The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)

(2013) F Heinrich et al.   AQUATIC MICROBIAL ECOLOGY

Substrate type drives variation in reactor microbiomes of anaerobic digesters

(2013) Wei Zhang et al.   BIORESOURCE TECHNOLOGY

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets

(2013) Lin Cai et al.   PLoS One

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

(2013) Nils Johan Fredriksson et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks

(2013) Federico M. Ibarbalz et al.   WATER RESEARCH

General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor

(2012) Taek-Seung Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

(2012) Feng Guo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Coverage evaluation of universal bacterial primers using the metagenomic datasets

(2012) Dan-Ping Mao et al.   BMC MICROBIOLOGY

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

Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies

(2012) Sotirios Vasileiadis et al.   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

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Characterizing microbial communities through space and time

(2011) Antonio Gonzalez et al.   CURRENT OPINION IN BIOTECHNOLOGY

Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing

(2011) Purnima S. Kumar 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

Bacterial community structures are unique and resilient in full-scale bioenergy systems

(2011) J. J. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale bacterial community dynamics and the taxa–time relationship within a full-scale activated sludge bioreactor

(2011) George F. Wells et al.   WATER RESEARCH

The underpinnings of the relationship of species richness with space and time

(2010) Samuel M. Scheiner et al.   ECOLOGICAL MONOGRAPHS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Bacterial community dynamics in two full-scale wastewater treatment systems with functional stability

(2010) X. Wang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Balance of Neutral and Deterministic Components in the Dynamics of Activated Sludge Floc Assembly

(2010) Joaquín M. Ayarza et al.   MICROBIAL ECOLOGY

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Temporal turnover and the maintenance of diversity in ecological assemblages

(2010) A. E. Magurran et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef 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

Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea

(2009) George F. Wells et al.   ENVIRONMENTAL MICROBIOLOGY

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Seasonal and Episodic Lake Mixing Stimulate Differential Planktonic Bacterial Dynamics

(2009) Ashley Shade et al.   MICROBIAL ECOLOGY

Nonrandom Assembly of Bacterial Populations in Activated Sludge Flocs

(2009) Joaquín M. Ayarza et al.   MICROBIAL ECOLOGY

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

(2009) Marcus J. Claesson et al.   PLoS One

How to get more out of molecular fingerprints: practical tools for microbial ecology

(2008) Massimo Marzorati et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors

(2008) Christopher J. Van Der Gast et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community dynamics in replicate membrane bioreactors – Natural reproducible fluctuations

(2008) Michael W. Falk et al.   WATER RESEARCH