Diversity at low abundance: The phenomenon of the rare bacterial biosphere

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

(2015) Mohamed Mysara et al.   BMC BIOINFORMATICS

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

(2015) Justyna Połka et al.   FOOD MICROBIOLOGY

Diversity of Lake Ladoga (Russia) bacterial plankton inferred from 16S rRNA gene pyrosequencing: An emphasis on picocyanobacteria

(2015) Maria Skopina et al.   JOURNAL OF GREAT LAKES RESEARCH

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity

(2015) Zachary T. Aanderud et al.   Frontiers in Microbiology

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Ecology: Finding Structure in the Rare Biosphere

(2014) Charles Bachy et al.   CURRENT BIOLOGY

Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams

(2014) Linda Wilhelm et al.   ENVIRONMENTAL MICROBIOLOGY

‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters

(2014) Caroline Sauret et al.   ENVIRONMENTAL POLLUTION

Probing environmental DNA reveals circum-Baltic presence and diversity of chlorophyll a/b-containing filamentous cyanobacteria (genus Prochlorothrix)

(2014) Nataliya Velichko et al.   HYDROBIOLOGIA

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Amphibian skin may select for rare environmental microbes

(2014) Jenifer B Walke et al.   ISME Journal

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities

(2014) Minseok Kim et al.   JOURNAL OF MICROBIOLOGY

Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea

(2014) Grazia Marina Quero et al.   Marine Genomics

Bacterial Diversity Assessment in Antarctic Terrestrial and Aquatic Microbial Mats: A Comparison between Bidirectional Pyrosequencing and Cultivation

(2014) Bjorn Tytgat et al.   PLoS One

Molecular Characterization and Analysis of a Novel Protein Disulfide Isomerase-Like Protein of Eimeria tenella

(2014) Hongyu Han et al.   PLoS One

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Winter bloom of a rare betaproteobacterium in the Arctic Ocean

(2014) Laura Alonso-Sáez et al.   Frontiers in Microbiology

The phenomenon of microbial uncultivability

(2013) SS Epstein   CURRENT OPINION IN MICROBIOLOGY

Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

(2013) Albert Leopold Müller et al.   ISME Journal

Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides

(2013) Mauricio Rodriguez-Lanetty et al.   MOLECULAR ECOLOGY

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters

(2013) M. Hugoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Culturing captures members of the soil rare biosphere

(2012) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Low sequencing efforts bias analyses of shared taxa in microbial communities

(2012) Leandro N. Lemos et al.   FOLIA MICROBIOLOGICA

‘Sponge-specific’ bacteria are widespread (but rare) in diverse marine environments

(2012) Michael W Taylor et al.   ISME Journal

Targeted recovery of novel phylogenetic diversity from next-generation sequence data

(2012) Michael D J Lynch et al.   ISME Journal

Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years

(2012) Júlia Rosa de Rezende et al.   ISME Journal

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

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance

(2011) Johanna Sjöstedt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing

(2011) Guillaume Lentendu et al.   FUNGAL DIVERSITY

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

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

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Activity of abundant and rare bacteria in a coastal ocean

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

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

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

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Experimental Choices and Analysis Noise on Surveys of the "Rare Biosphere"

(2009) T. J. Hamp et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hypotheses on the role of the protistan rare biosphere in a changing world

(2009) DA Caron et al.   AQUATIC MICROBIAL ECOLOGY

Defining the healthy "core microbiome" of oral microbial communities

(2009) Egija Zaura et al.   BMC MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Constant Flux of Diverse Thermophilic Bacteria into the Cold Arctic Seabed

(2009) C. Hubert et al.   SCIENCE

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

(2008) M. S. Elshahed et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

Scratching the surface of the rare biosphere with ribosomal sequence tag primers

(2008) Josh D. Neufeld et al.   FEMS MICROBIOLOGY LETTERS