The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics

(2013) G. Dubourg et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows

(2012) Juliane Günther et al.   BMC GENOMICS

Genomic sequence analysis and characterization of Sneathia amnii sp. nov

(2012) Michael D Harwich et al.   BMC GENOMICS

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

(2012) Charles K. Lee et al.   PLoS One

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Vaginal microbiome of reproductive-age women

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

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Use of a D-optimal mixture design to estimate the effects of diverse chloride salts on the growth parameters of Lactobacillus pentosus

(2009) F.N. Arroyo-López et al.   FOOD MICROBIOLOGY

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

High GC Contents of Primer 5′-End Increases Reaction Efficiency in Polymerase Chain Reaction

(2009) Naoki Shinoda et al.   NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS

PCR detection of nitrite reductase genes (nirK and nirS) and use of active consortia of constructed ternary adherent staphylococcal cultures via mixture design for a denitrification process

(2009) Besma Harbi et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Use of a D-optimal design with constrains to quantify the effects of the mixture of sodium, potassium, calcium and magnesium chloride salts on the growth parameters of Saccharomyces cerevisiae

(2008) J. Bautista-Gallego et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Predicting failure rate of PCR in large genomes

(2008) Reidar Andreson et al.   NUCLEIC ACIDS RESEARCH