MAGIC database facilitates understanding of early-life gut microbiome dynamics

The Metagenome-Assembled Genome Inventory for Children (MAGIC) database, which contains 20,172 global gut metagenomes from humans aged 0–7 years, characterizes the bacteriome and virome diversity of the global gut microbiome in early life.

Early-life human gut microbiota is thought to play a significant role in shaping the host’s immune system and metabolism, which can have long-lasting implications for health. However, existing microbiota databases are biased toward adult samples and lack data from African and Asian populations. [Nat Commun 2024;15:8323; Cell Host Microbe 2024;32:2212-2230.e8]

The MAGIC database, developed by researchers from the Chinese University of Hong Kong (CUHK), incorporates CUHK’s Chinese population–based MOMmy (MOther-infant Microbiota transmission and its link to long terM health of babY) metagenomic data. “This will help reinforce China’s role in studying early-life microbiome dynamics internationally,” said Professor Zhang Lin, Lead Scientist of the Microbiota I-Centre (MagIC), CUHK. [Cell Host Microbe 2024;32:2212-2230.e8; NCT04117321]

Extensive genomic diversity

The collected metagenomes are geographically diverse, spanning 34 countries/regions in Europe (48.7 percent), North America (28.7 percent), Africa (13.5 percent), Asia (4.9 percent), Oceania (3.8 percent), and South America (0.5 percent), with 81.7, 7.1 and 12.1 percent being from developed, emerging, and developing or least developed countries, respectively.

MAGIC features 3,200 prokaryotic and 139,624 viral genomes. “Remarkably, 8.5 percent of the prokaryotic and 63.9 percent of the viral genomes are unique to our database,” pointed out lead author, Dr Peng Ye, School of Public Health and Primary Care, CUHK. There was 6.7 percent improvement in read mapping rates, especially for samples collected from low-income countries.

Keystone species

The researchers also identified 54 keystone species within the early-life microbiome, including several species of Bifidobacterium, such as Bifidobacterium longum and Bifidobacterium infantis, and four phages. Keystone species could facilitate stabilization, resilience and diversity of the microbial community within the gut of an infant, thereby playing a significant role establishing a healthy microbiome.

“Importantly, MAGIC has shown that the abundance of some of these keystone species is related to health outcomes, such as allergies and atopic dermatitis in children,” wrote Dr Edoardo Pasolli of the Department of Agricultural Sciences, University of Naples Federico II, in an accompanying editorial. [Cell Host Microbe 2024;32:2047-2049]

Implications

“By identifying keystone microbial species, we can better understand their roles in infant health and disease development. This knowledge lays the foundation for us to go from zero to one when preventing conditions such as allergies early in life,” commented Professor Siew Ng, Director of MagIC, CUHK.

“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,” concluded Professor Heinmin Tun. “By addressing gaps in age and geographical representation, our database brings new hope for advancing fundamental microbiome science and clinical research to promote health through microbiome-targeting therapies.”