteriaceae

11.3 (3.1–17.0)

0.04 (0.02–17.1)

8.3 (2.4–19.5)

0.26

0.78

Bacteroidetes

0.13 (0.04–0.62)

30.1 (0.1–61.2)

0.11 (0.05–0.66)

0.58

0.88

  Bacteroidaceae

8.0 (0.06–63.1)

3.6 (0.03–28.3)

3.9 (0.11–52.7)

0.56

0.88

  Porphyromonadaceae

0.01 (0.00–0.07)

0.00 (0.00–0.00)

0.01 (0.00–0.07)

0.07

0.5

Firmicutes

31.2 (13.3–55.0)

8.5 (4.5–31.2)

39.2 (16.1–52.8)

0.12

0.63

  Streptococcaceae

0.50 (0.3–2.1)

0.15 (0.11–1.2)

0.40 (0.16–1.6)

0.24

0.78

  Clostridiaceae

0.77 (0.05–4.4)

3.9 (0.43–16.4)

0.64 (0.09–2.6)

0.74

0.88

  Lachnospiraceae

2.1 (0.05–10.2)

5.0 (0.81–28.5)

1.7 (0.05–8.3)

0.71

0.88

  Rumminococcaceae

0.08 (0.01–1.8)

3.5 (0.16–9.5)

0.05 (0.00–2.5)

0.41

0.88

  Vellionellaceae

3.4 (0.36–10.7)

2.7 (0.93–13.1)

4.9 (0.92–22.7)

0.54

0.88

Proteobacteria

33.2 (11.4–51.8)

44.4 (13.9–79.9)

34.2 (13.5–50.4)

0.67

0.88

  Enterobacteriaceae

16.1 (8.9–35.7)

25.6 (15.9–73.1)

21.8 (8.0–47.1)

0.46

0.88

Verrucomicrobia

0.00 (0.00–0.01)

0.00 (0.00–0.00)

0.00 (0.00–0.01)

0.33

0.85

  Verrucomicrobiaceae

0.00 (0.00–0.00)

0.00 (0.00–0.02)

0.00 (0.00–0.01)

0.23

0.78

F/B ratio

169.0 (22.8–859.8)

18.2 (0.07–1230.1)

218 (35.0–980.4)

0.33

0.85

F/P ratio

1.2 (0.35–3.1)

0.41 (0.12–0.75)

1.1 (0.6–3.1)

0.13

0.63

E/B ratio

1.5 (0.13–353.6)

287 (3.4–907.5)

4.3 (0.19–214.4)

0.57

0.88

Caesarean, emergency

49 (45.4%)

10 (9.3%)

49 (45.4%)

Actinobacteria

7.4 (1.4–20.5)

5.6 (3.3–13.5)

6.1 (0.4–16.9)

0.72

0.88

  Bifidobacteriaceae

3.5 (0.08–7.0)

28.8 (12.7–71.9)***

3.4 (0.57–18.1)

0.003

0.05

Bacteroidetes

0.10 (0.03–0.23)

0.15 (0.1–50.6)

0.10 (0.05–1.3)

0.14

0.63

  Bacteroidaceae

31.2 (0.07–66.7)

0.19 (0.08–22.1)

5.0 (0.07–67.1)

0.77

0.88

  Porphyromonadaceae

0.01 (0.00–0.14)

0.00 (0.00–0.13)

0.01 (0.00–0.04)

0.19

0.72

Firmicutes

33.3 (19.6–55.1)

48.1 (15.1–67.3)

33.9 (17.5–59.5)

0.74

0.88

  Streptococcaceae

0.59 (0.15–1.5)

3.5 (1.7–6.8)**

0.58 (0.21–1.1)

0.003

0.05

  Clostridiaceae

0.38 (0.04–7.5)

0.17 (0.01–3.1)

0.70 (0.02–3.7)

0.64

0.88

  Lachnospiraceae

2.9 (0.05–7.3)

3.8 (0.05–5.7)

1.6 (0.26–9.1)

0.77

0.88

  Rumminococcaceae

0.14 (0.00–2.6)

0.01 (0.01–0.91)

0.08 (0.00–0.58)

0.25

0.78

  Vellionellaceae

3.8 (0.56–10.9)

2.3 (0.2–4.8)

2.2 (0.41–13.0)

0.6

0.88

Proteobacteria

36.7 (19.3–56.4)

27.8 (12.6–38.2)

22.0 (7.7–51.5)*

0.08

0.52

  Enterobacteriaceae

20.3 (6.3–40.1)

10.2 (5.7–55.2)

15.0 (8.1–43.1)

0.88

0.95

Verrucomicrobia

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.00 (0.00–0.01)

0.81

0.91

  Verrucomicrobiaceae

0.00 (0.00–0.01)

0.01 (0.00–0.02)

0.00 (0.00–0.01)

0.14

0.63

F/B ratio

281 (52.7–1092.0)

362 (0.23–777.5)

252 (10.9–910.5)

0.63

0.88

F/P ratio

1.2 (0.47–2.8)

1.4 (0.65–4.1)

1.8 (0.65–4.6)

0.22

0.78

E/B ratio

0.84 (0.09–480.7)

4.3 (0.7–322.8)

10.0 (0.13–336.3)

0.87

0.95