About methods, citation, and license · v0.9 · 2026-10-05

mpCGCdb (the marine polysaccharide CAZyme gene clusterer database) catalogs every carbohydrate-active enzyme gene cluster (CGC) found in 24,196 medium- and high-quality marine genomes (at least 50% complete, at most 10% contamination) from the Global Ocean Microbiome Catalog (Chen et al. 2024). These include metagenome-assembled, single-cell and isolate genomes, assembled for GOMC or taken from OceanDNA, the Ocean Microbiomics Database and NCBI. 22,607 of these genomes contain at least one CGC. Each CGC contains at least one CAZyme and, in nearly all cases, a transporter, along with neighbouring genes such as sulfatases, peptidases, signal-transduction proteins and transcription factors.

The 289,962 CGCs are linked through a sequence similarity network with 531 million edges, which we split into 67,685 similarity-colocalization network (SCoNe) communities using Leiden clustering. For each community we report a representative protein, its InterPro architecture, its distribution across GTDB taxa, and its CAZy or SulfAtlas activity where one is known.

If mpCGCdb informs your work, please cite:

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mpCGCdb uses the resources below. Please also cite the original sources for any of them you use.

1. Paoli et al. (2022). Biosynthetic potential of the global ocean microbiome. Nature. doi:10.1038/s41586-022-04862-3
2. Chen et al. (2024). Global marine microbial diversity and its potential in bioprospecting. Nature. doi:10.1038/s41586-024-07891-2
3. Nishimura et al. (2022). The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Scientific Data. doi:10.1038/s41597-022-01392-5
4. Parks et al. (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research. doi:10.1093/nar/gkab776
5. Zheng et al. (2023). dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Research. doi:10.1093/nar/gkad328
6. Stam et al. (2023). SulfAtlas, the sulfatase database: state of the art and new developments. Nucleic Acids Research. doi:10.1093/nar/gkac977
7. Saier et al. (2021). The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Research. doi:10.1093/nar/gkaa1004