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Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

https://doi.org/10.1128/aem.02810-10
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/s1369-5274(98)80029-5openalex-snapshot
A natural species concept for prokaryotes
inferredcites →https://doi.org/10.1093/bioinformatics/16.5.412openalex-snapshot
Assessing the accuracy of prediction algorithms for classification: an overview
inferredcites →https://doi.org/10.1093/bioinformatics/bth226openalex-snapshot
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/nar/gkm864openalex-snapshot
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
inferredcites →https://doi.org/10.1093/nar/gkn491openalex-snapshot
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
inferredcites →https://doi.org/10.1093/nar/gkp285openalex-snapshot
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
inferredcites →https://doi.org/10.1098/rstb.2006.1920openalex-snapshot
The bacterial species definition in the genomic era
inferredcites →https://doi.org/10.1099/00207713-44-4-846openalex-snapshot
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
inferredcites →https://doi.org/10.1099/ijs.0.64483-0openalex-snapshot
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
inferredcites →https://doi.org/10.1111/j.1462-2920.2009.02051.xopenalex-snapshot
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02193.xopenalex-snapshot
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1128/aem.71.12.7724-7736.2005openalex-snapshot
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
inferredcites →https://doi.org/10.1128/aem.71.3.1501-1506.2005openalex-snapshot
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
inferredcites →https://doi.org/10.1128/jb.180.18.4765-4774.1998openalex-snapshot
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
inferredcites →https://doi.org/10.1146/annurev.micro.56.012302.160634openalex-snapshot
What are Bacterial Species?
inferredcites →https://doi.org/10.1371/journal.pcbi.1000844openalex-snapshot
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1000255openalex-snapshot
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0008230openalex-snapshot
A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

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The simultaneous addition of chitosan and peat enhanced the removals of antibiotics resistance genes during biogas residues composting
inferred← citeshttps://doi.org/10.1016/j.envres.2026.125817openalex-snapshot
A multi-state assessment of per- and polyfluoroalkyl substances (PFAS), pesticides, and antibiotic resistance genes in white-tailed deer (Odocoileus virginianus) of the United States
inferred← citeshttps://doi.org/10.1016/j.eti.2025.104446openalex-snapshot
Taxonomic structure and functional assembly of the broad-spectrum sulfonylurea herbicide-degrading microbial consortium L1 under different herbicide substrates
inferred← citeshttps://doi.org/10.1016/j.foodres.2021.110676openalex-snapshot
Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system
inferred← citeshttps://doi.org/10.1016/j.funeco.2018.01.004openalex-snapshot
Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing
inferred← citeshttps://doi.org/10.1016/j.heliyon.2025.e43530openalex-snapshot
Material Matters: Unraveling the effect of biodegradable plastic polyhydroxybutyrate (PHB), conventional high-density polyethylene (HDPE), and bamboo on the bacterial community of marine eulittoral sediments
inferred← citeshttps://doi.org/10.1016/j.ibiod.2012.07.017openalex-snapshot
Contribution of make-up water to the microbial community in an oilfield from which oil is produced by produced water re-injection
inferred← citeshttps://doi.org/10.1016/j.ibiod.2012.08.001openalex-snapshot
Microbial community structure and microbial activities related to CO2 storage capacities of a salt cavern
inferred← citeshttps://doi.org/10.1016/j.ibiod.2013.01.014openalex-snapshot
Microbiological survey for analysis of the brown spots on the walls of the tomb of King Tutankhamun
inferred← citeshttps://doi.org/10.1016/j.ibiod.2014.08.013openalex-snapshot
Microbially enhanced oil recovery from miniature model columns through stimulation of indigenous microflora with nitrate
inferred← citeshttps://doi.org/10.1016/j.ijantimicag.2017.03.017openalex-snapshot
Effects of oral antibiotics and isotretinoin on the murine gut microbiota
inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2014.09.031openalex-snapshot
Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)
inferred← citeshttps://doi.org/10.1016/j.ijpx.2019.100021openalex-snapshot
A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro
inferred← citeshttps://doi.org/10.1016/j.it.2018.09.007openalex-snapshot
The Impact of Intratumoral and Gastrointestinal Microbiota on Systemic Cancer Therapy
inferred← citeshttps://doi.org/10.1016/j.jbc.2022.102530openalex-snapshot
The role of FXR and TGR5 in reversing and preventing progression of Western diet–induced hepatic steatosis, inflammation, and fibrosis in mice
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2012.03.009openalex-snapshot
Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2013.07.004openalex-snapshot
