ArticleGigaScience2021
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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140 citing papers in PubMed, 208 citations in OpenAlex.
- Biosynthetic Diversity of Marine-DerivedMarine drugs · 2026Review
- Comparative Genomics Reveals Extensive Biosynthetic Diversity and Lineage-Specific Metabolic Potential AcrossJournal of fungi (Basel, Switzerland) · 2026Article
- Diverse biosynthetic pathways in Arctic hydrothermal biofilms.Nature communications · 2026Article
- Genomic catalogue of giant viruses reveals expanded diversity and functional potential.Nature microbiology · 2026Article
- Genome mining guided identification of new furo[3,2-c]pyridones phaeopyridones A-C from the endophytic fungus Phaeobotryon negundinis 12020.Natural products and bioprospecting · 2026Article
- Evolutionary strategies of late-stage diversification in bacterial biosynthetic gene clusters.Essays in biochemistry · 2026Review
- Inter-species horizontal transfer of biosynthetic gene clusters: an evolutionary driver for chemical diversity in bacterial communities.Essays in biochemistry · 2026Review
- A guide to Direct Pathway Cloning (DiPaC) for natural product discovery.Essays in biochemistry · 2026Review
- Heterologous expression of NRPS and PKS pathways in Escherichia coli: from bottlenecks to biosynthetic platforms.Essays in biochemistry · 2026Review
- Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.World journal of microbiology & biotechnology · 2026Article
- Unveiling the Taxonomic Diversity and Unprecedented Biosynthetic Treasure of the Phylum Myxococcota.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Fine-grained structural classification of biosynthetic gene cluster-encoded products.Bioinformatics (Oxford, England) · 2026Article
- DiscERN: an automated genome mining tool for the discovery of evolutionarily related natural products.Nature communications · 2026Article
- Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters inmSystems · 2026Article
- Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.Nature communications · 2026Article
- Advances in tools, strategies, and applications of mining of microbial genomes for novel antimicrobials: a comprehensive review.Folia microbiologica · 2026Review
- Genomic and chemical analyses of 713 marine biofilm-derived bacterial strains.Applied and environmental microbiology · 2026Article
- A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.Nature communications · 2026Article
- Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.Environmental microbiome · 2026Article
- The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.Nature communications · 2026Article
80 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. However, current tools are hindered by a bottleneck caused by the expensive network-based approach used to group these BGCs into gene cluster families (GCFs).
resultsHere, we introduce BiG-SLiCE, a tool designed to cluster massive numbers of BGCs. By representing them in Euclidean space, BiG-SLiCE can group BGCs into GCFs in a non-pairwise, near-linear fashion. We used BiG-SLiCE to analyze 1,225,071 BGCs collected from 209,206 publicly available microbial genomes and metagenome-assembled genomes within 10 days on a typical 36-core CPU server. We demonstrate the utility of such analyses by reconstructing a global map of secondary metabolic diversity across taxonomy to identify uncharted biosynthetic potential. BiG-SLiCE also provides a "query mode" that can efficiently place newly sequenced BGCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration.
conclusionsBiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global and searchable interconnected network of BGCs. As more genomes are sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available via https://github.com/medema-group/bigslice.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.