ArticlePeerJ2018
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 148 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
148 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Atmospheric Microbial Transport to Antarctica and Its Ecological Implications: A Systematic Review.Environmental microbiology · 2026Pooled it
- Guideline for designing microbiome studies in neoplastic diseases.GeroScience · 2024Guideline
- Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.Scientific reports · 2022Pooled it
- Pilot study evaluating tolerability and changes in fecal microbiota associated with novel probiotic administration to dogs with diarrhea.Frontiers in veterinary science · 2025Trial
- Physical activity enhances the improvement of body mass index and metabolism by inulin: a multicenter randomized placebo-controlled trial performed in obese individuals.BMC medicine · 2022Trial
- Randomised, double-blind, placebo-controlled trial of oral probiotic Streptococcus salivarius M18 on head and neck cancer patients post-radiotherapy: a pilot study.Scientific reports · 2020Trial
- Task geometry alignment enables parameter independent and accurate genomic search.Scientific reports · 2026Article
- Land-Use Shapes Soil Fungal Communities and Functional Guilds in Tropical Forest Ecosystems.Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Integrated multi-omics profiling of gut bacterial extracellular vesicles links cargo composition to host transcriptional responses.bioRxiv : the preprint server for biology · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- Global climate gradients structure soilbioRxiv : the preprint server for biology · 2026Article
- Submucosal microbiota profile in peri-implant health, peri-implant mucositis, and different severity levels of peri-implantitis.BMC oral health · 2026Article
- Article
- CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches.PloS one · 2026Article
- Modulation of the rumen microbiome and metabolism in dairy cows by altering the concentrate feeding pattern and the inclusion ofFrontiers in microbiomes · 2026Article
- The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia.Gut microbes · 2025Article
- Capturing sequence ambiguity among taxa in a primer-specific manner to improve taxonomic classification of amplicon sequencing.Nucleic acids research · 2025Article
- Dynamic airborne mycobiome in the metropolitan city transit system is driven by seasonality and station type.Microbiology spectrum · 2025Article
- Cannabis use, microbial diversity, andmedRxiv : the preprint server for health sciences · 2025Article
- Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.Molecular ecology · 2025Article
88 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
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal.
Indexed as
Identifiers
What OpenQuestion holds
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.