Phoenix 2: A locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2017.11.016openalex-snapshot
Control of microbial sulfide production by limiting sulfate dispersal in a water-injected oil field
inferred← citeshttps://doi.org/10.1016/j.jenvman.2019.109857openalex-snapshot
Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms
inferred← citeshttps://doi.org/10.1016/j.jes.2015.09.025openalex-snapshot
Bacterial communities in different locations, seasons and segments of a dairy wastewater treatment system consisting of six segments
inferred← citeshttps://doi.org/10.1016/j.jff.2019.103440openalex-snapshot
Wheat bran thermal treatment in a hot air oven does not affect the fermentation and colonisation process by human faecal microbiota
inferred← citeshttps://doi.org/10.1016/j.jff.2019.103484openalex-snapshot
2′-Fucosyllactose alters the composition and activity of gut microbiota from formula-fed infants receiving complementary feeding in a validated intestinal model
inferred← citeshttps://doi.org/10.1016/j.jfp.2023.100169openalex-snapshot
Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment
inferred← citeshttps://doi.org/10.1016/j.jglr.2017.03.003openalex-snapshot
Metagenomic analysis in Lake Onego (Russia) Synechococcus cyanobacteria
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2021.126080openalex-snapshot
A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost
inferred← citeshttps://doi.org/10.1016/j.joen.2024.05.010openalex-snapshot
An In Vitro Evaluation of the Antimicrobial Efficacy of a Novel Irrigant Using Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1016/j.jpowsour.2022.231347openalex-snapshot
Impact of cathodic biofouling on the uneven performance of individual units and scale-up power efficiency in parallel-connected air-cathode microbial fuel cells
inferred← citeshttps://doi.org/10.1016/j.jpsychires.2016.12.007openalex-snapshot
The gut microbiome composition associates with bipolar disorder and illness severity
inferred← citeshttps://doi.org/10.1016/j.jseaes.2014.02.014openalex-snapshot
Distributions and assemblages of microbial communities along a sediment core retrieved from a potential hydrate-bearing region offshore southwestern Taiwan
inferred← citeshttps://doi.org/10.1016/j.jwpe.2022.102868openalex-snapshot
Denitrification in perspective of carbon neutralization: CO2 emission reduction and electricity generation by Fe-anode and bio-cathode MFC
inferred← citeshttps://doi.org/10.1016/j.meatsci.2016.02.034openalex-snapshot
Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs
inferred← citeshttps://doi.org/10.1016/j.micres.2022.127244openalex-snapshot
The association between the respiratory tract microbiome and clinical outcomes in patients with COPD
inferred← citeshttps://doi.org/10.1016/j.mimet.2013.07.004openalex-snapshot
MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence
inferred← citeshttps://doi.org/10.1016/j.mimet.2017.01.017openalex-snapshot
A quantitative SMRT cell sequencing method for ribosomal amplicons
inferred← citeshttps://doi.org/10.1016/j.neuron.2025.10.006openalex-snapshot
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
inferred← citeshttps://doi.org/10.1016/j.neuroscience.2018.11.048openalex-snapshot
The Acute Influence of Acid Suppression with Esomeprazole on Gastrointestinal Microbiota and Brain Gene Expression Profiles in a Murine Model of Restraint Stress
inferred← citeshttps://doi.org/10.1016/j.ocsci.2020.08.003openalex-snapshot
Effect of rice-rice-rape rotation on physicochemical property and bacterial community of rhizosphere soil
inferred← citeshttps://doi.org/10.1016/j.pedobi.2020.150700openalex-snapshot
Functional shifts of soil microbial communities associated with Alliaria petiolata invasion
inferred← citeshttps://doi.org/10.1016/j.pmpp.2020.101590openalex-snapshot
Comparative analysis of bacterial and fungal endophytes responses to Candidatus Liberibacter asiaticus infection in leaf midribs of Citrus reticulata cv. Shatangju
inferred← citeshttps://doi.org/10.1016/j.protis.2017.03.005openalex-snapshot
The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale
inferred← citeshttps://doi.org/10.1016/j.psj.2026.106574openalex-snapshot
The impact of polystyrene nanoplastics on the chicken gut and liver: Based on transcriptomics and microbiomics
inferred← citeshttps://doi.org/10.1016/j.rsma.2025.104197openalex-snapshot
Characterization of microbial diversity in the harbour and ballast water of ships in the Gulf of Mannar, India using environmental DNA
inferred← citeshttps://doi.org/10.1016/j.rvsc.2021.08.011openalex-snapshot
Inclusion of small intestinal absorption and simulated mucosal surfaces further improve the Mucosal Simulator of the Canine Intestinal Microbial Ecosystem (M-SCIME™)
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2014.10.012openalex-snapshot
Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2016.03.220openalex-snapshot
Soil biochar amendment shapes the composition of N2O-reducing microbial communities
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2018.05.094openalex-snapshot
Aquifer recharge with stormwater runoff in urban areas: Influence of vadose zone thickness on nutrient and bacterial transfers from the surface of infiltration basins to groundwater
