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De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Seamless R and C++ Integration with Rcpp
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Comparison of the predicted and observed secondary structure of T4 phage lysozyme
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Advancing Our Understanding of the Human Microbiome Using QIIME
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Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
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Pyrosequencing enumerates and contrasts soil microbial diversity
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Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
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Defining seasonal marine microbial community dynamics
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Secondary structure improves OTU assignments of 16S rRNA gene sequences
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.2676openalex-snapshot
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
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QIIME allows analysis of high-throughput community sequencing data
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A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btr381openalex-snapshot
UCHIME improves sensitivity and speed of chimera detection
inferredcites →https://doi.org/10.1093/bioinformatics/bts552openalex-snapshot
Comparing clustering and pre-processing in taxonomy analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu085openalex-snapshot
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
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/gkp285openalex-snapshot
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
inferredcites →https://doi.org/10.1093/nar/gkr349openalex-snapshot
ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
inferredcites →https://doi.org/10.1093/nar/gkt241openalex-snapshot
Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units
inferredcites →https://doi.org/10.1111/1462-2920.12610openalex-snapshot
Limits to robustness and reproducibility in the demarcation of operational taxonomic units
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A new method for non‐parametric multivariate analysis of variance
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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.00342-13openalex-snapshot
Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
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
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Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil
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Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile
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Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis
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Alignment and clustering of phylogenetic markers - implications for microbial diversity studies
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Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows
inferredcites →https://doi.org/10.1186/s40168-015-0081-xopenalex-snapshot
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
inferredcites →https://doi.org/10.1186/s40168-015-0098-1openalex-snapshot
Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
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.pcbi.1003594openalex-snapshot
Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
inferredcites →https://doi.org/10.1371/journal.pone.0027310openalex-snapshot
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
inferredcites →https://doi.org/10.1371/journal.pone.0070837openalex-snapshot
A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs
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R: A Language and Environment for Statistical Computing
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inferredcites →https://doi.org/10.48550/arxiv.1403.2805openalex-snapshot
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VSEARCH: versatile open-source tool for microbiome analysis
inferredcites →https://doi.org/10.7717/peerj.545openalex-snapshot
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
inferredcites →https://doi.org/10.7717/peerj.593openalex-snapshot
Swarm: robust and fast clustering method for amplicon-based studies
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Isolation of Cultivation-Resistant Oomycetes, First Detected as Amplicon Sequences, from Roots of Herbicide-Terminated Winter Rye
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Responses of Bacterial and Fungal Community Structure to Different Rates of 1,3-Dichloropropene Fumigation
inferred← citeshttps://doi.org/10.1097/cm9.0000000000000871openalex-snapshot
A guide to human microbiome research: study design, sample collection, and bioinformatics analysis
inferred← citeshttps://doi.org/10.1099/jmm.0.001756openalex-snapshot
Microbiome depiction through user-adapted bioinformatic pipelines and parameters
inferred← citeshttps://doi.org/10.1101/2020.08.09.243188openalex-snapshot
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
inferred← citeshttps://doi.org/10.1101/2020.10.05.326504openalex-snapshot
RESCRIPt: Reproducible sequence taxonomy reference database management for the masses
inferred← citeshttps://doi.org/10.1101/2021.03.23.436606openalex-snapshot
A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution
inferred← citeshttps://doi.org/10.1101/2021.06.16.448699openalex-snapshot
Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies
inferred← citeshttps://doi.org/10.1101/2021.08.09.455616openalex-snapshot
OTUs clustering should be avoided for defining oral microbiome
inferred← citeshttps://doi.org/10.1101/2021.08.23.457424openalex-snapshot
