1. A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.
- Author
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Peng, Ye, Zhu, Jie, Wang, Shilan, Liu, Yingzhi, Liu, Xin, DeLeon, Orlando, Zhu, Wenyi, Xu, Zhilu, Zhang, Xi, Zhao, Shilin, Liang, Suisha, Li, Hang, Ho, Brian, Ching, Jessica Yuet-Ling, Cheung, Chun Pan, Leung, Ting Fan, Tam, Wing Hung, Leung, Tak Yeung, Chang, Eugene B., and Chan, Francis Ka Leung
- Abstract
Existing microbiota databases are biased toward 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 to 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 the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species. [Display omitted] • MAGIC features 3,299 prokaryotic and 139,624 viral species-level genomes • MAGIC improves early-life microbiome profiling with extended genomic information • Candidate keystone species are associated with diseases, geography, and age • Extended Bifidobacterium longum pangenome reveals evolutionary insights Existing microbiota databases are biased toward adults, hindering infant gut microbiome profiling. Peng et al. introduce the metagenome-assembled genome inventory for children (MAGIC), featuring 3,299 prokaryotic and 139,624 viral genomes. MAGIC enables characterization of early-life microbiome dynamics, identification of candidate keystone species, and strain-level study of target species. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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