ArticleMicroorganisms2023
Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required.
Article in Microorganisms, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.Journal of fish diseases · 2026Article
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.Cancer reports (Hoboken, N.J.) · 2026Article
- Unveiling Protist Composition and Diversity Patterns With eDNA Metabarcoding: Comparing Short- and Long-Read Approaches.Ecology and evolution · 2026Article
- Hidden Partners in Diversity: Acidobacteriota and Their Distribution in the Cape Floristic Region.MicrobiologyOpen · 2026Article
- Harnessing the gut microbiome to combat tuberculosis: a technological and clinical review.Frontiers in cellular and infection microbiology · 2026Review
- The prevalence and distribution ofFrontiers in microbiomes · 2026Article
- Antidepressant Effects ofFoods (Basel, Switzerland) · 2025Article
- Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in thebioRxiv : the preprint server for biology · 2025Article
- Pathogen virulence genes: Advances, challenges and future directions in infectious disease research (Review).International journal of molecular medicine · 2025Review
- Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities.Scientific reports · 2025Article
- Evaluation of V3-V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates.mSphere · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Prospective Comparative Study of an Oral Synbiotic and a Myoinositol-Based Herbal Supplement in Modifying Hormone Levels and the Gut Microbiome in Non-cystic Acne.Dermatology and therapy · 2025Article
- SkinDuoInternational journal of molecular sciences · 2025Observational
- Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.Journal of clinical microbiology · 2025Article
- Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.International journal of molecular sciences · 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
- Nasal Microbiota Profiling as a Predictive Secondary Tool for COVID-19 Diagnosis: The Critical Role of Taxonomic Resolution.Microorganisms · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.
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Registered trials
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