Florian Fournes
@flofournes.bsky.social
📤 96
📥 116
📝 4
Bacterial Genomes Adaptation_ CBI-Université de Toulouse 🇨🇵
reposted by
Florian Fournes
Justine Collier
24 days ago
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience
www.cell.com/iscience/ful...
🎊Congrats to my fantastic lab members
@noemiematthey.bsky.social
, Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
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Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein
Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics
https://www.cell.com/iscience/fulltext/S2589-0042%2826%2900124-0
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Paula Ramiro-Martínez
about 1 month ago
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story
www.pnas.org/doi/10.1073/...
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Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
https://www.pnas.org/doi/10.1073/pnas.2526088123
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Franklin Nobrega
about 1 month ago
Preprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).
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A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection
Bacteria must distinguish phage attack from normal homeostatic processes, yet the danger signals that trigger many defence systems remain unknown. Here, we show that a PUA-Calcineurin-CE-HAD module from Escherichia coli ECOR28 confers broad anti-phage protection by binding Dam-methylated deoxyadenosine monophosphate (m6-dAMP) generated during phage-induced chromosome degradation. Ligand binding converts a preassembled PUA-Calcineurin-CE hexamer loaded with six HAD phosphatases into a polymerising filament. The filament acts as a high-flux dNTP sink through a two-enzyme cascade: HAD first dephosphorylates dATP to dADP, and Calcineurin-CE then converts dADP to dAMP. dNTP collapse halts phage replication and enforces abortive infection. Multiple mobile-element DNA mimic proteins block filament assembly, revealing a direct phage counter-defence. More broadly, our findings extend a conserved, cross-kingdom paradigm of immune filament assembly to nucleotide-depletion antiviral defence and suggest modified-nucleotide sensing by related PUA-Calcineurin-CE modules as a widespread, underappreciated bacterial strategy. ### Competing Interest Statement The authors have declared no competing interest. NIHR Southampton Biomedical Research Centre, https://ror.org/01qqpzg67, Postdoctoral Bridging Fellowship F.L.N. is supported by a Wessex Health Partners (WHP) and National Institute for Health and Care Research Wessex Experimental Medicine Network (NIHR WEMN), Seed fund National Institutes of Health, GM145888, U24 GM129539) Maloris Foundation Memorial Sloan Kettering Cancer Center, P30-CA008748 Simons Foundation, SF349247 New York State Assembly
https://www.biorxiv.org/content/10.64898/2026.01.15.699771v1
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Xavier Charpentier
about 2 months ago
Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.
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Wiep Klaas Smits (ExpBac/CMAT)
about 2 months ago
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation
www.biorxiv.org/content/10.6...
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A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation
DNA methylation is a widespread phenomenon in bacteria that can regulate gene expression, although the mechanisms underlying this epigenetic regulation are often poorly understood. In Clostridioides d...
https://www.biorxiv.org/content/10.64898/2025.12.24.696351v1
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bioRxiv Microbiology
3 months ago
Plasmid copy number affects the DNA methylation-driven expression dynamics of the CfrBI restriction-modification system and impacts phage restriction
https://www.biorxiv.org/content/10.64898/2025.12.04.692298v1
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Calum H. G. Johnston
3 months ago
Pleased to share our recent article in PNAS - a collaboration with
@jessicaandreani.bsky.social
& Pablo Radicella, with important roles played by many members of each team. A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes
www.pnas.org/doi/10.1073/...
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A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS
Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and...
https://www.pnas.org/doi/10.1073/pnas.2511180122
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Devani Romero Picazo
4 months ago
Finally out from
@daganlab.bsky.social
! 🌱🦠🧬 Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events url:
academic.oup.com/mbe/article/...
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Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events
Abstract. Plasmids are important drivers of evolutionary transformations and ecological adaptation in prokaryotes. Plasmids supplying the host with benefic
https://academic.oup.com/mbe/article/42/11/msaf273/8305669
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bioRxiv Microbiology
4 months ago
Fast assembly and in vivo coalescence of ParB biocondensates involved in bacterial DNA partition
https://www.biorxiv.org/content/10.1101/2025.10.27.684735v1
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Ricardo Henriques
4 months ago
🦠🔬🤖🧑💻
#mAIcrobe
is out! With
@pinholab.bsky.social
's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making
#DeepLearning
for phenotyping accessible! Easy to use, plus model training 📜
www.biorxiv.org/content/10.1...
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Nature Communications
4 months ago
Chromosome replication and cell division cycles are not synchronized in Staphylococcus aureus, with cells exhibiting two segregated origins of replication at the start of the cell cycle
#bacteria
#microbiology
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Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus - Nature Communications
Our understanding of chromosome organization and dynamics in spherical bacteria, such as Staphylococcus aureus, remains limited. Here, the authors show that chromosome replication and cell division cycles are not synchronized in S. aureus, with cells exhibiting two segregated origins of replication at the start of the cell cycle.
https://bit.ly/43p95sF
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Florian Fournes
Florian Roisné-Hamelin
5 months ago
Delighted to announce our latest work on how Wadjet loads onto and establishes topological entrapment of plasmid DNA prior to initiating loop extrusion. At
@gruberlab.bsky.social
, Dubochet Center for Imaging and BSI
@igbmc.bsky.social
www.cell.com/molecular-ce...
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Justine Collier
6 months ago
🤩 Exciting Summer! 🤩 Two of my former postdocs in Switzerland🇨🇭 obtained Lecturer positions (Maîtres de Conférences) in French universities 🇨🇵 : congrats to Antonio Frandi and Florian Fournès !!!! 👏 La relève est assurée! All the best to both of you for this new start. 🤩
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Stephan Gruber
6 months ago
Our Wadjet-II paper by
@roisnehamelinf.bsky.social
is out in polished form:
www.cell.com/structure/fu...
With a great preview by
@kevincorbett.bsky.social
&
@amardeeep.bsky.social
highlighting the potential of Wadjets: Wadjet—Keeping a watchful eye on circular DNA.
www.cell.com/structure/fu...
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Ethan Garner
10 months ago
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
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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...
https://doi.org/10.1101/2025.05.18.654715
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Wiep Klaas Smits (ExpBac/CMAT)
6 months ago
The Escherichia coli replication initiator DnaA is titrated on the chromosome
www.nature.com/articles/s41...
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The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications
A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...
https://www.nature.com/articles/s41467-025-63147-1
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Florian Fournes
Didier Mazel
6 months ago
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...
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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…
https://www.sciencedirect.com/science/article/pii/S1369527425000797
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Javier Santoyo
7 months ago
Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome.
#BacterialExtrachromosomalElements
#OralMicrobiome
@natcomms.nature.com
🧬
www.nature.com/articles/s41...
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Shraddha Shitut
12 months ago
Excited to share our paper published in
@currentbiology.bsky.social
that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment !
www.cell.com/current-biol...
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reposted by
Florian Fournes
7 months ago
Excited to share another study from my lab @fordhamchem now out
@narjournal.bsky.social
:
doi.org/10.1093/nar/...
. Most bacterial DNA polymerases must interact with the sliding clamp DnaN for their function, but we show that it’s more complicated in B. subtilis DNA replication. (1/4)
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The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune their activity in DNA replication
Abstract. Ring-shaped sliding clamp proteins are essential components of the replication machinery across all domains of life. DNA polymerases bind the cla
https://doi.org/10.1093/nar/gkaf721
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One of the best places to conduct scientific research with a wonderfull project and a great PI!!
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7 months ago
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Daniela Barillà
7 months ago
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link:
rdcu.be/exnOc
Many years in the making, great collaboration with
@archaellum.bsky.social
&
@tunglejic.bsky.social
Thanks
@ukri.org
BBSRC &
@leverhulme.ac.uk
for funding, reviewers & editor!! 🙏
#microsky
#archaeasky
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Jesse Shapiro
8 months ago
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)
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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...
https://www.nature.com/articles/s41467-025-60699-0
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Matthew Cobb
8 months ago
Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing:
www.youtube.com/watch?v=7-tn...
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The Most Beautiful Experiment: Meselson and Stahl
YouTube video by Science Communication Lab
https://www.youtube.com/watch?v=7-tnuAqEp9g
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Pierre Dupuy
9 months ago
After a PhD and two postdocs, I’m very proud to be joining the CNRS as a Chargé de recherche, this is a meaningful milestone. Huge thanks to Claude Bruand,
@michaelglickman.bsky.social
, and
@oneyrolles.bsky.social
for their guidance and support. Olivier, let’s turn this into exciting discoveries!
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Jan-Willem Veening
9 months ago
New tenure track assistant professor position in molecular microbiology in our department
@dmf-unil.bsky.social
@unil.bsky.social
! We are casting a wide net for an experimental molecular microbiologist. Apply here:
wwwfbm.unil.ch/releve/appli...
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DMF: Tenure Track Assistant Professor towards Associate Professor in Molecular Microbiology - Site des postulations FBM
https://wwwfbm.unil.ch/releve/application/announce/show/133
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Céline Loot
9 months ago
www.pasteur.fr/fr/journal-r...
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Les bactéries utilisent les mêmes outils pour résister aux antibiotiques et aux virus
La résistance des bactéries aux antibiotiques est un phénomène qui s’accentue, créant un problème de santé publique majeur. Parmi les possibles alternatives aux antibiotiques, l’utilisation de virus i...
https://www.pasteur.fr/fr/journal-recherche/actualites/bacteries-utilisent-memes-outils-resister-aux-antibiotiques-aux-virus
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Zeynep Baharoglu
10 months ago
Marie Curie fellowship, post-doc hosting oppotunity in my lab. MSCA Post-doctoral Fellowship at IBPC Paris on RNA modifications in bacteria (FRANCE) 🦠💫
euraxess.ec.europa.eu/jobs/hosting...
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https://euraxess.ec.europa.eu/jobs/hosting/msca-post-doctoral-fellowship-ibpc-paris-rna-modifications-bacteria-france
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Céline Loot
10 months ago
At least 10% of the V. cholerae integron cassettes have novel antiphage activities (see below). Considering that there are 25,000 distinct cassettes of unknown function, integrons constitute an extraordinary and almost inexhaustible reservoir of antiphage functions!
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Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
https://www.science.org/doi/10.1126/science.ads0768
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Baptiste Darracq
10 months ago
White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) ! In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones.
www.science.org/doi/10.1126/...
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Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
https://www.science.org/doi/10.1126/science.ads0768
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Ákos T Kovács
10 months ago
Biofilm architecture determines the dissemination of conjugative plasmids
#PNAS
from
@sbigot.bsky.social
,
@knutdrescher.bsky.social
labs
www.pnas.org/doi/10.1073/...
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Biofilm architecture determines the dissemination of conjugative plasmids | PNAS
Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic res...
https://www.pnas.org/doi/10.1073/pnas.2417452122
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Nathan Fraikin
10 months ago
Our set of new prokaryote-optimized fluorescent proteins is now published !
#microbiology
#microsky
#microscopy
🧫🦠🔬
www.science.org/doi/10.1126/...
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A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging
Bright and photostable monomeric fluorescent proteins enable long-term time-lapse imaging in E. coli.
https://www.science.org/doi/10.1126/sciadv.ads6201
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Jan-Willem Veening
10 months ago
Now online
@narjournal.bsky.social
academic.oup.com/nar/article/...
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MV Mazzuoli
10 months ago
OUT NOW! 👇🏼We built a make-or-break Prime editing tool—have a read to discover how it’s changing the way we do genomic engineering.
www.nature.com/articles/s41...
@JWVeening @AxelJans & all others authors! 👏🏻
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Florian Fournes
Zeynep Baharoglu
12 months ago
Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein
www.biorxiv.org/content/10.1...
Another orphan cytosine methyltransferase in bacteria
#microsky
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Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein
While methylated cytosines are known to play important roles in eukaryotes, their significance in bacteria remains poorly understood especially when they are added on genomes by DNA methyltransferases...
https://www.biorxiv.org/content/10.1101/2025.03.21.644545v1?ct=ct
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Florian Fournes
Stephan Gruber
12 months ago
Happy to share the beautiful structure of a Wadjet SMC complex by
@roisnehamelinf.bsky.social
, with support from the DCI and
@drhonsworth.bsky.social
! This is a type II Wadjet with unique characteristics including a tandem KITE subunit, distinct coiled coil architecture and a deviant hinge.
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bioRxiv Microbiology
about 1 year ago
Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion
https://www.biorxiv.org/content/10.1101/2025.02.23.639760v1
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Noémie Matthey
over 1 year ago
It's really nice to see the huge flow of new people coming here! Maybe it's time for a quick presentation. Hi 👋 I'm Noémie, I love science 🧬 and especially microbes 🔬 I do scientific illustrations for paper, cover or logo. And I'm the illustrator behind the Bacterial World blog:
sarahs-world.blog
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Pedro Dorado-Morales
about 1 year ago
Interested in the plasmidverse? Then, don't think twice and join the International Society for Plasmid Biology Virtual Seminars Series. 👇
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"The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae | Nucleic Acids Research | Oxford Academic"
academic.oup.com/nar/article/...
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The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae
Abstract. Bacterial genomes contain a plethora of secondary replicons of divergent size. Circular replicons must carry a system for resolving dimeric forms
https://academic.oup.com/nar/article/53/2/gkae1300/7951707?searchresult=1
about 1 year ago
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Marie-Eve VAL
about 1 year ago
1/ 🔬 Our work, "Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae", is now published in Nature Communications. Here's a thread on how we think Chr1 and Chr2 replication is coordinated in Vibrio. 🧵 Link :
www.nature.com/articles/s41...
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Michael
about 1 year ago
Very happy to see our study "printed"
www.science.org/doi/10.1126/...
. We report how mechanics are related with DNA recombination efficiency. Great work by Kate
@cmcb-tud.bsky.social
@tudresden.bsky.social
in collab with
@celineloot.bsky.social
and
@amazeld.bsky.social
@pasteur.fr
. Synopsis 👇1/4
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