ArticleNature microbiology2025
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.
Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Indoor Microbiome: Sampling, Analysis and Emerging Trends.Environmental microbiology reports · 2026Pooled it
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to alpine permafrost degradation.Nature communications · 2026Article
- Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.Bioinformatics (Oxford, England) · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Bacterial biosynthetic superclusters: emerging drivers of synergistic natural products against antimicrobial resistance.Essays in biochemistry · 2026Review
- Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.BMC genomics · 2026Article
- Bacterial Diversity, Structure, and Function in Rhizosphere and Bulk Soils of Grapevines: Comparing Gravelly, Calcareous, and Aeolian Sandy Textures.Microorganisms · 2026Article
- Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.Microbial ecology · 2026Article
- Microbiome research beyond description and association.Science China. Life sciences · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- SNooPy: a statistical framework for long-read metagenomic variant calling.Nucleic acids research · 2026Article
- Advancing microbiology through foundational science.Nature microbiology · 2026Article
- Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.Scientific data · 2026Article
- An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales.bioRxiv : the preprint server for biology · 2026Article
- Review
- Global terrestrial distribution of N2O-reducing Acidobacteriota members.The ISME journal · 2026Article
- Article
- GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.Nucleic acids research · 2026Article
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.
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