TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

(2018) Søren M Karst et al.   NATURE BIOTECHNOLOGY

Ananke: temporal clustering reveals ecological dynamics of microbial communities

(2017) Michael W. Hall et al.   PeerJ

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

(2017) Alexandra M. Linz et al.   mSphere

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI

(2017) Joshua J. Hamilton et al.   mSystems

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

(2016) Josef Wagner et al.   BMC MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Biogeography of globally distributed bacteria in temperate and boreal Québec lakes as revealed by tag pyrosequencing of 16S rRNA genes

(2015) MT Cottrell et al.   AQUATIC MICROBIAL ECOLOGY

Bacterial diversity along a 2600 km river continuum

(2015) Domenico Savio et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

(2015) Jason Nicholas Woodhouse et al.   ISME Journal

Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb)

(2015) Aram Mikaelyan et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

MiDAS: the field guide to the microbes of activated sludge

(2015) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River

(2015) Clara Ruiz-González et al.   Frontiers in Microbiology

A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan

(2015) Ryan J. Newton et al.   Frontiers in Microbiology

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

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

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

Catchment-scale biogeography of riverine bacterioplankton

(2014) Daniel S Read et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

(2014) Henning Seedorf et al.   PeerJ

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

(2013) Sarah P. Preheim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

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

Lineage-Specific Responses of Microbial Communities to Environmental Change

(2012) Nicholas D. Youngblut et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier

(2012) Irene LG Newton et al.   BMC MICROBIOLOGY

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

(2012) Sarahi L Garcia et al.   ISME Journal

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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

Variability of Prokaryotic Community Structure in a Drinking Water Reservoir (Marathonas, Greece)

(2011) Despoina S. Lymperopoulou et al.   MICROBES AND ENVIRONMENTS

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

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