Uncovering the biosynthetic potential of soil metagenomes

Sequencing of DNA extracted from environmental samples can provide key insights into the biosynthetic potential of uncultured bacteria. However, the high complexity of soil metagenomes, which can contain thousands of bacterial species per gram of soil, imposes significant challenges to identify biosynthetic gene clusters in the genomes of low abundance species due to the massive sequencing depth required for their assembly. To facilitate the discovery of novel metabolites produced by rare members of the soil microbiome, we developed a targeted sequencing workflow termed CONKAT-seq (co-occurrence network analysis of targeted sequences) that detects physically clustered biosynthetic domains, a hallmark of bacterial secondary metabolism. Using CONKAT-seq, we show that a single soil sample can contain more than a thousand uncharacterized biosynthetic gene clusters, most of which originate from low frequency genomes. Our approach allows scalable exploration of largely untapped biosynthetic diversity across multiple soils and can guide the discovery of new secondary metabolites from rare members of the soil microbiome.