The core virome of preterm human milk is associated with lipidomic profiles

Phages in term human milk (HM) may benefit infants by preventing pathobiont overgrowth in their gastrointestinal tract (GIT) or transduce function through bacterial infection and integration. Lipids are associated with viral carriage in HM, but this has not been classified taxonomically or in preterm HM (pHM). Phage-lipid association may promote vertical transmission of phages to the infant GIT. We here compare the phage and lipid profiles in 113 pHM samples expressed over the first 100 days of life. Shotgun metagenomics and untargeted lipidomics revealed significant longitudinal increases in phage and lipid richness in pHM. Core phage communities were characterised by specific viral families, significantly correlated with lipid class abundances. This is the first taxonomic report of phage-lipid interactions in pHM and highlights the importance of phage carriage in pHM. Results suggest an evolved strategy for phage carriage in pHM and illustrates their importance in early life microbiota development.