Youssef El Mouali

Uropathogenic Escherichia coli invade luminal prostate cells via FimH–PPAP receptor binding - Nature Microbiology Uropathogenic Escherichia coli infection of a murine prostate organoid model reveals a bacterial FimH–host prostatic acid phosphatase adhesin-receptor interaction enabling invasion and replication wit...

Our first paper is out today in @natmicrobiol.nature.com!

We introduce a prostate organoid model and show that UPEC invades prostate cells via FimH binding to the prostate-specific protein PAPP. A step toward targeted therapies against bacterial prostatitis. 🎉

#UTI #UPEC #Organoids #AMR

Harnessing the microbiome for cancer therapy Nature Reviews Microbiology, Published online: 05 January 2026; doi:10.1038/s41579-025-01268-6In this Review, Hajjar, Mars and Kashyap discuss the role of the microbiome in cancer development and progression and in treatment response. They also consider the potential of the microbiome as a therapeutic target and as a prognostic and predictive biomarker, and outline major knowledge gaps in the field.

New online! Harnessing the microbiome for cancer therapy

Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv

RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

New paper from the lab!
Led by Patrick Müller: we show that non-antibiotic compounds — but not macrolide antibiotics — can induce an efflux pump that protects Bacteroidaceae from macrolides.
A neat twist on drug–microbe interactions... www.tandfonline.com/doi/full/10....

Small RNA promotes negative feedback of the master virulence regulator PhoP by repressing the PhoQ sensor enhancer UgtL in acidic pH | mSphere To cause disease, pathogens must express their virulence genes at the right time and in proper levels. Here, we establish that a small RNA (sRNA) restricts the activation of a regulator critical for t...

Check out our new article! Congrats to Michelle Prophete, Alex Mabel and Payton Bowman for their great work!

Small RNA promotes negative feedback of the master virulence regulator PhoP by repressing the PhoQ sensor enhancer UgtL in acidic pH | mSphere journals.asm.org/doi/10.1128/...

🔊 Interested in doing a PhD on RNA-binding proteins in an abundant microbiota species and becoming a member of the German Priority Programme “Illuminating Gene Functions in the Human Gut Microbiome”? Apply here: www.uni-wuerzburg.de/karriere/sin...

Muchas Felicidades!!! 👏👏 👏

RNAcanvas: interactive drawing and exploration of nucleic acid structures Abstract. Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. H

🧪 #RNAsky

If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!

academic.oup.com/nar/article/...

Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri Abstract. The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this l

🧵 New paper alert!
Our first dive into non-human hosts: the gut microbiome of the critically endangered lemur Indri indri 🐒🌱
Led by talented MSc student Francisca Labisa-Morais!
📄 @isme-microbes.bsky.social
academic.oup.com/ismej/advanc...

Nonuniversality of inflammaging across human populations - Nature Aging Analyzing readouts of inflammaging across four cohorts, Franck and colleagues identify strong variation and observe that inflammaging, in its known form, primarily emerges in industrialized—but not nonindustrialized—populations.

Human populations with less industrialized lifestyles may not experience inflammaging, a chronic low-grade inflammation that is linked with ageing, according to research published in @nataging.nature.com:

#Ageing

Unraveling the tempo and mode of horizontal gene transfer in bacteria Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facil…

www.sciencedirect.com/science/arti...

Nearly missed my bus stop reading this fascinating review :)

Advancing RNA phage biology through meta-omics Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i

I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies.

#PhageSky

doi.org/10.1093/nar/...

A geological timescale for bacterial evolution and oxygen adaptation Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the ge...

#weekendreading🔬📑

A geological timescale for bacterial evolution and oxygen adaptation

@science.org #microsky

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

Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition Nature Communications - Acute systemic immune activation may affect gut-luminal colonisation dynamics. Here, the authors show that LPS exposure in mice elevates gut-luminal oxygen species levels,...

