Manuel Ares-Arroyo
aresarroyom.bsky.social
Manuel Ares-Arroyo
@aresarroyom.bsky.social
Ramón y Cajal Fellow | Head of Biology of Mobile Genetic Elements Unit | Fisabio Foundation | Plasmids, MGEs, AMR, bacteria evolution
Pinned
Big news! Deeply honored to receive an #ERCStG from @erc.europa.eu! 🍾

Over the next five years, E-MOTION will study how interactions between Mobile Genetic Elements shape bacterial evolution in clinical settings.

Exciting science and opportunities ahead: stay tuned, positions will be opening soon!
📣 Good news! 📣

Results of the ERC 2026 Starting Grant call are out!

Funding worth a total of €705 million will go to 421 early-career researchers across Europe.

Discover who, what and where 👉 link.europa.eu/9M3MmN

🧪 #ERCStG #FrontierResearch #HorizonEurope
🇪🇺 @scienceinnovation.ec.europa.eu
Reposted by Manuel Ares-Arroyo
Finally out! 🎉
After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!)
Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus.
www.nature.com/articles/s41...

⬇️ 1/4
Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance - Nature Communications
Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...
www.nature.com
September 16, 2026 at 11:50 AM
As a wonderful way to wrap up these past few months, I’m deeply honored to receive the Plasmid Biology Prize from the International Society for Plasmid Biology at #ISPB2026 Berlin. 🍾🥳

Many thanks to the Society, and to all the friends, colleagues, and mentors I’m lucky to meet at these meetings.
September 15, 2026 at 5:12 PM
Reposted by Manuel Ares-Arroyo
I have an email alert for the word #plasmid. Yes, I'm that person. Today it brought me a paper comparing bacterial plasmids with #ecDNA in cancer (same tricks, different kingdoms).

"A paper a day keeps ignorance away" 👇

www.nature.com/articles/s41...
The shared evolutionary capacities of plasmids and extrachromosomal DNA - Nature Reviews Genetics
Plasmids in bacteria and extrachromosomal DNA in cancer both generate copy-number variation, alter gene expression and promote rapid adaptation. In this Perspective, Shaw and Henssen explore their sha...
www.nature.com
September 14, 2026 at 5:20 PM
Reposted by Manuel Ares-Arroyo
Interesting paper

'Plasmid–Host Networks Reveal Persistent Mobile Elements Across Wastewater Treatment'

www.nature.com/articles/s41...
Plasmid–Host Networks Reveal Persistent Mobile Elements Across Wastewater Treatment - Nature Communications
Using Hi-C metagenomics, this study maps how plasmids associate with bacterial hosts across wastewater treatment. They find that plasmid host range narrows from influent to effluent, and a few bacteri...
www.nature.com
September 12, 2026 at 11:06 AM
Reposted by Manuel Ares-Arroyo
Fascinating stuff - Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes academic.oup.com/mbe/advance-...
Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes
Abstract. Toxin-antitoxin systems (TAs) are widespread in bacterial genomes. Yet, their integration, persistence, and impact in chromosome dynamics remain
academic.oup.com
September 13, 2026 at 2:20 PM
Reposted by Manuel Ares-Arroyo
Why did some #viruses evolve to be #giants while others did not? Our perspective piece on this topic with Eugene Koonin. www.pnas.org/doi/10.1073/...
Why did some viruses evolve to be giants while others did not? | PNAS
Viruses are ubiquitous mobile genetic elements that are obligate symbionts of cellular life forms and replicate exclusively within host cells. The ...
www.pnas.org
September 11, 2026 at 5:10 PM
Reposted by Manuel Ares-Arroyo
It's finally published! What a journey @brownlab.bsky.social and I have been on with this one (ask me about it over a pint 🍻). Super excited to be able to say that it's finally out in Trends (author gift link to follow)! 🦠🧫 #phagesky
September 11, 2026 at 5:36 AM
Reposted by Manuel Ares-Arroyo
Please share!

We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬
More details & applications on funder website by 21st Oct 👇🏻

gw4biomed.ac.uk/developing-c...
Developing CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTP
Project Code IIAR27Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Antimicrobial resistance (AMR) poses a major thre...
gw4biomed.ac.uk
September 10, 2026 at 7:00 AM
Reposted by Manuel Ares-Arroyo
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome?

We are looking for a PhD student to work on this question in Bath!
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
gw4biomed.ac.uk
September 9, 2026 at 8:08 AM
Reposted by Manuel Ares-Arroyo
A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔

doi.org/10.1093/gbe/...
Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak
Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out
doi.org
September 7, 2026 at 7:35 AM
Reposted by Manuel Ares-Arroyo
705 million euro in ERC Starting Grants has just been awarded to 421 researchers across Europe.

In the coming months many will start to hire staff and set up their own research groups.

Keep an eye 👀 on the ERC team positions advertised on the #Euraxess website. 👉 buff.ly/7xrOtMp
September 6, 2026 at 12:30 PM
Big news! Deeply honored to receive an #ERCStG from @erc.europa.eu! 🍾

Over the next five years, E-MOTION will study how interactions between Mobile Genetic Elements shape bacterial evolution in clinical settings.

Exciting science and opportunities ahead: stay tuned, positions will be opening soon!
📣 Good news! 📣

Results of the ERC 2026 Starting Grant call are out!

