Eduardo P. C. Rocha

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.

The paper identifies and characterizes defence hotspots in P2-like phages and P4-like satellites, revealing rapid modular evolution of antiviral systems through gene swapping and recombination.

The paper identifies a missing component of the ComB T4SS in H. pylori essential for DNA uptake, showing it is a hexameric ATPase interacting with ComB4.

This study identifies prophage-encoded receptor-binding proteins (RBPs) mediating capsule specificity in Klebsiella pneumoniae, revealing structural diversity and functional activity beyond classical depolymerases.

The paper shows capsule exchange in Klebsiella pneumoniae has minimal fitness costs and preserves virulence traits across genetic backgrounds, suggesting plug-and-play dynamics in capsule loci.

The paper identifies novel origins of transfer (oriTs) in Genomic Islands, revealing their role as hitchhikers on conjugative elements and their contribution to bacterial genetic adaptation.

The paper introduces tyPPing, a method for detecting and typing phage-plasmids with high accuracy, outperforming existing tools in sensitivity and scalability.

The paper shows mobile genetic elements drive a fusion-deletion cycle in plasmids, shaping their evolution and antimicrobial resistance in Staphylococcus aureus.

This study identifies the Y. pseudotuberculosis T4BSS as a virulence factor contributing to FESLF pathogenicity through immune modulation during oral infection.

The paper identifies virulent phage genomes in bacterial assemblies, challenging the assumption that virulent phages cannot persist in bacterial cells.

The paper investigates viral-host lineage stability and mobile element diversity in a marine community, finding that ecological constraints promote long-term stability and diversity of phages and mobile genetic elements.

The paper quantifies the role of natural transformation in gene acquisition in bacteria, finding it contributes to a small percentage of novel genes but potentially includes high-impact antibiotic resistance genes.

This study examines how antibiotic treatment affects the gut phageome, finding reduced diversity and increased virulent phage blooms, which may help restore bacterial diversity through kill-the-winner dynamics.

The paper shows that plasmids with antibiotic resistance genes are highly mobile, have broad host ranges, and evolve faster than other plasmids, facilitating the spread of antibiotic resistance across bacterial species.

This study examines broad-host-range Vibrio phages, identifying genetic features and ecological trade-offs that influence their host range and environmental distribution.

The paper investigates plasmid-chromosome transcriptional interactions in multidrug-resistant bacteria, finding that a plasmid-encoded regulator drives chromosomal operon overexpression, enhancing bacterial fitness and carbapenem resistance dissemination.

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.

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.

The paper quantifies transformation rates in bacterial pathogens and links them to intragenomic conflicts with mobile genetic elements, showing similar evolutionary trends across species.

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

The paper identifies anti-phage defence systems encoded by sedentary chromosomal integron cassettes in Vibrio cholerae, showing 16 cassettes provide phage resistance.

This paper introduces rhea, a reference-free method for detecting structural variants in microbiomes using long-read coassembly graphs, showing improved performance over existing methods in simulated and real metagenomic data.

The paper investigates how inverted sedentary chromosomal integrons (SCIs) in Vibrio cholerae recover their original orientation through homologous recombination, maintaining cassette stability and bacterial fitness.

The paper shows toxin-antitoxin systems regulate cassette recombination dynamics in chromosomal integrons by killing cells when excision rates are too high.

The paper demonstrates that integron integrase can insert cassettes outside classical att sites, leading to new recombination sites called attG and expanding integron roles in bacterial evolution.

The paper identifies phage-plasmids as intermediaries facilitating genetic exchange between phages and plasmids, leading to the creation of novel elements and horizontal gene transfer.

MacSyFinder v2 improves molecular system detection in microbial genomes with enhanced modeling, search engine, and updated models.

The paper identifies conjugative origins of transfer in plasmids and chromosomes, revealing functional dependencies that explain plasmid mobility and antimicrobial resistance gene distribution.

IntegronFinder 2.0 identifies and analyzes integrons in bacterial genomes, revealing a large diversity of integrons and antibiotic resistance genes in Klebsiella pneumoniae.

The paper identifies 780 phage-plasmids across diverse bacterial phyla, groups them into 8 families based on gene repertoire similarity, and highlights their conserved phage genes and variable plasmid-like genes.