Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

(2018) Evan P. Starr et al.   Microbiome

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

Comparative genomics of the DNA damage-inducible network in the Patescibacteria

(2017) Miquel Sánchez-Osuna et al.   ENVIRONMENTAL MICROBIOLOGY

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

(2017) Stefan M Neuenschwander et al.   ISME Journal

Single-cell sequencing unveils the lifestyle and CRISPR-based population history of Hydrotalea sp. in acid mine drainage

(2017) J. D. Medeiros et al.   MOLECULAR ECOLOGY

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

(2017) Cindy J. Castelle et al.   Scientific Reports

Motility and adhesion through type IV pili in Gram-positive bacteria

(2016) K. H. Piepenbrink et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap

(2016) Xian Zhang et al.   BMC GENETICS

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies

(2016) Victor S. Pylro et al.   MICROBIAL ECOLOGY

Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont

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

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

(2016) Karthik Anantharaman et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics

(2015) Rose S. Kantor et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

(2015) Christopher T. Brown et al.   NATURE

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark

(2015) Siyu Zhang et al.   Standards in Genomic Sciences

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

(2015) William C. Nelson et al.   Frontiers in Microbiology

Catalytic properties, functional attributes and industrial applications of β-glucosidases

(2015) Gopal Singh et al.   3 Biotech

Catalytic properties, functional attributes and industrial applications of β-glucosidases

(2015) Gopal Singh et al.   3 Biotech

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

(2014) Francisco Dini-Andreote et al.   ISME Journal

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

(2014) Zheng-Shuang Hua et al.   ISME Journal

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

(2014) Victor S. Pylro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecological controls on the prevalence of candidate division TM7 in polar regions

(2014) Tristrom J. Winsley et al.   Frontiers in Microbiology

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

(2013) Alexis P Yelton et al.   BMC GENOMICS

Molecular basis of active copper resistance mechanisms in Gram-negative bacteria

(2013) Kinga Bondarczuk et al.   CELL BIOLOGY AND TOXICOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Multiple Vibrio fischeri genes are involved in biofilm formation and host colonization

(2012) Alba Chavez-Dozal et al.   FEMS MICROBIOLOGY ECOLOGY

Contemporary environmental variation determines microbial diversity patterns in acid mine drainage

(2012) Jia-Liang Kuang et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Glycerol utilization by Rhizobium leguminosarum requires an ABC transporter and affects competition for nodulation

(2012) H. Ding et al.   MICROBIOLOGY-SGM

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

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Response of Gram-positive bacteria to copper stress

(2009) Marc Solioz et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Type IV Pili Are Required for Virulence, Twitching Motility, and Biofilm Formation ofAcidovorax avenaesubsp.citrulli

(2009) Ofir Bahar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity

(2009) L. Macomber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS