José R Penadés
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jrpenades.bsky.social
José R Penadés
@jrpenades.bsky.social
320 followers 20 following 9 posts

Frustrated football player, I moved to a less relevant work: microbiologist interested on mobile genetic elements

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Biology 59%
Environmental science 21%
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Reposted by José R. Penadés

craigmaclean.bsky.social
Craig MacLean @craigmaclean.bsky.social · 4d
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.
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…
www.sciencedirect.com

Reposted by Simon Roux, Mart Krupovìč, José R. Penadés

soreklab.bsky.social
Sorek Lab @soreklab.bsky.social · 4d
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👇

Reposted by José R. Penadés

Reposted by José R. Penadés

lowlab.bsky.social
Harry Low’s Lab @lowlab.bsky.social · 6d
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-...

Reposted by José R. Penadés

biorxiv-microbiol.bsky.social
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 12d
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases https://www.biorxiv.org/content/10.1101/2025.10.29.685425v1

Reposted by José R. Penadés

Reposted by José R. Penadés

paulbrainey.bsky.social
Paul Rainey @paulbrainey.bsky.social · 13d
@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/...
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...
www.pnas.org

Reposted by José R. Penadés

craigmaclean.bsky.social
Craig MacLean @craigmaclean.bsky.social · 15d
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...
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...
www.biorxiv.org

Reposted by José R. Penadés

natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · 17d
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...
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.
www.nature.com

Reposted by José R. Penadés

Reposted by José R. Penadés

asantoslopez.bsky.social
Alfonso Santos Lopez @asantoslopez.bsky.social · 19d
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...
www.cell.com

Reposted by José R. Penadés

Reposted by Jesse M. Shapiro, José R. Penadés

sanmillan.bsky.social
Alvaro San Millan @sanmillan.bsky.social · 19d
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...
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...
www.cell.com

Reposted by José R. Penadés

imperiallifesci.bsky.social
Imperial Life Sciences @imperiallifesci.bsky.social · 21d
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...
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...
www.nature.com

Reposted by José R. Penadés

epcrocha.bsky.social
Eduardo Rocha @epcrocha.bsky.social · 27d
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👇
Lytic phages form modular isolation networks and exhibit long-term genetic stability

jrpenades.bsky.social
José R Penadés @jrpenades.bsky.social · 27d
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...
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...
www.biorxiv.org

Reposted by José R. Penadés

Reposted by José R. Penadés

brockhurstlab.bsky.social
Michael Brockhurst @brockhurstlab.bsky.social · Oct 6
PS Simon’s tail fibre protein structure models showing the variants causing altered surface receptor binding specificity are Lovell-y

Reposted by José R. Penadés

brockhurstlab.bsky.social
Michael Brockhurst @brockhurstlab.bsky.social · Oct 6
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

Reposted by Jesse M. Shapiro, Simon Roux, José R. Penadés , and 1 more

brockhurstlab.bsky.social
Michael Brockhurst @brockhurstlab.bsky.social · Oct 6
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...
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...
www.biorxiv.org

Reposted by José R. Penadés

biorxiv-microbiol.bsky.social
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Oct 5
The Staphylococcus aureus LXG-domain toxins EsxX and SAR0287 do not promote virulence in a zebrafish larval infection model https://www.biorxiv.org/content/10.1101/2025.10.04.680436v1

Reposted by José R. Penadés

cnb-csic.bsky.social
Centro Nacional de Biotecnología (CNB) @cnb-csic.bsky.social · Oct 2
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

Reposted by José R. Penadés

Reposted by José R. Penadés

Reposted by José R. Penadés

craigmaclean.bsky.social
Craig MacLean @craigmaclean.bsky.social · Sep 30
Builds on pre-print posted earlier this week and gratuitously reposted here

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

Reposted by Jesse M. Shapiro, José R. Penadés

craigmaclean.bsky.social
Craig MacLean @craigmaclean.bsky.social · Sep 30
New pre-print
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky

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

Reposted by José R. Penadés, Alan McNally

bugsinblood.bsky.social
Andy Edwards @bugsinblood.bsky.social · Sep 29
Now published! www.nature.com/articles/s41...

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

Reposted by José R. Penadés

craigmaclean.bsky.social
Craig MacLean @craigmaclean.bsky.social · Sep 29
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...
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...
www.biorxiv.org

Reposted by José R. Penadés, Alan McNally

brockhurstlab.bsky.social
Michael Brockhurst @brockhurstlab.bsky.social · Sep 26
Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...