Ecology and exploration of the rare biosphere

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

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

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares 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

Amphibian skin may select for rare environmental microbes

(2014) Jenifer B Walke et al.   ISME Journal

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

(2014) Andrew C Doxey et al.   ISME Journal

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Commonness and rarity in the marine biosphere

(2014) S. R. Connolly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

(2014) Y. Verastegui et al.   mBio

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

(2014) Ryan J. Williams et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean

(2013) KL Vergin et al.   AQUATIC MICROBIAL ECOLOGY

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

(2013) Andrea K. Bartram et al.   FEMS MICROBIOLOGY ECOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

(2013) Jianjun Wang et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Shifts in the Microbial Community Composition of Gulf Coast Beaches Following Beach Oiling

(2013) Ryan J. Newton et al.   PLoS One

Evidence for a persistent microbial seed bank throughout the global ocean

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

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

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Microbial community assembly, theory and rare functions

(2013) Mujalin K. Pholchan et al.   Frontiers in Microbiology

Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach

(2012) Noha Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Culturing captures members of the soil rare biosphere

(2012) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

‘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

Secondary structure improves OTU assignments of 16S rRNA gene sequences

(2012) Patrick D Schloss   ISME Journal

Unraveling assembly of stream biofilm communities

(2012) Katharina Besemer et al.   ISME Journal

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

(2012) Byron C Crump et al.   ISME Journal

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data

(2012) T. Frisli et al.   JOURNAL OF APPLIED MICROBIOLOGY

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

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

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

An Early-Branching Microbialite Cyanobacterium Forms Intracellular Carbonates

(2012) E. Couradeau et al.   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

The Rare Bacterial Biosphere

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

Progress in Understanding Harmful Algal Blooms: Paradigm Shifts and New Technologies for Research, Monitoring, and Management

(2011) Donald M. Anderson et al.   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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

(2011) Angélique Gobet et al.   ISME Journal

The Western English Channel contains a persistent microbial seed bank

(2011) J Gregory Caporaso et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Microbial seed banks: the ecological and evolutionary implications of dormancy

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

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu 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

Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses

(2011) Ryosuke Nakai et al.   POLAR BIOLOGY

Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

(2011) E. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Macroecology of unicellular organisms - patterns and processes

(2011) Janne Soininen   Environmental Microbiology Reports

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Reduction of rare soil microbes modifies plant-herbivore interactions

(2010) W. H. Gera Hol et al.   ECOLOGY LETTERS

The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

(2010) David L. Kirchman et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10

(2010) K. C.- Y. Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

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

(2010) Michael Pester et al.   ISME Journal

Big sulfur bacteria

(2010) Bo Barker Jørgensen   ISME Journal

Soil Microbial Abundance and Diversity Along a Low Precipitation Gradient

(2010) Ami Bachar et al.   MICROBIAL ECOLOGY

Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the "Killing the Winner" Hypothesis Revisited

(2010) C. Winter et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

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

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys

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

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model

(2010) T. Miki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined niche and neutral effects in a microbial wastewater treatment community

(2010) I. D. Ofiteru et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

(2009) DA Caron et al.   AQUATIC MICROBIAL ECOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert 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

Salt marsh sediment bacteria: their distribution and response to external nutrient inputs

(2009) Jennifer L Bowen et al.   ISME Journal

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing

(2009) Vladimir Lazarevic et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Unsuitable distinction between viable and deadStaphylococcus aureusandStaphylococcus epidermidisby ethidium bromide monoazide

(2009) H. Kobayashi et al.   LETTERS IN APPLIED MICROBIOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince 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

Removal of Free Extracellular DNA from Environmental Samples by Ethidium Monoazide and Propidium Monoazide

(2008) A. O. Wagner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

(2008) Stephen J Bent et al.   ISME Journal

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal