BGC Atlas v2: biosynthetic gene clusters with taxonomic and environmental context at scale

Abstract

Genomic and metagenomic studies have revealed that microbes have the capacity to produce an enormous diversity of secondary metabolites. These compounds play important roles in microbial interactions and are also a major source of medicines and other useful natural products, yet only a small fraction of this biosynthetic potential has been experimentally characterized. BGC Atlas was developed to explore this largely uncharacterized diversity by placing biosynthetic gene clusters (BGCs) into genomic and environmental context. Here, we present BGC Atlas v2, which expands the collection more than eightfold to more than 16 million predicted BGCs and extends it from metagenomic assemblies to metagenome-assembled genomes (MAGs), single-amplified genomes and isolate genomes. The new release provides taxonomic assignments for nearly all BGCs, harmonized environmental metadata, nested searches across biosynthetic, taxonomic, environmental and geographic properties, and protein-sequence searches against BGC-encoded genes. Its scale also reveals how much bacterial and archaeal biosynthetic diversity remains unexplored. By connecting pathways to related families, organisms and environments, BGC Atlas v2 supports natural-product discovery and investigations of prokaryotic biosynthetic diversity across taxa and ecosystems. BGC Atlas v2 is freely available at https://bgc-atlas.cs.uni-tuebingen.de.