Eduardo Rocha
@epcrocha.bsky.social
Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris
Pinned
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Reposted by Eduardo Rocha
🚨L'ENS de Lyon recrute un.e maître de conférence qui rejoindra le CIRI pour développer ses recherches sur l'immunité bactérienne, les transferts horizontaux et les MGE.
📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !
📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !
📢 Recruitment of an Associate Professor (Maître de conférences) in Bacteriology at CIRI and ENS de Lyon.
Research at @ciri-lyon.bsky.social @francoisrousset.bsky.social
@labxc.bsky.social
Anti-phage Immunity, Horizontal gene/ MGE transfer
📚 Teaching at ENS de Lyon within the Department of Biology.
Research at @ciri-lyon.bsky.social @francoisrousset.bsky.social
@labxc.bsky.social
Anti-phage Immunity, Horizontal gene/ MGE transfer
📚 Teaching at ENS de Lyon within the Department of Biology.
January 14, 2026 at 5:02 PM
🚨L'ENS de Lyon recrute un.e maître de conférence qui rejoindra le CIRI pour développer ses recherches sur l'immunité bactérienne, les transferts horizontaux et les MGE.
📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !
📖 Une très belle opportunité d'enseigner à des étudiants brillants tout en menant des recherches excitantes !
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
January 14, 2026 at 11:41 AM
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 11:26 AM
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Reposted by Eduardo Rocha
📢 We are hiring 📢 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
January 14, 2026 at 8:55 AM
📢 We are hiring 📢 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology
Reposted by Eduardo Rocha
Happy to share our recent preprint:
"DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity"
www.biorxiv.org/content/10.6...
@spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social
"DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity"
www.biorxiv.org/content/10.6...
@spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social
January 14, 2026 at 8:57 AM
Happy to share our recent preprint:
"DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity"
www.biorxiv.org/content/10.6...
@spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social
"DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity"
www.biorxiv.org/content/10.6...
@spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social
Reposted by Eduardo Rocha
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
January 14, 2026 at 5:10 AM
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
Reposted by Eduardo Rocha
Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.
📢 Recruitment of an Associate Professor (Maître de conférences) in Bacteriology at CIRI and ENS de Lyon.
Research at @ciri-lyon.bsky.social @francoisrousset.bsky.social
@labxc.bsky.social
Anti-phage Immunity, Horizontal gene/ MGE transfer
📚 Teaching at ENS de Lyon within the Department of Biology.
Research at @ciri-lyon.bsky.social @francoisrousset.bsky.social
@labxc.bsky.social
Anti-phage Immunity, Horizontal gene/ MGE transfer
📚 Teaching at ENS de Lyon within the Department of Biology.
January 13, 2026 at 2:01 PM
Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.
Reposted by Eduardo Rocha
New bioRxiv preprint from our Lesterlin lab
How early gene expression coupled to DNA processing boosts resistance plasmid spread.
With @nfrk92.bsky.social in collab with Y. Yamaichi lab
👉 doi.org/10.64898/202...
How early gene expression coupled to DNA processing boosts resistance plasmid spread.
With @nfrk92.bsky.social in collab with Y. Yamaichi lab
👉 doi.org/10.64898/202...
Coupling DNA processing to early gene expression drives antibiotic resistance plasmid dissemination
The rapid global spread of antibiotic resistance is mediated by conjugative plasmids, yet how these elements establish immediately after entering new bacterial hosts remains poorly understood. Here we...
doi.org
January 12, 2026 at 8:56 AM
New bioRxiv preprint from our Lesterlin lab
How early gene expression coupled to DNA processing boosts resistance plasmid spread.
With @nfrk92.bsky.social in collab with Y. Yamaichi lab
👉 doi.org/10.64898/202...
How early gene expression coupled to DNA processing boosts resistance plasmid spread.
With @nfrk92.bsky.social in collab with Y. Yamaichi lab
👉 doi.org/10.64898/202...
