New research has uncovered insights into the factors shaping the composition of human breast milk, highlighting the impact of coffee consumption and genetic differences. A recent study explored the biological and dietary influences behind hundreds of molecular variations in breast milk.
Drawing from the Mothers and Infants Linked for Healthy Growth (MILK) study, researchers found that maternal diet had the most significant association with the milk metabolome among the evaluated maternal factors. They identified substantial variation in milk metabolites, categorizing them into seven groups of related compounds.
Methodology
The study analyzed data from 349 participants who provided milk samples approximately one month after giving birth. These participants planned to breastfeed exclusively and had uncomplicated pregnancies, though 15% had gestational diabetes. Milk samples were collected two hours after feeding, processed, and stored at −80°C until analysis.
Researchers employed three mass spectrometry techniques: gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and liquid chromatography–tandem mass spectrometry (LC-MS/MS). They also assessed milk macronutrients, hormones, and cytokines. Maternal dietary intake was evaluated using the Diet History Questionnaire (DHQ), with data available for 344 participants.
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Key Findings
The study revealed that coffee and caffeine intake were strongly linked to the presence of quinic acid and 1,3-dimethyluric acid in milk. Dietary factors accounted for 34% of quinic acid variation and 12.5% of proline-betaine variation, a metabolite tied to citrus consumption. Higher alcohol consumption was associated with lower levels of sphingosine-1-phosphate (S1P), a lipid involved in intestinal and immune development.
Gene expression analysis showed that higher levels of quinolinate phosphoribosyltransferase (QPRT) were linked to lower quinolinic acid, consistent with its metabolic role. Genome-wide association studies (GWAS) identified nine significant genetic associations with milk metabolites.
Models incorporating dietary, clinical, and genetic data from 183 participants explained a median of 13.2% of metabolite variation for 246 metabolites. Dietary factors were the primary contributors in 168 models (68%). These findings indicate that milk composition is influenced by multiple maternal factors, with diet playing the most significant role.
The study lays the groundwork for exploring whether milk metabolites reflect maternal nutrition or impact infant development. However, it was observational and did not establish effects on infant health. Limitations include assessing milk at one month postpartum, reliance on dietary questionnaires, and a predominantly European-ancestry population with a small genetic sample. Researchers analyzed 458 metabolites and identified 1,038 significant diet–metabolite correlations, with 88% being positive, showing the strong link between diet and milk composition.
Milk-cell RNA sequencing provided gene expression data for 299 participants, while genetic data from 197 supported genome-wide analyses. Statistical methods included correlation testing and machine learning to explore dietary and metabolite relationships.
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Researchers compared genetic associations in milk metabolites with plasma studies and evaluated the contributions of dietary, clinical, and genetic factors. They also identified links between milk metabolites and gene expression in milk cells.
Genetic Associations
Notable associations included variants near PDE6A, linked to purine metabolism, and GNE, associated with a form of sialic acid.
The GNE association was linked to a milk expression quantitative trait locus, suggesting a specific role in lactation. Comparisons with plasma studies revealed both shared and milk-specific genetic associations. The variant did not clearly relate to the 19 milk oligosaccharides measured.
This observational study did not establish infant health effects and assessed milk at one month postpartum. Analyzing 458 metabolites using three mass spectrometry platforms marks a significant advancement in breast milk research, offering insights into the interplay of maternal diet, genetics, and milk composition. Human milk provides essential nutrients and bioactive compounds critical for infant growth, immune development, and microbial colonization in the first 1,000 days of life. The findings are available on the bioRxiv preprint server, with the reference Demerath bioRxiv 2026.08.11.744248; DOI: 10.64898/2026.08.11.744248.