Eduardo Rocha

Manuscript accepted just in time for #ESEB2025 @eseb2025.bsky.social
@julielebris.bsky.social will present phenotypic heterogeneity in some #ESKAPE pathogens 🧫 !
S34.01 - Mechanisms of adaptation to changing conditions in microorganisms
Those not going to Barcelona, stay tuned for details!

Horizontal Gene Transfer Inference: Gene Presence–Absence Outperforms Gene Trees Abstract. Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new env

@swstkm.bsky.social & @martinlercher.bsky.social evaluate HGT inference methods, showing that those analyzing gene family presence/absence patterns across species trees outperform approaches based on gene tree-species tree reconciliation.

🔗 doi.org/10.1093/molbev/msaf166

#evobio #molbio #HGT

Thanks, Alvaro!

Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓

A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon
research.pasteur.fr/en/job/a-two...

A Phylogenetic Host‐Range Index Reveals Ecological Constraints in Phage Specialisation and Virulence Phages are typically known for having a limited host range, targeting particular strains within a bacterial species, but accurately measuring their specificity remains challenging. Factors like the g...

After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.social‬ @inrae-pv.bsky.social‬ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/...
These are our key findings:

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive chan...

The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻

www.biorxiv.org/content/10.1...

Great to see this out. The impact of antibiotics on the gut phages and what it tells us of the disruption associated with antibiotics . www.cell.com/cell-reports... Check @eugenpfeifer.bsky.social thread

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...

The #ESEB2025 meeting in Barcelona is getting closer, there are still places available but time for registration is running up. Are you going to miss the main evolutionary biology event in Europe this year?
👇
eseb2025.com/registration/

thanks! I keep forgetting that I must add them...

Thanks to co-authors María Pilar Garcillán-Barcia, Fernando de la Cruz & lab young coll on plasmids @charlescoluzzi.bsky.social @eugenpfeifer.bsky.social @aresarroyom.bsky.social @amandinen.bsky.social @matthieu-haudiquet.bsky.social @julmini.bsky.social @olayarendueles.bsky.social ++ many not here.

the evolution of plasmid mobility

Plasmid mobility can evolve rapidly. Some plasmids evolve faster than others and carry preferentially certain cargo functions, such as antibiotic resistance, other change in terms of mobility from helpers to hitchers, from phages to conjugative, others may simply die out. 8/9

plasmids strike back

Plasmids can be targeted by bacteria and other MGEs (including other plasmids) for destruction by multiple defense systems. But they can also fight back creating a diversity of positive and negative interactions with cells and other MGEs. 7/9

plasmids pick their hosts

Some plasmids seem to be able to pick their hosts (and/or being picked by their hosts). This involves molecular interactions promoting targeted conjugation or phage-plasmid infection. 6/9

Phage-plasmids versus conjugative plasmids

Other plasmids are also phages, others are satellites of phages. This brings balance to the world of mobile genetic elements, both phages and conjugative elements can be of type integrative (in the chromosome) or plasmids. Advantages and disadvantages of these types are open to understanding. 5/9

mechanisms of hitchers and lazy plasmids to transfer between cells.

Most plasmids require other plasmids to transfer between cells (hitchers) or enjoy some sort of lazy mobility. This is only now being quantified and understood in detail. 4/9

statistics on plasmids

Now that there are tens of thousands of completely sequenced plasmids, one gets the opportunity not only to understand their diversity but also study their molecular biology at the light of their ecology and impact on microbial populations. 3/9

conjugation history and distribution of ralaxases and conjugative systems

Conjugation is now understood in exquisite detail in a few systems, but many questions remain: What exactly happens in the recipient cell? How does it occur in some major clades (Cyanobacteria, Archaea)? What is the cost of the process (for donors and recipients)? 2/9

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

New paper alert! 🚨

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate.

We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.

Let's dive in! 🧵👇

Viromics approaches for the study of viral diversity and ecology in microbiomes Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity.

www.biorxiv.org/content/10.1...

Heads up! 📢
The 5th Session of the ISPB Virtual Seminars is tomorrow, from 8:00 to 9:00 UTC. Hope to see you there virtually!
#Plasmid #ISPB #VirtualSeminar

#Joboffer #CNRS CPJ computational biology in our unit. Deadline for submitting your application is July 14. See details below. Come to join us!

@univparissaclay.bsky.social @cea.fr @genopole.bsky.social

Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by @campy-bara.bsky.social www.biorxiv.org/content/10.1...

PhD Project: Discovering Novel Mechanisms of Phage Genome Evolution We are looking for an awesome PhD student to join our research team to investigate how bacteriophages (phages) generate targeted mutations that enable them to evolve and infect new bacterial hosts. Yo...

PhD opportunities at @flindersuniversity.bsky.social in Adelaide, Australia's most liveable city, to study genetics in #phage

We will also have genetics #postdoc positions too!

#microsky #phagesky

www.linkedin.com/pulse/phd-pr...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...