Delivery mode, birth order, and sex impact neonatal microbial colonization

Abstract

The initial microbial colonization of the infant gut during birth plays a critical role in shaping both immediate and long-term health outcomes. While mode of delivery is a known determinant of this colonization process, the potential impacts of infant sex and birth order remain underexplored. This study investigates the influence of delivery mode, infant sex, and birth order (maternal parity) on the microbial communities in first-pass meconium samples from neonates, using 16S rRNA gene sequencing. We found that delivery mode impacted the presence of detectable microbial communities. Specifically, only 17% of samples from neonates delivered by elective Cesarean section showed any microbial presence, compared to approximately two-thirds of samples from neonates exposed to maternal vaginal microbes (emergency C-section or vaginal delivery). Among vaginally delivered neonates without antibiotic exposure, birth order was associated with taxonomic shifts. Neonates born to primiparous mothers had a lower abundance of Bifidobacterium, a keystone species in the infant gut microbiome. Unexpectedly, the gut microbiota differed by infant sex, with males having lower alpha diversity and shifts in microbial community composition (PERMANOVA p = 0.008), characterized by elevated levels of Enterobacteriales, which was both less prevalent and less abundant in female neonates. These findings highlight the intricate interplay between delivery mode, infant sex, and birth order in shaping the early gut microbiome.

Keywords: Gut microbiota; birth mode; birth order; delivery mode; first-pass meconium; infant sex; neonatal colonization; parity.

Figure 1.

Relative abundance of 20 most abundant bacterial genera in first-pass meconium samples with >100 sequencing reads. (a) Cesarean section (C-section), (b) vacuum extraction, and c) spontaneous vaginal delivery. Neonates exposed to peripartum antibiotics are indicated by red text. One neonate delivered by elective C-section is indicated by an asterisk, all other C-sections are emergency.

Figure 2.

Relative abundance of 20 most abundant bacterial orders in meconium samples of spontaneously vaginally delivered neonates differ by parity and sex. Individual sample identifiers are noted below taxonomic bars. Neonates with peripartum antibiotic exposure are indicated by red text.

Figure 3.

Overall community composition varies by infant sex. (a) Alpha diversity, measured by the total number of ASVs detected in each sample, was significantly lower in male (n = 7) neonates compared to females (n = 10). Mean ± SD for first-born females (173.4 ± 85.9, n = 5), first-born males (111.0 ± 164.1, n = 3), later born females (220.8 ± 154.3, n = 5), and later born males (45.25 ± 59.4, n = 3). Significance assessed by linear regression (lm function in the stats package in R). (b) Beta diversity differed significantly by infant sex (R2 = 14.9%, p = 0.008) but not by parity (R2 = 0.05, p = 0.70). Significance assessed by PERMANOVA (adonis2 function in the vegan package in R). Females are noted as red and males as blue, primiparous samples as closed circles and multiparous as closed triangles.