ArticleFrontiers in microbiology2020
Comparison of Bioinformatics Pipelines and Operating Systems for the Analyses of 16S rRNA Gene Amplicon Sequences in Human Fecal Samples.
Article in Frontiers in microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 3 of them syntheses that pooled it.
What it found
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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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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
50 citing papers in PubMed, 3 syntheses or guidelines pooled it, 77 citations in OpenAlex.
- The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.Heart failure reviews · 2022Pooled it
- Systematic Review of the Effects of Exercise and Physical Activity on the Gut Microbiome of Older Adults.Nutrients · 2022Pooled it
- A Systematic Review of Arts-Based Interventions Delivered to Children and Young People in Nature or Outdoor Spaces: Impact on Nature Connectedness, Health and Wellbeing.Frontiers in psychology · 2022Pooled it
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Can the leafhopper microbiome unlock new strategies for its control?Journal of economic entomology · 2026Review
- Dataset characterising dominant bacterial phylotypes across animal manure-enriched composting microcosms for crude oil waste sludge bioremediation.Data in brief · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Review
- QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters.Parasites & vectors · 2025Article
- Wounds and the Microbiota: The Healing Interplay Between Host and Microbial Communities.International journal of molecular sciences · 2025Review
- PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.Current issues in molecular biology · 2025Article
- Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.Clinics and practice · 2025Review
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.Molecular ecology resources · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods.Environmental microbiome · 2025Article
- Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer's disease?Current opinion in psychiatry · 2025Review
- Founders Can Increase Determinism of Community Assembly.Ecology and evolution · 2025Article
- Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition.mSystems · 2025Article
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplicon high-throughput sequencing of 16S ribosomal RNA (rRNA) gene is currently the most widely used technique to investigate complex gut microbial communities. Microbial identification might be influenced by several factors, including the choice of bioinformatic pipelines, making comparisons across studies difficult. Here, we compared four commonly used pipelines (QIIME2, Bioconductor, UPARSE and mothur) run on two operating systems (OS) (Linux and Mac), to evaluate the impact of bioinformatic pipeline and OS on the taxonomic classification of 40 human stool samples. We applied the SILVA 132 reference database for all the pipelines. We compared phyla and genera identification and relative abundances across the four pipelines using the Friedman rank sum test. QIIME2 and Bioconductor provided identical outputs on Linux and Mac OS, while UPARSE and mothur reported only minimal differences between OS. Taxa assignments were consistent at both phylum and genus level across all the pipelines. However, a difference in terms of relative abundance was identified for all phyla (
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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.