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
| 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 | |
IQR interquartile range, F/B Firmicutes/Bacteroidetes, F/P Firmicutes/Proteobacteria, E/B Enterobacteriaceae/Bacteroidaceae, FDR false discovery rate
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
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