Relative abundance of dominant phyla, families and genera in fecal samples, by mode of delivery and infant diet*
| Taxon† | Relative abundance,‡ %, mean ± SE | p value | Relative abundance,‡ %, mean ± SE | p value | ||
|---|---|---|---|---|---|---|
| Vaginal delivery n = 18 | Cesarean delivery n = 6 | Not breastfed n = 9 | Breastfed n = 15 | |||
| Actinobacteria | ||||||
| Bifidobacteriaceae | 36.6 ± 7.8 | 48.6 ± 14.8 | > 0.1 | 34.4 ± 9.8 | 42.8 ± 9.4 | > 0.1 |
| Bifidobacterium | 36.6 ± 7.8 | 48.6 ± 14.8 | > 0.1 | 34.4 ± 9.8 | 42.8 ± 9.4 | > 0.1 |
| Coriobacteriaceae | 1.8 ± 0.9 | 0.3 ± 0.1 | > 0.1 | 1.6 ± 1.0 | 1.3 ± 0.9 | > 0.1 |
| Eggerthella | 0.5 ± 0.3 | 0.3 ± 0.2 | > 0.1 | 0.6 ± 0.4 | 0.4 ± 0.2 | > 0.1 |
| Bacteroidetes | ||||||
| Bacteroidaceae | 1.0 ± 0.4 | 0.0 ± 0.0 | 0.03 | 0.7 ± 0.4 | 0.8 ± 0.4 | > 0.1 |
| Bacteroides | 1.0 ± 0.4 | 0.0 ± 0.0 | 0.02§ | 0.7 ± 0.4 | 0.8 ± 0.4 | > 0.1 |
| Proteobacteria | ||||||
| Enterobacteriaceae | 13.7 ± 2.7 | 6.2 ± 3.1 | > 0.1 | 9.5 ± 2.6 | 13.2 ± 3.3 | > 0.1 |
| Escherichia–Shigella | 13.6 ± 2.7 | 1.0 ± 0.7 | < 0.001§ | 8.3 ± 2.9 | 11.8 ± 3.4 | > 0.1 |
| Pasteurellaceae | 0.1 ± 0.1 | 0.6 ± 0.6 | > 0.1 | 0.0 ± 0.0 | 0.4 ± 0.3 | 0.04 |
| Haemophilus | 0.1 ± 0.1 | 0.6 ± 0.6 | > 0.1 | 0.0 ± 0.0 | 0.4 ± 0.3 | 0.06 |
| Firmicutes | ||||||
| Clostridiaceae | 2.8 ± 2.0 | 2.1 ± 1.0 | > 0.1 | 1.4 ± 0.5 | 3.4 ± 2.3 | > 0.1 |
| Clostridium | 2.8 ± 2.0 | 2.1 ± 1.0 | > 0.1 | 1.4 ± 0.5 | 3.4 ± 2.3 | > 0.1 |
| Enterococcaceae | 1.6 ± 0.6 | 0.9 ± 0.8 | > 0.1 | 1.8 ± 0.9 | 1.3 ± 0.5 | > 0.1 |
| Enterococcus | 1.6 ± 0.6 | 0.9 ± 0.8 | > 0.1 | 1.8 ± 0.9 | 1.3 ± 0.5 | > 0.1 |
| Erysipelotrichaceae | 4.6 ± 2.0 | 7.1 ± 3.8 | > 0.1 | 3.0 ± 1.1 | 6.6 ± 2.8 | > 0.1 |
| Lachnospiraceae | 22.8 ± 5.7 | 19.5 ± 6.3 | > 0.1 | 33.1 ± 8.9 | 15.3 ± 4.2 | > 0.1 |
| Blautia | 2.2 ± 1.4 | 5.4 ± 4.9 | > 0.1 | 4.3 ± 2.6 | 2.1 ± 2.0 | > 0.1 |
| Coprococcus | 0.9 ± 0.7 | 0.6 ± 0.6 | > 0.1 | 0.9 ± 0.5 | 0.8 ± 0.8 | > 0.1 |
| Peptostreptococcaceae | 1.2 ± 0.5 | 1.2 ± 0.7 | > 0.1 | 2.9 ± 0.8 | 0.2 ± 0.1 | 0.002§ |
| Ruminococcaceae | 0.7 ± 0.3 | 0.4 ± 0.3 | > 0.1 | 1.2 ± 0.5 | 0.2 ± 0.2 | 0.08 |
| Streptococcaceae | 4.7 ± 2.4 | 8.7 ± 6.8 | > 0.1 | 3.0 ± 1.1 | 7.3 ± 3.8 | > 0.1 |
| Streptococcus | 4.6 ± 2.4 | 8.7 ± 6.8 | > 0.1 | 3.0 ± 1.1 | 7.3 ± 3.8 | > 0.1 |
| Veillonellaceae | 5.0 ± 1.8 | 3.6 ± 2.0 | > 0.1 | 3.6 ± 2.2 | 5.4 ± 1.9 | > 0.1 |
| Veillonella | 5.0 ± 1.8 | 3.6 ± 2.0 | > 0.1 | 3.5 ± 2.2 | 5.3 ± 1.9 | > 0.1 |
| Verrucomicrobia | ||||||
| Verrucomicrobiaceae | 0.6 ± 0.6 | 0.6 ± 0.6 | > 0.1 | 1.6 ± 1.2 | 0.0 ± 0.0 | 0.001§ |
| Akkermansia | 0.6 ± 0.6 | 0.6 ± 0.6 | > 0.1 | 1.6 ± 1.2 | 0.0 ± 0.0 | 0.001§ |
Note: SE = standard error.
↵* We assessed differential abundance of bacterial taxa using Metastats.
↵† Taxa were excluded from this analysis if they did not exceed 1% relative abundance in at least 1 sample or were not present in at least 3 infants.
↵‡ Values represent the percentages of all 16S gene sequences analyzed, after quality processing as described in Appendix 1 (available at www.cmaj.ca/lookup/suppl/doi:10.1503/cmaj.121189/-/DC1).
↵§ p < 0.05 after correction for multiple testing.