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Reposted by Marie-Eve VAL

Jan-Willem Veening @veeninglab.com · 4d

Finally out, such an awesome piece of work, very proud of this one: www.cell.com/cell-systems... #MicroSky

Reposted by Marie-Eve VAL

Zeynep Baharoglu @zeynepbaharoglu.bsky.social · Sep 6

So excited our antibiotic potentiation story is out 🤩 Led by the extraordinary @manonlang.bsky.social with @fox-science.bsky.social & @amazeld.bsky.social +amazing collaborators @immunobladder.bsky.social @imaneelmeouche.bsky.social 🦠 We believe it can make a difference in #AMR infections!

Uridine as a potentiator of aminoglycosides through activation of carbohydrate transporters

Uridine boosts aminoglycoside treatment efficiency against antibiotic-susceptible as well as antibiotic-resistant E. coli strains.

www.science.org

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Reposted by Marie-Eve VAL

Karina Ilchenko @karinailchenko.bsky.social · Sep 3

🚨 New preprint! 🧬

𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.

We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use

📖 www.biorxiv.org/content/10.1...

Efficient detection and typing of phage-plasmids

Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...

www.biorxiv.org

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Reposted by Marie-Eve VAL

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

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Reposted by Marie-Eve VAL

Eduardo Rocha @epcrocha.bsky.social · Sep 3

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

Karina Ilchenko @karinailchenko.bsky.social · Sep 3

🚨 New preprint! 🧬

𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.

We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use

📖 www.biorxiv.org/content/10.1...

Efficient detection and typing of phage-plasmids

Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...

www.biorxiv.org

16 47

Reposted by Marie-Eve VAL

Chris Creevey @hairyllama.bsky.social · Aug 22

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

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...

biorxiv.org

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Reposted by Marie-Eve VAL

Ethan Garner @fleshball.bsky.social · May 20

I’m excited that the work by Diego Ramirez and Lei Yin is out, where they gained several key insights into what provides the force underlying bacterial cell division doi.org/10.1101/2025....

To divide, cells must first bend the membrane inward, a process that’s energetically expensive

The interplay of membrane tension and FtsZ filament condensation on the initiation and progression of cell division in B. subtilis

The first step of cell division is deforming the planar cell membrane inward towards the cytoplasm. As deforming membranes is energetically costly, biology has developed various protein systems to acc...

doi.org

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Reposted by Marie-Eve VAL

Sarah Bigot @sbigot.bsky.social · Aug 20

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...

www.nature.com

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Reposted by Marie-Eve VAL

Alicia Calvo-Villamañán @aliciapcv.bsky.social · Aug 20

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

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...

rdcu.be

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Marie-Eve VAL @val-meve.bsky.social · Aug 20

#microsky In this review, we summarize the current literature across bacterial phyla on large extrachromosomal replicons. Current Opinion in Microbiology: doi.org/10.1016/j.mi....

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Marie-Eve VAL @val-meve.bsky.social · Aug 20

Congratulations to PhD students Jasmin Ostermayer and Noa Guzzi (co–first authors 🎉), together with Jakub Czarnecki and Alfonso Soler-Bistué, for compressing the diverse, lineage-wide literature on large extrachromosomal replicons into <5000 words and 80 references 😅

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Reposted by Marie-Eve VAL

Didier Mazel @amazeld.bsky.social · Aug 20

For those who love bacterial replicons, The ultimate review, from our lab, signed by the master of their evolution.
‪@val-meve.bsky.social‬ www.sciencedirect.com/science/arti...

Taming wild replicons: evolution and domestication of large extrachromosomal replicons

Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…

www.sciencedirect.com

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Reposted by Marie-Eve VAL

Nature Portfolio @natureportfolio.nature.com · Aug 16

A paper in Nature Microbiology reports that the use of AI to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising source of future antibiotics. #medsky 🧪

Deep learning reveals antibiotics in the archaeal proteome - Nature Microbiology

Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising source of future antibiotics.

go.nature.com

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Reposted by Marie-Eve VAL

Nature Microbiology @natmicrobiol.nature.com · Aug 8

#NatMicroPicks

Synthetic evolution overdrive 🦠🔧🚅

A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.

#SynBio #MicroSky

www.science.org/doi/10.1126/...

An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli

Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....

www.science.org

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Reposted by Marie-Eve VAL

Didier Mazel @amazeld.bsky.social · Jul 28

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon
research.pasteur.fr/en/job/a-two...

A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

research.pasteur.fr

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Reposted by Marie-Eve VAL

Eduardo Rocha @epcrocha.bsky.social · Jul 23

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/...

graphical abstract of the article the extended mobility of plasmids

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Reposted by Marie-Eve VAL

Saloni @scientificdiscovery.dev · Jul 21

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...

AlphaFold - A practical guide

www.ebi.ac.uk

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Reposted by Marie-Eve VAL

Nature Microbiology @natmicrobiol.nature.com · Jul 4

#NatMicroPicks

Vibrio in competition! 🦠💉

An orphan T6SS effector in non-toxigenic Vibrio cholerae targets susceptible strains by disrupting ion balance, shaping Vibrio population dynamics and offering a model for precision antimicrobials.

#MicroSky

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

A Vibrio-specific T6SS effector reshapes microbial competition by disrupting Vibrio bioenergetics

Liu et al. report that a Vibrio-specific T6SS effector, TseVs, selectively disrupts Vibrio bioenergetics while sparing non-target microbes via an immunity-independent mechanism. This work reveals how ...

www.cell.com

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Reposted by Marie-Eve VAL

Daniela Barillà @danielabarilla.bsky.social · Jul 2

York calling! 📣 🧬🧬🧬

Join us at www.biochemistry.org/events-and-t...

⏳⏰ Early bird deadline approaching soon, 16 July! Do not miss out! Half of the talks selected from abstracts.
@damelab.bsky.social @vslioy.bsky.social @graingerlab.bsky.social @biochemsoc.bsky.social @biophychrom.bsky.social

View of a street in York with old houses on both sides and the towers of York Minster in the background.

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Reposted by Marie-Eve VAL

Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 2

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

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...

doi.org

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Reposted by Marie-Eve VAL

Tung Le @tunglejic.bsky.social · Jul 2

Finally published! Many thanks to the reviewers and editor whose comments & suggestions improved this work significantly more than the first preprint version!!!

www.pnas.org/doi/10.1073/...

Expanding the diversity of bacterial DNA partitioning: A CTP-independent ParABS system for plasmid partitioning in Streptomyces | PNAS

The ATP- and CTP-dependent ParA-ParB-parS segrosome is a macromolecular complex that segregates chromosomes/plasmids in most bacterial species. CTP...

www.pnas.org

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Reposted by Marie-Eve VAL

Janet Iwasa @jiwasa.bsky.social · Jul 2

Check out this new review (with animations, natch) of mechanisms of licensing origins of DNA replication - a wonderful (and continuing!) collaboration with Bruce Stillman @cshlnews.bsky.social and John Diffley @crick.ac.uk! www.nature.com/articles/s41...

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Reposted by Marie-Eve VAL

Tami Lieberman @contaminatedsci.bsky.social · Jun 30

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

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Reposted by Marie-Eve VAL

Pierre Lê-Bury @pierrelebury.bsky.social · Jul 1

1/8 - New in @natcomms.nature.com !
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...

In-host evolution of Yersinia enterocolitica during a chronic human infection - Nature Communications

This study documents the evolution of antibiotic resistance and major growth defects in Yersinia enterocolitica in a patient over 14 years, revealing genetic changes that shed light on bacterial adapt...

www.nature.com

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Reposted by Marie-Eve VAL

Jesse Shapiro @bjesseshapiro.bsky.social · Jul 1

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial:

Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).

www.nature.com/articles/s41...

(1/n)

Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications

The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...

www.nature.com

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