A census-based estimate of Earth's bacterial and archaeal diversity

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

Genome watch: Microbial diversity knows no borders

(2018) Lindsay J. Pike et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial diversification through geological time

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Biological Species Are Universal across Life’s Domains

(2017) Louis-Marie Bobay et al.   Genome Biology and Evolution

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

25 years of serving the community with ribosomal RNA gene reference databases and tools

(2017) Frank Oliver Glöckner et al.   JOURNAL OF BIOTECHNOLOGY

Evidence for early life in Earth’s oldest hydrothermal vent precipitates

(2017) Matthew S. Dodd et al.   NATURE

A null model for microbial diversification

(2017) Timothy J. Straub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

(2017) Brendan B. Larsen et al.   QUARTERLY REVIEW OF BIOLOGY

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Towards a balanced view of the bacterial tree of life

(2017) Frederik Schulz et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

(2017) Albert Barberán et al.   mSphere

A macroecological theory of microbial biodiversity

(2017) William R. Shoemaker et al.   Nature Ecology & Evolution

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Reply to Willis: Powerful predictions of biodiversity from ecological models and scaling laws

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extrapolating abundance curves has no predictive power for estimating microbial biodiversity

(2016) Amy Willis   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The vast unknown microbial biosphere

(2016) Carlos Pedrós-Alió et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Status of the Archaeal and Bacterial Census: an Update

(2016) Patrick D. Schloss et al.   mBio

After All, Only Millions?

(2016) Rudolf Amann et al.   mBio

Reply to “The Underestimation of Global Microbial Diversity”

(2016) Rudolf Amann et al.   mBio

The Underestimation of Global Microbial Diversity

(2016) Jay T. Lennon et al.   mBio

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

(2016) Louie Wurch et al.   Nature Communications

Estimating and comparing microbial diversity in the presence of sequencing errors

(2016) Chun-Huo Chiu et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

Endemic hydrothermal vent species identified in the open ocean seed bank

(2016) Giorgio Gonnella et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Estimating diversity via frequency ratios

(2015) Amy Willis et al.   BIOMETRICS

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis

(2015) J. William Schopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

(2014) Ali May et al.   BIOINFORMATICS

An improved nonparametric lower bound of species richness via a modified good-turing frequency formula

(2014) Chun-Huo Chiu et al.   BIOMETRICS

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

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

(2014) Johan Decelle et al.   PLoS One

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects

(2014) Frank O. Aylward et al.   mBio

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

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

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

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

(2013) Wei Chen et al.   PLoS One

Marine bacteria exhibit a bipolar distribution

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

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

Estimating population diversity with CatchAll

(2012) J. Bunge et al.   BIOINFORMATICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria

(2012) Takashi Okubo et al.   MICROBES AND ENVIRONMENTS

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

(2012) KAREN E. SULLAM et al.   MOLECULAR ECOLOGY

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

(2012) V. G. Fonseca et al.   NUCLEIC ACIDS RESEARCH

Population size estimation based upon ratios of recapture probabilities

(2011) Irene Rocchetti et al.   Annals of Applied Statistics

The Rare Bacterial Biosphere

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Drivers of bacterial  -diversity depend on spatial scale

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

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

(2009) Chih-Horng Kuo et al.   Biology Direct

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

(2009) Talima Pearson et al.   BMC BIOLOGY

The nonrandom microheterogeneity of 16S rRNA genes inVibrio splendidusmay reflect adaptation to versatile lifestyles

(2009) Sigmund Jensen et al.   FEMS MICROBIOLOGY LETTERS

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Classification of Bacteria and Archaea: Past, present and future

(2009) Karl Heinz Schleifer   SYSTEMATIC AND APPLIED MICROBIOLOGY

Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments

(2008) Ana Casanueva et al.   EXTREMOPHILES

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH