Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements

M Ares-Arroyo, C Coluzzi, JA Moura de Sousa… - PLoS …, 2024 - journals.plos.org
Mobile genetic elements shape microbial gene repertoires and populations. Recent results
reveal that many, possibly most, microbial mobile genetic elements require helpers to …

[HTML][HTML] Plasmid classifications

MP Garcillán-Barcia, S Redondo-Salvo, F de la Cruz - Plasmid, 2023 - Elsevier
Plasmids are universally present in bacteria and play key roles in the dissemination of
genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive …

Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2024 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome

MG Durrant, A Fanton, J Tycko, M Hinks… - Nature …, 2023 - nature.com
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific
integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as …

Population-level impacts of antibiotic usage on the human gut microbiome

K Lee, S Raguideau, K Sirén, F Asnicar… - Nature …, 2023 - nature.com
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic
microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their …

<? mode longmeta?> IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

AP Camargo, L Call, S Roux, S Nayfach… - Nucleic acids …, 2024 - academic.oup.com
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They
drive horizontal gene transfer, impacting ecological and evolutionary processes within …

Phage–host coevolution in natural populations

D Piel, M Bruto, Y Labreuche, F Blanquart… - Nature …, 2022 - nature.com
Coevolution between bacteriophages (phages) and their bacterial hosts occurs through
changes in resistance and counter-resistance mechanisms. To assess phage–host …

The defense island repertoire of the Escherichia coli pan-genome

D Hochhauser, A Millman, R Sorek - PLoS genetics, 2023 - journals.plos.org
It has become clear in recent years that anti-phage defense systems cluster non-randomly
within bacterial genomes in so-called “defense islands”. Despite serving as a valuable tool …

Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

E Pfeifer, JA Moura de Sousa, M Touchon… - Nucleic acids …, 2021 - academic.oup.com
Plasmids and temperate phages are key contributors to bacterial evolution. They are usually
regarded as very distinct. However, some elements, termed phage–plasmids, are known to …

Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

M Ares-Arroyo, C Coluzzi, EPC Rocha - Nucleic acids research, 2023 - academic.oup.com
Plasmids can be transferred between cells by conjugation, thereby driving bacterial
evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer …