Maria Letizia Di Martino

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 https://www.biorxiv.org/content/10.1101/2025.06.16.659909v1

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...

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

“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.

Determinants of divergent Salmonella and Shigella epithelial colonization strategies resolved in human enteroids and colonoids | mBio Pathogenic bacteria employ partially overlapping sets of virulence factor functions to colonize host epithelia but can differ markedly in their pathogenesis and disease kinetics. This work combines ba...

Out now @mbio.bsky.social !: We provide a time-resolved map comparing #Salmonella and #Shigella epithelial colonization strategies in human #enteroids and #colonoids. Connecting the dots among decades of molecular findings reg. underlying virulence factors.

journals.asm.org/doi/10.1128/...

#EESInfection was very inspiring and enriching! Thanks for all new connections and for the opportunity to present our soon to be published story on TraDIShigella during infection of human intestinal organoids! Stay tuned to read the full story!

Only 328 days to go! We're very busy behind the scenes getting thigns ready for the meeting! In the meantime you can add your email address for updates here: coming-soon.embo.org/w26-04

Was great fun to have the emminent @lbarquist.bsky.social visit for the @scilifelab.se The Svedberg seminar this week.

Few can explain computation and statistics so that even wetlab biologists get it, but here is one:

www.utm.utoronto.ca/biology/peop...

www.helmholtz-hiri.de/en/research/...

So great to finally meet you too! Thanks for all the patient computational-to-biological translations over the years. It has been really great working together. I suspect it won’t be long before we find another crazy adventure to dive into!

Today our favorite #mastcell infection-ologist Chris von Beek nailed his #PhD thesis to the group log. Looking forward to an exciting defense. They grow up so fast...

Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...

OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice

#microsky 🧪

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

Biased sampling confounds machine learning prediction of antimicrobial resistance Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train...

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪

www.biorxiv.org/content/10.1...

ProQ prevents mRNA degradation through inhibition of poly(A) polymerase Abstract. The RNA-binding protein ProQ interacts with many transcripts in the bacterial cell. ProQ binding is associated with increased messenger RNA (mRNA

New paper from the lab out now. ProQ prevents polyadenylation to stabilise mRNA in Salmonella.
Fantastic work by Sofia Bergman and Christopher Birk.

Micromix: web infrastructure for visualizing and remixing microbial ‘omics data Abstract. Micromix is a flexible web platform for sharing and integrating microbial omics data, including RNA sequencing and transposon-insertion sequencin

Interested in collecting, sharing, and interacting with large collections of bacterial functional genomics data (RNA-seq, Tn-seq/TraDIS, etc.)? Check out our new web platform, Micromix, with case studies for Salmonella and Bacteroides! 🧫🧬🖥️🧪 Thread 1/n

academic.oup.com/gigascience/...