E. P. C. Rocha

The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae

The paper identifies that XerCD recombination is used by large plasmids and chromids for dimer resolution, similar to chromosomes, and shows this is required for their faithful inheritance.

Two D-loop resolution systems enable natural genetic transformation in bacteria

This study identifies two D-loop resolution systems in bacteria, YraN/ComM and CoiA/RadA, that work together to process the transformation D-loop during natural genetic transformation.

Identification of novel origins of transfer across bacterial plasmids

The paper identifies 21 novel origins of transfer (oriTs) in bacterial plasmids, filling gaps in oriT diversity and enabling exploration of conjugation in plasmids lacking conjugation genes.

Latent evolution of biofilm formation depends on life-history and genetic background

This study shows that biofilm formation evolves rapidly in response to environmental changes and is influenced by genetic background and nutrient availability.

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

This study reports the emergence of a novel non-aggregative colony morphology in Klebsiella variicola and demonstrates social exploitation through negative frequency-dependent selection.

Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes.

This study shows that horizontal gene transfer influences the likelihood of acquiring antibiotic resistance mutations in core genes of E. coli.

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency

The paper shows how bacterial capsule traits influence phage susceptibility and plasmid conjugation efficiency, with implications for horizontal gene transfer and population dynamics.

Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts

The paper quantifies domain mosaicism in phage proteins to show how protein modularity contributes to functional diversity and diversification across bacterial hosts.

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

This study shows plasmids avoid restriction-modification system targets, with smaller plasmids adapting via sequence composition and larger ones via protective genes.

Identification and characterization of thousands of bacteriophage satellites across bacteria

The paper develops a tool to identify bacteriophage satellites in bacterial genomes, expanding their known number to ~5000 and revealing their diversity and genomic organization.

A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

The paper identifies a new family of phage-inducible chromosomal islands that produce small capsids using phage tails and spread without harming their helper phages.

Competition between phage-resistance mechanisms determines the outcome of bacterial co-existence

This study coevolves bacterial strains under different phage pressures, showing that resistance mechanisms compete, with genetic resistance becoming dominant over time.

Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion

This paper identifies phage-plasmids carrying antibiotic resistance genes and demonstrates their ability to transfer resistance across bacteria.

Evolution of plasmid mobility: origin and fate of non-conjugative plasmids

This study examines how plasmid mobility evolves by analyzing gene repertoires and relaxases, finding that mobility transitions are linked to significant gene changes and the emergence of new plasmid types.

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

The paper identifies P4-like bacteriophage satellites in Enterobacterales genomes, showing their prevalence, conserved core structure, and broad host range.

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

The paper shows that capsule inactivation by phage pressure in Klebsiella pneumoniae facilitates conjugation-mediated gene flow, linking virulence and antibiotic resistance evolution.

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

The paper investigates prophage interactions in Klebsiella, finding that capsule serotype determines infection success and that phage predation accelerates capsule loss, driving serotype switches.

Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions

The paper shows that bacterial capsule maintenance and fitness advantage depend on growth conditions, with nutrient-poor media favoring capsule retention and nutrient-rich media allowing its loss.

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

This study investigates genetic exchanges among bacteriophages, identifying factors influencing gene flow and its impact on phage and bacterial evolution.

Unlinked rRNA genes are widespread among Bacteria and Archaea

The paper shows that unlinked 16S and 23S rRNA genes are common in many bacterial and archaeal phyla, not just rare exceptions, and are associated with specific ecological and metabolic traits.

Parallels between experimental and natural evolution of legume symbionts

This study compares natural and experimental evolution of legume symbionts, finding similar patterns of purifying selection and adaptation through quorum-sensing systems.

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems

The paper investigates the interaction between NHEJ repair and type II-A CRISPR-Cas systems, finding that Csn2 inhibits NHEJ while NHEJ does not affect CRISPR-Cas.