Objective·To analyze the diversity and composition of the maternal gut microbiota and vaginal microbiota in late pregnancy,neonatal meconium microbiota and vernix caseosa microbiota,and analyze the similarities,differences and correlations.Methods·This is a prospective study.Maternal stool samples and vaginal swabs in late-pregnancy,and neonatal meconium samples were collected from 11 mother-infant pairs at Xinhua Hospital,Shanghai Jiao Tong University School of Medicine from August to November 2018;the vernix caseosa from three sites(forehead,axilla,and inguinal crease)and meconium samples were collected from 14 healthy newborns at International Peace Maternity and Child Health Hospital,Shanghai Jiao Tong University School of Medicine in December 2018.All births were vaginal deliveries.The 16S rRNA gene V3?V4 region sequencing was used.The diversity,composition and similarities/differences of the maternal gut microbiota,the vaginal microbiota,and the neonatal meconium microbiota from the 11 mother-infant pairs,as well as the neonatal vernix caseosa microbiota and the meconium microbiota from the 14 newborns were analyzed.Results·The number of operational taxonomic units(OTUs),ACE index,Chao1 index,and Shannon index of maternal gut microbiota were all higher than those of vaginal microbiota;the ACE indices and the Chao1 indices of the vernix caseosa microbiota at three sites were all higher than those of meconium microbiota(P<0.01).The β diversity varied among the maternal gut microbiota,vaginal microbiota,and neonatal meconium microbiota(P<0.01).The β diversity of neonatal vernix caseosa microbiota from three sites(forehead,axilla,and inguinal crease)was similar,but different from meconium microbiota(P<0.01).At the phylum level,the dominant bacteria were Firmicutes(52.76%)and Bacteroidetes(41.67%)in the maternal gut microbiota,Firmicutes(74.36%)and Actinobacteria(21.25%)in the maternal vaginal microbiota,and Firmicutes(84.22%)and Proteobacteria(8.80%)in the neonatal vernix caseosa microbiota.The dominant bacterium in the neonatal meconium was Proteobacteria in the two batches of samples(81.11%and 88.72%,respectively).At the genus level,the dominant bacteria were Bacteroides(35.42%)and Faecalibacterium(10.12%)in the maternal gut microbiota,Lactobacillus(69.10%)and Bifidobacterium(11.30%)in the vaginal microbiota,and Lactobacillus(79.81%)and Pseudomonas(3.23%)in the vernix caseosa microbiota.The dominant bacterium in the neonatal meconium was Escherichia in the two batches of samples(55.21%and 31.18%,respectively).Conclusion·The α diversity of maternal gut microbiota is higher than that of vaginal microbiota and neonatal meconium microbiota,and it is higher in neonatal vernix caseosa than that in meconium microbiota.The Firmicutes is the predominant phylum in the maternal late-pregnancy gut microbiota,vaginal microbiota,and neonatal vernix microbiota.Lactobacillus is the predominant genus in both maternal vaginal and neonatal vernix caseosa microbiota.Proteobacteria in phylum and Escherichia in genus are predominant in meconium microbiota.The microbiota composition is similar in vernix caseosa at different body sites,but there are differences between the vernix caseosa microbiota and meconium microbiota.