New round of PhD studentships in microbial engineering, including one with me on engineering non-canonical DNA mismatch repair into E. coli 🦠🧬 www.findaphd.com/phds/project...

Feel like doing a SynBio PhD in Spain? Check this offer, many fellowships available 👉🏻 lifehub.csic.es/synbio-cofund/

Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

Hey y’all, New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae www.microbiologyresearch.org/content/jour...

🧬New paper out! We report the first isolation of viable B. bacteriovorus predators from human gut microbiota. www.frontiersin.org/journals/mic.... Great work of Mario Romero @migueldiezfdz.bsky.social @josete600.bsky.social and @rosacampo.bsky.social

In this issue: Fresh light on horse evolution, mangrove restoration as coastal flood protection, and the links between aerobic metabolism and planetary oxygenation. In PNAS: https://ow.ly/yB6J50Y5ykK

And what a beautiful @pnas.org cover @paularamiro.bsky.social and @jerorb.bsky.social !!!!!! You should be very proud!

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/...

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...

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

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

Coupling DNA processing to early gene expression drives antibiotic resistance plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.01.09.698686v1

🚨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

New preprint out: Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics www.biorxiv.org/content/10.6... @mingyan-igi.bsky.social

🎁 Getting a paper acceptance right before Christmas break is one of the best feelings. 100% recommend. Happy holidays, everyone! 🎄✨

Genomic Flexibility Through Extrachromosomal Amplifications: A Leishmania Survival Strategy https://www.biorxiv.org/content/10.64898/2025.12.13.692850v1

Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social #MicroSky #Mevosky journals.plos.org/plosbiology/...

My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)

The December cover of Genome Biology and Evolution features Rojas-Triana et al., who publish a Review on the adaptive potential of extrachromosomal circular DNA across taxa. 🔗 doi.org/10.1093/gbe/evaf223 #genome #evolution

Collateral sensitivity and genetic vulnerability of antibiotic resistance

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...

On the plane after a fantastic few days in Liverpool at #MicroEvo25 organised by the @microbiologysociety.org. The science, the people, and the city were all way above expectations. I’m definitely coming back. Had an absolute blast!

What a week! Thanks to everyone who attended the UK Phage Therapy workshop and #MicroEvo25 in Liverpool… every talk, poster, question, chat, and round of applause helps to build our microbial evolution community! Thanks to @microbiologysociety.org and @ukri.org for support

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/...

🚨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

🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)

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/...

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Finally out from @daganlab.bsky.social! 🌱🦠🧬 Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events url: academic.oup.com/mbe/article/...

Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!

#microsky 😮 journals.plos.org/plosgenetics...

Exciting news! I have two positions open in my lab at the UoManchester: one PDRA and one Research Tech. Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!

Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social

🚨 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

Se busca candidat@ xa un contrato Juan de la Cierva en el lab @miguelmatilla.bsky.social en la @eezcsic.bsky.social (Granada). @canalugr.bsky.social @csic.es @csicdivulga.bsky.social Info en: aei.gob.es/convocatorias/… Las personas interesadas deben de ponerse vía: [email protected]

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/ Please share widely! #QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED

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...

Integrating theory and machine learning to reveal determinants of plasmid copy number https://www.biorxiv.org/content/10.1101/2025.10.23.684078v1

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...

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...

Dissecting the fitness effects of a carbapenem resistance plasmid in clinical Enterobacterales using plasmid-wide CRISPRi screens @aliciapcv.bsky.social @jorgesastred.bsky.social @sanmillan.bsky.social @cnb-csic.bsky.social #bacteria #plasmids

1/3 To those interested in microbial iron & metal transport: In 1992, the late JB Neilands (UCB), the pioneer in the study of Fe transport entrusted me with his collection of purified siderophores from a wide range of microbes—many of them unique chemical species that can no longer be reproduced

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...

After the coffee break, we had a round table about dealing with evolution of drug resistance & synergies among EvoMG fields. We had a panel representing the different related "areas": Isabel Veiga (Plasmodium), David Posada (Cancer), Jero Rodriguez (Bacteria), Ana Abecasis (Virus).