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 Metagenome-Assembled Genome Inventory for Children (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 novel. 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 previously uncharted genomes that enable characterization of dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.现有微生物组数据库多偏向成人样本，这严重阻碍了婴儿肠道微生物组的精准解析。本研究从0至7岁儿童的大量原始宏基因组与富集病毒样颗粒的宏基因组数据集中，构建了儿童宏基因组组装基因组库（Metagenome-Assembled Genome Inventory for Children, MAGIC），该库涵盖3299个原核生物物种级基因组与139624个病毒物种级基因组，其中分别有8.5%和63.9%为尚未被报道的全新物种。MAGIC可优化早期生命微生物组的解析流程，其在宏基因组读段比对环节的提升效果在非洲人群中最为显著。随后本研究鉴定出54个候选关键物种，包括若干双歧杆菌属（Bifidobacterium）物种与4种噬菌体，这些物种形成的类群丰度随时间呈现动态波动。该类群的丰度在早产婴儿中显著降低，且与儿童过敏症存在显著关联。通过分析长双歧杆菌（Bifidobacterium longum）的泛基因组，本研究发现了噬菌体介导的进化与群体感应相关的生态适应证据。综上，MAGIC数据库获取了此前未被探明的微生物基因组资源，可为早期生命微生物组的动态特征解析、候选关键物种鉴定以及目标物种的菌株级研究提供有力支撑。