ArticleFEMS microbiology ecology2021
Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?
Article in FEMS microbiology ecology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- Species- and strain-level assessment usingGut microbesTrial
- Gastric Microbiota from Populations with High Risk of Gastric Cancer in Nariño, Colombia.International journal of molecular sciences · 2026Article
- A multiplex assay to detect mosquito species, bloodmeal host source and Plasmodium in malaria vectors using Nanopore amplicon sequencing.Medical and veterinary entomology · 2026Article
- Significant impact of threshold adjustments on microbiome characterization following Nanopore sequencing.ISME communications · 2026Article
- Evaluation of V3-V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates.mSphere · 2025Article
- Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.Genome medicine · 2025Article
- Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status.BMC veterinary research · 2025Article
- Bioinformatic strategies in metagenomics of chronic prostatitis.World journal of urology · 2025Article
- Dehalogenating Desulfoluna spp. are ubiquitous in host-specific sponge microbiomes of the Great Barrier Reef.The ISME journal · 2025Article
- Third generation sequencing analysis detects significant differences in duodenal microbiome composition between functional dyspepsia patients and control subjects.Neurogastroenterology and motility · 2025Article
- Article
- Identification of a terpene synthase arsenal using long-read sequencing and genome assembly of Aspergillus wentii.BMC genomics · 2024Article
- Cross-comparison of gut metagenomic profiling strategies.Communications biology · 2024Article
- High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.PNAS nexus · 2024Article
- Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.Journal of water and health · 2024Article
- Differential Reshaping of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream (Microorganisms · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans.BMC microbiology · 2024Article
- RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.PeerJ · 2024Article
- Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing.PloS one · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.
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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.