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Background: Mothers are the primary source of bacteria for newborns, but it is unclear whether mother-to-newborn transmission occurs prior to, during or after birth. Similarly, the effect of the delivery mode on neonatal microorganisms has been the focus of controversy. Methods: Healthy maternal and neonatal pairs that underwent vaginal birth and caesarean section were enrolled in this study. Meconium, placenta, membrane and amniotic fluid samples for newborns and vaginal, rectal and oral samples for mothers were collected. All samples were amplified and sequenced by a 16S rRNA gene primer set targeting bacteria and archaea. Findings: A total of 550 samples from 36 mother-neonate pairs with vaginal births and 42 mother-neonate pairs with caesarean sections were included in this study. The negative controls showed that the data analysis in this study was not affected by contamination. There was a high diversity of microbial communities in the pregnancy environment of the foetus. Meconium samples could be divided into three distinct types that were not influenced by the delivery method. Interpretation: The distribution patterns of bacterial communities in the meconium, placenta, and foetal membranes were highly similar and had nothing to do with the mode of delivery. For approximately half of the placental microorganisms, the same sequence could be found in the vaginal, rectal, and oral samples of the mother. Keywords: Meconium, Microbiota, Delivery mode, Archaea

Background: Mothers are the primary source of bacteria for newborns, but it is unclear whether the structuring of the infant microbiome is the result of mother-to-newborn transmission prior, during or after birth. Similarly, the effect of delivery mode on neonatal microorganisms has been the focus of controversy. Methods: Approximately the same number of healthy maternal and neonatal pairs of vaginal birth and caesarean section were enrolled in this study. Meconium, placenta, membranes and amniotic fluid samples of newborns and vaginal, rectal and oral samples of mothers were collected. All samples were amplified and sequenced by a 16S rRNA gene primer set targeting bacteria and archaea. Findings: A total of 550 samples from 36 mother-neonate pairs with vaginal births and 42 mother-neonate pairs with caesarean sections were included in this study. A negative control showed that all data analysis in this study was not affected by contamination. Indeed, there was a high diversity of microbial communities in the pregnant environment of the foetus. The microbial community composition of neonatal samples was not affected by the mode of delivery. Approximately half of all meconium microorganisms were found in the vaginal, rectal and oral samples of the mother. Interpretation: The origin and influencing factors of pioneer microorganisms in neonates were studied. How these microorganisms enter the breeding environment and their roles need further study. Funding Statement: the National Natural Science Foundation of China (81860437) and Yunnan Province Innovation Team of Intestinal Microecology Related Disease Research and Technological Transformation (China). Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: This project was approved by the Ethics Committee of Yan’an affiliated Hospital of Kunming Medical University (2019-077-01). Mothers were made aware of the nature of the study, specifically consented to give their personal information, and gave written informed consent for their and their child’s participation.