Genetic Competence Drives Genome Diversity in Bacillus subtilis

Beyond the Black Queen Hypothesis

(2016) Alix Mas et al.   ISME Journal

Steady at the wheel: conservative sex and the benefits of bacterial transformation

(2016) Ole Herman Ambur et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Theory of prokaryotic genome evolution

(2016) Itamar Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defying Muller’s Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

(2016) Mizue Naito et al.   mBio

Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes

(2016) Evgeni Bolotin et al.   Scientific Reports

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

(2016) Nicholas J. Croucher et al.   PLOS BIOLOGY

Fitness Trade-Offs in Competence Differentiation of Bacillus subtilis

(2016) Melih Yüksel et al.   Frontiers in Microbiology

A new view of the tree of life

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

Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species

(2015) Evgeni Bolotin et al.   Genome Biology and Evolution

Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-SymbioticSpiroplasma

(2015) Wen-Sui Lo et al.   Genome Biology and Evolution

ComGA-RelA interaction and persistence in theBacillus subtilis K-state

(2015) Jeanette Hahn et al.   MOLECULAR MICROBIOLOGY

From Cell Differentiation to Cell Collectives: Bacillus subtilis Uses Division of Labor to Migrate

(2015) Jordi van Gestel et al.   PLOS BIOLOGY

Interactions of Salmonella with animals and plants

(2015) Agnès Wiedemann et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

(2014) Pere Puigbò et al.   BMC BIOLOGY

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

(2014) Vincent P. Richards et al.   Genome Biology and Evolution

Gut Adhesive Bacillus subtilis Spores as a Platform for Mucosal Delivery of Antigens

(2014) Milene Tavares Batista et al.   INFECTION AND IMMUNITY

Natural Competence and the Evolution of DNA Uptake Specificity

(2014) J. C. Mell et al.   JOURNAL OF BACTERIOLOGY

Sporulation during Growth in a Gut Isolate of Bacillus subtilis

(2014) C. R. Serra et al.   JOURNAL OF BACTERIOLOGY

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

Developmentally-Regulated Excision of the SPβ Prophage Reconstitutes a Gene Required for Spore Envelope Maturation in Bacillus subtilis

(2014) Kimihiro Abe et al.   PLoS Genetics

Plant innate immunity against human bacterial pathogens

(2014) Maeli Melotto et al.   Frontiers in Microbiology

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

(2013) Alan McNally et al.   Genome Biology and Evolution

Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus

(2013) V. Bhandari et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Ecological and Mechanistic Insights Into the Direct and Indirect Antimicrobial Properties of Bacillus subtilis Lipopeptides on Plant Pathogens

(2013) J. Falardeau et al.   JOURNAL OF CHEMICAL ECOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

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

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria

(2013) H. Luo et al.   mBio

The fungus-growing termite Macrotermes natalensis harbors bacillaene-producing Bacillus sp. that inhibit potentially antagonistic fungi

(2013) Soohyun Um et al.   Scientific Reports

Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability

(2013) Louis-Marie Bobay et al.   PLoS Genetics

Interrelationships of Food Safety and Plant Pathology: The Life Cycle of Human Pathogens on Plants

(2012) Jeri D. Barak et al.   Annual Review of Phytopathology

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

(2012) Rolf S Kaas et al.   BMC GENOMICS

Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?

(2012) Xavier Charpentier et al.   CURRENT OPINION IN MICROBIOLOGY

Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

(2012) A. Ahmed et al.   JOURNAL OF BACTERIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

(2012) J. J. Morris et al.   mBio

Phylogenetic Analysis of Bacillus subtilis Strains Applicable to Natto (Fermented Soybean) Production

(2011) Yuji Kubo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

COMPETENCE INCREASES SURVIVAL DURING STRESS IN STREPTOCOCCUS PNEUMONIAE

(2011) Daniel J. P. Engelmoer et al.   EVOLUTION

Complete Genome Sequence of Bacillus subtilis BSn5, an Endophytic Bacterium of Amorphophallus konjac with Antimicrobial Activity for the Plant Pathogen Erwinia carotovora subsp. carotovora

(2011) Y. Deng et al.   JOURNAL OF BACTERIOLOGY

Extreme genome reduction in symbiotic bacteria

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

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus

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

Ecology of Speciation in the Genus Bacillus

(2010) N. Connor et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept

(2010) Tristan Lefébure et al.   Genome Biology and Evolution

Genome Sequence of Bacillus subtilis subsp. spizizenii gtP20b, Isolated from the Indian Ocean

(2010) L. Fan et al.   JOURNAL OF BACTERIOLOGY

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Optimal Strategy for Competence Differentiation in Bacteria

(2010) C. Scott Wylie et al.   PLoS Genetics

Episodic Selection and the Maintenance of Competence and Natural Transformation in Bacillus subtilis

(2009) P. J. Johnsen et al.   GENETICS

Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov.

(2009) A. P. Rooney et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

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

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Bistability, Epigenetics, and Bet-Hedging in Bacteria

(2008) Jan-Willem Veening et al.   Annual Review of Microbiology

Stochastic switching to competence

(2008) Madeleine Leisner et al.   CURRENT OPINION IN MICROBIOLOGY

Self-destructive cooperation mediated by phenotypic noise

(2008) Martin Ackermann et al.   NATURE

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH