ArticlePloS one2013
Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers, 6 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
146 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Standardized 16S Meta-Analysis Reveals Consistent Host-Associated Patterns in Laminariales Epiphytic Microbiomes.MicrobiologyOpen · 2026Pooled it
- Association between primary Sjögren's syndrome and gut microbiota disruption: a systematic review and meta-analysis.Clinical rheumatology · 2024Pooled it
- Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth.BMC biology · 2023Pooled it
- Microbiome changes associated with acute and chronic pancreatitis: A systematic review.Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] · 2021Pooled it
- Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials.Genome medicine · 2016Pooled it
- Microbiome of the paranasal sinuses: Update and literature review.American journal of rhinology & allergyPooled it
- Paucibacterial Microbiome and Resident DNA Virome of the Healthy Conjunctiva.Investigative ophthalmology & visual science · 2016Trial
- Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.PloS one · 2016Trial
- Root Exudates from Coexisting Plant Species Differentially Shape Soil Microbial Communities and Nutrient Dynamics in a Desert Steppe.Microorganisms · 2026Article
- Species-level profiling ofPeerJ · 2026Article
- Molecular phylogeny of the Acer-feeding aphid subfamily Drepanosiphinae (Insecta: Hemiptera: Aphididae) and the evolution of its endosymbiotic consortia.Zoological letters · 2025Article
- Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.Renal failure · 2025Review
- Microbial Consortium ofPlants (Basel, Switzerland) · 2025Article
- Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data.Microorganisms · 2025Article
- Exploring the bacterial communities in date palm roots in saline versus non-saline environment.BMC plant biology · 2025Article
- MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.Microbial ecology · 2025Article
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- NovelFrontiers in microbiology · 2025Article
- Microbiome associated to an HEnvironmental microbiome · 2024Article
- LysoPE mediated by respiratory microorganism Aeromicrobium camelliae alleviates H9N2 challenge in mice.Veterinary research · 2024Article
86 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
3 authors.
Funding
Abstract
Massively parallel high throughput sequencing technologies allow us to interrogate the microbial composition of biological samples at unprecedented resolution. The typical approach is to perform high-throughout sequencing of 16S rRNA genes, which are then taxonomically classified based on similarity to known sequences in existing databases. Current technologies cause a predicament though, because although they enable deep coverage of samples, they are limited in the length of sequence they can produce. As a result, high-throughout studies of microbial communities often do not sequence the entire 16S rRNA gene. The challenge is to obtain reliable representation of bacterial communities through taxonomic classification of short 16S rRNA gene sequences. In this study we explored properties of different study designs and developed specific recommendations for effective use of short-read sequencing technologies for the purpose of interrogating bacterial communities, with a focus on classification using naïve Bayesian classifiers. To assess precision and coverage of each design, we used a collection of ∼8,500 manually curated 16S rRNA gene sequences from cultured bacteria and a set of over one million bacterial 16S rRNA gene sequences retrieved from environmental samples, respectively. We also tested different configurations of taxonomic classification approaches using short read sequencing data, and provide recommendations for optimal choice of the relevant parameters. We conclude that with a judicious selection of the sequenced region and the corresponding choice of a suitable training set for taxonomic classification, it is possible to explore bacterial communities at great depth using current technologies, with only a minimal loss of taxonomic resolution.
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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.