Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI

(2019) Rebecca Vongsa et al.   BMC MICROBIOLOGY

Clostridioides difficile contamination in the environment of a clinical microbiology laboratory and laboratory workers

(2019) E. Reigadas et al.   CLINICAL MICROBIOLOGY AND INFECTION

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

Author Correction: Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Association Between Bacteremia From Specific Microbes and Subsequent Diagnosis of Colorectal Cancer

(2018) Thomas N.Y. Kwong et al.   GASTROENTEROLOGY

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression

(2018) Smruti Pushalkar et al.   Cancer Discovery

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

The urinary microbiome associated with bladder cancer

(2018) Viljemka Bučević Popović et al.   Scientific Reports

The immune microenvironment in vulvar (pre)cancer: review of literature and implications for immunotherapy

(2018) Ziena Abdulrahman et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin

(2018) Zhen He et al.   GUT

The oral microbiota: dynamic communities and host interactions

(2018) Richard J. Lamont et al.   NATURE REVIEWS MICROBIOLOGY

Community profiling of the urinary microbiota: considerations for low-biomass samples

(2018) Lisa Karstens et al.   Nature Reviews Urology

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Reply to Meisel et al.

(2017) Patrick L.J.M. Zeeuwen et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling

(2017) Stefan A. Boers et al.   Scientific Reports

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

(2017) Anna Vesty et al.   PLoS One

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

(2017) Yenkai Lim et al.   Scientific Reports

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies

(2016) Emmanouil Angelakis et al.   Scientific Reports

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

(2015) Fiona Fouhy et al.   PLoS One

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Processing faecal samples: a step forward for standards in microbial community analysis

(2014) Alba Santiago et al.   BMC MICROBIOLOGY

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment

(2013) Aleksandar D. Kostic et al.   Cell Host & Microbe

Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

(2013) E. E. Hilt et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Evidence of Uncultivated Bacteria in the Adult Female Bladder

(2012) A. J. Wolfe et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

(2012) Nastassia V. Patin et al.   MICROBIAL ECOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Visualizing non-metric similarities in multiple maps

(2011) Laurens van der Maaten et al.   MACHINE LEARNING

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Review of squamous premalignant vulvar lesions

(2008) H.P. van de Nieuwenhof et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY