The influence of maternal gut and vaginal microbiota on gastrointestinal colonization of neonates born vaginally and per caesarean section

Background: Early life microbial colonization of the neonatal gastrointestinal tract is crucial for imprinting of the immune system. Vertical transmission of maternal microbes is considered the key source of initial neonatal microbial colonization. We aimed to evaluate the role of the maternal vaginal and rectal microbiota in early neonatal gastrointestinal colonization in vaginally- and caesarean section-born neonates. Methods: Maternal vaginal and rectal swabs were collected shortly before delivery. Neonatal fecal samples were collected at day 0, 7 and 28 postnatally in both vaginally-born (n = 23) and caesarean-section born (n = 40) neonates (total n = 63). All samples were analyzed by 16 S rRNA sequencing. The relative abundances of amplicon sequence variants (ASVs) shared between maternal swabs and fecal neonatal samples were compared in vaginally-versus caesarean section-born neonates. Results: The median relative abundance of ASVs shared in the maternal rectal and vaginal swabs with all neonatal samples was low (below 10% for rectal or vaginal swabs with any of the three time-points). When focusing on vaginally- versus caesarean section-born neonates, there were no differences in the relative abundance of shared ASVs with the maternal vaginal swabs, and only on day 7 in the rectal swabs (p = 0.002). However, in both delivery routes, the relative abundance of ASV shared with the maternal rectal swab was higher (median 19% in vaginally-born neonates and 2% in caesarean section-born neonates) compared to the relative abundance of the ASVs shared with the maternal vaginal swab (0% for both vaginally- and caesarean section-born neonates) on day 28. Conclusions: We observed that only a limited amount of ASVs were transferred from maternal rectal and vaginal compartments to the neonatal gastrointestinal tract. ASVs from the maternal gastrointestinal tract contributed to neonatal gut colonization to a greater extent than ASVs from the maternal genital tract at one month of age. Our findings contribute to an increased understanding of factors influencing neonatal gastrointestinal colonization in both caesarean section and vaginal birth, of importance as characteristics of early colonization have been associated with health outcomes later in life. Trial registration: The original trial is registered with the Dutch Clinical Trial Registry (Trial registration number: NTR6000, https://www.trialregisternl/trial/5845) and the study protocol was published online.