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
🚨#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...
Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
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...
www.findaphd.com
November 18, 2025 at 9:38 AM
🚨#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...
Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
Reposted by Eduardo Rocha
Kissing evolved at least 21 million years ago. www.sciencedirect.com/science/arti... @matildabrindle.bsky.social
November 19, 2025 at 8:40 AM
Kissing evolved at least 21 million years ago. www.sciencedirect.com/science/arti... @matildabrindle.bsky.social
Reposted by Eduardo Rocha
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
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...
rdcu.be
November 18, 2025 at 9:01 PM
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
Reposted by Eduardo Rocha
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons
Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti
academic.oup.com
November 17, 2025 at 3:44 PM
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Reposted by Eduardo Rocha
Happy to share our latest T6SS review:
nature.com/articles/s41...
Thank you, Jan, Danny (@dannyjamesward.bsky.social), Joana (@joanampereira.bsky.social), as well as reviewers and editors @natrevmicro.nature.com!
nature.com/articles/s41...
Thank you, Jan, Danny (@dannyjamesward.bsky.social), Joana (@joanampereira.bsky.social), as well as reviewers and editors @natrevmicro.nature.com!
The type VI secretion system and associated effector proteins - Nature Reviews Microbiology
In this Review, Basler and colleagues examine the type VI secretion system (T6SS), focusing on the diversity of antibacterial T6SS effectors and the evolutionary forces that shape them. They explain h...
nature.com
November 17, 2025 at 10:08 AM
Happy to share our latest T6SS review:
nature.com/articles/s41...
Thank you, Jan, Danny (@dannyjamesward.bsky.social), Joana (@joanampereira.bsky.social), as well as reviewers and editors @natrevmicro.nature.com!
nature.com/articles/s41...
Thank you, Jan, Danny (@dannyjamesward.bsky.social), Joana (@joanampereira.bsky.social), as well as reviewers and editors @natrevmicro.nature.com!
Reposted by Eduardo Rocha
PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇
www.findaphd.com
November 18, 2025 at 11:41 AM
PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇
Reposted by Eduardo Rocha
It’s out ! Evolution of Bordetella parapertussis, the second agent of whooping cough: many parallelisms with Bordetella pertussis, including rapid adaptation by loss of the pertactin vaccine antigen. Just published in @microbiosoc MGen journal
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis
Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths. Bordetella parapertussis (Bpp) contributes significantly to the burden of whooping coug...
www.microbiologyresearch.org
November 16, 2025 at 6:01 PM
It’s out ! Evolution of Bordetella parapertussis, the second agent of whooping cough: many parallelisms with Bordetella pertussis, including rapid adaptation by loss of the pertactin vaccine antigen. Just published in @microbiosoc MGen journal
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Eduardo Rocha
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
Dynamics of dN/dS within recombining bacterial populations
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...
www.biorxiv.org
November 16, 2025 at 3:26 PM
The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.
Reposted by Eduardo Rocha
The origin of plasmid core genes remains poorly understood - Picazo et al. show that acquisition of LLP-1/LPP-2 plasmids by the bacteria Pantoea introduced genetic redundancy with chromosomal genes, followed by waves of differential gene loss.
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
November 14, 2025 at 8:36 AM
The origin of plasmid core genes remains poorly understood - Picazo et al. show that acquisition of LLP-1/LPP-2 plasmids by the bacteria Pantoea introduced genetic redundancy with chromosomal genes, followed by waves of differential gene loss.
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf273
#evobio #molbio
Reposted by Eduardo Rocha
Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus!
Please RT (or is it RB? not sure how our lingo has changed!)
Please RT (or is it RB? not sure how our lingo has changed!)
🚨 15 days left to apply!
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
November 14, 2025 at 10:22 AM
Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus!
Please RT (or is it RB? not sure how our lingo has changed!)
Please RT (or is it RB? not sure how our lingo has changed!)
Reposted by Eduardo Rocha
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 12, 2025 at 3:43 AM
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Reposted by Eduardo Rocha
We are happy to share a new paper from our lab:
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42...
which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42...
which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals - Communications Biology
Co-abundance analysis of 938 healthy individuals uncovers how host factors shape gut microbiome interactions, highlighting a core set of 200 impacted genera and additional factor-specific interactions...
www.nature.com
November 10, 2025 at 5:00 PM
We are happy to share a new paper from our lab:
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42...
which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42...
which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.
