ArticleNature communications2019
Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Genome mining reveals an architecturally expanded pyoluteorin-associated biosynthetic gene cluster and a divergent flavin-dependent halogenase-like sequence in deep-sea Pseudomonas Aeruginosa from the Gulf of Guinea.Antonie van Leeuwenhoek · 2026Article
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- Resistance-CONKAT-seq Guided Discovery of a ClpP Active Natural Product from a Soil Metagenome.ACS chemical biology · 2026Article
- The WormFood CURE: Screening for bioactive metabolites that antagonize thebioRxiv : the preprint server for biology · 2026Article
- Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.Environmental microbiology · 2026Article
- Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.Nature communications · 2026Article
- Microbial secondary metabolites: advancements to accelerate discovery towards application.Nature reviews. Microbiology · 2025Review
- Synthetic Biology in Natural Product Biosynthesis.Chemical reviews · 2025Review
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research.Angewandte Chemie (International ed. in English) · 2025Review
- Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.Advanced biotechnology · 2024Review
- SecMet-FISH: labeling, visualization, and enumeration of secondary metabolite producing microorganisms.FEMS microbiology ecology · 2024Article
- Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes.Communications biology · 2024Article
- Present and future outlooks on environmental DNA-based methods for antibiotic discovery.Current opinion in microbiology · 2023Review
- Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.Microbiology spectrum · 2023Article
- Article
- sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome.Bioinformatics (Oxford, England) · 2023Article
- Bacterial natural product discovery by heterologous expression.Journal of industrial microbiology & biotechnology · 2023Review
- Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.Nature microbiology · 2022Article
- Multiplexed mobilization and expression of biosynthetic gene clusters.Nature communications · 2022Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
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 explore secondary metabolites potentially produced by rare members of the soil microbiome. Here, we develop 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. Following targeted amplification of conserved biosynthetic domains in a highly partitioned metagenomic library, CONKAT-seq evaluates amplicon co-occurrence patterns across library subpools to identify chromosomally clustered domains. 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 which are practically inaccessible through untargeted sequencing. CONKAT-seq allows scalable exploration of largely untapped biosynthetic diversity across multiple soils, and can guide the discovery of novel secondary metabolites from rare members of the soil microbiome.
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