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.
All the quality and taxonomy information of the genomes in SMAG catalog can be viewed at web-based user interface SMAG_interface
The soil metagenome-assembled genome sequences of SMAG project can be downloaded in fasta format through SMAG_40039; SMAG_40039_MD5;
SMAG MAGs after dereplication (N=21,077) was deposited at SMAG_drep_21077; SMAG_drep_21077_md5;
The uSGBs (N=16,530) can be downloaded at 16,530_uSGBs; 16530_uSGBs_md5;
The virus identified from SMAG can be downloaded from mag_virus.
The SMAG catalog of the soil metagenomes, SNV catalogs and viruses predicted from SMAG for this publication are available at Zenodo.
To upload the large gz file, we split it into smaller file with the prefix “mag.tar.gz”, downloaders can use the cat ./mag.tar.gz* > mag.tar.gz; tar -xjvf <mag.tar.gz> to process the MAGs.
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.
Other associated data supporting the findings are available from the corresponding author(bma@zju.edu.cn) upon reasonable request. Also you can contact lucy20@zju.edu.cn for details.
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).