Manuel Ares-Arroyo

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

New preprint out on bioRxiv!

www.biorxiv.org/content/10.6...

Can conjugative plasmids be used to control plasmid and pathogen spread?

Follow me down the rabbit hole that led to this story 🧵

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...

Two cartoon images of children with plasmids for faces about to fight. Commentators are saying "Plasmid-borne CRISPR-Cas systems provide significant defensive benefits" and "Yes, but toxin-antitoxin systems on competitor plasmids constrain the offensive CRISPR-Cas benefit"

Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile
journals.plos.org/plosbiology/... 1/6

Type IV secretion systems: reconciling diversity through a unified nomenclature This review presents a comprehensive overview of Type IV Secretion Systems (T4SSs), focusing on their structural, functional, and evolutionary diversity ac

Happy to share a new review proposing a unified nomenclature for T4SSs.
Great collaboration with Peter J Christie, Gabriel Waksman, Ronnie Per-Arne Berntsson and our team.
academic.oup.com/femsre/artic...
#T4SS#Microbiology

New pre-print with @wtmatlock.bsky.social!!!
www.biorxiv.org/content/10.6...
What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

🚨 New preprint 🚨

How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence?

A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship!

www.biorxiv.org/content/10.6...

Fluorescence micrograph. Emma Miller and Alex Merz, unpublished.

🧵 After years out of the field, I and my lab are again working on bacterial type IV pili. We have just posted our first preprints, and I'm excited to share what we have discovered.

This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.

1/

On this fabulous day celebrating André Citroën's birthday 🥖🚗, I’m happy to share my main paper from my postdoc in @jrpenades.bsky.social Lab.
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!

www.biorxiv.org/content/10.6...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

Un poste de Maître de Conférence est ouvert pour rejoindre notre unité à Lyon !

Possibilité de rejoindre mon équipe pour travailler sur:
- caractérisation des mécanismes de défense anti-phage
- transfert horizontal et interactions entre éléments génétiques mobiles

N'hésitez pas à me contacter

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

Plasmid mutation rates scale with copy number | PNAS Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...

New paper out in PNAS!!! 🎉

Do more plasmid copies mean faster evolution?

🧵 Dive into the story

www.pnas.org/doi/10.1073/...

Bacteriophages mobilize bacterial defense systems via lateral transduction Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.

#microsky #phagesky #phage defence

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

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

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🧵

Thank you very much, João!

Thanks, Siân! I'm happy you liked it!

Thanks, Théo!

Merci beaucoup, Zamin!!

Thank you, Aude!

This was a really joint effort, impossible to achieve without the hard work, advise and help, of all the co-authors: @rjunker.bsky.social , @amandinen.bsky.social , Marie Touchon, and @epcrocha.bsky.social at @pasteur.fr.

As take-home message, conjugation isn't just for plasmids. The mobilome is a tangled network where both conjugative plasmids and ICEs are hitched by a wide range of mobilizable plasmids and IMEs, all of them spreading critical genes across bacterial genomes.

iOriTs are an overlooked class of Mobile Genetic Elements that evolved to remain in bacterial chromosomes while piggybacking on others to transfer between cells. They are important, since understanding these minimal hitchers can help predict the spread of critical traits in high-risk pathogens.

Unlike plasmids, iOriTs carry few antibiotic resistance genes in these species. Instead, they're usually carriers of critical virulence factors and represent MGE-defence hotspots. Interestingly, our results suggest iOriTs may be reservoirs of novel defence genes!