Eduardo Rocha
@epcrocha.bsky.social
Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris
Pinned
Eduardo Rocha
@epcrocha.bsky.social
· Oct 14
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
Reposted by Eduardo Rocha
@laasya2.bsky.social @deepaagashe.bsky.social et al. quantified the growth cost of mistranslation rates and exposure to antibiotics in E. coli, finding that altered translation accuracy can shape adaptive outcomes.
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
December 19, 2025 at 6:53 PM
@laasya2.bsky.social @deepaagashe.bsky.social et al. quantified the growth cost of mistranslation rates and exposure to antibiotics in E. coli, finding that altered translation accuracy can shape adaptive outcomes.
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
Reposted by Eduardo Rocha
How do bacteria deal with double costs? And how costly are unusual levels of mistranslation anyway? In short - antibiotics are more of an issue than less/more mistranslation, but the latter changes how populations deal with antibiotics. For the long story, check out our new paper!
So happy that this work simultaneously measuring the costs of antibiotic exposure and mistranslation is finally out in MBE! Work from @deepaagashe.bsky.social (who was ultra patient!) and my labs. Do see the research highlight here, with Nishant's lovely graphic. academic.oup.com/mbe/article/...
How Life's “Mistakes” Impact Adaptation
Even in a colony of genetically identical bacteria, no two individuals are exactly alike. This phenomenon, known as phenotypic “noise,” is a long-standing
academic.oup.com
December 19, 2025 at 12:19 PM
How do bacteria deal with double costs? And how costly are unusual levels of mistranslation anyway? In short - antibiotics are more of an issue than less/more mistranslation, but the latter changes how populations deal with antibiotics. For the long story, check out our new paper!
Reposted by Eduardo Rocha
Preprint alert📢!
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host?
➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied
Here is what we found. www.biorxiv.org/content/10.6...
#MicroSky #PhageSky
🧵
➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied
Here is what we found. www.biorxiv.org/content/10.6...
#MicroSky #PhageSky
🧵
Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community
Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, partic...
www.biorxiv.org
December 18, 2025 at 2:11 PM
Preprint alert📢!
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host?
➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied
Here is what we found. www.biorxiv.org/content/10.6...
#MicroSky #PhageSky
🧵
➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied
Here is what we found. www.biorxiv.org/content/10.6...
#MicroSky #PhageSky
🧵
Reposted by Eduardo Rocha
@julietteluiselli.bsky.social et al. introduce a mathematical model of genome size evolution, showing that the noncoding fraction of the genome is shaped by biases in mutational neutrality, and robustness selection arising from structural mutations
🔗 doi.org/10.1093/molbev/msaf315
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf315
#evobio #molbio
December 16, 2025 at 12:14 PM
@julietteluiselli.bsky.social et al. introduce a mathematical model of genome size evolution, showing that the noncoding fraction of the genome is shaped by biases in mutational neutrality, and robustness selection arising from structural mutations
🔗 doi.org/10.1093/molbev/msaf315
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf315
#evobio #molbio
Reposted by Eduardo Rocha
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:53 PM
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Eduardo Rocha
Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission
Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...
journals.plos.org
December 12, 2025 at 12:09 PM
Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Reposted by Eduardo Rocha
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/...
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
academic.oup.com
December 12, 2025 at 8:57 AM
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/...
Reposted by Eduardo Rocha
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
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
December 10, 2025 at 6:06 PM
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
Reposted by Eduardo Rocha
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...
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
academic.oup.com
December 9, 2025 at 6:22 PM
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...
Reposted by Eduardo Rocha
🔬 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
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
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...
research.pasteur.fr
December 8, 2025 at 8:53 AM
🔬 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
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
Reposted by Eduardo Rocha
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
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
December 7, 2025 at 12:54 PM
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
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
Reposted by Eduardo Rocha
Impact of Host and Bacterial Metabolism on Antibiotic Susceptibility
#AMR #amrsky
pubs.acs.org/doi/10.1021/...
#AMR #amrsky
pubs.acs.org/doi/10.1021/...
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...
pubs.acs.org
December 7, 2025 at 2:57 PM
Impact of Host and Bacterial Metabolism on Antibiotic Susceptibility
#AMR #amrsky
pubs.acs.org/doi/10.1021/...
#AMR #amrsky
pubs.acs.org/doi/10.1021/...
Reposted by Eduardo Rocha
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)
Antibiotic Resistance Microbiology Dataset Mass General Brigham (ARMD-MGB) v1.0.0
ARMD-MGB contains detailed microbiology and clinical metadata for >225,000 patients and >970,000 cultures collected over 10 years
physionet.org
December 5, 2025 at 7:39 AM
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)
Reposted by Eduardo Rocha
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?
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
We've just released our new preprint! 🐀✨
doi.org/10.1101/2025...
How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift?
@camilleberthelot.bsky.social
👇 A short thread on what we found in African mole-rats.
doi.org/10.1101/2025...
How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift?
@camilleberthelot.bsky.social
👇 A short thread on what we found in African mole-rats.
Coordinated shifts in gene expression and regulation during mole-rat evolution
Changes in gene expression and regulation are central to mammalian phenotypic evolution. Yet, distinguishing adaptive gene expression shifts from neutral divergence remains challenging. Here, we integ...
doi.org
December 4, 2025 at 4:50 PM
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?
In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
Reposted by Eduardo Rocha
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
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
Home
pangbank.genoscope.cns.fr
December 3, 2025 at 10:49 PM
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
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
Reposted by Eduardo Rocha
🦠🧪🧬🚨 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-...
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
academic.oup.com
December 3, 2025 at 2:34 AM
🦠🧪🧬🚨 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-...
Reposted by Eduardo Rocha
Taming wild replicons: evolution and domestication of large extrachromosomal replicons
#MicroSky
www.sciencedirect.com/science/arti...
#MicroSky
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
December 2, 2025 at 2:25 PM
Taming wild replicons: evolution and domestication of large extrachromosomal replicons
#MicroSky
www.sciencedirect.com/science/arti...
#MicroSky
www.sciencedirect.com/science/arti...
Reposted by Eduardo Rocha
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.
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...
www.sib.swiss
December 2, 2025 at 8:24 AM
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.
Reposted by Eduardo Rocha
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 👇
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...
doi.org
November 30, 2025 at 7:51 PM
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 👇
Reposted by Eduardo Rocha
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
🔗 doi.org/10.1093/molbev/msaf259
#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
doi.org
November 26, 2025 at 5:42 PM
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
🔗 doi.org/10.1093/molbev/msaf259
#evobio #molbio
Reposted by Eduardo Rocha
🧬🛡️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...
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...
November 27, 2025 at 9:35 AM
🧬🛡️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...
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...
Reposted by Eduardo Rocha
Cumulative cgMLST : Our novel preprint is out @biorxiv doi.org/10.1101/2025...
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...
doi.org
November 26, 2025 at 2:27 PM
Cumulative cgMLST : Our novel preprint is out @biorxiv doi.org/10.1101/2025...
Reposted by Eduardo Rocha
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/...
A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...
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...
www.pnas.org
November 26, 2025 at 7:44 AM
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/...
A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...
Reposted by Eduardo Rocha
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
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
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
doi.org
November 20, 2025 at 3:48 PM
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
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
Reposted by Eduardo Rocha
#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/...
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/...
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
academic.oup.com
November 23, 2025 at 4:39 PM
#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/...
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/...