ReviewComputational and structural biotechnology journal2021
Nanopore sequencing and its application to the study of microbial communities.
Review in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 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
104 citing papers in PubMed, 192 citations in OpenAlex.
- Species- and strain-level assessment usingGut microbesTrial
- A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.Microbial genomics · 2026Article
- Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.Veterinary and animal science · 2026Article
- Genomic and Phenotypic Evaluation of the Gliadin-Degrading Probiotic Bacillus amyloliquefaciens EG025 from Cheonggukjang for Celiac Disease Treatment.Probiotics and antimicrobial proteins · 2026Article
- Review
- Critical assessment of intratumor and low-biomass microbiome using long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Animals : an open access journal from MDPI · 2026Article
- Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation.FEMS microbiology reviews · 2026Review
- Significant impact of threshold adjustments on microbiome characterization following Nanopore sequencing.ISME communications · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Training in metataxonomics-integrated risk assessment for foodborne pathogens in the Polish and Spanish dairy chain (DAIRYPOL).EFSA journal. European Food Safety Authority · 2025Article
- The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research.npj antimicrobials and resistance · 2025Review
- Next-generation sequencing of the tonsillar microbiome in severe acute tonsillitis: comparison with healthy controls and culture-based findings.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.BMC microbiology · 2025Article
- Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis.BMC microbiology · 2025Article
- Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.Journal of assisted reproduction and genetics · 2025Article
- Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.Microorganisms · 2025Review
- Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.MethodsX · 2025Article
44 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 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable technologies. The use of long reads has allowed to address several previously unsolved issues in the field, such as the resolution of complex genomic structures, and facilitated the access to metagenome assembled genomes (MAGs). Furthermore, the low cost and portability of platforms together with the development of rapid protocols and analysis pipelines have featured nanopore technology as an attractive and ever-growing tool for real-time in-field sequencing for environmental microbial analysis. This review provides an up-to-date summary of the experimental protocols and bioinformatic tools for the study of microbial communities using nanopore sequencing, highlighting the most important and recent research in the field with a major focus on infectious diseases. An overview of the main approaches including targeted and shotgun approaches, metatranscriptomics, epigenomics, and epitranscriptomics is provided, together with an outlook to the major challenges and perspectives over the use of this technology for microbial studies.
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What OpenQuestion holds
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.