Youssef El Mouali
@youssefelmouali.bsky.social
Microbiome and RNA. Postdoc at Till Strowig Lab Helmholtz HZI. Former Jörg Vogel Lab Helmholtz HIRI. Alumni @UniBarcelona
Excellent review article Metabolic strategies of Enterobacteriaceae gut colonization | Nature Reviews Microbiology share.google/hKziCqmwDr3D...
Metabolic strategies of Enterobacteriaceae gut colonization - Nature Reviews Microbiology
In this Review, Schubert and Hardt explore the metabolic strategies that Enterobacteriaceae use to establish themselves in the gut, and how they adapt to inflammatory conditions in this environment.
share.google
“Right now, in some underfunded lab, a scientist is chasing a question that sounds pointless…No one can say if they will succeed. But a century of experience says that funding people to do this work is a good bet. If we stop making that bet, we will pay for it in cures no one will know to miss.”
Victor Ambros@vambros.bsky.social · 2mo agoA column by Jeff Coller: “The Science That Turned Lizard Venom Into GLP-1s Is Under Attack” www.nytimes.com/2026/06/20/o...
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. https://scim.ag/4nTQ3nq
S. copri keeps pace with modern lifestyles Subset of Segatella copri strains have acquired an additional oxygen regulator via horizontal gene transfer, which confers increased oxygen tolerance. These strains are more prevalent in industrialized countries www.cell.com/cell-host-mi...
Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...
cell.com
Die Studie der Erstautor:innen @youssefelmouali.bsky.social & @caroline-tawk.bsky.social ist heute bei @cp-cellhostmicrobe.bsky.social erschienen. Das Team aus der Abteilung von Till Strowig vermutet, dass die Sauerstofftoleranz einen Selektionsvorteil bieten könnte. www.cell.com/cell-host-mi...
Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...
cell.com
Unser Darm ist normalerweise eine sauerstofffreie Zone und viele Bakterien im #Darmmikrobiom vertragen keinen Sauerstoff. Ein HZI-Team zeigt nun aber, dass das #Darmbakterium Segatella copri in industrialisierten Ländern häufiger sauerstofftolerant ist. www.helmholtz-hzi.de/media-center...
Genetisches Bonusmaterial macht Darmbakterium Segatella copri sauerstofftolerant
HZI-Studie identifiziert funktionelle Unterschiede in Segatella-Stämmen aus verschiedenen Regionen der Welt
helmholtz-hzi.de
New paper out in @cp-cellhostmicrobe.bsky.social! Microbes evolving with modern lifestyles 🧬🦠 S. copri uses PerR to manage oxygen stress, but some strains acquired OxyR via HGT, boosting oxygen tolerance. These strains are enriched in industrialized populations. www.cell.com/cell-host-mi...
Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...
cell.com
Read our new Review Article on antibiotic-induced gut microbiome dysbiosis: Michael Knopp, Camille Goemans et al discuss risks and strategies for mitigation link.springer.com/article/10.1...
New preprint from the Ghigo lab (@jmghigolab.bsky.social): crossfeeding B. theta <--> E. coli within a microfluidics system. Shows spatial structure and oxygen availability can qualitatively transform the nature and ecological outcome of microbial interactions. www.biorxiv.org/content/10.6...
biorxiv.org
My super department @warwicklifesci.bsky.social is hiring 6 assistant profs in the wake of recent retirements. We're looking for people in microbiology/infection, cellular disease / immunity; environmental biology; and plant/crop science. #MicroSky warwick-careers.tal.net/vx/lang-en-G...
Assistant Professor x6 (111522-0426) - University of Warwick
Title: Assistant Professor x6 (111522-0426). Application Deadline: . Position Type: Permanent
warwick-careers.tal.net
Happy to share our new work on how phages escape bacterial immunity. We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation. www.nature.com/articles/s41... #PhageSky #MicroSky
Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications
Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...
nature.com
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...
biorxiv.org
Beyond Viral Suppression: How the Right #HIV Drug Helps the Gut Heal Itself @rutgerwalls.bsky.social @fcatalamoll.bsky.social @irsicaixa.es @hospitalclinic.bsky.social #Microbiome
Beyond Viral Suppression: How the Right HIV Drug Helps the Gut Heal Itself
Can specific HIV drugs heal the gut? For late-stage patients, viral suppression isn't enough to stop chronic inflammation. Our 2-year trial reveals that dolutegravir, unlike darunavir, profoundly restores the gut microbiome, offering a new pathway to long-term health and reduced inflammation.
dlvr.it
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
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...
nature.com
New online! Harnessing the microbiome for cancer therapy
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.
nature.com
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/...
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
doi.org
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.
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...
journals.plos.org
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....
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/...
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...
journals.asm.org
🔊 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...
Job offer for a PhD student position at the Chair of Microbiology
uni-wuerzburg.de
🧪 #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/...
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
academic.oup.com
🧵 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...
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
academic.oup.com
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
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.
spklr.io
www.sciencedirect.com/science/arti... Nearly missed my bus stop reading this fascinating review :)
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…
sciencedirect.com
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/...
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
doi.org
#weekendreading🔬📑 A geological timescale for bacterial evolution and oxygen adaptation @science.org #microsky www.science.org/doi/10.1126/...
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...
science.org
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
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,...
rdcu.be
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...
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
doi.org
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:
Vitor Heidrich@vheidrich.bsky.social · last yr.Thrilled to share our review (with @mireiavallesc.bsky.social and Nicola Segata) on "Human microbiome acquisition and transmission" just published @naturerevmicro.bsky.social
