Fig. 5: Dynamics of the neonatal gut microbiome in early life.

a Time points for neonatal sample collection. b Chao1 and Shannon diversity indices in the neonatal gut microbiome (Day 0: n = 27, Day 1: n = 28, Day 4: n = 43, Month 1: n = 39). Each p-value is shown in Supplementary Table 5. c Principal coordinates analysis (PCoA) plots based on unweighted and weighted UniFrac distances of bacterial compositions in the neonatal gut microbiome. Each p-value is shown in Supplementary Table 6. d Comparison of the relative abundances of bacterial genera in the neonatal gut microbiome between Day 1 and Day 4. e Comparison of the relative abundances of bacterial genera in the neonatal gut microbiome between Day 4 and Month 1. f PCoA plots based on unweighted and weighted UniFrac distances at each time point, comparing bacterial composition in the neonatal gut microbiome between vaginally delivered and cesarean-section-delivered offspring. g Multivariable association analysis of bacterial genera in the neonatal gut microbiome, comparing vaginally delivered and cesarean-section-delivered offspring at each time point. Data are presented as means ± standard errors of the mean. *p < 0.05, **p < 0.01, ****p < 0.0001. Pairwise comparisons (two-sided) were performed using estimated marginal means, accounting for repeated measures, and adjusted for multiple comparisons using the Benjamini-Hochberg method in panel (b). Bacterial compositions were compared using permutational analysis of variance with permutations restricted within each participant, and adjusted for multiple comparisons using the Benjamini-Hochberg method in panels (c) and (f).