Fig. 1: The neonatal microbiotas within three days postpartum.

The neonatal buccal (NB), rectal (NR), and stool (NS) microbiotas on day 0 (within 24 h postpartum), day 1 (24–48 h postpartum), and day 2 (48–72 h postpartum) after birth and the maternal buccal (MB), rectal (MR), and vaginal (MV) microbiotas collected on the last visit of pregnancy were used in the diversity analyses. The experimental design, including case number, is shown in Fig. S1a. a Alpha diversity (Shannon index) of the neonatal microbiotas on different days. P values were quantified using the two-sided Mann–Whitney U test. Lines in the boxplots represent maximum, 75% quantile, median, 25 quantile, and minimum values from top to bottom. b Beta diversity of the NB, NR, and NS and MB, MR, and MV microbiotas quantified by the Bray-Curtis distance and visualized by the t-distributed stochastic neighbor embedding plot. c Pairwise analysis of the difference between two microbiotas was performed using the Adonis test with default parameters. The significance is indicated by asterisks. ***P value ≤ 0.001. d The significant changes in the relative abundance of taxa in the neonatal microbiotas are shown by a dot plot and are highlighted by asterisks. The relative abundance changes of taxa that are abundant in any studied microbiota are also visualized. Relative abundance change was tested by the ALDEx2 package with default parameters in R and quantified by the per-taxon median difference between two conditions. Adjusted P values were generated by the Benjamini-Hochberg correction of the Mann–Whitney U test.