ArticleNature biotechnology2019
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 197 papers, 1 of them a synthesis that pooled it.
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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
197 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The microbial dark matter and "wanted list" in worldwide wastewater treatment plants.Microbiome · 2023Pooled it
- Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.NPJ biofilms and microbiomes · 2026Trial
- Trial
- Microbial transmission and ecology of human and environmental microbial communities in childcare centers.Research square · 2026Article
- Article
- GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.Science China. Life sciences · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- The Gut Microbiome Profile of Lions in Etosha National Park, Namibia.Research square · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.Scientific reports · 2026Article
- Review
- Article
- Organohalide respiration by a Desulforhopalus-dominated community.The ISME journal · 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
- Long-read sequencing for cancer liquid biopsy: advancing precision oncology.Frontiers in oncology · 2026Review
- The role of the gut microbiome in antibiotic-driven antimicrobial resistance.Frontiers in microbiology · 2026Review
137 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
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.
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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.