Jorge Sastre Domínguez

What is the best strategy to win any contest?

Eliminate your opponents of course.

Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.

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

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.

Now published in @natcomms.nature.com rdcu.be/eOf63

Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...

So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...

Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments The repeatability of evolution is fundamentally important for understanding the origin and diversification of life as well as for developing evolutionary forecasting tools. Repeatability is limited by...

For the predicting evolution crowd

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

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/...

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...

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...

Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky

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

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics

We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...

If you like time travel & biology, this 🧵is for you👇

Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

Mutations in the circadian cycle drive adaptive plasticity in cyanobacteria | PNAS Circadian clocks allow organisms to anticipate daily fluctuations in light and temperature, but how this anticipatory role promotes adaptation to d...

I am so proud to be part of this work, that we initiated Fernando de la Cruz and I, when he was on sabbatical in my lab in 2009... it took so much time for this achievement, 1000 thanks to Raúl Fernández-López! this brought me back to my PhD on cyanobacteria genetics. www.pnas.org/doi/10.1073/...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed Mutations within promoters and coding sequences are both involved in adaptation, but their relative contributions remain to be compared directly. Using the fungal enzyme cytosine deaminase, we examine...

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky

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

Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...

Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇

Check out @julielebris.bsky.social’s thread on our latest manuscript describing phenotypic heterogeneity in capsule production in Klebsiella & Acinetobacter @klebclub.bsky.social

This work started when I was still in @pasteur.fr & got finished in @cbitoulouse.bsky.social
#microsky #phagesky

We are hiring a PhD student! Are you fascinated by microbes and evolution? Come join us in Barcelona!

Serotype swapping in Klebsiella spp. by plug-and-play Understanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic inter...

How complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes?
That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus.
The paper: www.biorxiv.org/content/10.1...
Thread👇

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Identifican el coste fisiológico de mantener la resistencia microbiana en enterobacterias - CNB

El grupo de Álvaro San Millán revela el coste de mantener la resistencia en enterobacterias

El trabajo traza un mapa funcional del plásmido pOXA-48, con potencial para guiar nuevas terapias contra resistencias

bit.ly/4p0fCmY

@sanmillan.bsky.social @aliciapcv.bsky.social @jorgesastred.bsky.social

Extremely glad to see this out!!

Wonderful work by all the lab, especially @aliciapcv.bsky.social. Don't miss her thread!!

Thank you so much!!! 😄

Thank you very much!!! 😁😁

Our new manuscript is out! A bit of everything cool:

Plasmids ✅
Insertion Sequences ✅
AMR Evolution ✅
Microbial Communities ✅
Databases analyses ✅
Mathematical modeling ✅

See the scientific thread below of Jorge Sastre, who has brilliantly led this work with @palomarodera.bsky.social

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:

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

New paper in collaboration with the @asantoslopez.bsky.social lab!

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

Kudos to all the authors involved in this work, what a team!!!! @palomarodera.bsky.social @javierdelafuente.bsky.social S. Martinez-Gonzalez, S. Quesada, M. Valencoso-Requena, @aliciapcv.bsky.social C. Costas, @ayari.bsky.social @asantoslopez.bsky.social and @sanmillan.bsky.social

Summing up, our results indicate that conjugative plasmids not only fuel AMR evolution through gene dissemination, but also through IS-mediated inactivation of chromosomal genes.

Clinically, our study could explain the observed rise of combined AMR phenotypes, such as carbapenems and colistin!