ArticlePloS one2020
Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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
15 citing papers in PubMed, 29 citations in OpenAlex.
- Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.The ISME journal · 2026Article
- Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland.FEMS microbiology letters · 2026Article
- A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset.Scientific data · 2025Article
- Intermittent fasting induced cerebral ischemic tolerance altered gut microbiome and increased levels of short-chain fatty acids to a beneficial phenotype.Neurochemistry international · 2024Article
- Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing.Urolithiasis · 2024Article
- Article
- Strategies for Bovine Respiratory Disease (BRD) Diagnosis and Prognosis: A Comprehensive Overview.Animals : an open access journal from MDPI · 2024Review
- Isolation, identification, and biological characterization of bacterial endophytes isolated from Gunnera perpensa L.FEMS microbiology letters · 2024Article
- Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status.Frontiers in endocrinology · 2024Observational
- Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection.Scientific reports · 2022Article
- Bovine respiratory microbiota of feedlot cattle and its association with disease.Veterinary research · 2022Review
- Detection ofFrontiers in microbiomes · 2022Article
- Incorporation of Data From Multiple Hypervariable Regions when Analyzing Bacterial 16S rRNA Gene Sequencing Data.Frontiers in genetics · 2022Article
- 16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis.PeerJ · 2022Article
- Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing.mSystems · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is improved through reduced unassigned reads by including a survey of near-full-length sequences specific to the target environment, using a niche of interest represented by the upper respiratory tract (URT) of cattle. We created a custom Bovine URT database from these longer sequences for assignment of shorter, less expensive reads in comparisons of the upper respiratory tract among individual animals. This process improves the ability to detect changes in the microbial populations of a given environment, and the accuracy of defining the content of that environment at increasingly higher taxonomic resolution.
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.