Reposted by Eduardo Rocha
Neisseria gonorrhoeae carries an unusually large number of restriction–modification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...
doi.org
January 13, 2026 at 1:40 PM
Neisseria gonorrhoeae carries an unusually large number of restriction–modification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...
Reposted by Eduardo Rocha
NLR-like immunity in bacteria
A new study from the Alex Gao lab. The scope of this work is incredible!!!
www.biorxiv.org/content/10.6...
A new study from the Alex Gao lab. The scope of this work is incredible!!!
www.biorxiv.org/content/10.6...
Diverse bacterial pattern recognition receptors sense the conserved phage proteome
Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...
www.biorxiv.org
January 5, 2026 at 1:59 PM
NLR-like immunity in bacteria
A new study from the Alex Gao lab. The scope of this work is incredible!!!
www.biorxiv.org/content/10.6...
A new study from the Alex Gao lab. The scope of this work is incredible!!!
www.biorxiv.org/content/10.6...
Reposted by Eduardo Rocha
📢 Job opening — Bioinformatics Engineer
Join the MicroScope platform (LABGeM, CEA/Genoscope) to develop tools and pipelines for microbial genomics.
📍 Evry, France | ⏳ Fixed-term contract
🔗 bit.ly/3Z5WSXc
@ifb-elixir-fr.bsky.social
Join the MicroScope platform (LABGeM, CEA/Genoscope) to develop tools and pipelines for microbial genomics.
📍 Evry, France | ⏳ Fixed-term contract
🔗 bit.ly/3Z5WSXc
@ifb-elixir-fr.bsky.social
Ingénieur en bioinformatique pour le développement de la plateforme MicroScope - LABGeM
Localisé au CEA/Genoscope, un centre de recherche scientifique dédié à la génomique environnementale, le Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme (LABGeM, UMR8030, l...
bit.ly
January 12, 2026 at 11:36 AM
📢 Job opening — Bioinformatics Engineer
Join the MicroScope platform (LABGeM, CEA/Genoscope) to develop tools and pipelines for microbial genomics.
📍 Evry, France | ⏳ Fixed-term contract
🔗 bit.ly/3Z5WSXc
@ifb-elixir-fr.bsky.social
Join the MicroScope platform (LABGeM, CEA/Genoscope) to develop tools and pipelines for microbial genomics.
📍 Evry, France | ⏳ Fixed-term contract
🔗 bit.ly/3Z5WSXc
@ifb-elixir-fr.bsky.social
Reposted by Eduardo Rocha
PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...
jobs.uni-jena.de/jobposting/c...
PhD student bioinformatics: Phage genomic modules: data mining, visualisation, and databasing
jobs.uni-jena.de
January 12, 2026 at 11:41 AM
PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...
jobs.uni-jena.de/jobposting/c...
Reposted by Eduardo Rocha
Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
January 11, 2026 at 7:43 PM
Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Reposted by Eduardo Rocha
We’re looking for a postdoc to join the Hendrickson lab!
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...
Research Associate / Postdoctoral Fellow - Honeybee Bacteriophages and Advanced Biotechnology -
University of Canterbury | Te Whare Wānanga o Waitaha
jobs.canterbury.ac.nz
January 9, 2026 at 12:27 AM
We’re looking for a postdoc to join the Hendrickson lab!
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...
Reposted by Eduardo Rocha
Canada Research Chairs www.canada.ca/en/impact-pl...: $1M/year for 8 years, plus up to $6M in CFI infrastructure support. Looking for leading researchers abroad interested in AMR research, antibiotic discovery (Pandemicstopai.ca), phages. Email short vision + CV. Tight deadlines: March 10 & June 15
Canada Impact+ Research Chairs - Canada.ca
www.canada.ca
January 8, 2026 at 7:18 PM
Canada Research Chairs www.canada.ca/en/impact-pl...: $1M/year for 8 years, plus up to $6M in CFI infrastructure support. Looking for leading researchers abroad interested in AMR research, antibiotic discovery (Pandemicstopai.ca), phages. Email short vision + CV. Tight deadlines: March 10 & June 15
Reposted by Eduardo Rocha
Bacteria do compute and can be reprogrammed for new capacities—but not exactly by following Turing’s rules. Evolution, context dependence, and the soft-matter nature of living hardware redefine what computation means in biology. From @angelgm.bsky.social Lab 👉🏻 www.sciencedirect.com/science/arti...
