Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial Dysbiosis Is Associated with Human Breast Cancer

(2014) Caiyun Xuan et al.   PLoS One

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Application of special oligotrophic media for cultivation of bacterial communities originated from ultrapure water

(2013) Zsuzsa Kéki et al.   ACTA MICROBIOLOGICA ET IMMUNOLOGICA HUNGARICA

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates

(2013) Zongxin Ling et al.   BMC GENOMICS

Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome

(2013) Ami S. Bhatt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Detection of Transient Bacteraemia following Dental Extractions by 16S rDNA Pyrosequencing: A Pilot Study

(2013) Alfonso Benítez-Páez et al.   PLoS One

Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status

(2013) William G. Branton et al.   PLoS One

Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

(2013) Joanna S. Kuehn et al.   PLoS One

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya

(2013) Yury M. Shtarkman et al.   PLoS One

Mining RNA–Seq Data for Infections and Contaminations

(2013) Thomas Bonfert et al.   PLoS One

Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota

(2013) Philip Cooper et al.   PLoS One

Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

(2013) N. DeLeon-Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering

(2013) Girish Srinivas et al.   Nature Communications

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing

(2013) Lisa Oberauner et al.   Scientific Reports

Bacterial communities and species-specific associations with the mucus of Brazilian coral species

(2013) Camila Carlos et al.   Scientific Reports

Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

(2013) Xin-Yue Cheng et al.   Scientific Reports

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

(2013) Leopoldo N Segal et al.   Microbiome

Longitudinal analysis of the lung microbiome in lung transplantation

(2012) Klaudyna Borewicz et al.   FEMS MICROBIOLOGY LETTERS

New perspectives on viable microbial communities in low-biomass cleanroom environments

(2012) Parag Vaishampayan et al.   ISME Journal

A global survey of the bacteria within earthworm nephridia

(2012) Seana K. Davidson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Multiple Sources of Contamination in Samples from Patients Reported to Have XMRV Infection

(2012) Mary F. Kearney et al.   PLoS One

A Longitudinal Study of Streptococcus pneumoniae Carriage in a Cohort of Infants and Their Mothers on the Thailand-Myanmar Border

(2012) Paul Turner et al.   PLoS One

Midgut Microbiota of the Malaria Mosquito Vector Anopheles gambiae and Interactions with Plasmodium falciparum Infection

(2012) Anne Boissière et al.   PLoS Pathogens

Bacterial communities in an ultrapure water containing storage tank of a power plant

(2011) Veronika Bohus et al.   ACTA MICROBIOLOGICA ET IMMUNOLOGICA HUNGARICA

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept

(2011) J. Amar et al.   DIABETOLOGIA

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

(2011) Valerie J McKenzie et al.   ISME Journal

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

An Efficient Strategy for Broad-Range Detection of Low Abundance Bacteria without DNA Decontamination of PCR Reagents

(2011) Shy-Shin Chang et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Development of an ethidium monoazide-enhanced internally controlled universal 16S rDNA real-time polymerase chain reaction assay for detection of bacterial contamination in platelet concentrates

(2011) Poorvi Patel et al.   TRANSFUSION

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One

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

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

Reagent decontamination to eliminate false-positives in Escherichia coli qPCR

(2008) Sarah S. Silkie et al.   JOURNAL OF MICROBIOLOGICAL METHODS