ArticleGenome research2023
Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Going Mobile: Using Portable Genomic Technologies for PCR-Free In Situ Species Identification and Real-Time Molecular Systematics.Ecology and evolution · 2025Article
- Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment.npj antimicrobials and resistance · 2025Review
- Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.Scientific data · 2025Article
- Microbial functional diversity and redundancy: moving forward.FEMS microbiology reviews · 2025Review
- Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.The ISME journal · 2025Article
- Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.ISME communications · 2025Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.Briefings in bioinformatics · 2023Article
- Present and future outlooks on environmental DNA-based methods for antibiotic discovery.Current opinion in microbiology · 2023Review
- Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.Frontiers in microbiology · 2022Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.
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Registered trials
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