Dalia H. Almasud

تخصص المعلوماتية الحيوية · دفعة 2026

Breast Milk Microbiome Shifts from Environmental to Infant-Oral Signatures Across Lactation Stages

Human breast milk contains a living bacterial community whose composition is not fixed. This project investigated whether that composition changes systematically across the postpartum period, and whether such change reflects a biologically coherent shift consistent with retrograde inoculation, the transfer of bacteria from an infant's developing oral microbiome back into milk during nursing. Using 16S rRNA sequencing data from 540 breast milk samples spanning the first several years postpartum (Qiita Study 11366, Chambers Breast Milk Microbiome), samples were grouped into four clinical lactation stages and analyzed for diversity, differential abundance, and compositional structure. Microbial diversity increased significantly across stages (Kruskal-Wallis, p=2.7×10⁻⁷), and community composition also differed significantly by stage (PERMANOVA, R²=1.82%, p=0.001). Twenty-three genera changed significantly with stage (DESeq2, padj<0.1): oral-associated genera consistently increased while environmental and enteric genera consistently declined, a pattern independently cross-validated with a second, compositional-data-based method (ALDEx2, 91% overlap). One ambiguous taxon, a SILVA placeholder cluster, was resolved via BLAST to a dominant sequence matching Prevotella melaninogenica at 100% identity, a documented infant oral colonizer. Together, these results show that breast milk composition shifts consistently over the postpartum period toward genera linked to the infant oral microbiome, a pattern consistent with, though not proof of, retrograde inoculation.

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