Cross-Species Analysis of Milk Extracellular Vesicles Reveals a Conserved Innate Core and a Divergent, Human-Specific Adaptive Immune Fraction

Abstract

Milk-derived extracellular vesicles (EVs) carry proteins and microRNAs that mediate immune communication between mother and offspring, yet which inflammation-related cargo is conserved—and which is species specific—across mammals remains poorly defined. We assembled MetaMilkDB, a provenance-tracked database integrating proteomic, transcriptomic, metabolomic and pathway-level evidence for milk-EVs across four species (Homo sapiens, Bos taurus, Capra hircus, Ovis aries), combining curated studies with in-house EV proteomics (265,009 measurements). Of 4958 EV protein families, 570 (11.5%) formed a conserved core containing five inflammation markers (HP, LTF, MUC1, MUC15, TLR2), four re-detected in our in-house proteomes. This core was an innate scaffold and was not itself enriched for inflammation; instead, inflammation cargo concentrated in the species-specific fraction, overwhelmingly in human milk (45/966 vs. 6/1222 shared; odds ratio 9.9; q = 1.6 × 10−10), forming a secretory-immunoglobulin and complement module absent from ruminant cargo. A parallel layer of inflammation-annotated EV-microRNAs showed heterogeneous conservation across species and converged on TLR/NF-κB-related immune regulation. Milk-EV immunity is organized on two axes—a conserved innate scaffold shared across species and a divergent, largely human adaptive-immune fraction—clarifying which cargo is a candidate cross-species biomarker and which may underlie species-specific immune transfer.