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2018.06.067openalex-snapshot
Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2020.136707openalex-snapshot
Yard vegetation is associated with gut microbiota composition
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.163160openalex-snapshot
Energy-related wastewater contamination alters microbial communities of sediment, water, and amphibian skin
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.165840openalex-snapshot
Elevational changes in soil properties shaping fungal community assemblages in terrestrial forest
inferred← citeshttps://doi.org/10.1016/j.soilbio.2020.107930openalex-snapshot
Bacterial predation limits microbial sulfate-reduction in a coastal acid sulfate soil (CASS) ecosystem
inferred← citeshttps://doi.org/10.1016/j.syapm.2015.02.006openalex-snapshot
Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system
inferred← citeshttps://doi.org/10.1016/j.tjnut.2023.07.009openalex-snapshot
The Gut Microbiota Differ in Exclusively Breastfed and Formula-Fed United States Infants and are Associated with Growth Status
inferred← citeshttps://doi.org/10.1016/j.trsl.2012.05.003openalex-snapshot
The human gut microbiome: current knowledge, challenges, and future directions
inferred← citeshttps://doi.org/10.1016/j.trsl.2016.06.002openalex-snapshot
The gut microbiota and inflammatory bowel diseases
inferred← citeshttps://doi.org/10.1016/j.ttbdis.2020.101535openalex-snapshot
Within-population diversity of bacterial microbiomes in winter ticks (Dermacentor albipictus)
inferred← citeshttps://doi.org/10.1016/j.watres.2014.11.024openalex-snapshot
Molecular analysis of single room humidifier bacteriology
inferred← citeshttps://doi.org/10.1016/j.watres.2019.01.002openalex-snapshot
Diagnosing water treatment critical control points for cyanobacterial removal: Exploring benefits of combined microscopy, next-generation sequencing, and cell integrity methods
inferred← citeshttps://doi.org/10.1016/j.watres.2020.116223openalex-snapshot
Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification
inferred← citeshttps://doi.org/10.1016/j.wroa.2022.100157openalex-snapshot
Ammonia oxidation by novel “Candidatus Nitrosacidococcus urinae” is sensitive to process disturbances at low pH and to iron limitation at neutral pH
inferred← citeshttps://doi.org/10.1016/j.xcrm.2026.102846openalex-snapshot
Type I interferon signaling in hematopoietic cells impairs neutrophil antibacterial function in the middle ear during viral co-infection
inferred← citeshttps://doi.org/10.1016/s2095-3119(15)61230-8openalex-snapshot
Long-term rice-rice-green manure rotation changing the microbial communities in typical red paddy soil in South China
inferred← citeshttps://doi.org/10.1017/9781107707399.015openalex-snapshot
Phylogenetic Techniques in Geomicrobiology
inferred← citeshttps://doi.org/10.1021/acs.est.6b03108openalex-snapshot
Bacterial Diversity in Ships’ Ballast Water, Ballast-Water Exchange, and Implications for Ship-Mediated Dispersal of Microorganisms
inferred← citeshttps://doi.org/10.1021/acs.est.6b06064openalex-snapshot
Longitudinal and Source-to-Tap New Orleans, LA, U.S.A. Drinking Water Microbiology
inferred← citeshttps://doi.org/10.1021/acs.est.7b01518openalex-snapshot
Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning
inferred← citeshttps://doi.org/10.1021/acsinfocus.7e5035openalex-snapshot
Statistical Data Analysis of Microbiomes and Metabolomics
inferred← citeshttps://doi.org/10.1021/es203748bopenalex-snapshot
Toluene Depletion in Produced Oil Contributes to Souring Control in a Field Subjected to Nitrate Injection
inferred← citeshttps://doi.org/10.1021/es400341bopenalex-snapshot
Long-term Operation of Microbial Electrosynthesis Systems Improves Acetate Production by Autotrophic Microbiomes
inferred← citeshttps://doi.org/10.1021/es500763eopenalex-snapshot
Carbon Dioxide and Hydrogen Sulfide Associations with Regional Bacterial Diversity Patterns in Microbially Induced Concrete Corrosion
inferred← citeshttps://doi.org/10.1029/2020jg006209openalex-snapshot
Biogeochemical Gradients in a Serpentinization‐Influenced Aquifer: Implications for Gas Exchange Between the Subsurface and Atmosphere
inferred← citeshttps://doi.org/10.1038/ajg.2014.73openalex-snapshot
Analyzing the Human Microbiome: A “How To” guide for Physicians
inferred← citeshttps://doi.org/10.1038/ismej.2011.187openalex-snapshot
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences
inferred← citeshttps://doi.org/10.1038/ismej.2012.102openalex-snapshot
Secondary structure improves OTU assignments of 16S rRNA gene sequences
inferred← citeshttps://doi.org/10.1038/ismej.2013.188openalex-snapshot
Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians
inferred← citeshttps://doi.org/10.1038/ismej.2013.65openalex-snapshot
Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges
inferred← citeshttps://doi.org/10.1038/ismej.2014.117openalex-snapshot
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
inferred← citeshttps://doi.org/10.1038/ismej.2014.139openalex-snapshot
Disturbance and temporal partitioning of the activated sludge metacommunity
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