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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

From: Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios

Birth scenarios Dominant taxaa   Pet exposure status (N = 746)
No exposure
337 (45.2%)
Median (IQR)
Only prenatal
60 (8.0%)
Median (IQR)
Both pre- and postnatal
349 (46.8%)
Median (IQR)
P FDRp
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
  1. IQR interquartile range, F/B Firmicutes/Bacteroidetes, F/P Firmicutes/Proteobacteria, E/B Enterobacteriaceae/Bacteroidaceae, FDR false discovery rate
  2. Post hoc comparisons between no exposure group and either group of exposure were done by Mann-Whitney U test. *P < 0.05; **P < 0.01; ***P < 0.0001
  3. aDominant taxa have overall median relative abundance >1% at −3–4 months; phyla are in the plain text and families are italicized. Comparisons by nonparametric Kruskal-Wallis test with FDR correction for multiple testing