Funding worth a total of €705 million will go to 421 early-career researchers across Europe.

Discover who, what and where 👉 link.europa.eu/9M3MmN

🧪 #ERCStG #FrontierResearch #HorizonEurope
🇪🇺 @scienceinnovation.ec.europa.eu
September 3, 2026 at 2:33 PM
Reposted by Manuel Ares-Arroyo
It’s out! 🥹🎉

We’re so incredibly happy and proud to see this work out in the world.

And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you!

doi.org/10.1038/s415...
@natmicrobiol.nature.com
September 3, 2026 at 9:34 AM
Reposted by Manuel Ares-Arroyo
Distinct plasmid- and host-encoded mechanisms drive small plasmid copy number-mediated heteroresistance in Escherichia coli | bioRxiv
Distinct plasmid- and host-encoded mechanisms drive small plasmid copy number-mediated heteroresistance in Escherichia coli
Antibiotic heteroresistance, the presence of a rare resistant subpopulation within an otherwise susceptible bacterial population, poses a significant clinical challenge. Understanding its genetic mechanisms is critical for early detection and treatment efficacy. Here, we investigate the contribution of small plasmids to heteroresistance using a clinical bloodstream Escherichia coli isolate carrying a 12 kb ColE1-type plasmid (p12). We show that this plasmid drives transient β-lactam heteroresistance through massive increases in plasmid copy number. Two distinct genetic mechanisms drive this amplification: mutations in the plasmid RNAI/RNAII that deregulate replication control, and a chromosomal recD mutation that induces multimerization and a shift toward rolling-circle replication. Notably, this recD-mediated amplification is restricted to small ColE1 and F- plasmids. This study highlights the crucial role of small plasmids in resistance evolution, demonstrating that they can cause this phenotype via alternative genetic pathways, without the involvement of traditional large resistance plasmids. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2024-03665, 2024-06136, 2021-02091 NIH Common Fund, https://ror.org/001d55x84, 1U19AI158080-01
www.biorxiv.org
August 21, 2026 at 12:02 AM
Reposted by Manuel Ares-Arroyo
New paper led by Liam Shaw, with Arancha Peñil Celis, @aresarroyom.bsky.social, @adalijuanluo.bsky.social & Fernando de la Cruz. academic.oup.com/nar/article/...
This is very much Liam’s story, but I loved playing a small part in it 🧵
The leading region of many plasmids is adapted for translational efficiency
Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first
academic.oup.com
August 20, 2026 at 1:15 PM
Reposted by Manuel Ares-Arroyo
#MicroSky
maybe we should update this post?
August 19, 2026 at 1:34 PM
Reposted by Manuel Ares-Arroyo
Excited to share that our paper on Horizontal Gene Transfer is now out in its final form in @gigascience.bsky.social! 🥳 By analysing 163 high-quality ant genomes, we show that HGT from bacteria is widespread across the ants and likely has adaptive functions!

doi.org/10.1093/giga...
🐜📸: Alex Wild
July 2, 2026 at 3:35 PM
Reposted by Manuel Ares-Arroyo
Excited to share our latest preprint from the lab! 🧬

We found that IS110 elements, typically considered small, can grow into large elements that carry cargo and disseminate antimicrobial resistance. We also experimentally validated the smallest and largest IS110s characterized to date.
Canonically minimal RNA-guided insertion sequences expand into large elements that disseminate antimicrobial resistance https://www.biorxiv.org/content/10.64898/2026.08.14.744561v1
August 18, 2026 at 5:32 PM
Reposted by Manuel Ares-Arroyo
1st genome sequenced (Sanger 1977), 1st genome
synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social
Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
www.biorxiv.org
August 3, 2026 at 10:42 AM
Reposted by Manuel Ares-Arroyo
Plasmid biology is compressed in host chromosomal architecture | bioRxiv www.biorxiv.org/content/10.6...
August 13, 2026 at 6:43 AM
Reposted by Manuel Ares-Arroyo
One of our most popular preprints of 2025 is now published in @science.org. Congrats to @brianhie.bsky.social, @samuelhking.bsky.social, and team on establishing a framework for generating and evaluating AI-generated genomes.

- Access the paper: www.science.org/doi/10.1126/...
August 6, 2026 at 6:43 PM
Reposted by Manuel Ares-Arroyo
Broken chromosomes don’t stay home: Tunneling nanotubes carry damaged DNA between human cells
Broken chromosomes don’t stay home: Tunneling nanotubes carry damaged DNA between human cells
In a recent Cell paper, Maurais et al. show that genomic instability drives human cells to transfer fragmented chromosomes to neighbors via tunneling nanotubes (TNTs), with heritable functional consequences, raising fundamental questions about intercellular communication, genome surveillance, and cancer evolution.
dlvr.it
August 7, 2026 at 7:14 PM
Reposted by Manuel Ares-Arroyo
Some bacteria use the CRISPR/Cas systems as transcriptional repressors of other anti-phage systems, such that when CRISPR interfered with, gene expression of repressed anti-phage systems goes up www.nature.com/articles/s41...
CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature
CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...
www.nature.com
July 22, 2026 at 5:21 PM
Reposted by Manuel Ares-Arroyo