ArticleNature communications2019
Species abundance information improves sequence taxonomy classification accuracy.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 2 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.
The trial behind it
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
124 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Multi-cohort ensemble learning framework for vaginal microbiome-based endometrial cancer detection.Frontiers in cellular and infection microbiology · 2025Pooled it
- A Mediterranean Diet Pattern Improves Intestinal Inflammation Concomitant with Reshaping of the Bacteriome in Ulcerative Colitis: A Randomised Controlled Trial.Journal of Crohn's & colitis · 2023Trial
- Gut Microbial Stability is Associated with Greater Endurance Performance in Athletes Undertaking Dietary Periodization.mSystems · 2022Trial
- Treatment With Multi-Species Probiotics Changes the Functions, Not the Composition of Gut Microbiota in Postmenopausal Women With Obesity: A Randomized, Double-Blind, Placebo-Controlled Study.Frontiers in cellular and infection microbiology · 2022Trial
- Soil Microbial Assembly Mirrors a Savanna Mosaic Amid Plant Invasion and Soil Disturbance.Ecology and evolution · 2026Article
- Changes to Skin Microbiome Community Dynamics Support Resistance to Enzootic and Epizootic Strains of Batrachochytrium dendrobatidis (Bd) in the Spotted Salamander (Ambystoma maculatum).Molecular ecology · 2026Article
- The oral microbiome is associated with stress, adversity, and mental health in young adults.Scientific reports · 2026Article
- Direct microbiota profiling of apheresis-associated products for microbiological insights in cell therapy.Scientific reports · 2026Article
- Sampling Design and Sample Processing Affect Soil Biodiversity Assessments.Molecular ecology resources · 2026Article
- Profiling gut microbiota of colorectal cancer in Indonesia: a focus on beneficial taxa depletion.Gut pathogens · 2026Article
- Microbiome-Metabolome Crosstalk as a Driver of COVID-19 Severity.Medical sciences (Basel, Switzerland) · 2026Article
- Enhanced pathogen detection and gut microbiome alterations in pyogenic liver abscess: insights from next-generation sequencing.Gut pathogens · 2026Article
- Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems.NPJ biofilms and microbiomes · 2026Article
- Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.NPJ biofilms and microbiomes · 2026Article
- Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods and a Vagina-Specific 16S rRNA Gene Database.Microorganisms · 2026Article
- SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity.Nucleic acids research · 2026Article
- RNA-based characterization of ribosomally active microbial communities during beef slaughtering.Frontiers in microbiology · 2026Article
- Soil microbiome analysis of a northeastern deciduous forest in SUNY Old Westbury, Long Island, New York.microPublication biology · 2026Article
- Gut microbiota and pathobiont exposure influences disease incidence in non-obese diabetic mice.Frontiers in microbiology · 2026Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments.
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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.