Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota

Abstract

Gut microbiota is one of the largest microbial communities within the human body, yet its origins and early developmental processes remain not fully understood. This study collected samples from 26 mother-infant pairs from the third trimester to 14 days postpartum, using 16S rDNA sequencing and Source Tracker analysis to investigate the dynamic changes and sources of early infant gut microbiota. Results showed that maternal gut microbiota at 32 weeks of gestation was the primary source of meconium microbiota in vaginally delivered infants and continued to influence day-14 gut microbiota, while maternal vaginal microbiota contributed minimally (<1%). Regardless of bacterial presence in breast milk, maternal gut microbiota remained a critical source for day-14 gut microbiota of vaginally delivered infants. Placental microbiota was also an important source of meconium microbiota across different delivery modes. In cesarean-delivered infants, the origins of gut microbiota were more complex, with a higher proportion of "transient bacteria" in meconium, potentially impacting the stable colonization of gut microbiota. However, by day 14, the gut microbiota of cesarean and vaginally delivered infants became similar post-breastfeeding. Correlation network analysis revealed intricate maternal-infant microbial interactions, indicating that maternal microbes may influence the colonization of infant gut microbiota. Shared taxa analysis showed that functional flora might exist in the placenta. Meanwhile, beneficial anaerobes like Bifidobacterium significantly increased in infant day-14 gut microbiota, suggesting their potential role in gut health. Overall, this study provides novel insights into the colonization and developmental patterns of early infant gut microbiota.

Importance: Gut microbiota exerts a significant impact on an individual's long-term health; however, its origins and colonization processes remain to be fully elucidated. This study revealed that early infant gut microbiota of vaginally delivered infants primarily derived from maternal gut microbiota, which began colonizing the fetus as early as 32 weeks of gestation. In contrast, the contribution of maternal vaginal microbiota to early infant gut microbiota was quite limited. Moreover, placental microbiota also constituted an important source for the fetal gut microbiota. These findings provide novel insights into the developmental mechanisms of infant gut microbiota and highlight the important role of maternal microbes in the early colonization of infant gut microbiota.

Keywords: 16S rDNA; correlation network; gut microbiota; infant; microbial transmission.

Fig 1

α and β diversity analyses of early infant gut microbiota. (a) Shannon index and (b) Simpson index were utilized to assess α diversity. Group differences were tested using the Kruskal-Wallis test, with pairwise comparisons conducted using the Wilcoxon rank-sum test with Bonferroni correction for multiple testing. Statistical significance is indicated by **P < 0.01 and ***P < 0.001. (c) Principal coordinates analysis (PCoA) based on Weighted_Unifrac distances and (d) Unweighted_Unifrac distances was performed to visualize the clustering of samples. Different colors represent distinct groups, and the percentages on the axes indicate the proportion of variance explained by each principal component. (e–h) Anosim analysis based on Bray-Curtis dissimilarity was performed to evaluate the differences in microbial community structure between groups at different time points. CIF1, meconium microbiota of cesarean-section infants; CIF2, gut microbiota of 14-day-old infants delivered by cesarean section; VIF1, meconium microbiota of vaginally delivered infants; VIF2, gut microbiota of 14-day-old vaginally delivered infants.

Fig 2

Relative abundances of the top 20 microbes in early infant gut microbiota at the phylum and genus levels. (a) Phylum-level composition of the top 20 microbes ranked by relative abundance in meconium and day-14 gut microbiota of infants. (b) Genus-level composition of the top 20 microbes ranked by relative abundance in meconium and day-14 gut microbiota of infants. CIF1, meconium microbiota of cesarean-section infants; CIF2, gut microbiota of 14-day-old infants delivered by cesarean section; VIF1, meconium microbiota of vaginally delivered infants; VIF2, gut microbiota of 14-day-old vaginally delivered infants.

