Distinct early gut microbiota patterns by delivery mode within 100 hours of birth

<h4>Background</h4>Disruptions in the early-life gut microbiome have been reported to be associated with various health conditions. However, few studies have investigated the establishment of the gut microbiota in the immediate postnatal period.<h4>Aim</h4>To characterize the gut microbiota of neonates within the first 100 hours after birth.<h4>Methods</h4>A total of 512 healthy neonates born at a tertiary hospital were enrolled in this study. Stool samples were collected between March 2024 and December 2024 and categorized by delivery mode and stool collection time. Microbiota diversity and composition were assessed using full-length 16S rDNA sequencing. Stool samples from 140 neonates with predominant breastfeeding were analyzed.<h4>Results</h4>Of the 140 neonates, 70 (50%) were female, 66 (47.1%) were delivered by vaginal delivery (VD), 74 (52.9%) were delivered by cesarean section (CS), and 87 (62.1%) were firstborn. The time of stool collection ranged from 13.2 minutes to 109.82 hours. A significant difference in the time of stool collection was observed between CS and VD neonates (43.0 hours; 95%CI: 35.8-50.1 <i>vs</i> 32.4 hours; 95%CI: 27.8-36.9; <i>P</i> = 0.016). Gut microbiota analysis revealed that CS was associated with higher alpha diversity (Chao1 and Shannon indices; <i>P</i> < 0.001) and beta diversity (<i>P</i> < 0.001). A reduction in the gut microbiota diversity was observed 48 hours after birth <i>(P</i> < 0.001). <i>Escherichia coli</i> predominated in the VD samples. <i>Bifidobacterium</i> species, including <i>Bifidobacterium longum</i>, <i>Bifidobacterium pseudocatenulatum</i>, and <i>Bifidobacterium bifidum</i>, emerged significantly 48 hours after birth. CS neonates exhibited a higher relative abundance of skin- and environmental-associated taxa, including <i>Staphylococcus</i>, <i>Streptococcus</i>, and <i>Pseudomonas</i>, and markedly reduced colonization by <i>Bifidobacterium</i> species despite predominant breastfeeding.<h4>Conclusion</h4>Despite predominant breastfeeding, CS neonates showed reduced colonization by <i>Bifidobacterium</i> and a greater abundance of skin- and environment-associated taxa within the first 100 hours of life. These findings indicate that delivery mode can be a key determinant of early microbial assembly and highlight the need for targeted strategies to support the establishment of beneficial microbiota in CS-delivered infants.