mMGE

mMGE catalogs and annotates extrachromosomal mobile genetic elements (eMGEs) in human metagenomes, providing a curated resource of their sequences, taxonomy, gene content, prevalence, and host associations.

Key Features:

• Non-redundant catalog: Contains 517,251 non-redundant eMGEs derived from 66,425 human metagenomic samples from diverse body sites.
• Composition: Distinguishes 92,492 plasmids and 424,759 phages within the catalog.
• Clustering: Organizes approximately half of the eMGEs into 70,074 clusters using relaxed clustering criteria.
• Annotations: Provides sequence characteristics, taxonomy affiliations, gene contents, and associated prokaryotic hosts for each eMGE.
• Prevalence metrics: Computes prevalence of individual eMGEs and of clusters within and across samples.

Scientific Applications:

• eMGE distribution analysis: Compare abundance and distribution of eMGEs across human body sites and metagenomic samples.
• Host–element association studies: Investigate associations between eMGEs and prokaryotic hosts inferred from annotations.
• Phenotype association: Explore potential associations between eMGEs (or clusters) and human phenotypes or distribution preferences.
• Evolutionary and community impact: Study roles of phages and plasmids in genome evolution and microbial community structuring via horizontal transfer.

Methodology:

Compiled a non-redundant catalog from 66,425 human metagenomic samples; grouped ~50% of eMGEs into 70,074 clusters based on relaxed criteria; annotated each eMGE for sequence characteristics, taxonomy, gene content, and associated prokaryotic hosts; and calculated prevalence of individual eMGEs and clusters within and across samples.