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? 🤔
🧵👇
Congrats Pedro et al!! Beautiful story!
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
Pictured is a map of plasmids, which are DNA molecules that can be transferred between bacteria. Each ring and dot represents an evolved plasmid and a mutation, respectively. Image credit: Paula Ramiro-Martínez.
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!
Thank you!!
Thank you, Carmen!
Thank you, Vaughn! It’s usually tough to compete with all the cute animal covers they usually pick, so I’m really proud this one got chosen!
Thank you!
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/...
