Jorge Sastre Domínguez
@jorgesastred.bsky.social
PhD student in the Plasmid Biology and Evolution (PBE) and Evolution of Microbes and Mobile Genetic Elements labs. Bioinformatics 💻 Evolutionary Biology 🦠 Antimicrobial resistance 💊 📍CNB - CSIC
In 2014, Jason Rosch and I met at a GRC in Tuscany and sketched an idea on a cocktail napkin: what if we evolved S.pneumo in mice, treated them with antibiotics, varied their immune systems and watched what won? 11 years and a huge team effort later, it's out in @cp-cellhostmicrobe.bsky.social 🧵
We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)
Nature@nature.com · last wk.Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature
Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.
go.nature.com
Out Now! Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections #MicroSky
Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections
Nature Microbiology, Published online: 23 July 2026; doi:10.1038/s41564-026-02414-3Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to tobramycin during chronic lung infection within patients.
go.nature.com
Out Now! Klebsiella pneumoniae inhibits vasodilation through capsule and T6SS-dependent pathways #MicroSky
Klebsiella pneumoniae inhibits vasodilation through capsule and T6SS-dependent pathways
Nature Microbiology, Published online: 21 July 2026; doi:10.1038/s41564-026-02425-0Vasodilation is inhibited by Klebsiella pneumonia through a multipronged approach involving type VI secretion system activity and the VgrG4 effector, plus capsule, to limit eNOS-dependent and endothelial hyperpolarization routes to vasodilation.
go.nature.com
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
César de la Fuente@delafuentelab.bsky.social · 2w agoBiology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...
Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...
Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology
The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...
nature.com
So it turns out that after these six years, there was almost no further increase. One of the big surprises in the world of drug resistance: in many cases resistance levels stop increasing even when we don't change how we use the drugs.
Rather: small N + strong selection = beneficial mutations linked to DNA repair mutants that ⬆️ mutation supply We tried to be accurate here @catarmbruster.bsky.social www.cell.com/cell-reports... Grateful that evolutionary biology is being used in microbial pathogenesis, now need more pop-gen
Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis
Armbruster et al. find that infection-site biogeography impacts evolution of the opportunistic pathogen, Pseudomonas aeruginosa. In the sinuses of adults with cystic fibrosis, P. aeruginosa residing i...
cell.com
Can harmful gene loss become an evolutionary opportunity? In our new work in @molbioevol.bsky.social , lab-evolved E. coli lines recovering from metabolic gene loss did more than return to normal: some surpassed wild type on nutrients never seen during lab evolution. 📎 doi.org/10.1093/molb...
🔬🦠 Comment #Klebsiella parvient-elle à changer de capsule aussi fréquemment pour mieux s’adapter à son environnement ? Les travaux de @julielebris.bsky.social mis à la une par @cnrsbiologie.bsky.social 👏 -avec @epcrocha.bsky.social #MicroSky @cbitoulouse.bsky.social
CNRS Biologie@cnrsbiologie.bsky.social · 3mo ago#ResultatScientifique🔎| Une bactérie capable de changer de « bouclier » pour mieux s’adapter à son environnement : une stratégie étonnante de Klebsiella pneumoniae qui éclaire ses capacités d’évolution et de résistance. ✍️ @olayarendueles.bsky.social @julielebris.bsky.social ▶️ buff.ly/q8AKHo1
The version of record of our revised preprint is finally out today. In it, we introduce a fast and reliable methdology for the full factorial design of microbial communities, i.e. constructing every monoculture, pair, trio, four-member,... n-member co-culture of N strains. doi.org/10.7554/eLif...
Full factorial construction of synthetic microbial communities
A rapid, inexpensive, and easy to implement experimental protocol enables the construction of combinatorially complete sets of microbial consortia.
doi.org
Check it out, this is a truly useful dataset! #mevosky
Paloma Rodera@palomarodera.bsky.social · 3mo agoNew paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...
New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...
biorxiv.org
New book "A Primer for Experimental Evolution" with coauthors Michael Rose, Margarida Matos, and Joe Graves. www.worldscientific.com/worldscibook... A compact primer for students and colleagues interested in planning and designing experiments to address questions in evolutionary biology.
