Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data

(2023) Yiwen Wang et al.   BRIEFINGS IN BIOINFORMATICS

Advances in the oral microbiota and rapid detection of oral infectious diseases

(2023) Xuan Xiao et al.   Frontiers in Microbiology

MKMR: a multi-kernel machine regression model to predict health outcomes using human microbiome data

(2023) Bing Li et al.   BRIEFINGS IN BIOINFORMATICS

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

(2023) Dileep Kishore et al.   mSystems

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

(2022) Margaret D Weinroth et al.   JOURNAL OF ANIMAL SCIENCE

In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs

(2022) Alba Regueira-Iglesias et al.   Frontiers in Cellular and Infection Microbiology

A Simultaneous Feature Selection and Compositional Association Test for Detecting Sparse Associations in High-Dimensional Metagenomic Data

(2022) Andrew L. Hinton et al.   Frontiers in Microbiology

Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery

(2022) Concepcion Sanchez-Cid et al.   Biomolecules

Investigating differential abundance methods in microbiome data: A benchmark study

(2022) Marco Cappellato et al.   PLoS Computational Biology

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

(2021) Lingjing Jiang et al.   BIOMETRICS

Robust covariance estimation for high‐dimensional compositional data with application to microbial communities analysis

(2021) Yong He et al.   STATISTICS IN MEDICINE

Salivary Microbiome Variation in Early Childhood Caries of Children 3–6 Years of Age and Its Association With Iron Deficiency Anemia and Extrinsic Black Stain

(2021) Rui Han et al.   Frontiers in Cellular and Infection Microbiology

Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences

(2021) Ze-Gang Wei et al.   Frontiers in Microbiology

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters

(2021) Rodrigo García-López et al.   Genes

Using machine learning approaches for multi-omics data analysis: A review

(2021) Parminder S. Reel et al.   BIOTECHNOLOGY ADVANCES

Flexible co‐data learning for high‐dimensional prediction

(2021) Mirrelijn M. Nee et al.   STATISTICS IN MEDICINE

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

(2021) Zhengqiao Zhao et al.   PLoS Computational Biology

Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases

(2021) Charlotte Thomas et al.   Diagnostics

Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse

(2021) Senlin Liu et al.   PLoS One

Multivariable association discovery in population-scale meta-omics studies

(2021) Himel Mallick et al.   PLoS Computational Biology

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation

(2021) Michael Greenacre et al.   Frontiers in Microbiology

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

(2020) Jesse R. Willis et al.   Microorganisms

A novel deep learning method for predictive modeling of microbiome data

(2020) Ye Wang et al.   BRIEFINGS IN BIOINFORMATICS

Species-level evaluation of the human respiratory microbiome

(2020) Olufunmilola Ibironke et al.   GigaScience

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

(2020) Ana Elena Pérez-Cobas et al.   Microbial Genomics

Oral Microbiota Composition Predicts Early Childhood Caries Onset

(2020) A. Grier et al.   JOURNAL OF DENTAL RESEARCH

Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting

(2020) Egija Zaura et al.   PERIODONTOLOGY 2000

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Intra‐oral single site comparisons of periodontal and peri‐implant microbiota in health and disease

(2019) Xiao‐Lin Yu et al.   CLINICAL ORAL IMPLANTS RESEARCH

The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease

(2019) Alex M. Valm   JOURNAL OF MOLECULAR BIOLOGY

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis

(2019) Anna Lundmark et al.   Frontiers in Cellular and Infection Microbiology

Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation

(2019) Aneesha Acharya et al.   Frontiers in Cellular and Infection Microbiology

Rarefaction, Alpha Diversity, and Statistics

(2019) Amy D. Willis   Frontiers in Microbiology

Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

(2019) Duo Jiang et al.   Frontiers in Genetics

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

(2018) Ehsaneddin Asgari et al.   BIOINFORMATICS

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Artificial Intelligence in Cardiology

(2018) Kipp W. Johnson et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Oral microbiota reveals signs of acculturation in Mexican American women