The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO 2 fixation
inferred← citeshttps://doi.org/10.1101/2022.07.27.501757openalex-snapshot
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
inferred← citeshttps://doi.org/10.1101/2024.11.06.622322openalex-snapshot
Microbiome impact of ibezapolstat and other Clostridioides difficile infection relevant antibiotics using humanized mice
inferred← citeshttps://doi.org/10.1101/286526openalex-snapshot
A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing
inferred← citeshttps://doi.org/10.1101/604314openalex-snapshot
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
inferred← citeshttps://doi.org/10.1109/ssci51031.2022.10022184openalex-snapshot
Semi-supervised and Incremental VSEARCH for Metagenomic Classification
inferred← citeshttps://doi.org/10.1109/tcbb.2023.3253138openalex-snapshot
Comparison of Methods for Biological Sequence Clustering
inferred← citeshttps://doi.org/10.1111/1755-0998.12692openalex-snapshot
PipeCraft: Flexible open‐source toolkit for bioinformatics analysis of custom high‐throughput amplicon sequencing data
inferred← citeshttps://doi.org/10.1111/1755-0998.13329openalex-snapshot
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species
inferred← citeshttps://doi.org/10.1111/1755-0998.13340openalex-snapshot
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences
inferred← citeshttps://doi.org/10.1111/1755-0998.70090openalex-snapshot
MetaZooGene Intercalibration Experiment ( MZG ‐ ICE ): Metabarcoding Marine Zooplankton Diversity of the Global Ocean
inferred← citeshttps://doi.org/10.1111/1758-2229.13209openalex-snapshot
Consistent spatial patterns in microbial taxa of red squirrel gut microbiomes
inferred← citeshttps://doi.org/10.1111/2041-210x.13316openalex-snapshot
ReClustOR: a re‐clustering tool using an open‐reference method that improves operational taxonomic unit definition
inferred← citeshttps://doi.org/10.1111/ele.70031openalex-snapshot
Central Taxa Are Keystone Microbes During Early Succession
inferred← citeshttps://doi.org/10.1111/jav.02083openalex-snapshot
Experimental old nest material predicts hoopoe Upupa epops eggshell and uropygial gland microbiota
inferred← citeshttps://doi.org/10.1111/jpy.12763openalex-snapshot
A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome
inferred← citeshttps://doi.org/10.1111/jvim.16824openalex-snapshot
The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective
inferred← citeshttps://doi.org/10.1111/mec.14478openalex-snapshot
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
inferred← citeshttps://doi.org/10.1111/mec.14542openalex-snapshot
The impact of bacteriophages on phyllosphere bacterial abundance and composition
inferred← citeshttps://doi.org/10.1111/nph.14752openalex-snapshot
Moving beyond de novo clustering in fungal community ecology
inferred← citeshttps://doi.org/10.1111/omi.12434openalex-snapshot
Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis
inferred← citeshttps://doi.org/10.1111/prd.12359openalex-snapshot
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting
inferred← citeshttps://doi.org/10.1111/tpj.14170openalex-snapshot
Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions
inferred← citeshttps://doi.org/10.1126/science.add5787openalex-snapshot
Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target
inferred← citeshttps://doi.org/10.1128/aac.01604-24openalex-snapshot
The impact of ibezapolstat and other Clostridioides difficile infection-relevant antibiotics on the microbiome of humanized mice
inferred← citeshttps://doi.org/10.1128/aem.01756-16openalex-snapshot
Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: a Cross-Sectional Cohort Study in Malawi
inferred← citeshttps://doi.org/10.1128/aem.02343-19openalex-snapshot
Reintroducing mothur: 10 Years Later
inferred← citeshttps://doi.org/10.1128/aem.02576-16openalex-snapshot
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing
inferred← citeshttps://doi.org/10.1128/aem.02627-17openalex-snapshot
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
inferred← citeshttps://doi.org/10.1128/mbio.00201-16openalex-snapshot
Status of the Archaeal and Bacterial Census: an Update
inferred← citeshttps://doi.org/10.1128/mbio.01018-16openalex-snapshot
Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome
inferred← citeshttps://doi.org/10.1128/mra.01238-24openalex-snapshot
clustur: an R package for clustering features using sparse distance matrices
inferred← citeshttps://doi.org/10.1128/msphere.00336-23openalex-snapshot
Machine learning classification by fitting amplicon sequences to existing OTUs
inferred← citeshttps://doi.org/10.1128/msphere.00410-18openalex-snapshot
Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
inferred← citeshttps://doi.org/10.1128/msphere.00916-21openalex-snapshot
OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs
inferred← citeshttps://doi.org/10.1128/mspheredirect.00073-17openalex-snapshot
OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
inferred← citeshttps://doi.org/10.1128/msystems.00003-15openalex-snapshot
Open-Source Sequence Clustering Methods Improve the State Of the Art
inferred← citeshttps://doi.org/10.1128/msystems.00027-16openalex-snapshot
Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods
inferred← citeshttps://doi.org/10.1128/msystems.00032-16openalex-snapshot
16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
inferred← citeshttps://doi.org/10.1128/msystems.00300-21openalex-snapshot
Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection
inferred← citeshttps://doi.org/10.1128/spectrum.00344-21openalex-snapshot
The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients
inferred← citeshttps://doi.org/10.1128/spectrum.00362-23openalex-snapshot
Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment
inferred← citeshttps://doi.org/10.1155/ijm/6677609openalex-snapshot
Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety
inferred← citeshttps://doi.org/10.1163/23524588-20230057openalex-snapshot
Effects of black soldier fly meal feeding on rainbow trout gut microbiota, immune-related gene expression, and Lactococcus petauri resistance
inferred← citeshttps://doi.org/10.1177/0036850419881855openalex-snapshot
High-throughput DNA sequencing technologies for water and wastewater analysis
inferred← citeshttps://doi.org/10.1186/s12859-018-2349-1openalex-snapshot
GeFaST: An improved method for OTU assignment by generalising Swarm’s fastidious clustering approach
inferred← citeshttps://doi.org/10.1186/s12859-019-2663-2openalex-snapshot
SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
inferred← citeshttps://doi.org/10.1186/s12859-019-2965-4openalex-snapshot
iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis
inferred← citeshttps://doi.org/10.1186/s12859-020-03666-4openalex-snapshot
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
inferred← citeshttps://doi.org/10.1186/s12859-020-03829-3openalex-snapshot
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
inferred← citeshttps://doi.org/10.1186/s12859-021-04232-2openalex-snapshot
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
inferred← citeshttps://doi.org/10.1186/s12890-023-02789-7openalex-snapshot
Restoring the epigenetic landscape of lung microbiome: potential therapeutic approach for chronic respiratory diseases
inferred← citeshttps://doi.org/10.1186/s12890-025-03795-7openalex-snapshot
Airway Candida diversity in COPD patients and its differential stimulatory effects on lung inflammation in mice
inferred← citeshttps://doi.org/10.1186/s13059-018-1450-0openalex-snapshot
HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
inferred← citeshttps://doi.org/10.1186/s40168-017-0314-2openalex-snapshot
A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
inferred← citeshttps://doi.org/10.1186/s40168-019-0743-1openalex-snapshot
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
inferred← citeshttps://doi.org/10.1186/s40168-020-00957-zopenalex-snapshot
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
inferred← citeshttps://doi.org/10.1186/s40168-021-01059-0openalex-snapshot
Identifying biases and their potential solutions in human microbiome studies
inferred← citeshttps://doi.org/10.1186/s40748-021-00131-9openalex-snapshot
Methods for exploring the faecal microbiome of premature infants: a review
inferred← citeshttps://doi.org/10.12688/f1000research.9227.2openalex-snapshot
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005518openalex-snapshot
ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009581openalex-snapshot
RESCRIPt: Reproducible sequence taxonomy reference database management
inferred← citeshttps://doi.org/10.1371/journal.pone.0169563openalex-snapshot
Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics
inferred← citeshttps://doi.org/10.1371/journal.pone.0171017openalex-snapshot
Microbiome sharing between children, livestock and household surfaces in western Kenya
inferred← citeshttps://doi.org/10.1371/journal.pone.0172811openalex-snapshot
Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis
inferred← citeshttps://doi.org/10.1371/journal.pone.0222763openalex-snapshot
Enriched taxa were found among the gut microbiota of centenarians in East China
inferred← citeshttps://doi.org/10.1371/journal.pone.0224444openalex-snapshot
Latitudinal gradient of cyanobacterial diversity in tidal flats
inferred← citeshttps://doi.org/10.1371/journal.pone.0243241openalex-snapshot
CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
inferred← citeshttps://doi.org/10.1371/journal.pone.0253502openalex-snapshot
Clinical utility of subgingival plaque-specific bacteria in salivary microbiota for detecting periodontitis
inferred← citeshttps://doi.org/10.15368/theses.2021.42openalex-snapshot
LOTUS: A Web-Based Computational Tool for the Preliminary Investigation of a Novel MST Method Utilizing a Library of 16S rRNA Bacteroides OTUs
inferred← citeshttps://doi.org/10.15389/agrobiology.2022.2.222engopenalex-snapshot
MICROBIOTA AND REPRODUCTION IN AGRICULTURAL MAMMALS(review)
inferred← citeshttps://doi.org/10.15389/agrobiology.2022.2.222rusopenalex-snapshot
МИКРОБИОТА И РЕПРОДУКЦИЯ У СЕЛЬСКОХОЗЯЙСТВЕННЫХ ВИДОВ МЛЕКОПИТАЮЩИХ (обзор)
inferred← citeshttps://doi.org/10.18174/440534openalex-snapshot
Causes and consequences of soil bacterial rarity
inferred← citeshttps://doi.org/10.18174/575174openalex-snapshot
Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
inferred← citeshttps://doi.org/10.18632/oncotarget.10597openalex-snapshot
Deciphering bacterial community changes in zucker diabetic fatty rats based on 16S rRNA gene sequences analysis
inferred← citeshttps://doi.org/10.18632/oncotarget.20477openalex-snapshot
Polysaccharides from Chrysanthemum morifolium Ramat ameliorate colitis rats by modulating the intestinal microbiota community
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2370012/v1openalex-snapshot
Multi-omics analysis to examine microbiota and metabolites in the colon of different breeds of swine
inferred← citeshttps://doi.org/10.21203/rs.3.rs-304542/v1openalex-snapshot
The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients
inferred← citeshttps://doi.org/10.21203/rs.3.rs-923879/v1openalex-snapshot
Sporamin Intervention Altered the Gut Microbiome and Tumor Tissue Transcriptome in Mice Intraperitoneally Xenografted With the Human Colorectal Carcinoma LoVo Cells
inferred← citeshttps://doi.org/10.21533/scjournal.v9i1.184openalex-snapshot
A De Novo Clustering Method: Snowball for Assigning 16S Operational Taxonomic Units
inferred← citeshttps://doi.org/10.21533/scjournal.v9i1.186openalex-snapshot
Genomic Signal Processing Techniques for Taxonomy Prediction
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