Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

(2021) Jorge A Moura de Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

(2021) Lina M León et al.   NUCLEIC ACIDS RESEARCH

Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities

(2021) Jordi van Gestel et al.   Nature Communications

Molecular Basis of Lysis–Lysogeny Decisions in Gram-Positive Phages

(2021) Aisling Brady et al.   Annual Review of Microbiology

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

(2021) Matthieu Haudiquet et al.   PLOS BIOLOGY

Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

(2021) Jingqiu Liao et al.   Nature Microbiology

A regulatory cascade controls Staphylococcus aureus pathogenicity island activation

(2021) Andreas F. Haag et al.   Nature Microbiology

Regulation of prophage induction and lysogenization by phage communication systems

(2021) John B. Bruce et al.   CURRENT BIOLOGY

The arbitrium system controls prophage induction

(2021) Aisling Brady et al.   CURRENT BIOLOGY

To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

(2021) Jorge A. Moura de Sousa et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages

(2021) Fatima Aysha Hussain et al.   SCIENCE

Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements

(2021) Suzanne Humphrey et al.   Nature Communications

Staphylococcal phages and pathogenicity islands drive plasmid evolution

(2021) Suzanne Humphrey et al.   Nature Communications

Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

(2021) James P. J. Hall et al.   PLOS BIOLOGY

Population genomics of Klebsiella pneumoniae

(2020) Kelly L. Wyres et al.   NATURE REVIEWS MICROBIOLOGY

The role of hosts, plasmids and environment in determining plasmid transfer rates: A meta-analysis

(2020) Richard J. Sheppard et al.   PLASMID

Diversity and Function of Phage Encoded Depolymerases

(2020) Leandra E. Knecht et al.   Frontiers in Microbiology

Lipopolysaccharide O-antigens - bacterial glycans made to measure

(2020) Chris Whitfield et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

(2020) Guillaume Gautreau et al.   PLoS Computational Biology

Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

(2020) Stephanie G Hays et al.   eLife

Assembly of Bacterial Capsular Polysaccharides and Exopolysaccharides

(2020) Chris Whitfield et al.   Annual Review of Microbiology

The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages

(2020) Marta Lourenço et al.   Cell Host & Microbe

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

(2020) Jorge A. M. de Sousa et al.   ISME Journal

Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation

(2020) Yue Wang et al.   ISME Journal

Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages

(2020) Lorena Rodríguez-Rubio et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

(2020) Marie Touchon et al.   PLoS Genetics

Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms

(2020) Charles Bernard et al.   ISME Journal

Prokaryotic viperins produce diverse antiviral molecules

(2020) Aude Bernheim et al.   NATURE

A Family of Viral Satellites Manipulates Invading Virus Gene Expression and Can Affect Cholera Toxin Mobilization

(2020) Zachary K. Barth et al.   mSystems

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation

(2019) Jorge A. Moura de Sousa et al.   Scientific Reports

Bacteria and archaea on Earth and their abundance in biofilms

(2019) Hans-Curt Flemming et al.   NATURE REVIEWS MICROBIOLOGY

Regulation of Gram-Positive Conjugation

(2019) Verena Kohler et al.   Frontiers in Microbiology

Bacteriophages benefit from generalized transduction

(2019) Alfred Fillol-Salom et al.   PLoS Pathogens

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

(2019) Nelson Frazão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse conjugative elements silence natural transformation in Legionella species

(2019) Isabelle Durieux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic transduction by phages and chromosomal islands: The new and noncanonical

(2019) Yin Ning Chiang et al.   PLoS Pathogens

The Ecology and Evolution of Pangenomes

(2019) Michael A. Brockhurst et al.   CURRENT BIOLOGY

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

Cis-Acting Relaxases Guarantee Independent Mobilization of MOBQ4 Plasmids

(2019) M. Pilar Garcillán-Barcia et al.   Frontiers in Microbiology

Plasmid persistence: costs, benefits, and the plasmid paradox

(2018) Amanda C. Carroll et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations

(2018) J. Jutkina et al.   SCIENCE OF THE TOTAL ENVIRONMENT

CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction

(2018) Bridget N. J. Watson et al.   mBio

Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa

(2018) Anneke van der Zee et al.   Frontiers in Microbiology

Factors driving effective population size and pan-genome evolution in bacteria

(2018) Louis-Marie Bobay et al.   BMC EVOLUTIONARY BIOLOGY

Genome hypermobility by lateral transduction

(2018) John Chen et al.   SCIENCE

Phage mobility is a core determinant of phage–bacteria coexistence in biofilms

(2017) Matthew Simmons et al.   ISME Journal

Prokaryote genome fluidity is dependent on effective population size

(2017) Nadia Andrea Andreani et al.   ISME Journal

Communication between viruses guides lysis–lysogeny decisions

(2017) Zohar Erez et al.   NATURE

Disentangling the effects of selection and loss bias on gene dynamics

(2017) Jaime Iranzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

Dissemination of antibiotic resistance genes from antibiotic producers to pathogens

(2017) Xinglin Jiang et al.   Nature Communications

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

Plasmid vesicles mimicking virions

(2017) Patrick Forterre et al.   Nature Microbiology

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

(2017) Wesley Loftie-Eaton et al.   Nature Ecology & Evolution

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Evolutionary Ecology of Prokaryotic Immune Mechanisms

(2016) Stineke van Houte et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

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

Plasmid transfer in biofilms: a perspective on limitations and opportunities

(2016) Thibault Stalder et al.   npj Biofilms and Microbiomes

Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance

(2015) Wesley Loftie-Eaton et al.   MOLECULAR BIOLOGY AND EVOLUTION

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

Analysis of SOS-Induced Spontaneous Prophage Induction in Corynebacterium glutamicum at the Single-Cell Level

(2013) A. M. Nanda et al.   JOURNAL OF BACTERIOLOGY

Plasmid-Encoded ComI Inhibits Competence in the Ancestral 3610 Strain of Bacillus subtilis

(2013) M. A. Konkol et al.   JOURNAL OF BACTERIOLOGY

Fixation probability of mobile genetic elements such as plasmids

(2013) Samuel J. Tazzyman et al.   THEORETICAL POPULATION BIOLOGY

The interconnection between biofilm formation and horizontal gene transfer

(2012) Jonas Stenløkke Madsen et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Evolution of Conjugation and Type IV Secretion Systems

(2012) Julien Guglielmini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasmid-mediated horizontal gene transfer is a coevolutionary process

(2012) Ellie Harrison et al.   TRENDS IN MICROBIOLOGY

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Selfish genetic elements, genetic conflict, and evolutionary innovation

(2011) J. H. Werren   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes

(2011) H. K. Allen et al.   mBio

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

Mobility of Plasmids

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

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

Escherichia coli genes affecting recipient ability in plasmid conjugation: Are there any?

(2009) Daniel Pérez-Mendoza et al.   BMC GENOMICS

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Autonomous plasmid-like replication of a conjugative transposon

(2009) Catherine A. Lee et al.   MOLECULAR MICROBIOLOGY

Microbial co-habitation and lateral gene transfer: what transposases can tell us

(2009) Sean D Hooper et al.   GENOME BIOLOGY

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

Recombination frequency in plasmid DNA containing direct repeats—predictive correlation with repeat and intervening sequence length

(2008) Pedro H. Oliveira et al.   PLASMID