ArticleNature biotechnology2020
Complete, closed bacterial genomes from microbiomes using nanopore sequencing.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 204 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
204 citing papers in PubMed, 415 citations in OpenAlex.
- Parallel evolution of chimeric genes in microbial evolution experiments.Microbial genomics · 2026Article
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Maternal and infant gut microbiome.iMeta · 2026Review
- Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.Journal of microbiology (Seoul, Korea) · 2026Article
- Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.Microbial genomics · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- CAMP: a modular metagenomics analysis system for integrated multistep data exploration.NAR genomics and bioinformatics · 2026Article
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- Review
- Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.Biology methods & protocols · 2026Review
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.Microbiology spectrum · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.Microbial genomics · 2025Article
- Automated environmental metagenomics using Oxford nanopore sequencing.BMC genomics · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.mSystems · 2025Article
144 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.
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Registered trials
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.