ArticleGenes2021
Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol.
Article in Genes, 2021. 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, 16 citations in OpenAlex.
- Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Enhancing low-level genome-edited crop detection and identification in food mixtures using nanopore adaptive sampling: Rice-Soybean mixture as proof-of-concept.NPJ science of food · 2026Article
- Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA.NAR genomics and bioinformatics · 2025Article
- Nanopore R10.4 metagenomic detection of blaNature communications · 2024Article
- Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.BMC medical genomics · 2024Article
- Fructooligosaccharides benefits on glucose homeostasis upon high-fat diet feeding require type 2 conventional dendritic cells.Nature communications · 2024Article
- Unraveling metagenomics through long-read sequencing: a comprehensive review.Journal of translational medicine · 2024Review
- Functional alterations and predictive capacity of gut microbiome in type 2 diabetes.Scientific reports · 2023Article
- Benchmarking second and third-generation sequencing platforms for microbial metagenomics.Scientific data · 2022Article
- Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism.International journal of molecular sciences · 2022Article
- Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study.Frontiers in microbiology · 2022Article
- Characterization of the Gut Microbiota in Individuals with Overweight or Obesity during a Real-World Weight Loss Dietary Program: A Focus on the Bacteroides 2 Enterotype.Biomedicines · 2021Article
- Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities, which reflect naturally occurring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina, and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. This protocol can be implemented in a clinical or research setting, bringing rapid personalized whole-genome profiling of target microbiome species.
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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.