Table 3.
Relative abundance of dominant genera in faecal microbiota of infants at 3–4 months, according to birth scenarios and pet exposure
| Birth scenarios | Dominant generaa | Pet exposure status (N = 746) | ||||
|---|---|---|---|---|---|---|
| No exposure 337 (45.17%) Median (IQR) |
Only prenatal 60 (8.0%) Median (IQR) |
Both pre- and postnatal 349 (46.78%) Median (IQR) |
P | FDRp | ||
| Vaginal, IAP− |
171 (45.6%) | 32 (8.5%) | 172 (45.9%) | |||
| Bifidobacterium | 5.3 (1.8–14.9) | 2.2 (0.68–13.0) | 6.3 (1.6–17.8) | 0.21 | 0.63 | |
| Bacteroides | 31.2 (0.36–62.4) | 29.9 (2.4–62.9) | 31.5 (0.61–60.7) | 0.66 | 0.86 | |
| Parabacteroides | 0.01 (0.00–0.5) | 0.16 (0.00–2.9) | 0.01 (0.00–0.51) | 0.13 | 0.51 | |
| Streptococcus | 0.62 (0.13–2.1) | 0.46 (0.21–1.4) | 0.59 (0.21–1.8) | 0.81 | 0.86 | |
| Unclassified Clostridiaceae | 0.03 (0.00–0.45) | 0.09 (0.00–0.46) | 0.07 (0.01–0.49) | 0.45 | 0.81 | |
| Clostridium | 0.01 (0.00–0.38) | 0.01 (0.00–0.29) | 0.02 (0.00–0.42) | 0.15 | 0.51 | |
| Unclassified Lachnospiraceae | 0.02 (0.00–1.6) | 0.38 (0.02–4.8)* | 0.05 (0.01–1.5)* | 0.02 | 0.16 | |
| Ruminococcus | 0.02 (0.00–1.2) | 0.43 (0.01–1.5)* | 0.05 (0.00–2.6)* | 0.03 | 0.21 | |
| Oscillospira | 0.00 (0.00–0.04) | 0.07 (0.00–2.3)* | 0.01 (0.00–0.7)*** | <0.001 | 0.04 | |
| Veillonella | 1.5 (0.16–14.9) | 2.9 (0.13–9.1) | 1.6 (0.24–7.6) | 0.89 | 0.91 | |
| Unclassified Enterobacteriaceae | 15.5 (7.0–31.9) | 5.4 (1.3–28.4)** | 13.3 (4.6–34.8) | 0.02 | 0.16 | |
| Akkermansia | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.42 | 0.81 | |
| Vaginal, IAP+ |
75 (42.6%) | 14 (8.0%) | 87 (49.4%) | |||
| Bifidobacterium | 2.0 (0.06–9.9) | 2.2 (0.36–4.1) | 3.7 (0.27–16.8) | 0.25 | 0.69 | |
| Bacteroides | 0.67 (0.05–59.2) | 33.7 (0.04–56.3) | 12.0 (0.05–69.6) | 0.84 | 0.88 | |
| Parabacteroides | 0.01 (0.00–0.03) | 0.00 (0.00–1.12) | 0.00 (0.00–0.02) | 0.95 | 0.95 | |
| Streptococcus | 0.43 (0.21–1.6) | 0.47 (0.12–0.93) | 0.59 (0.2–3.6) | 0.34 | 0.81 | |
| Unclassified Clostridiaceae | 0.08 (0.01–0.88) | 0.30 (0.01–3.5) | 0.09 (0.01–1.0) | 0.49 | 0.81 | |
| Clostridium | 0.03 (0.00–0.86) | 0.07 (0.02–1.9) | 0.04 (0.00–1.0) | 0.47 | 0.81 | |
| Unclassified Lachnospiraceae | 0.02 (0.00–3.8) | 0.66 (0.01–4.1) | 0.08 (0.01–3.2) | 0.55 | 0.83 | |
| Ruminococcus | 0.01 (0.00–0.44) | 0.02 (0.00–1.28) | 0.03 (0.01–1.88)*** | 0.004 | 0.1 | |
| Oscillospira | 0.00 (0.00–0.56) | 0.02 (0.00–2.8) | 0.01 (0.00–0.65) | 0.66 | 0.86 | |
| Veillonella | 3.2 (0.3–13.9) | 0.63 (0.19–13.7) | 2.7 (0.24–11.8) | 0.69 | 0.86 | |
| Unclassified Enterobacteriaceae | 20.3 (8.7–37.3) | 21.8 (9.8–503) | 12.5 (3.6–37.0)* | 0.06 | 0.29 | |
| Akkermansia | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.74 | 0.86 | |
