Eduardo Rocha

Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance Abstract. Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despit

We've come full circle! I began my postdoctoral career by identifying the peptidyl deformylase gene. Today, we show that half of bacterial species harbor multiple PDF genes (up to 7, for always a single Met-tRNA transformylase), and while the role of these PDFs ... academic.oup.com/mbe/article/...

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation Abstract. Conjugative plasmids are a major driving force for the dissemination of antimicrobial resistance. During conjugation, plasmid DNA is transferred

academic.oup.com/nar/article/... Collaboration with Y. Yamaichi. Killing donor bacteria in conjugation mixes using water enables transcriptomic profiling of early plasmid genes ! Superb tool for studying zygotic induction of these early genes, which include anti-SOS and anti-RM factors. #microsky

Editorial: society journals matter—supporting science through renewed commitment Scientific publishing is in flux. Commercial publishers have expanded their influence, driven by profit margins and citation metrics. At the same time, a g

Your societies need you #MicroSky! Editorial from the European Academy of Microbiology Task Force: Society journals matter—supporting science through renewed commitment: academic.oup.com/microlife/ar...

Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

🔬 Call to create junior research groups at the Institut Pasteur

Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies

📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD

Apply now 📝 research.pasteur.fr/en/call/crea...

#JobOpportunity #Research

Entre 2023 et 2024 les dépenses 🇪🇺de R&D en % du PIB ↘️
Tout va bien (non) (bis)

En dépit des grandes déclarations de "[put invest. R&D] at the centre of our economy. We will increase our research spending to focus more on strategic priorities" commission.europa.eu/document/dow...
#helloESR

Impact of Host and Bacterial Metabolism on Antibiotic Susceptibility Antimicrobial resistance (AMR) is a global healthcare emergency, directly causing 1.3 million deaths per year and predicted to increase dramatically over the coming decades. Understanding the molecula...

Impact of Host and Bacterial Metabolism on Antibiotic Susceptibility

#AMR #amrsky

pubs.acs.org/doi/10.1021/...

Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)

New preprint from our lab, spearheaded by @maelledaunesse.bsky.social and in collaboration with Diego Villar!

In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?

We’re excited to announce the launch of the beta version of PanGBank website! 🧬🌐
pangbank.genoscope.cns.fr

PanGBank is a web-based platform for exploring, analyzing, and downloading pangenomes created with #PPanGGOLiN.

🔗 Dive in, test it out, and let us know what you think!

#pangenome

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Taming wild replicons: evolution and domestication of large extrachromosomal replicons Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…

Taming wild replicons: evolution and domestication of large extrachromosomal replicons

#MicroSky

www.sciencedirect.com/science/arti...

Somewhat ironic that we pay extra for "author services" (under subscription or APC) and then get deleterious edits

Not yet. But I have been getting reviews that do seem to be done by AI (post-edited or not). Some of them look well-structured, but very vague, highlighting secondary aspects, as if they concerned some other paper on a closely related topic.

Amos Bairoch, Swiss pioneer of bioinformatics, passes away We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...

We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We honour his legacy by continuing to build the future of bioinformatics.

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

Kwun et al. test whether transformation is an efficient mechanism for deleting prophage despite sensitivity to the ssDNA imported by competence machinery, identifying key interfaces in the evolutionary arms race between prophage and their hosts.

🔗 doi.org/10.1093/molbev/msaf259

#evobio #molbio

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

Cumulative cgMLST provides increased discrimination of nested phylogenetic groups Background Core genome multilocus sequence typing (cgMLST) is a powerful method for bacterial strain genotyping. However, the size of the core genome decreases as the phylogenetic breadth of the targe...

Cumulative cgMLST : Our novel preprint is out @biorxiv doi.org/10.1101/2025...

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and...

Pleased to share our recent article in PNAS - a collaboration with @jessicaandreani.bsky.social & Pablo Radicella, with important roles played by many members of each team.

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi

In a new MBE Perspective, @jomcinerney.bsky.social introduces the concepts of epaktovars and xenotypes, providing a framework for describing phenotypic convergence and shared genetic material resulting from gene transfer across diverse lineages.

🔗 doi.org/10.1093/molbev/msaf279

#evobio #molbio

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

#microsky #phagesky #phage

Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.

academic.oup.com/mbe/article/...

⭐ NAR Breakthrough! ⭐

🔬 New study by Betancurt et al. uses #PacBio single-molecule sequencing to build a long-read fidelity assay that reveals how different #DNApolymerase families make distinct errors.
🧬 Read more: doi.org/10.1093/nar/...
@nebiolabs.bsky.social @pasteur.fr
#NARBreakthrough

INCEPTION Symposium 2025 - Research INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.

The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.

tinyurl.com/5yx2wmz5

(1/n)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Bacterial immune systems as causes and consequences of microbiome structure Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...

MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin... PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️

Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

Kissing evolved at least 21 million years ago. www.sciencedirect.com/science/arti... @matildabrindle.bsky.social

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf