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...

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!🧵👇

🚨 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!👇👇

Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...

Great article about EvolvingSTEM & Dr. Abigail Matela's leadership to infuse dozens of schools w/ authentic microbiology research experiences that demonstrate evolution in real time. We've engaged more than 11,000 students over 11 years! 😅 🧪 🧫 www.hotmetalcampus.com/news-researc...

Multiple fully funded PhD/postdoc positions available: experimental evolution of tumour suppression, egalitarian & fraternal ETIs, jumbo phage ecology & genetics. Related EoIs welcome. Email CV/statement of motivation written in own words. Open until filled. Grateful for reposting 🙏

@vscooper.micropopbio.org & @isabelott.bsky.social let me crash their high-school bacteria hunt while I was working on my book "Life's Edge." Their paper's now out, featuring lots of mutants (including my very own CZ1A).

Now out in AEM @asm.org! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy journals.asm.org/eprint/FBU9M...

So happy to see this finally published in @plosbiology.org! This is the first chapter of @julielebris.bsky.social PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics w/ @epcrocha.bsky.social #microsky @klebclub.bsky.social Link below- Check out her 🧵 for more details!

Happy to have participated in this beautiful work on the human gut resistome in populations exposed to minimal anthropogenic pollution 🥳. Do not miss it!

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👇

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...

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

Out Now! Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation #MicroSky

Check out the latest version of our paper — peer-reviewed, polished, and published. Hope you like it! www.nature.com/articles/s41...

Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼

New preprint on the limits of detecting higher-order interactions in microbial communities. www.biorxiv.org/content/10.6... We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.

Given that clonal biofilms of single bacterial species rapidly diversify into niche specialists, how do biofilms of multiple species evolve? A 🧵 featuring new collaborative pubs: 1. www.biorxiv.org/content/10.6... 2. www.nature.com/articles/s41...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

What a fantastic new addition to my lab! 🚀 Welcome @albertohca.bsky.social to the @uam.es family! Stay tuned for the science we’re going to build together in the coming years!

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover. 🔗 www.biorxiv.org/content/10.6...

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...

Emerging advances in prokaryotic transposition: TnPedia as a promising tool www.cell.com/trends/micro... #jcampubs

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

New preprint from the lab! Stress-Induced Cooperation Promotes Tolerance in Resource-Limited Auxotrophic Microbial Consortia. Great and long journey with great collaborators.

We’re very happy to share the results from the last chapter of my PhD, now out as a preprint on bioRxiv www.biorxiv.org/content/bior...

🚨Call for papers🚨 Microbial Evolution: Impacts on Human Health in the society journal Evolution, Medicine, and Public Health Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa EIC: me This will be great, please submit and share! academic.oup.com/emph/pages/m...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

🚨🚨🚨 We're looking for a research tech to work on alt splicing, pancreatic islets and diabetes. The goal is to set a high-throughput platform to investigate the role of alternative exons in beta cell biology! Interested in joining our lab at @melisupf.bsky.social? 👇 www.upf.edu/documents/d/...

Preprint alert📢! 
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host? ➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied Here is what we found. 
www.biorxiv.org/content/10.6... 
#MicroSky #PhageSky 🧵

It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons! 🧪 #socialviruses #evosky

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...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

🚨 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

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...

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...

✨New paper from @jrpenades.bsky.social and @sanmillan.bsky.social labs. We found that non-conjugative plasmids 🧬 tend to have low mobility to promote functional diversity ⚔️💊 in bacterial communities🦠🦠. Brilliant work by Akshay, @asantoslopez.bsky.social and others. www.cell.com/cell-reports...

📢¡Oferta de trabajo en el CBM! El grupo de David Ruano ofrece un contrato predoctoral para desarrollar un nuevo método diagnóstico del SIBO (Small Intestinal Bacterial Overgrowth). Plazo hasta el 30 oct. Info👇 www.cbm.uam.es/index.php/jo...

🚨🚨🚨 Two super well-funded PhD grants from our MSCA Doctoral Network @evomg-dn.bsky.social at our lab at @melisupf.bsky.social, @crg.eu and the @evomg-bcn.bsky.social Program. If you're excited about evolution, genomics and biomedical research, this is your DN! 😃 Further info: www.evomg-dn.eu and 👇

Session 3 (Thr 09/10 in the afternoon) was dedicated to Microbes, microbiome and antibiotic resistance.

Nuestro compañero Álvaro San Millán (@sanmillan.bsky.social), investigador en el #CNB_CSIC ha recibido el Premio María Moliner, que reconoce la labor de quienes se inician en la dirección de tesis doctorales, destacando su compromiso en el acompañamiento del talento emergente. ¡Enhorabuena!👏

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...

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...

View from the lab now. Did I mention that we are recruiting faculty microbiologists? www.linkedin.com/posts/vaughn...

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

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine. 1) MMG (my dept): fundamental research in med micro 2) Peds ID / I4Kids institute 3) Center for Vaccine Research 🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

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