Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

(2021) Weibing Xun et al.   Microbiome

Reproducibility: expect less of the scientific paper

(2021) Olavo B. Amaral et al.   NATURE

Global homogenization of the structure and function in the soil microbiome of urban greenspaces

(2021) Manuel Delgado-Baquerizo et al.   Science Advances

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

(2020) Jasmine Chong et al.   Nature Protocols

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

(2020) Haris Zafeiropoulos et al.   GigaScience

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

(2020) Marius Welzel et al.   BMC BIOINFORMATICS

Moving to a World Beyond “p 

(2019) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

What Have We (Not) Learnt from Millions of Scientific Papers with P Values?

(2019) John P. A. Ioannidis   AMERICAN STATISTICIAN

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Systematic processing of ribosomal RNA gene amplicon sequencing data

(2019) Julien Tremblay et al.   GigaScience

Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy

(2018) Casey Chen et al.   ISME Journal

The Proposal to Lower P Value Thresholds to .005

(2018) John P. A. Ioannidis   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Sinking particles promote vertical connectivity in the ocean microbiome

(2018) Mireia Mestre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

(2018) Patrick D. Schloss   mBio

Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

(2018) Christopher J. Stewart et al.   PeerJ

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

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

(2018) Jacob T. Nearing et al.   PeerJ

The Microbiome and Risk for Obesity and Diabetes

(2017) Anthony L. Komaroff   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

(2017) Mohamed Mysara et al.   GigaScience

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

(2017) Sarah L. Westcott et al.   mSphere

Statisticians issue warning over misuse of P values

(2016) Monya Baker   NATURE

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

The fickle P value generates irreproducible results

(2015) Lewis G Halsey et al.   NATURE METHODS

The global ocean microbiome

(2015) M. A. Moran   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

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

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

(2014) Ali May et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

(2014) Thomas S. B. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

Changes in Abundance of Oral Microbiota Associated with Oral Cancer

(2014) Brian L. Schmidt et al.   PLoS One

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

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

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

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

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

(2011) Wim Crielaard et al.   BMC Medical Genomics

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

(2008) P.C.Y. Woo et al.   CLINICAL MICROBIOLOGY AND INFECTION