What it is
MGnify is the canonical name of the metagenomic dataset used in the reports; no additional alias or stable external identifier was reported in the sources. 1,2
Key facts from the sources
MGnify provided 260,652 environmental metagenome-assembled genomes (MAGs), meaning genomes reconstructed from metagenomic sequencing data. 1
After filtering out host-associated biomes, 30,497 MAGs remained in the environmental analysis. 1
Of these environmental MAGs, 22,356 had usable geospatial coordinates, corresponding to 73.3% coordinate coverage of the filtered environmental MAG set. 1
Among the 22,356 MAGs with coordinates, 2.8% carried at least one metal-resistance type. 1
The report combined MGnify MAG data with geospatial metadata retrieved through the european nucleotide archive batch API. 1
The resulting analysis supports environmental-resistome by identifying global prevalence, biome enrichment and depletion, and geographic hotspots of environmental bacterial metal resistance. 1
The coordinate coverage and sampling limitations inform environment-embedding-geography, particularly the distinction between per-sample coordinate gaps and geographic gaps. 1
In the plant-microbiome study, MGnify supplied metagenomic genus-level comparisons alongside pangenome-derived plant-association data. 2 This refines the environmental-resistome use of MGnify by showing that the dataset also supports ecological comparisons of plant-associated communities, rather than only geospatial metal-resistance analysis. 2
MGnify detected 17 genera across all three analyzed crop rhizospheres; 117 genera were unique to tomato, 54 to maize, and 5 to barley. 2 Its plant-associated genera had a higher median mobilome burden than non-plant genera, 3.7 versus 2.8 mobile elements per genome, with Mann–Whitney p = 1.49×10⁻⁵. 2 This supports using MGnify for genus-scale ecological and mobile-element comparisons, while not establishing genome-level horizontal-transfer rates. 2
The MGnify and pangenome classifications had only 11.7% Jaccard overlap, reflecting different measurements: metagenomic detection versus isolation metadata. 2 MGnify BGC, mobilome, and defense data were available only for the soil biome in that analysis, so its comparisons did not directly contrast rhizosphere with bulk soil. 2
The soil-metal functional-genomics analysis extends MGnify’s use from MAG-level resistance prevalence and genus-level ecology to functional gene-content analysis: its MGnify Spark-table inputs covered 51,748 soil samples, nine metals, and 2,355 significant COG–metal associations at FDR < 0.05. 3 The dominant transporter and biosynthesis signals are relevant to environmental-resistome, but the observational associations refine rather than establish the interpretation of MGnify-derived metal responses because co-contamination, conditional model fit, effect sizes, and spatial validation remain unresolved. 3
Source
- Global Biogeography of Environmental Bacterial Metal Resistance — report summary describing the MGnify-derived environmental MAG dataset and its global metal-resistance analysis. 1
- Plant Microbiome Ecotypes — Compartment-Specific Functional Guilds and Their Genetic Architecture — report summary describing MGnify-based plant-associated genus, rhizosphere, and mobilome comparisons. 2
- Soil Metal Concentrations Drive Functional Gene Shifts — report summary describing MGnify-linked soil metal and functional gene-content associations. 3