Maternal transmission and limited virulent phage replication shape early infant gut virome maturation

Early life gut microbiome dynamics are increasingly recognized as important determinants of microbiome maturation, yet the ecological dynamics of its associated bacteriophages remain poorly resolved. Here, we performed bulk and virus like particle (VLP)-enriched metagenomic sequencing and fecal metabolomic profiling of longitudinal fecal samples from 32 mother-infant dyads, incorporating an exogenous phage spike in to enable absolute quantification of viral loads. Our results show that early infant gut phageome is defined by a profound lack of virulent phage genome copies while temperate phages remain relatively stable, challenging previous assumptions. We further identified extensive maternal sharedness of mainly virulent phages predicted to infect Bacteroidaceae, which could explain recovery of virulent phage absolute abundances. Virulent phage concentrations were further associated with several fecal metabolites including primary bile acids. These findings revise the current model of infant phageome assembly highlighting the underappreciated role of virulent phages.