Do Different Samples From Pregnant Women and Their Neonates Share the Common Microbiome: A Prospective Cohort Study

Abstract Background We characterized the microbiome composition from various samples in pregnant women and their neonates and evaluated the association between the distribution of microbiome and obstetric factors. Results A prospective study was performed in live births delivered at a single tertiary center between March 2020 and January 2021. Samples collected from pregnant women and their newborns included maternal cervicovaginal discharge (VD), amniotic fluid (AF), umbilical cord blood (CB), neonatal gastric liquid (GL), and meconium. Next-generation sequencing was used to analyze the composition of the microbiome from the samples. We identified 19,597,239 bacterial sequences from the 641 samples. The alpha diversity of the negative control group was slightly higher than that of the VD group. The samples were separated well based on the microbiome pattern unique to their body sites despite the significant batch effects present within our dataset. We observed a higher relative abundance of Lactobacillus at the genus level but lower abundances of Aerococcus, Fusobacterium, Gardnerella, Peptoniphilus, Porphyromonas, and Prevotella in VD. In evaluating the association with clinical data, Staphylococcus in M showed a strong association with preterm birth. The lists of bacterial taxa were connected to the weights of newborn babies in the CB group. The microbiome pattern of GL was similar to that of AF, but not technically identical. Twins did not demonstrate significant differences in the composition of microbiomes from neonate samples. Conclusions In this study, samples known to be traditionally sterile, such as AF and CB, showed specific bacterial taxa although they were extremely close to negative controls. The microbiome patterns were grouped according to the body compartments where the samples had been obtained, not according to the mother-fetus/infant pairs. Further studies lowering the possibility of contamination and redeeming the low-biomass specimens are necessary to determine the relationship between microbiomes and specific pathological complications during pregnancy.