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👇

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...

New preprint! We show that conjugation accelerates the segregation of #plasmid alleles -> horizontal transfer is a route for allele segregation in MGE evolution. Led by Lisa Hartmann, with @mariosanter.bsky.social &Nils Hülter. Naturally, reviewed by @qedscience.bsky.social! doi.org/10.64898/202...

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

Glad to see our latest work out in Nature Microbiology!! Extremely grateful to everyone involved in the project. Check it out!! 👇🏻👇🏻

Final version of our last paper is out! www.nature.com/articles/s41...

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.

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

How do evolutionary forces shape bacterial adaptation to the plant environment? 🌱🦠 Curious? Read our new review in @femsjournals.bsky.social Microbiology Reviews. #PlantMicrobiome #MicrobialEvolution #HostMicrobeInteractions #Rhizosphere #Microbiome 🔗 doi.org/10.1093/fems...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

New preprint out on bioRxiv! www.biorxiv.org/content/10.6... Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵

A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination https://www.biorxiv.org/content/10.64898/2026.02.21.707213v1

BRIG v1.0.0 Released — BLAST Ring Image Generator This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1. BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]

Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution... www.biorxiv.org/content/10.6...

🚨 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)

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

New pre-print with @wtmatlock.bsky.social!!! www.biorxiv.org/content/10.6... What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

Conjugation structures plasmid populations through host-lineage restriction https://www.biorxiv.org/content/10.64898/2026.02.19.706745v1

CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin–antitoxin activity when horizontally transferred | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003658

SFI’s Santiago Elena has been elected a fellow of the American Academy of Microbiology. He joins 62 fellows in the 2026 class. His work explores how RNA viruses adapt to hosts and manipulate cellular resources. Since joining SFI in 2008, he has organized several working groups on virus evolution.

A short research stay in 2019 (back in the pre-COVID era) at José R. Penadés lab turned into the third chapter of my PhD and today it finally sees the light.

Sometimes, adaptation to one #antibiotics can make bacteria more vulnerable to other drugs. #CollateralSensitivity. 💡 By following the evolution of a β-lactamase, we uncovered how mutations can both create and mitigate such collateral sensitivity networks. www.biorxiv.org/content/10.6...

Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1

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...