Breast Milk Oxylipin Signature Predicts Infant Gut Microbiota Maturation: A Prospective Lipidomics–Metagenomics Cohort Study

Introduction: Breast milk provides essential lipids shaping the infant gut microbiome, but the role of bioactive oxidized lipids (oxylipins) remains unknown. This study investigates whether breast milk oxylipins predict early-life gut microbiota maturation.

Methods: In a prospective cohort of 95 mother-infant dyads, breast milk samples were collected at 1, 3, and 6 months postpartum. Oxylipins were profiled using ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) targeting 56 oxylipins from the COX, LOX, and CYP pathways. Infant fecal metagenomes were sequenced (shotgun) at corresponding time points. Data on delivery mode (vaginal/C-section), maternal and infant antibiotic exposure (yes/no, timing), maternal diet (food frequency questionnaire), and feeding practices (exclusive/predominant/partial breastfeeding) were collected and included as covariates. Multi-omics integration was performed using sparse partial least squares (sPLS) regression with adjustment for these confounders.

Results: Among 42 detected oxylipins, 12,13-DiHOME, 9,10-DiHOME, and 5-HETE emerged as the strongest predictors (VIP score >1.8) independent of confounders. Infants in the high-DiHOME cluster exhibited accelerated microbiota maturation, with a 2.4-fold higher Bifidobacterium dominance (p<0.001) and increased α-diversity (Shannon index: 3.2 vs. 2.1, p<0.01) by 3 months. These oxylipins correlated with upregulation of bacterial CAZymes involved in HMO utilization (r=0.68, p<0.001). The oxylipin signature explained 47% of the variance in gut microbial composition at 6 months, outperforming traditional lipid classes (triglycerides, phospholipids). Infants with a “pro-maturation” oxylipin profile had significantly lower incidence of colic and atopic dermatitis at 12 months (OR=0.31, 95% CI: 0.15–0.64).

Conclusions: This study identifies a novel breast milk oxylipin signature—12,13-DiHOME and 5-HETE—that predicts infant gut microbiota maturation and immune outcomes, revealing a previously unrecognized role of dietary oxylipins in early-life microbial programming.