ArticleCommunications biology2021
Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.
Article in Communications biology, 2021. 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, 55 citations in OpenAlex.
- When context matters: community and environmental context to elicit natural products.Essays in biochemistry · 2026Review
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.Nature communications · 2026Article
- Retraction for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.Microbiology spectrum · 2026Article
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.BMC genomics · 2025Article
- Automated environmental metagenomics using Oxford nanopore sequencing.BMC genomics · 2025Article
- Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.Microorganisms · 2025Review
- Microbial secondary metabolites: advancements to accelerate discovery towards application.Nature reviews. Microbiology · 2025Review
- Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.Indian journal of microbiology · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Whole genome sequencing of Penicillium and Burkholderia strains antagonistic to the causal agent of kauri dieback disease (Phytophthora agathidicida) reveals biosynthetic gene clusters related to antimicrobial secondary metabolites.Molecular ecology resources · 2025Article
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.GigaScience · 2025Article
- Shotgun metagenomics reveals antibiotic resistome dynamics and metabolic specialization in fungal-dominated microbiomes.Frontiers in microbiology · 2025Article
- The encoded and expressed biosynthetic potential of Greenland Ice Sheet microbes.Frontiers in microbiology · 2025Article
- Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.Scientific reports · 2024Article
- MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.Microbiome · 2024Article
- Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.Nature methods · 2024Article
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Authors and funding
19 authors at 3 institutions in 2 countries.
Funding
Abstract
Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.
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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.