Youssef El Mouali
@youssefelmouali.bsky.social
Microbiome and RNA. Postdoc at Till Strowig Lab Helmholtz HZI. Former Jörg Vogel Lab Helmholtz HIRI. Alumni @UniBarcelona
Pinned
The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization
El Mouali et al. characterized the RNA landscape of the human gut-residing bacteria
Segatella copri using in vitro and gut-derived samples. They identified a small RNA
regulator essential for gut colo...
www.cell.com
It was time to move here!
Check out our recent paper on the essential role of a small RNA for Segatella copri gut colonization. Mechanistic insights on the lifestyle of the mysterious (but incredibly abundant) Segatella/Prevotella copri in the gut.
www.cell.com/cell-host-mi...
Check out our recent paper on the essential role of a small RNA for Segatella copri gut colonization. Mechanistic insights on the lifestyle of the mysterious (but incredibly abundant) Segatella/Prevotella copri in the gut.
www.cell.com/cell-host-mi...
Reposted by Youssef El Mouali
🧪 #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/...
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
August 28, 2025 at 10:33 PM
🧪 #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/...
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/...
Reposted by Youssef El Mouali
🧵 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...
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
August 1, 2025 at 9:05 AM
🧵 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...
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...
Reposted by Youssef El Mouali
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
#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
June 30, 2025 at 6:57 PM
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
#Ageing
Reposted by Youssef El Mouali
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/...
#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
April 23, 2025 at 8:57 AM
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/...
#PhageSky
doi.org/10.1093/nar/...
Reposted by Youssef El Mouali
#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
@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...
www.science.org
April 4, 2025 at 3:45 PM
#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
@science.org #microsky
www.science.org/doi/10.1126/...
Reposted by Youssef El Mouali
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
👉🏼 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
March 23, 2025 at 9:15 AM
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
👉🏼 rdcu.be/eelLn
Reposted by Youssef El Mouali
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...
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
March 24, 2025 at 4:30 PM
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...
doi.org/10.1159/isbn...
Reposted by Youssef El Mouali
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:
This was a fun writing process with @vheidrich.bsky.social and Nicola Segata! See Vitor's summary thread below:
Thrilled to share our review (with @mireiavallesc.bsky.social and Nicola Segata) on "Human microbiome acquisition and transmission" just published @naturerevmicro.bsky.social
March 21, 2025 at 4:43 PM
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:
This was a fun writing process with @vheidrich.bsky.social and Nicola Segata! See Vitor's summary thread below:
Reposted by Youssef El Mouali
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:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
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.
www.nature.com
February 18, 2025 at 11:02 AM
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:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
Reposted by Youssef El Mouali
📣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...
Apply here: www.uni-wuerzburg.de/karriere/sin...
PhD student position at the Chair for Microbiology
www.uni-wuerzburg.de
February 14, 2025 at 8:25 AM
📣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...
Apply here: www.uni-wuerzburg.de/karriere/sin...
Reposted by Youssef El Mouali
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...
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...
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...
www.nature.com
February 7, 2025 at 3:15 PM
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...
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...
Reposted by Youssef El Mouali
Starting my Bluesky adventure by highlighting a new paper from the lab!
"A human gut bacterium antagonizes neighboring bacteria by altering their protein folding ability" @cp-cellhostmicrobe.bsky.social
@yalemedicine.bsky.social Andrew Goodman
www.cell.com/cell-host-mi...
@yalemedicine.bsky.social Andrew Goodman
www.cell.com/cell-host-mi...
A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability
Antagonism shapes microbiomes. Lim et al. identify a mechanism used by human gut commensals
to antagonize related bacteria. The secreted effector Bte1 alters the protein-folding
machinery of targeted ...
www.cell.com
February 5, 2025 at 8:40 PM
Starting my Bluesky adventure by highlighting a new paper from the lab!
Reposted by Youssef El Mouali
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/...
academic.oup.com/gigascience/...
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
academic.oup.com
February 4, 2025 at 8:22 PM
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/...
academic.oup.com/gigascience/...
Reposted by Youssef El Mouali
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...
www.nature.com/articles/s41...
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.
www.nature.com
February 3, 2025 at 2:46 PM
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...
www.nature.com/articles/s41...
Reposted by Youssef El Mouali
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.
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.
February 3, 2025 at 12:45 PM
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.
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.
Reposted by Youssef El Mouali
OUT NOW: Microbiota-derived succinate promotes EHEC virulence via lysine succinylation
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
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...
www.nature.com
January 31, 2025 at 3:59 PM
OUT NOW: Microbiota-derived succinate promotes EHEC virulence via lysine succinylation
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Reposted by Youssef El Mouali
Reposted by Youssef El Mouali
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 🦠🧫
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
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...
www.science.org
January 24, 2025 at 4:30 AM
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 🦠🧫
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
Reposted by Youssef El Mouali
📢 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...
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...
www.medrxiv.org
December 5, 2024 at 2:00 PM
📢 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...
Reposted by Youssef El Mouali
🦠🔬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...
https://www.nature.com/articles/s41467-023-36135-6
@MangesLab @QMULBartsTheLon...
The gut microbiome and early-life growth in a population ...
Here, using metagenomics, the authors show that the gut m...
www.nature.com
November 22, 2024 at 10:06 AM
🦠🔬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...
https://www.nature.com/articles/s41467-023-36135-6
@MangesLab @QMULBartsTheLon...
Reposted by Youssef El Mouali
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
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…
buff.ly
January 8, 2025 at 7:51 PM
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
Reposted by Youssef El Mouali
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
January 22, 2025 at 5:31 PM
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
Reposted by Youssef El Mouali
NEW COMMENT: Microbiome science needs more microbiologists
@abaumler.bsky.social and Lauren Radlinski argue that integrating microbiologists and fundamental microbiological concepts should help advance microbiome science
www.nature.com/articles/s41...
@abaumler.bsky.social and Lauren Radlinski argue that integrating microbiologists and fundamental microbiological concepts should help advance microbiome science
www.nature.com/articles/s41...
Microbiome science needs more microbiologists - Nature Microbiology
Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.
www.nature.com
January 23, 2025 at 10:55 AM
NEW COMMENT: Microbiome science needs more microbiologists
@abaumler.bsky.social and Lauren Radlinski argue that integrating microbiologists and fundamental microbiological concepts should help advance microbiome science
www.nature.com/articles/s41...
@abaumler.bsky.social and Lauren Radlinski argue that integrating microbiologists and fundamental microbiological concepts should help advance microbiome science
www.nature.com/articles/s41...