ArticleInternational journal of molecular sciences2020
Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Article
- Fecal microbiome associated with egg production efficiency in laying hens.Animal bioscience · 2026Article
- Article
- Significant impact of threshold adjustments on microbiome characterization following Nanopore sequencing.ISME communications · 2026Article
- Analysis of the overall development trends and hotspots in the research field of the human gut virome.Virology journal · 2025Review
- Review
- Effects of Maternal Pre-Pregnancy BMI on Preterm Infant Microbiome and Fecal Fermentation Profile-A Preliminary Cohort Study.Nutrients · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.Archives of microbiology · 2024Article
- The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.Applied and environmental microbiology · 2023Article
- Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing.Cancers · 2023Article
- Variable Region Sequences Influence 16S rRNA Performance.Microbiology spectrum · 2023Article
- Article
- Species-Level Characterization of the Microbiome in Breast Tissues with Different Malignancy and Hormone-Receptor Statuses Using Nanopore Sequencing.Journal of personalized medicine · 2023Article
- Comparative analysis of full-length 16s ribosomal RNA genome sequencing in human fecal samples using primer sets with different degrees of degeneracy.Frontiers in genetics · 2023Article
- Amplicon_sorter: A tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences.Ecology and evolution · 2022Article
- Application of third-generation sequencing in cancer research.Medical review (2021) · 2021Article
- Decreased secondary faecal bile acids in children with ulcerative colitis and Clostridioides difficile infection.Alimentary pharmacology & therapeutics · 2021Article
- Gut Microbiota Composition and Its Metabolites in Different Stages of Chronic Kidney Disease.Journal of clinical medicine · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified, bar-coded, and sequenced using the Illumina MiSeq and ONT MinION sequencers and corresponding kits. Mapping of the sequenced amplicon using MinION to the entire 16S rRNA gene was analyzed with the cloud-based EPI2ME algorithm. V3-V4 reads generated using MiSeq were aligned by applying the CLC genomics workbench. More than 90% of sequenced reads generated using distinct sequencers were accurately classified at the genus or species level. The misclassification of sequenced reads at the species level between the two approaches was less substantial as expected. Taken together, the comparative results demonstrate that MinION sequencing platform coupled with the corresponding algorithm could function as a practicable strategy in classifying bacterial community to the species level.
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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.