The Metagenome-Assembled Genome Inventory for Children (MAGIC)

Existing microbiota databases are biased towards adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a **M**etagenome-**A**ssembled **G**enome **I**nventory for **C**hildren (**MAGIC**) from a large collection of bulk and viral-like particle-enriched metagenomes from 0-7 years of age, encompassing `3,299` prokaryotic and `139,624` viral species-level genomes, `8.5%` and `63.9%` of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified `54` candidate keystone species, including several *Bifidobacterium spp.* and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the *B. longum* pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.