Laura Álvaro-Llorente

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

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 pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens - Nature Communications This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the carbapenemase OXA-48 has a role in the plasmid-associated fitness costs.

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

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes. Background: Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is w...

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

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

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! 🧵👇

Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli - Nature Communications pOXA-48 plasmids have emerged as key vectors of carbapenem resistance within Enterobacteriaceae. In this study, the authors use a transposon sequencing (Tn-seq) approach to identify genetic determinan...

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

Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli - Nature Communications pOXA-48 plasmids have emerged as key vectors of carbapenem resistance within Enterobacteriaceae. In this study, the authors use a transposon sequencing (Tn-seq) approach to identify genetic determinan...

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

Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...

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

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses phage attachment at the membrane and assembles a transmembrane complex that halts infection by blocking phage DNA re...

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/...

The prototypic crAssphage is a linear phage-plasmid Schmidtke et al. demonstrate that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid with a broad ho...

#phagesky

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

Experimental evolution in an era of molecular manipulation Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00867-6In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the underlying genetics and forces that shape phenotypic evolution.

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 Abstract. Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and di

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/...

graphical abstract of the article the extended mobility of plasmids

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! 👇

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨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 - Nature Communications The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate dete...

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

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

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

New-to-nature biocompatible chemistry for plastic waste upcycling - Nature Chemistry Synthetic and biological chemistry are traditionally seen as separate fields. Now, a biocompatible chemical reaction enables an engineered microbe to convert plastic waste into valuable compounds unde...

#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!

The Respiratory Tract Microbiome and Human Health The respiratory tract microbiome (RTM) trains the immune system and protects against infections. Changes in the RTM are linked to various respiratory diseases. High-throughput methodologies and compu...

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/...

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome - Nature A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistanc...

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 Abstract. Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin–antitoxin (TA) systems. However,

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/...