José R Penadés

An unprecedented DNA recognition–mimicry switch governs induction in arbitrium phages Temperate phages integrate multiple information sources to regulate lysis-lysogeny transitions. SPBeta-like phages use arbitrium signalling and DNA damage to control repressor activity during lytic in...

Excited to share our latest work with @albertomarina.bsky.social and @avigdoreldar.bsky.social labs, where we decipher the mechanism by which SPβ-like phages sense the SOS response to control the lysis–lysogeny switch. www.biorxiv.org/content/10.1...

Grantham PhD opportunities The Grantham Institute - Climate Change and the Environment invites PhD applications that support projects in some of our priority research areas. In...

🚨 PhD Opportunity in my lab🚨
Harnessing Phage Satellites for Next-Generation Biological Crop Protection
🗓 Deadline: 12 Jan
🔗 Apply: tinyurl.com/425x8ahj
🔗 Project : tinyurl.com/22uanm86
Interested in Structural Microbiology, Phage Biology & SynBio - Apply Now!

Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1

Bacterial immune systems as causes and consequences of microbiome structure Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...

👏 Dos proyectos del #CNB seleccionados en la convocatoria de Investigación en Salud 2025 de la @caixaresearch.bsky.social

Ambos abordan un gran reto global: la resistencia a los antimicrobianos.

#HealthResearch #FundaciónlaCaixa
@sanmillan.bsky.social @jaescudero.bsky.social

f.mtr.cool/jejatlbssz

1/ Antibiotic resistance causes ➕ than 1 M deaths each year and understanding why this happens is key to stopping it.

With #HealthResearch support, @sanmillan.bsky.social is investigating how different plasmids (DNA fragments) coexist in bacteria and confer resistance.

https://tinyurl.com/3bysv6cr

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

#microsky #phagesky #phage

Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.

academic.oup.com/mbe/article/...

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

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...

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...

mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pne…

New paper: www.sciencedirect.com/science/arti...
Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇

Please RT. Post-doc opportunity alert! 💥 closing 10th December.. Come join our team (www.thelowlab.org) at Imperial, London, working on the structure and mechanism of bacterial secretion systems.

For more details and to apply please see

www.imperial.ac.uk/jobs/search-...

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...

@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/...

Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases https://www.biorxiv.org/content/10.1101/2025.10.29.685425v1

Bacterial TIR-based immune systems sense phage capsids to initiate defense - Nature Microbiology After sensing capsids, the Thoeris antiphage defense system triggers a cascade that leads to NAD+ cleavage and cell arrest, which are dynamics that are mirrored in some mammalian immune pathways.

New article alert: Bacterial TIR-based immune systems sense phage capsids to initiate defense

Out now in Nature Microbiology by Cameron G. Roberts, Chloe B. Fishman, Zhiying Zhang, Dalton V. Banh, Dinshaw J. Patel & Luciano A. Marraffini

#microsky

www.nature.com/articles/s41...

Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome

Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky

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

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

Do plasmids really move around that much? Well, maybe not always

Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social

This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social

www.cell.com/cell-reports...

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...

The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin...

New paper just out from #OurImperial @tcostalab.bsky.social

The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain.

www.nature.com/articles/s41...

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👇

Well, I guess I just learned that svg don't work great here. Check the figures in the preprint!

Phages communicate across species to shape microbial ecosystems Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

Our latest work reveals that arbitrium phages cross-communicate across species! These tiny viruses “listen” to signals from others, coordinating lysis-lysogeny decisions across species.
Original idea from @albertomarina.bsky.social and, as usual, he was right.
www.biorxiv.org/content/10.1...

PS Simon’s tail fibre protein structure models showing the variants causing altered surface receptor binding specificity are Lovell-y

5-years in the making this paper has been a real journey!

Also, a fun collaboration with @frimanscience.bsky.social @jofoth.bsky.social Edze Westra, Simon Lovell, Aras Kadioglu

#mevosky #phagesky

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

Check it out! A proper team effort from past and present group members and a great collaboration with @sergemostowylab.bsky.social

El proyecto "Descubrir actividades de resistencia antimicrobiana más allá de la resistencia" de
@sanmillan.bsky.social (#CNB, @csic.es) y @jaescudero.bsky.social (@ucm.es) recibe una ayuda del Programa #Fundamentos de Fundación BBVA.

ℹ️Lee la noticia aquí👇

bit.ly/48cvkp1

Evolutionary rescue accelerates competitive exclusion in a parasite community Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

New pre-print: Eco-evolutionary responses of phage to different thermal regimes.

Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2

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

Now published! www.nature.com/articles/s41...

Very nice collaboration with Hoogenboom ( @ucl.ac.uk ) and Bonev ( @uniofnottingham.bsky.social ) labs.

Evolutionary rescue accelerates competitive exclusion in a parasite community Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

Builds on pre-print posted earlier this week and gratuitously reposted here

www.biorxiv.org/content/10.1...
#Phagesky