🚀 Thrilled to share our first metaSPLiT preprint from @annabiosys.bsky.social's lab in collaboration with @gibbological.bsky.social! Explore hidden bacterial phenotypic heterogeneity in the human gut microbiome and discover the concept of "physiological guilds": www.biorxiv.org/content/10.6...

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

Most of our knowledge about bacterial functional roles in microbiomes comes from bulk measurements. Yet microbial communities are complex ecosystems in which functionally distinct bacterial subpopulat...

biorxiv.org

On my way to the French Gut Symposium in Paris #microbiome #FrenchGut

📣 Our lab is recruiting postdocs to lead new fully funded projects on mechanisms of microbiome–gut–brain signaling & microbial regulation of brain–body interactions in disease, w supportive clinical collaborators. Expertise in gut–brain, systems neuro, or neuroimmunology preferred. Please email 📧

A great meeting and great weather was a bonus 😁

SciFoodHealth@scifoodhealth.bsky.social · 5mo ago

🇪🇸 #DominoEU gathered in Madrid (15–17 April) to shape Year 4️⃣ after an intensive Year 3. 🔬 RCTs on kefir completed 📊 3,444 samples in cFMD 🌍 Living Labs across 6 countries & more. 🔄 Next phase: scaling up research & clinical work. 👀 Stay tuned & subscribe to the newsletter: www.domino-euproject.eu

A great meeting with a warm welcome from our spanish colleagues !

SciFoodHealth@scifoodhealth.bsky.social · 5mo ago

🇪🇸 #DominoEU gathered in Madrid (15–17 April) to shape Year 4️⃣ after an intensive Year 3. 🔬 RCTs on kefir completed 📊 3,444 samples in cFMD 🌍 Living Labs across 6 countries & more. 🔄 Next phase: scaling up research & clinical work. 👀 Stay tuned & subscribe to the newsletter: www.domino-euproject.eu

🇪🇸 #DominoEU gathered in Madrid (15–17 April) to shape Year 4️⃣ after an intensive Year 3. 🔬 RCTs on kefir completed 📊 3,444 samples in cFMD 🌍 Living Labs across 6 countries & more. 🔄 Next phase: scaling up research & clinical work. 👀 Stay tuned & subscribe to the newsletter: www.domino-euproject.eu

Vous souhaitez apprendre à annoter et comparer vous-même vos génomes bactériens ? Notre cycle de formation "Bioinformatique par la pratique" vous propose ce module de 2 jours à Jouy-en-Josas (19-20 mars 2026). 📝 Inscriptions et programme sur documents.migale.inrae.fr/trainings.html

Besoin de manipuler vous-même votre jeu de données #RNAseq, depuis les étapes de bioinformatique à l’analyse différentielle, sans passer par la ligne de commande unix ? Ce module de 3 jours à Jouy (16-18 mars) est pour vous ! 📝 Inscriptions et programme sur documents.migale.inrae.fr/trainings.html

Vous pratiquez R mais souhaitez faire des graphiques sophistiqués avec le package #ggplot2 ? Notre cycle de formation "Bioinformatique par la pratique" vous propose ce module d’un jour à Jouy-en-Josas (12 mars 2026). 📝 Inscriptions et programme sur documents.migale.inrae.fr/trainings.html

Besoin de vous former au langage R ? Notre cycle de formation "Bioinformatique par la pratique" propose ce module introductif à Jouy-en-Josas sur 2 jours (10 et 11 mars 2026). 📝 Inscriptions et programme sur documents.migale.inrae.fr/trainings.html

Thank you Lars. In the memory of Peer Bork. youtube.com/shorts/ymqyM...

In memory of Peer Bork #shorts

YouTube video by Lars Juhl Jensen

youtube.com

Sad day. @borklab.bsky.social bring so much to Science and notably in the #microbiome RIP Peer thank you for all your legacy. www.embl.org/news/embl-an...

In remembrance of Peer Bork  | EMBL

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

embl.org

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

nature.com

I presented new data from the French Gut project during the last Food System #Microbiomes congress in Wageningen fme.micalis.fr/congress/202...

The FME lab communicates about the links between the microbiome, nutrition and health.