A Primer for Experimental Evolution
worldscientific.com
Happy to share that our latest research on the eco-evolutionary dynamics of MDR plasmids and PDPs is now out (open access vAuthor) in The ISME Journal doi.org/10.1093/isme... Here, we explored how plasmid-dependent phages (PDPs) act as a selective pressure against the spread of multidrug resistance
Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmids
Abstract. Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are part
doi.org
What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇
biorxiv.org
🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇
Multireplicon plasmids emerge under predictable rules and drive the spread of antimicrobial resistance across bacterial hosts
Plasmids are DNA molecules that replicate independently of the bacterial chromosome and are typically associated with the spread of antimicrobial resistance (AMR) and virulence determinants, among other relevant traits. Fusion events between plasmids generate larger, complex backbones that carry two or more replication systems, known as multireplicon plasmids. Despite decades of study, we are still far from understanding how multireplicon plasmids arise, persist, and shape the evolution of AMR. Here, we analyzed 24,000 non-redundant plasmids across bacterial genera and found that more than 30% of them encoded multiple replicons. Compared to single-replicon plasmids, multireplicon plasmids were larger, were enriched in genes encoding antimicrobial, metal, and biocide resistance as well as virulence factors, and showed higher mobility and a broader host range. We also found that multireplicon assembly is not random. Some replicon pairs repeatedly merge into stable multireplicon plasmids, while other pairs rarely fuse even when they commonly coexist intracellularly. We also show that replicon pairs tend to be localized either in close proximity to one another or on opposite poles of the plasmid. We further highlight that multireplicon plasmids can be broadly classified into two groups: long-term coevolving replicon pairs and transient associations that lack a shared evolutionary history. Finally, we reveal the molecular mechanisms underlying multireplicon formation and highlight the role of insertion sequences in their formation and maintenance. Together, our work sheds light on the abundance, gene content, evolutionary patterns, and formation dynamics of multireplicon plasmids and pinpoints their relevance to bacterial evolution and human health. ### Competing Interest Statement The authors have declared no competing interest. Instituto de Salud Carlos III, https://ror.org/00ca2c886, PI23/01945, PFIS - FI22/00265, Miguel Servet - CP22/00164 European Research Council, https://ror.org/0472cxd90, HorizonGT, 101077809 Fundación Ramón Areces, "Ayudas Fundación Ramón Areces para la realización de Tesis Doctorales en Ciencias de la Vida y de la Materia 2025" Coordenação de Aperfeicoamento de Pessoal de Nível Superior, https://ror.org/00x0ma614, 88881.128025/2025-01
biorxiv.org
Ignacio (Nacho) de Quinto@nachodequinto.bsky.social · 3mo agoWhat if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇
Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...
science.org
Latest from the lab! Between clinical S. aureus, most gene transfer mechanisms are blocked, yet lateral transduction remains highly efficient. Restriction modification-defective strains act as gateways for horizontal gene transfer, enabling DNA flow across populations. rdcu.be/fbNQK
Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution
Nature Communications - The efficiency of horizontal gene transfer between different bacterial lineages is often unclear. Here, Figueroa et al. show that lateral transduction is the primary driver...
rdcu.be
Out in @natcomms.nature.com! We show that while most MGEs are blocked by RM systems🛡️, the chromosome is still mobile! 🧬And that cells with defective systems act as "gateways" for HGT. Can you find the hidden Easter egg🐇🥚? Hint: There's a nod to my 🇲🇽 heritage in one of the figures! rdcu.be/fbUC8
Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution
Nature Communications - The efficiency of horizontal gene transfer between different bacterial lineages is often unclear. Here, Figueroa et al. show that lateral transduction is the primary driver...
rdcu.be
New paper from Hugh Cottingham, @katholt.bsky.social , @yekwah.bsky.social @nenadmacesic.bsky.social and co. Great to see the speed/accuracy tradeoff info here, I don't think I've seen it laid out like this before. www.microbiologyresearch.org/content/jour...
🔊 Looking for a Research Assistant in Bacterial Evolution to join my lab 🦠 🥼Main duties: Research (AMR + microbiome) + lab assistance. ⏲️ Post duration: 30 months 🗓️ Closing date for applications: 20th April 2026 💰 Salary: ~£35k Details and how to apply: tinyurl.com/2a3v66y7 Please share!
This link will take you to a page that’s not on LinkedIn
lnkd.in
Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez
We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇
The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...
rdcu.be
New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Here is it! Super new science from us on horizontal gene transfer & bact defense systems! Liyana OW YONG discovered the first-of-its-kind defense factor AbjA that triggers 'abortive conjugation' as a defense mechanism, by targeting the T4SS! How neat?! #MicroSky 1/7 www.biorxiv.org/content/10.6...
biorxiv.org
Shu-Sin Chng@figlegend.bsky.social · last yr.Extremely proud of newly minted PhD Dr Nur Liyana bte Ayub Ow Yong for her work in our lab! Some new science coming soon so stay tuned! 🎉🎉
Phd Position alert 🚨 Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. It’s not going to be just regular fun. It’s going to ASTRAfun. 🤓 www.uu.nl/en/organisat...
PhD Position in Computational Modelling of Fungal Evolution
How do giant mobile elements called ‘Starships’ reshape fungal plant pathogens? Help us computationally model their spread and impact in nature and agriculture!
uu.nl
