| Summary: | Inter-subject variability in human milk microbiome is well known; however, its origins and possible relationship to the mother’s diet are still debated. We investigated associations between maternal nutrition, milk fatty acids composition and microbiomes in mother–infant dyads. Breast milk and infant fecal samples were collected across three time points (one week, one month and three months postpartum) from 22 mother–infant pairs. Food frequency questionnaires for the months of pregnancy and three months postpartum were collected. Milk fatty acids were analyzed by GC–MS and the microbiome in breast milk and infant feces was determined by 16S rRNA sequencing. Statistical interactions were computed using Spearman’s method and corrected for multiple comparisons. We found significant negative correlation between <i>Streptococcus</i> relative abundance in maternal milk and intake of unsaturated fatty acids and folic acid at one month postpartum. At three months postpartum, vitamin B-12 consumption was significantly associated with a single operational taxonomic unit belonging to <i>Streptococcus</i>. Comparison between milk microbiome and lipid composition showed, one-month postpartum, significant negative correlation between <i>Streptococcus</i> relative abundance and the abundance of oleic acid. Additional correlations were detected between <i>Staphylococcus hominis</i> and two medium-chain saturated fatty acids. Our results reinforce the hypothesis that maternal nutrition may affect milk microbiome.
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