The FME lab communicates about the links between the microbiome, nutrition and health in Food System Microbiome conference.

fme.micalis.fr

A new article, “𝘼 𝙨𝙘𝙤𝙥𝙞𝙣𝙜 𝙧𝙚𝙫𝙞𝙚𝙬 𝙤𝙛 𝙩𝙝𝙚 𝙝𝙚𝙖𝙡𝙩𝙝 𝙚𝙛𝙛𝙚𝙘𝙩𝙨 𝙤𝙛 𝙛𝙚𝙧𝙢𝙚𝙣𝙩𝙚𝙙 𝙛𝙤𝙤𝙙𝙨 𝙞𝙣 𝙨𝙥𝙚𝙘𝙞𝙛𝙞𝙘 𝙝𝙪𝙢𝙖𝙣 𝙥𝙤𝙥𝙪𝙡𝙖𝙩𝙞𝙤𝙣𝙨 𝙖𝙣𝙙 𝙩𝙝𝙚𝙞𝙧 𝙥𝙤𝙩𝙚𝙣𝙩𝙞𝙖𝙡 𝙧𝙤𝙡𝙚 𝙞𝙣 𝙥𝙧𝙚𝙘𝙞𝙨𝙞𝙤𝙣 𝙣𝙪𝙩𝙧𝙞𝙩𝙞𝙤𝙣” has been published in Frontiers in Nutrition as part of the COST Action PIMENTO. fme.micalis.fr/article/2025...

Understanding How Fermented Foods Shape Health Insights From a New PIMENTO Review

A scoping review of the health effects of fermented foods in specific human populations and their potential role in precision nutrition: current knowledge and gaps

fme.micalis.fr

cFMD v1.3.0 is here! 🚀 We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMD While we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood. 1/4

GitHub - SegataLab/cFMD: Public repository for cFMD - curatedFoodMetagenomicData

Public repository for cFMD - curatedFoodMetagenomicData - SegataLab/cFMD

github.com

tea time! #metagenomics #microbiome @metagenopolis.bsky.social

fme.micalis.fr/article/2025...

New tool suite - Food Microbiome Metabolic Modules (F3M)

Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes

fme.micalis.fr

📢 [𝐍𝐞𝐰 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧] 𝐀𝐧𝐭𝐢𝐛𝐢𝐨𝐭𝐢𝐜𝐬 𝐚𝐧𝐝 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐭𝐚: 𝐩𝐡𝐚𝐠𝐞𝐬, 𝐚𝐥𝐥𝐢𝐞𝐬 𝐨𝐟 𝐫𝐞𝐬𝐢𝐥𝐢𝐞𝐧𝐜𝐞. @metagenopolis.bsky.social @inrae-france.bsky.social with @inserm.fr @institutpasteur.bsky.social #microbiome #science #antibiotics #phages #research #health @eugenpfeifer.bsky.social www.cell.com/cell-reports...

Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages

Antibiotic-induced disruption of the gut microbiome leads to a transient loss of microbiome diversity (bacterial and viral) and causes blooms of bacteria and their viruses. Our analysis suggests that ...

cell.com

New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡 microbiomejournal.biomedcentral.com/articles/10.... #metagenomic #science #data #lefrenchgut @inrae-france.bsky.social @institutpasteur.bsky.social

Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2 - Microbiome

Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...

microbiomejournal.biomedcentral.com

Huge congratulations to our colleague @arnauvich.bsky.social for presenting his research on FODMAP restriction and gut microbiota in IBS patients at United European Gastroenterology Week 2025 in Berlin🇩🇪👏! #UEGWeek @myueg.bsky.social @vibmicrobes.bsky.social

It was nice to have a chance to present few result from French Gut project. fme.micalis.fr/congress/202... #microbiome #EESMicrobiome

The French Gut at EMBL Human Microbiome Symposium 2025

results from the French Gut project presented at the EMBL Human Microbiome Symposium

fme.micalis.fr

Starting my journey from Australia to Heidelberg 🇩🇪 to the @embl.org Human Microbiome conference It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited Still chance to attend it online 👇 www.embl.org/about/info/c...

The human microbiome

embl.org

Question: what’s one piece of advice you’d give to somebody starting out in quantitative ecology? #QuantitativeEcology #Statistics #R

www.science.org/content/arti...

Trump cuts subscriptions to Springer Nature journals

Other publishers appear unscathed in recent actions

science.org

A three-country analysis of the gut #microbiome indicates taxon associations with diet vary by taxon resolution and population journals.asm.org/doi/10.1128/...

A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population | mSystems

An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why ...

journals.asm.org

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances www.nature.com/articles/s41... #jcampubs

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...

nature.com

One Health World #Microbiome Partnership Summit is coming soon!

Agenda - World One Health Microbiome Summit

June 20, 2025 Académie Nationale de Médecine, Paris Please note that this program could change.

wmp.symposium.inrae.fr

Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social www.cell.com/trends/micro...

Analyzing human gut microbiome data from global populations: challenges and resources

Research on the human gut microbiome is expanding rapidly; yet, most published studies focus on populations from high-income regions such as North America and Europe. Underrepresentation of population...

cell.com

This is so cool - octopus can sense microbiomes: sending a gift link www.nytimes.com/2025/06/17/s...

Eight Arms to Taste Your Microbiome

nytimes.com