In Global Soil MAGs (SMAG) Project, we conducted the first large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalog) from 3,304 soil metagenomes. We identified 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which greatly expand archaeal and bacterial diversity across the tree of life. The uSGBs identified substantially increased the functional landscape and intra-species genome diversity of the soil microbiome, and provided large proportions of the 43,169 biosynthetic gene clusters and 8,545 CRISPR-Cas genes mined from the SMAG catalog.
Due to the high cost of long-term maintenance, we have decided to discontinue the use of https://smag.microbmalab.cn/ for data access and downloads. We strongly recommend using the following download options instead:
The SMAG catalog of the soil metagenomes, SNV catalogs and viruses predicted from SMAG for this publication are available at Zenodo.
To facilitate systematic discovery and convenient access to high-quality MAG resources, Dr. Rui Li from the Beijing Institute of Genomics has created an open-source index project, Awesome MAG.
SMAG has been included in this project, together with a detailed Download guide.
We thank Dr. Rui Li (lirui@big.ac.cn) for organizing and maintaining this helpful community resource.
All the 21,077 MAGs were deposited at cyverse_21077; All the 40,039 MAGs were deposited at cyverse_40039
The workflow used to generate the genomes, taxonomic analysis, and functional annotation, alongside the BGCs prediction, pan-genome, SNV annotations, and virus predictions can be found in github repository Pipeline.
Scripts used to generate the figures are available at Figure coding.
The source data underlying Figs. 1–6 and Supplementary Figs. 1-6 are provided as Source Data files and have been deposited in the Figshare database Data files.
The SMAG catalogue remain openly shared and available to all researchers and practitioners in relevant fields, please contact lucy20@zju.edu.cn for further questions or detailed inquiries.
Ma, B., Lu, C., Wang, Y. et al. A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nat Commun 14, 7318 (2023).