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All supplementary figures are listed in Additional_File_1.pdf. (PDF 4060 kb)

ImportanceEstablishment of the infant microbiome has lifelong implications on health and immunity. Gut microbiota of breastfed compared with nonbreastfed individuals differ during infancy as well as into adulthood. Breast milk contains a diverse population of bacteria, but little is known about the vertical transfer of bacteria from mother to infant by breastfeeding.ObjectiveTo determine the association between the maternal breast milk and areolar skin and infant gut bacterial communities.Design, setting, and participantsIn a prospective, longitudinal study, bacterial composition was identified with sequencing of the 16S ribosomal RNA gene in breast milk, areolar skin, and infant stool samples of 107 healthy mother-infant pairs. The study was conducted in Los Angeles, California, and St Petersburg, Florida, between January 1, 2010, and February 28, 2015.ExposuresAmount and duration of daily breastfeeding and timing of solid food introduction.Main outcomes and measuresBacterial composition in maternal breast milk, areolar skin, and infant stool by sequencing of the 16S ribosomal RNA gene.ResultsIn the 107 healthy mother and infant pairs (median age at the time of specimen collection, 40 days; range, 1-331 days), 52 (43.0%) of the infants were male. Bacterial communities were distinct in milk, areolar skin, and stool, differing in both composition and diversity. The infant gut microbial communities were more closely related to an infant's mother's milk and skin compared with a random mother (mean difference in Bray-Curtis distances, 0.012 and 0.014, respectively; P

Lineages detected reproducibly in placental samples and their proportional abundance. (DOC 47 kb)

Oligonucleotides used in this study. (DOC 34 kb)

Raw data from quantitative PCR analysis of 16S rRNA gene. (Aâ C) Representative amplification curves for 16S rRNA gene qPCR of placental and control samples in triplicate in the six subjects studied. (PDF 4964 kb)

Oligonucleotides used in this study. (DOC 34 kb)

Raw data from quantitative PCR analysis of 16S rRNA gene. (Aâ C) Representative amplification curves for 16S rRNA gene qPCR of placental and control samples in triplicate in the six subjects studied. (PDF 4964 kb)

Lineages detected reproducibly in placental samples and their proportional abundance. (DOC 47 kb)

Demographic and clinical characteristics of study participants. (DOC 29 kb)

Posterior probability distributions for the difference in DNA abundance between air swab negative controls and placenta (blue), saliva (red), vaginal swabs (orange), and other negative controls (green) as estimated by quantitative PCR analysis of 16S rRNA gene abundance for PSP (top) and MO BIO extractions (bottom). Each cycle difference in the cycle of threshold between samples was assumed to represent a 2-fold difference in DNA. Dashed vertical line indicates no change in 16S rRNA gene abundance compared to air swabs. (PDF 239 kb)

Analysis of microbiota composition using principal coordinate analysis of UniFrac distances. (A, E) Weighted UniFrac analysis of the full sample set. (B, F) Unweighted UniFrac analysis of the full sample set. (C, G) Weighted UniFrac analysis of placental and control samples only. (D, H) Unweighted UniFrac analysis of placental and control samples only. Aâ D corresponds to the PSP extraction method and Eâ H corresponds to the MO BIO extraction method. (PDF 288 kb)

Posterior probability distributions for the difference in DNA abundance between air swab negative controls and placenta (blue), saliva (red), vaginal swabs (orange), and other negative controls (green) as estimated by quantitative PCR analysis of 16S rRNA gene abundance for PSP (top) and MO BIO extractions (bottom). Each cycle difference in the cycle of threshold between samples was assumed to represent a 2-fold difference in DNA. Dashed vertical line indicates no change in 16S rRNA gene abundance compared to air swabs. (PDF 239 kb)