Reposted by Eduardo Rocha
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
The hitchhiker’s guide to cross-species DNA delivery
Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski,
et al. reveal how phage satellites assemble chimeric infective particles that deliver
DNA across species bound...
www.cell.com
November 9, 2025 at 9:39 AM
The hitchhiker’s guide to cross-species DNA delivery
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
Reposted by Eduardo Rocha
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Reposted by Eduardo Rocha
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Eduardo Rocha
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Eduardo Rocha
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae
Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...
journals.plos.org
November 3, 2025 at 11:58 PM
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
Reposted by Eduardo Rocha
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 1:55 PM
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
Reposted by Eduardo Rocha
Use antisense oligomers to silence phage genes and discover new biology.
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @helmholtzhzi.bsky.social @uni-wuerzburg.de
print: www.nature.com/articles/s41...
highlight: www.nature.com/articles/s41...
briefing: www.nature.com/articles/d41...
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @helmholtzhzi.bsky.social @uni-wuerzburg.de
print: www.nature.com/articles/s41...
highlight: www.nature.com/articles/s41...
briefing: www.nature.com/articles/d41...
October 31, 2025 at 8:08 AM
Use antisense oligomers to silence phage genes and discover new biology.
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @helmholtzhzi.bsky.social @uni-wuerzburg.de
print: www.nature.com/articles/s41...
highlight: www.nature.com/articles/s41...
briefing: www.nature.com/articles/d41...
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @helmholtzhzi.bsky.social @uni-wuerzburg.de
print: www.nature.com/articles/s41...
highlight: www.nature.com/articles/s41...
briefing: www.nature.com/articles/d41...
Reposted by Eduardo Rocha
📣 We are moving to Barcelona to join the amazing @crg.eu and explore how centrosomes & cilia work, evolve & respond to the environment. We are looking for
PhD students www.crg.eu/en/content/t...
Postdocs gimm.pt/jobs/postdoc...
Other calls to open, also for an experienced lab manager.
Get in touch!
PhD students www.crg.eu/en/content/t...
Postdocs gimm.pt/jobs/postdoc...
Other calls to open, also for an experienced lab manager.
Get in touch!
October 30, 2025 at 1:15 PM
📣 We are moving to Barcelona to join the amazing @crg.eu and explore how centrosomes & cilia work, evolve & respond to the environment. We are looking for
PhD students www.crg.eu/en/content/t...
Postdocs gimm.pt/jobs/postdoc...
Other calls to open, also for an experienced lab manager.
Get in touch!
PhD students www.crg.eu/en/content/t...
Postdocs gimm.pt/jobs/postdoc...
Other calls to open, also for an experienced lab manager.
Get in touch!
Reposted by Eduardo Rocha
I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
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
academic.oup.com
October 30, 2025 at 11:33 AM
I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Reposted by Eduardo Rocha
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Eduardo Rocha
That merely being “under review” by a Nature family journal is offered as a quality proxy for a paper is a tragic illustration of the extent to which academia is addicted to brands and outsources evaluation
October 25, 2025 at 6:37 PM
That merely being “under review” by a Nature family journal is offered as a quality proxy for a paper is a tragic illustration of the extent to which academia is addicted to brands and outsources evaluation
Reposted by Eduardo Rocha
Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...
Bacterial strain Taxonomy for Genomic Surveillance - GenEpi-BioTrain Webinar - Research
This workshop aims to provide participants with a comprehensive understanding of bacterial classification and nomenclature approaches used in genomic surveillance. Participants will gain insight into ...
research.pasteur.fr
October 21, 2025 at 1:47 PM
Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...
Reposted by Eduardo Rocha
Horizontal gene transfer, segregation loss, and the speed of microbial adaptation
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by David V McLeod and Sylvain Gandon
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by David V McLeod and Sylvain Gandon
Horizontal gene transfer, segregation loss, and the speed of microbial adaptation
Abstract. Microbial adaptation is driven by the circulation of mobile genetic elements (MGEs) among bacteria. On the one hand, MGEs can be viewed as selfis
doi.org
October 20, 2025 at 7:23 PM
Horizontal gene transfer, segregation loss, and the speed of microbial adaptation
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by David V McLeod and Sylvain Gandon
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by David V McLeod and Sylvain Gandon