| Caesarean, scheduled | 42 (48.3%) | 4 (4.6%) | 41 (47.1%) | |||
| Bifidobacterium | 5.0 (0.37–21.6) | 3.7 (0.51–19.9) | 8.2 (1.3–16.9) | 0.76 | 0.86 | |
| Bacteroides | 0.08 (0.04–0.44) | 30.0 (0.08–61.1) | 0.10 (0.05–0.42) | 0.49 | 0.81 | |
| Parabacteroides | 0.00 (0.00–0.01) | 0.00 (0.00–0.04) | 0.00 (0.00–0.01) | 0.74 | 0.86 | |
| Streptococcus | 0.80 (0.29–2.1) | 0.46 (0.13–0.75) | 1.6 (0.39–3.7) | 0.15 | 0.51 | |
| Unclassified Clostridiaceae | 0.15 (0.01–1.5) | 0.13 (0.02–1.7) | 0.40 (0.06–1.6) | 0.58 | 0.84 | |
| Clostridium | 0.04 (0.01–1.5) | 0.16 (0.02–0.59) | 0.28 (0.02–1.7) | 0.54 | 0.82 | |
| Unclassified Lachnospiraceae | 0.04 (0.00–8.7) | 2.0 (0.46–22.6) | 0.05 (0.00–7.1) | 0.42 | 0.81 | |
| Ruminococcus | 0.02 (0.00–1.9) | 0.00 (0.00–0.01) | 0.01 (0.00–1.7) | 0.26 | 0.69 | |
| Oscillospira | 0.00 (0.00–0.16) | 0.00 (0.00–0.01) | 0.03 (0.00–0.89)* | 0.04 | 0.24 | |
| Veillonella | 7.0 (1.04–16.3) | 3.6 (1.14–5.41) | 6.2 (1.57–29.7) | 0.53 | 0.82 | |
| Unclassified Enterobacteriaceae | 27.7 (10.1–45.2) | 34.9 (13.1–74.7) | 30.5 (10.8–47.8) | 0.79 | 0.86 | |
| Akkermansia | 0.00 (0.00–0.01) | 0.00 (0.00–0.00) | 0.00 (0.00–0.01) | 0.36 | 0.81 | |
| Caesarean, emergency | 49 (45.4%) | 10 (9.3%) | 49 (45.4%) | |||
| Bifidobacterium | 6.5 (1.2–18.0) | 4.8 (1.9–12.4) | 5.3 (0.18–16.8) | 0.75 | 0.86 | |
| Bacteroides | 0.08 (0.03–0.17) | 0.13 (0.05–17.1) | 0.09 (0.04–1.3) | 0.19 | 0.61 | |
| Parabacteroides | 0.00 (0.00–0.01) | 0.01 (0.00–0.02)* | 0.00 (0.00–0.01) | 0.05 | 0.27 | |
| Streptococcus | 1.2 (0.5–3.0) | 0.64 (0.13–5.1) | 0.96 (0.27–2.7) | 0.48 | 0.81 | |
| Unclassified Clostridiaceae | 0.36 (0.02–3.3) | 0.30 (0.01–0.67) | 0.31 (0.04–1.6) | 0.65 | 0.86 | |
| Clostridium | 0.19 (0.02–2.4) | 0.04 (0.00–1.1) | 0.20 (0.02–1.2) | 0.63 | 0.86 | |
| Unclassified Lachnospiraceae | 0.03 (0.01–5.2) | 0.39 (0.01–1.6) | 0.77 (0.01–9.2) | 0.41 | 0.81 | |
| Ruminococcus | 0.00 (0.00–0.03) | 0.00 (0.00–0.33) | 0.22 (0.00–4.6)** | 0.01 | 0.16 | |
| Oscillospira | 0.01 (0.00–0.45) | 0.00 (0.00–1.2) | 0.19 (0.01–2.8)** | 0.02 | 0.16 | |
| Veillonella | 9.2 (2.98–26.2) | 8.6 (4.3–42.4) | 8.1 (0.53–23.8) | 0.45 | 0.81 | |
| Unclassified Enterobacteriaceae | 34.1 (16.5–54.1) | 18.1 (7.5–32.9) | 16.4 (6.3–48.4) | 0.1 | 0.44 | |
| Akkermansia | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.00 (0.00–0.01) | 0.81 | 0.86 | |
IQR interquartile range, 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 genera have overall median relative abundance >1% at 3–4 months; phyla are in plain text and families are in italics. Comparisons by nonparametric Kruskal-Wallis test with FDR correction for multiple testing