ArticleGenes2023
Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution.
Article in Genes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Genomic insights into a versatile deep-sea methanotroph constituting the rare biosphere of a Brazilian carbonate mound complex.mSystems · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Revisiting multi-region 16S sequencing in gastric cancer.World journal of gastrointestinal oncology · 2026Article
- Secretory IgA amplification during immune checkpoint blockade enhances the control of tumor growth by enterotropic T cells.Science advances · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.Microbiology spectrum · 2025Article
- Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments.Environmental microbiology · 2025Article
- Nasal Microbiota Profiling as a Predictive Secondary Tool for COVID-19 Diagnosis: The Critical Role of Taxonomic Resolution.Microorganisms · 2025Article
- Article
- Improved resolution of microbial diversity in deep-sea surface sediments using PacBio long-read 16S rRNA gene sequencing.mSphere · 2024Article
- Impact of DNA extraction, PCR amplification, sequencing, and bioinformatic analysis on food-associated mock communities using PacBio long-read amplicon sequencing.BMC microbiology · 2024Article
- The Characteristics of Gut Microbiota and Its Relation with Diet in Postmenopausal Osteoporosis.Calcified tissue international · 2024Article
- Soil depth and physicochemical properties influence microbial dynamics in the rhizosphere of two Peruvian superfood trees, cherimoya and lucuma, as shown by PacBio-HiFi sequencing.Scientific reports · 2024Article
- High-Energy Supplemental Feeding Shifts Gut Microbiota Composition and Function in Red Deer (Animals : an open access journal from MDPI · 2024Article
- A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.Frontiers in microbiology · 2024Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.
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