ArticleiScience2020
Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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.
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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
18 citing papers in PubMed.
- Microbiome as a Tool to Monitor Aquarium Systems.Veterinary sciences · 2026Article
- Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.Journal of oral microbiology · 2026Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.bioRxiv : the preprint server for biology · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.Microbiology spectrum · 2024Article
- Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.The ISME journal · 2024Article
- Article
- Review
- Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Benchmarking second and third-generation sequencing platforms for microbial metagenomics.Scientific data · 2022Article
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing.NPJ biofilms and microbiomes · 2021Article
- Nanopore sequencing and its application to the study of microbial communities.Computational and structural biotechnology journal · 2021Review
- Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics.Frontiers in microbiology · 2021Article
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length and are therefore particularly relevant for microbiome studies. However, owing to the higher per-base error rates than typical short-read sequencing, the application of long-read sequencing on microbiomes remains largely unexplored. Here we deeply sequenced two human microbiota mock community samples (HM-276D and HM-277D) from the Human Microbiome Project. We showed that assembly programs consistently achieved high accuracy (∼99%) and completeness (∼99%) for bacterial strains with adequate coverage. We also found that long-read sequencing provides accurate estimates of species-level abundance (R = 0.94 for 20 bacteria with abundance ranging from 0.005% to 64%). Our results not only demonstrate the feasibility of characterizing complete microbial genomes and populations from error-prone Nanopore sequencing data but also highlight necessary bioinformatics improvements for future metagenomics tool development.
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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.