BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes
Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.
Authors
- Christian von Mering (ORCID: https://orcid.org/0000-0001-7734-9102)
- Caner Bağcı (ORCID: https://orcid.org/0000-0003-4428-9515)
- Satria A. Kautsar (ORCID: https://orcid.org/0000-0002-9815-511X)
- Shrikant Mantri (ORCID: https://orcid.org/0000-0002-7493-459X)
- Kai Blin (ORCID: https://orcid.org/0000-0003-3764-6051)
- Luděk Sehnal (ORCID: https://orcid.org/0000-0002-8038-3317)
- Matin Nuhamunada (ORCID: https://orcid.org/0000-0003-3177-8299)
- Alexey Gurevich (ORCID: https://orcid.org/0000-0002-5855-3519)
- Marnix H. Medema (ORCID: https://orcid.org/0000-0002-2191-2821)
- Nadine Ziemert (ORCID: https://orcid.org/0000-0002-7264-1857)
- Azat Tagirdzhanov (ORCID: https://orcid.org/0000-0002-6185-0821)
- Daniel Udwary (ORCID: https://orcid.org/0000-0002-3491-0198)
- Tilmann Weber (ORCID: https://orcid.org/0000-0002-8260-5120)
- Hemant Goyat
- Casimir Ladanyi
Institutions
- SIB Swiss Institute of Bioinformatics (CH)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- University of Zurich (CH)
- Novo Nordisk Foundation (DK)
- German Center for Infection Research (DE)
- Czech Academy of Sciences, Institute of Microbiology (CZ)
- Radix (United States) (US)
- Helmholtz Centre for Infection Research (DE)
- Helmholtz Institute for Pharmaceutical Research Saarland (DE)
- BRIC-National Agri-Food and Biomanufacturing Institute (IN)
- University of Tübingen (DE)
- Wageningen University & Research (NL)
- Saarland University (DE)
- Technical University of Denmark (DK)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-10-09
- DOI
- https://doi.org/10.1093/nar/gkae953
- Citations
- 30
- Primary Topic
- Microbial Natural Products and Biosynthesis
- Type
- article
- Field-Weighted Citation Impact
- 13.43
Funders
- U.S. Department of Energy
- Deutsches Zentrum für Infektionsforschung
- Universität des Saarlandes
- Novo Nordisk Fonden
- Office of Science
- National Agri-Food Biotechnology Institute