Fig 3

Venn diagrams of early infant gut microbiota. (a) Venn diagram showing the unique and shared OTU counts, sequence numbers (seq), and relative abundances between the meconium microbiota of vaginally delivered (VIF1) and cesarean-section infants (CIF1). (b) Venn diagram depicting unique and shared OTU counts, seq, and relative abundances between VIF2 and CIF2. (c) Venn diagram presenting shared and unique OTU counts, seq, and relative abundances between VIF1 and VIF2. (d) Venn diagram illustrating shared and unique OTU counts, seq, and relative abundances between CIF1 and CIF2. In each diagram, overlapping areas represent shared OTUs, while non-overlapping areas indicate unique OTUs, along with corresponding sequence counts and relative abundances. Relative abundances, expressed as percentages, were calculated by dividing the sequence counts of unique or shared OTUs by the total OTU sequence count within each group and multiplying by 100% to adjust for sample size discrepancies between groups. OTU, operational taxonomic unit; seq, sequences.

Fig 4

LEfSe analysis of gut microbiota during early infancy. (a) LEfSe analysis revealed distinct differences in composition between the meconium microbiota of vaginally delivered infants (VIF1) and that of cesarean-section infants (CIF1). (b) Significant variations were observed in composition between the VIF1 and the gut microbiota of 14-day-old vaginally delivered infants (VIF2). (c) Notable disparities in composition were indicated between the CIF1 and the gut microbiota of 14-day-old infants delivered by cesarean section (CIF2). LEfSe, Linear discriminant analysis effect size.

Fig 5

Contributions of maternal niche microbiota on the early infant gut microbiota. Results of Source Tracker analysis for the following groups: (a) meconium microbiota of vaginally delivered infants (VIF1, n = 8), (b) gut microbiota of 14-day-old vaginally delivered infants (VIF2, n = 16), (c) gut microbiota of 14-day-old vaginally delivered infants fed bacterial breast milk (BM, n = 10), (d) gut microbiota of 14-day-old vaginally delivered infants fed sterile BM (n = 4), (e) meconium microbiota of cesarean-section infants (CIF1, n = 7), and (f) gut microbiota of 14-day-old infants delivered by cesarean section (CIF2, n = 3). CTF, gut microbiota at term pregnancy in women with cesarean section delivery; CTO, maternal oral microbiota at term in women with cesarean section delivery; CTP, full-term placental microbiota of cesarean section; CTV, vaginal microbiota at term in women with cesarean section delivery; VLF, gut microbiota at 32 weeks in women with vaginal delivery; VLV, vaginal microbiota at 32 weeks of gestation in women with vaginal delivery; VTF, gut microbiota at term pregnancy in women with vaginal delivery; VTO, maternal oral microbiota at term in women with vaginal delivery; VTP, full-term placental microbiota of vaginal delivery; VTV, vaginal microbiota at term in women with vaginal delivery.

Fig 6

Correlation networks of cross-ecological and temporal interactions between maternal and infant microbiota. Correlation networks were constructed at the genus level for the following pairs: (a) meconium microbiota of vaginally delivered infants (VIF1) and maternal gut microbiota at 32 weeks (VLF); (b) VIF1 and full-term placental microbiota of vaginal delivery (VTP); (c) gut microbiota of 14-day-old vaginally delivered infants (VIF2) and VLF; (d) meconium microbiota of cesarean-section infants (CIF1) and full-term placental microbiota of cesarean section (CTP); (e) gut microbiota of 14-day-old infants delivered by cesarean section (CIF2) and full-term gut microbiota of women with cesarean section delivery (CTF). In the network diagrams, green dots denote infant gut microbiota, purple dots represent maternal gut microbiota, and blue dots indicate placental microbiota. Red arrows indicate the location of Bifidobacterium to highlight its associations with other genera in the network diagrams. Red lines signify positive correlations, while green lines indicate negative correlations. For each network, the top 200 genera based on relative abundance were selected from each microbial niche. However, in the CIF2-CTF network, only 35 genera were detected in CIF2; therefore, the top 35 genera by relative abundance from CTF were selected for analysis.