Exploring the computing power of microbes that shapes the environment
Microbes process input information into output responses through diverse genetic and metabolic mechanisms, effectively making them physical systems th…
www.sciencedirect.com
January 8, 2026 at 6:40 AM
Bacteria do compute and can be reprogrammed for new capacities—but not exactly by following Turing’s rules. Evolution, context dependence, and the soft-matter nature of living hardware redefine what computation means in biology. From @angelgm.bsky.social Lab 👉🏻 www.sciencedirect.com/science/arti...
Reposted by Eduardo Rocha
It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...
Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis
Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…
www.sciencedirect.com
January 7, 2026 at 2:13 PM
It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...
Reposted by Eduardo Rocha
Seeking expressions of interest from researchers abroad for a Canada Impact+ Research Chair ($1M/year × 8 + up to $6M CFI) in AI-enabled antibiotic discovery and/or AMR, phage & phage-based derivatives. Email me a short vision, CV, and 3–5 key papers. Deadline: March 10, 2026 (Intake 2: June 15).
January 7, 2026 at 1:19 AM
Seeking expressions of interest from researchers abroad for a Canada Impact+ Research Chair ($1M/year × 8 + up to $6M CFI) in AI-enabled antibiotic discovery and/or AMR, phage & phage-based derivatives. Email me a short vision, CV, and 3–5 key papers. Deadline: March 10, 2026 (Intake 2: June 15).
Reposted by Eduardo Rocha
New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
Constructing a “periodic table” of bacteria to map diversity in trait space
Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen
academic.oup.com
January 6, 2026 at 7:31 PM
New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
Reposted by Eduardo Rocha
📣 preprint alert!
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.
🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.
🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...
Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia
Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes d...
doi.org
January 6, 2026 at 10:29 AM
📣 preprint alert!
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.
🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.
🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...
The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky
#phagesky #microsky
January 5, 2026 at 4:41 PM
The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky
#phagesky #microsky
Reposted by Eduardo Rocha
As 2026 begins, the EAM, @Vdlorenzo.bsky.social, Paul B. Rainey and many others remind us the urgency of renewing support to Society Journals and, taking action to reward quality research and curb predatory publishing.
👉 buff.ly/V36xgMO
👉 buff.ly/T8QE90G
👉 buff.ly/V36xgMO
👉 buff.ly/T8QE90G
January 5, 2026 at 8:00 AM
As 2026 begins, the EAM, @Vdlorenzo.bsky.social, Paul B. Rainey and many others remind us the urgency of renewing support to Society Journals and, taking action to reward quality research and curb predatory publishing.
👉 buff.ly/V36xgMO
👉 buff.ly/T8QE90G
👉 buff.ly/V36xgMO
👉 buff.ly/T8QE90G
🚨 New paper from our lab in Cell Reports @cp-cellreports.bsky.social, led by Clara Douadi!
We show that bacteriophages can cross the intestinal barrier, with increased translocation in Crohn's disease.
🔗 www.cell.com/cell-reports...
Many thanks to all the authors!
We show that bacteriophages can cross the intestinal barrier, with increased translocation in Crohn's disease.
🔗 www.cell.com/cell-reports...
Many thanks to all the authors!
Differential translocation of bacteriophages across the intestinal barrier in health and Crohn’s disease
Intestinal barrier integrity is crucial for gut homeostasis. Douadi et al. show that
bacteriophages can cross this barrier without causing damage and that translocation
rates depend on the barrier sta...
www.cell.com
January 5, 2026 at 1:40 PM
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!