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Background  Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonate, which in turn can affect disease risk later in life. Very little is known about what factors shape the human milk microbiome. The goal of the present study was to examine the milk microbiota from a range of women who delivered vaginally or by caesarean (C) section, who gave birth to males or females, at term or preterm.    Methods  Milk was collected from 39 Caucasian Canadian women, and microbial profiles were analyzed by 16S ribosomal RNA (rRNA) sequencing using the Illumina platform.    Results  A diverse community of milk bacteria was found with the most dominant phyla being Proteobacteria and Firmicutes and at the genus level,  Staphylococcus ,  Pseudomonas ,  Streptococcus  and  Lactobacillus . Comparison of bacterial profiles between preterm and term births, C section (elective and non-elective) and vaginal deliveries, and male and female infants showed no statistically significant differences.    Conclusions  The study revealed the diverse bacterial types transferred to newborns. We postulate that there may be a fail-safe mechanism whereby the mother is “ready” to pass along her bacterial imprint irrespective of when and how the baby is born.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-015-0145-y) contains supplementary material, which is available to authorized users.

Human milk microbiota profiles in relation to birthing method, gestation and infant gender