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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products
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The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more
Kai Blin1, Simon Shaw1, Marnix H Medema2
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark.
Nucleic Acids Research
|October 31, 2023
Summary
The antiSMASH database, a key tool for natural product discovery, now offers version 4. It provides access to over 230,000 biosynthetic gene clusters from high-quality microbial genomes, aiding drug and crop protection development.
Area of Science:
- Microbiology
- Bioinformatics
- Natural Products Chemistry
Background:
- Microorganisms are prolific sources of natural products vital for medicine and agriculture.
- Genome mining using bioinformatics tools is crucial for discovering these valuable compounds.
- antiSMASH is a leading software for identifying biosynthetic gene clusters (BGCs) responsible for natural product synthesis.
Purpose of the Study:
- To present version 4 of the antiSMASH database, enhancing access to microbial natural product potential.
- To provide an updated and expanded collection of high-quality BGCs from diverse microbial genomes.
- To offer an interactive graphical user interface for exploring these BGCs.
Main Methods:
- Utilized antiSMASH version 7.1 for the detection of BGCs.
- Curated publicly available, dereplicated, high-quality microbial genomes (archaeal, bacterial, and fungal).
- Developed an interactive graphical user interface for database access and exploration.
Main Results:
- Version 4 of the antiSMASH database contains 231,534 high-quality BGC regions.
- The database integrates data from 592 archaeal, 35,726 bacterial, and 236 fungal genomes.
- The database is accessible via a user-friendly graphical interface at https://antismash-db.secondarymetabolites.org/.
Conclusions:
- The updated antiSMASH database significantly expands the resource for discovering microbial natural products.
- Version 4 facilitates efficient exploration of BGCs for drug discovery and crop protection agent development.
- This resource empowers researchers by providing a comprehensive and accessible collection of biosynthetic gene clusters.
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