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...

I'm pleased we discussed our research on the respiratory and intestinal microbiomes in the evolution of critically ill patients at #CSMicrobiome2026 @cellpressevents.bsky.social Great work of Iván Linares and @sandramingo.bsky.social

This paper is 💥 Really nice work by @nachodequinto.bsky.social

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👇

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...

🧬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

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...

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...

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

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

New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths. biorxiv.org/content/10.1101/2025.08.20.671315v1 @jomcinerney.bsky.social

New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇

Our paper “Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli” is now online in @natcomms.nature.com ✨ 👉 www.nature.com/articles/s41... @cnrs-rhoneauvergne.bsky.social @mmsb-lyon.bsky.social

First of all, we recommend reading a complementary study led by Yannick Baffert and @sbigot.bsky.social, in which they use Tn-seq to study the genetic determinants of pOXA-48 in plasmid maintenance and conjugation. Really cool piece of work that reaches similar conclusions to ours! 2/14

This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription. www.cell.com/cell/fulltex... Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

#phage #phagesky Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing | PNAS www.pnas.org/doi/10.1073/...

#phagesky www.cell.com/cell-host-mi...

ICYMI: New online! Experimental evolution in an era of molecular manipulation

Excited 🥳 to share our latest work on gut phages! Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌 Out in Cell Reports @cp-cellreports.bsky.social doi.org/10.1016/j.ce... Here's what we found 🤓

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa 🦠👏High-throughput tRNA epitranscriptome profiling using mass spec on P. aeruginosa transposon insertion library and links with metabolic networks #microsky #rnasky doi.org/10.1093/nar/...

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Had an amazing time at #FEMS2025 last week, where I presented our latest findings on collateral sensitivity mediated by beta-lactamases ☯️ Big thanks to everyone who came by! So proud of my colleagues for their brilliant talks and posters ✨

The perfect summer read is here! 👇🏽

A must read paper! 👇

🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...

Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41...

Universal rules govern plasmid copy number www.nature.com/articles/s41...

#NatMicroPicks E. coli making paracetamol from plastic waste! 🦠💊 A new biocompatible chemistry for plastic waste upcycling using microbes. #MicroSky #SynBio 🔧🧬 www.nature.com/articles/s41...

What determines who a phage can infect? We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort. 👇 A thread!

New mini-review on the respiratory microbiome and its contribution to human health from biotechnology 🫁🦠 @tmcoque.bsky.social @microbiotech.bsky.social enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

New antibiotic class discovered by researchers at @mcmasteruniversity.bsky.social & @illinoispress.bsky.social "A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome" in @nature.com Hope it can make it to market to help combat #AMR infections www.nature.com/articles/s41...

The Eligo team did it again! We just shared on biorxiv the work we did towards the development of a CRISPR-Cas therapy targeting Shiga Toxin producing E. coli (STEC). www.biorxiv.org/content/10.1...

A noncanonical intrinsic terminator in the HicAB toxin–antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids in @narjournal.bsky.social by Lin et al. academic.oup.com/nar/article/...