ArticleMicrobiology spectrum2025
QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.
Article in Microbiology spectrum, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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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.
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Who cites it
10 citing papers in PubMed.
- A QIIME2-based workflow for multi-amplicon 16S rRNA profiling.Microbiology resource announcements · 2026Article
- Pasture diversity and regenerative management shape ruminant gut microbiome dynamics within a real multi-year farming system.Frontiers in microbiology · 2026Article
- Gut microbiota and SCFA signatures in predicting postoperative infection sites in neurocritical care patients.Frontiers in microbiology · 2026Article
- Geographical and seasonal variations of soil microbiomes and metabolomes in the core production area of Jiang-flavor Baijiu: a multi-omics characterization.Frontiers in microbiology · 2026Article
- Functional and taxonomic shifts in rhizosphere microbiomes of summer legume cover crops.Frontiers in plant science · 2026Article
- The role ofFrontiers in oral health · 2026Review
- Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.International journal of genomics · 2026Review
- Polyphasic Characterisation of Microbiota Associated with Sant'Agostino Table Olives Flavoured withFoods (Basel, Switzerland) · 2025Article
- Microbial Selection and Functional Adaptation in Technical Snow: A Molecular Perspective from 16S rRNA Profiling.International journal of molecular sciences · 2025Article
- Reciprocal regulation of rumen microbiota and epithelial genes in response to small peptide supplementation for feed efficiency in beef cattle.Frontiers in veterinary science · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (
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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.