(2018) Kristi L. Hoffman et al.   PLoS One

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

(2018) Junyi Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model

(2018) Jian Xiao et al.   Frontiers in Microbiology

COREMIC: a web-tool to search for a niche associated CORE MICrobiome

(2018) Richard R. Rodrigues et al.   PeerJ

Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation

(2018) Jessica D. Forbes et al.   Computational and Structural Biotechnology Journal

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study

(2018) He Xu et al.   Frontiers in Microbiology

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing

(2018) Zhifang Zhou et al.   PeerJ

Batch effects correction for microbiome data with Dirichlet-multinomial regression

(2018) Zhenwei Dai et al.   BIOINFORMATICS

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

On the ecosystemic network of saliva in healthy young adults

(2017) Egija Zaura et al.   ISME Journal

Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing

(2017) Ignacio Sanz-Martin et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Dental caries and periodontal diseases in the ageing population: call to action to protect and enhance oral health and well-being as an essential component of healthy ageing - Consensus report of group 4 of the joint EFP/ORCA workshop on the boundaries be

(2017) Maurizio S. Tonetti et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Deciphering Diversity Indices for a Better Understanding of Microbial Communities

(2017) Bo-Ra Kim et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Subgingival dysbiosis in smoker and non-smoker patients with chronic periodontitis

(2017) Lorena Coretti et al.   Molecular Medicine Reports

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study

(2017) Sébastien Boutin et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

How conserved are the conserved 16S-rRNA regions?

(2017) Marcel Martinez-Porchas et al.   PeerJ

A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology

(2017) S. E. Adams et al.   Scientific Reports

Intricacies of assessing the human microbiome in epidemiologic studies

(2016) Courtney K. Robinson et al.   ANNALS OF EPIDEMIOLOGY

MetaCoMET: a web platform for discovery and visualization of the core microbiome

(2016) Yi Wang et al.   BIOINFORMATICS

The oral microbiome – an update for oral healthcare professionals

(2016) M. Kilian et al.   BRITISH DENTAL JOURNAL

Analysis and Interpretation of the Human Microbiome

(2016) James J. Ashton et al.   INFLAMMATORY BOWEL DISEASES

A family of interaction-adjusted indices of community similarity

(2016) Thomas Sebastian Benedikt Schmidt et al.   ISME Journal

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

(2016) Jianye Zhou et al.   PLoS One

Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study

(2016) Toru Takeshita et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota

(2015) Fei Teng et al.   Cell Host & Microbe

Beyond microbial community composition: functional activities of the oral microbiome in health and disease

(2015) Ana E. Duran-Pinedo et al.   MICROBES AND INFECTION

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A Filifactor alocis-centered co-occurrence group associates with periodontitis across different oral habitats

(2015) Hui Chen et al.   Scientific Reports

Subgingival microbiome in patients with healthy and ailing dental implants

(2015) Hui Zheng et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

qgraph: Network Visualizations of Relationships in Psychometric Data

(2015) Sacha Epskamp et al.   Journal of Statistical Software

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals

(2015) Yukuto Sato et al.   PLoS One

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

(2015) Jeff S. Bowman et al.   PLoS One

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

(2014) P. J. McMurdie et al.   BIOINFORMATICS

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Sequencing the human microbiome in health and disease

(2013) M. J. Cox et al.   HUMAN MOLECULAR GENETICS

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation

(2013) Loreto Abusleme et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing

(2013) Mi Zhou et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A comprehensive evaluation of multicategory classification methods for microbiomic data

(2013) Alexander Statnikov et al.   Microbiome

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

(2012) Sebastian Jünemann et al.   PLoS One

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Pyrosequencing as a tool for better understanding of human microbiomes

(2012) José F. Siqueira et al.   Journal of Oral Microbiology

Saliva microbiomes distinguish caries-active from healthy human populations

(2011) Fang Yang et al.   ISME Journal

Rethinking microbial diversity analysis in the high throughput sequencing era

(2011) Leandro N. Lemos et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

(2011) Ann L. Griffen et al.   PLoS One

Classification and regression trees

(2011) Wei-Yin Loh   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Bacterial diversity in the oral cavity of 10 healthy individuals

(2010) Elisabeth M Bik et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH