Huge thanks to Thibault Frisch, @sellinlab.bsky.social and all other co-authors and collaborators Petra Geiser, Margarita Κomi, Philip Karlsson, Anjeela Bhetwal, Laura Jenniches, @lbarquist.bsky.social , @holmqvist-lab.bsky.social , and @andrenmateus.bsky.social, for making this work possible!

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

This work builds on our recent Nature Genetics paper on Shigella colonization in intestinal organoids (rdcu.be/eqGgf), zooming in on one of the screen hits: pcnB.

The pcnB gene sustains Shigella flexneri virulence Author summary Bacterial infections represent a major global threat. Understanding the genetic determinants promoting infections is crucial to overcome this threat. Shigella is an intracellular bacter...

Thrilled to share that our study on how the pcnB gene sustains Shigella virulence is now published in PLOS Pathogens: journals.plos.org/plospathogen...

In short: pcnB ➝increased virulence-plasmid replication ➝ elevated T3SS expression ➝ enhanced invasion/spread within the intestinal epithelium.

Happy to announce that our paper is finally out! Thanks to @brozlab.bsky.social and co-authors @elliottbernard.bsky.social @ehartenian.bsky.social 🥳 the NLRP6 inflammasome is activated by sterile- or pathogen-induced endolysosomal damage @embojournal.org

IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇

Enhanced virulence and stress tolerance are signatures of epidemiologically successful Shigella sonnei
@sydneylmiles.bsky.social @katholt.bsky.social
🙏to transformative collaborative effort

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

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.

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!

Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria Mast cell phenotypic features influence anti-bacterial response. Connective tissue-like mast cells sense Salmonella through combined Toll-like-receptor (TLR) signaling and recognition of Type-III-sec....

Mast cell subsets respond uniquely to Salmonella infection. Read all about it in our latest paper in EJI. Another chapter in our deciphering of mast cell interactions with enterobacteria, driven by Chris von Beek.

onlinelibrary.wiley.com/doi/10.1002/...

Matrix-M adjuvant triggers inflammasome activation and enables antigen cross-presentation through induction of lysosomal membrane permeabilization - npj Vaccines npj Vaccines - Matrix-M adjuvant triggers inflammasome activation and enables antigen cross-presentation through induction of lysosomal membrane permeabilization

Such a rewarding collab it has been with our colleagues at #Novavax to dissect the MoA of their potent Matrix-M adjuvant. This project has really put the imaging skills of @erixoneriksson.bsky.social to the test. The fruits of this joint labour out now in NPJ Vaccines

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

RNA modifications digest Summer 2025 Bimonthly newsletter: RNA modifications and related topics, mostly in bacteria. Summer 2025, first issue!

🦠 Launching a bimonthly digest on RNA modifications and related topics in bacteria!🤩 First issue: Summer 2025. Shared here + by email, future ones will be quicker reads! 😅 #rnasky #microsky #ribosome Subscribe and share if you are interested! rnamodifupdates.substack.com/p/rna-modifi...

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature Genetics A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

#NatMicroPicks

Decoding Shigella’s Virulence Blueprint 🦠🧬

Combining organoid infection models with genome-wide mutagenesis allows mapping the full set of Shigella genes required for human gut colonization

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

@sellinlab.bsky.social @natgenet.nature.com

Prof. Lars Barquist. Story title: One the Map: Experimental Research Uses Cultured Mini-Organs to Study Infections

Could lab-grown mini-organs help scientists research a range of infections? A new study published in Nature Genetics shows how researchers have mapped how the Shigella bacterium infects the human gut.

Read our interview with study co-author — and UTM Biology prof — Lars Barquist at uoft.me/bI7.

Excited to be at #EESMicrobiology this week presenting our latest work on #Shigella gut #organoid infection screen from our recent Nature Genetics paper (see below)!
Stop by poster 109 or just look for me, happy to chat and connect!
#Microbiology #Shigella #Organoids #TraDIS

The pcnB gene sustains Shigella flexneri virulence www.biorxiv.org/content/10.1101/2025.06....

This is figure 2, which shows a genome-wide map of the Shigella geneset required to invade the human enteroid infection model.

A study in Nature Genetics establishes the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. go.nature.com/4e7fdKp 🧬 🧪

Huge congratulations to Thibault Frisch for leading this work to completion with remarkable insight and drive, and thanks to all co-authors for making it happen! @sellinlab.bsky.social, @lbarquist.bsky.social, @andrenmateus.bsky.social, @holmqvist-lab.bsky.social

pcnB (poly-A polymerase I) sustains replication of the Shigella virulence plasmid at levels optimal for virulence and boosts intraepithelial expansion in intestinal organoid monolayers.

New preprint out: www.biorxiv.org/content/10.1...
We followed up on our recent Nature Genetics paper mapping Shigella colonization in intestinal organoids with a deep dive into one of the screen hits: pcnB.

#Shigella #virulence #microsky

Organoid models advance dysentery control - Nature Genetics Shigella is a major human pathogen with a stark lack of pipelines linking genome content to clinical pathogenesis. An innovative study using large-scale organoid models, combined with genome-wide muta...

Thanks @sydneylmiles.bsky.social and @sergemostowylab.bsky.social for writing such a sharp and thoughtful editorial, which covers all the main points and potential caveats of our study published yesterday.

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

Thank you so much!

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

Our latest work combines human gut epithelial #organoid culture with experimental #Shigella #infections, transposon mutagenesis, and statistical modeling. This has led to the mapping of the comprehensive geneset that drives Shigella epithelial colonization.

Out @natgenet.nature.com:

rdcu.be/eqGgf

Stay tuned for a follow up story coming out soon!

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature Genetics A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

Very excited about our latest combining advanced cell culture, transposon-insertion sequencing, and statistical modeling to map Shigella virulence determinants in organoid models. Great collaboration w/ @mldm.bsky.social @sellinlab.bsky.social in @natgenet.nature.com

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

Lab-grown mini-organs help uncover how pathogens cause disease YouTube video by SciLifeLab

“we used mini organs, specifically mini-intestines, and infected them with a dangerous bacterium called Shigella” says @mldm.bsky.social‬

@sellinlab.bsky.social‬ (SciLifeLab & @uu.se) shows that cultured mini-organs can uncover how pathogens cause disease

youtu.be/xG_66ZGd_fk

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature Genetics A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

Thanks to lab-grown miniature intestines, researchers at #HIRI & Uppsala University have mapped how Shigella bacteria infect the human gut. This @natgenet.nature.com study opens the door to using cultured mini-organs to investigate a wide range of infections. 📍🦠
www.nature.com/articles/s41...

Organoid models advance dysentery control - Nature Genetics Shigella is a major human pathogen with a stark lack of pipelines linking genome content to clinical pathogenesis. An innovative study using large-scale organoid models, combined with genome-wide muta...

Finally thanks @sydneylmiles.bsky.social and @sergemostowylab.bsky.social for for highlighting our work with this cool editorial: www.nature.com/articles/s41...

Deeply grateful to @sellinlab.bsky.social for the unwavering support! And special thanks to our lab members Anjeela Bhetwal, @erixoneriksson.bsky.social, Ana Lopes, Angelika Ntokaki, and Martina Pasqua for their contributions. Also grateful to @andrenmateus.bsky.social and our clinical collaborators

This study was co-led with our outstanding collaborators @lbarquist.bsky.social and Laura Jenniches — whose computational expertise was key to making this possible.

One of the most exciting insights: Shigella uses tRNA-modifying enzymes and codon usage bias to fine-tune its virulence!

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

Thrilled to share our work is finally out at @natgenet.nature.com ! rdcu.be/eqGgf
Combining a scalable human gut organoid model with TraDIS and statistical modeling, we mapped how Shigella colonizes the intestine at genome-wide resolution.