I am very excited to share our latest publication on the effect of systemic #endotoxin on intestinal #microbiota spearheaded by the brilliant Sanne Kroon at the Hardt lab @eth-dbiol.bsky.social @ethzurich.bsky.social @naturecomms.bsky.social

👉🏼 rdcu.be/eelLn

Fast Facts: The Gut Microbiome ‘Fast Facts: The Gut Microbiome’, though pithy and concise, is amazingly comprehensive and takes the reader through all major aspects of the human gut micr

I have been teaching classes on the gut #microbiome for almost 20 years and always struggled to have a good book to recommend. Finally there is one. Fergus Shanahan's "Fast Facts: The Gut Microbiome" provides expert insight, is brilliant, and it is free.

doi.org/10.1159/isbn...

Our review on the acquisition and transmission of the human microbiome, now out @naturerevmicro.bsky.social 🦠 🔄

This was a fun writing process with @vheidrich.bsky.social and Nicola Segata! See Vitor's summary thread below:

Metagenomic estimation of dietary intake from human stool - Nature Metabolism Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...

#metagenomics #microbiome #microbiomesky

So what is MEDI? A combination of two things:

📣Fully funded PhD position available in our lab at @uniwuerzburg.bsky.social, in collaboration with Dr. Connolly at Newcastle University (@ruamicro.bsky.social). "Dissecting the RNA-centric landscape of microbiota-pathogen interactions in the gut”. 🦠

Apply here: www.uni-wuerzburg.de/karriere/sin...

Respiratory processes of early-evolved hyperthermophiles in sulfidic and low-oxygen geothermal microbial communities - Nature Communications The early evolution of microbial respiration under low-oxygen conditions is still incompletely understood. Here, the authors analyzed the genomics of filamentous geothermal communities and showed that...

How did microbes obtain energy for growth when oxygen was scarce, before the Great Oxidation Event?

The study of microbes in hot springs identifies pathways involving certain cytochrome oxidases that may have played a crucial role in early microbial evolution

🦠🧪

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

Starting my Bluesky adventure by highlighting a new paper from the lab!

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/...

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Happy to share our new paper in @naturemicrobiol.bsky.social on mapping spatial relationships of the human gut microbiome. We identified distinct spatial hubs between gut bacteria that reflect sub-community assemblies at the micron-scale. Led by Miles Richardson & co.
www.nature.com/articles/s41...

Keeping Up With the Boost Fellows, Freiburg
We visited cognitive neuroscientist and Boost fellow @denizkumral.bsky.social in Freiburg. Deniz moved there from the @mpicbs.bsky.social in Leipzig to the Imaging Memory and Consolidation Lab of Monika Schönauer at @uni-freiburg.de.

Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation - Nature Microbiology Gut microbiota-derived succinate promotes CitC succinyltransferase-dependent succinylation of PurR to alleviate T3SS repression and promote virulence in enterohaemorrhagic Escherichia coli and Citroba...

OUT NOW: Microbiota-derived succinate promotes EHEC virulence via lysine succinylation

#microsky 🧪

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

Expanding the human gut microbiome atlas of Africa - Nature A cross-sectional study from four African countries shows the importance of investigating the gut microbiome in previously under-represented populations and provides a framework for equitable microbio...

New in @nature.com

Expanding the human gut microbiome atlas of Africa

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

Highly multiplexed spatial transcriptomics in bacteria Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫

Interplay Between the Gut Microbiome and Typhoid Fever: Insights from Endemic Countries and a Controlled Human Infection Model Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi ( S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and...

📢 Thrilled to share our latest research! Certain gut bacteria may protect against typhoid fever by producing short-chain fatty acids www.medrxiv.org/content/10.1...

🦠🔬Our paper which maps the composition and function of the gut #microbiome in children throughout 1-18 months of life in rural Zimbabwe, is out today in @NatureComms! A quick 🧵on what we found 👇

https://www.nature.com/articles/s41467-023-36135-6
@MangesLab @QMULBartsTheLon...

Dynamics of the gut microbiome in individuals at risk of rheumatoid arthritis: a cross-sectional and longitudinal observational study Objectives This work aimed to resolve the conflicting reports on Prevotellaceae abundance in the development of rheumatoid arthritis (RA) and to observe structural, functional and temporal changes in…

Leeds study of 19 pts at-risk for RA (ACPA+ & arthralgia) finds low-diversity gut microbiome & in the 10 mos preceding the transition to RA, microbiome becomes more unstable w/ accumulation of Prevotellaceae, particularly Prevotella copri