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...

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

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...

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

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

📢 [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...

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

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

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...

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

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/...

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

One Health World #Microbiome Partnership Summit is coming soon!

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...

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

If you are an european citizen and you think we should ban conversion practices targeting LGBTQ+ citizens. You should sign this. Half of signature are from France, we need more countries! eci.ec.europa.eu/043/public/#...

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...

Dethlefsen and Relman new #microbiome article is always an event www.nature.com/articles/s41...

Wow! Our paper in @natmicrobiol.nature.com has just surpassed 10,000 views in less than a month!! a rare feat for a #plant #microbiome study! We argue that seed-borne bacteria are the architects of the wheat rhizobiome. Thanks to everyone who’s been engaging with our work :) doi.org/10.1038/s415...

If you're a PhD student, Master's student or researcher interested in #artificial #intelligence applications to microbial ecosystems and in particular the gut #microbiome, we're organizing a researchers' school here: ai-microbiome-school.onrender.com/speakers

The more I use python, the more I like R 🤷 #rstats

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology www.nature.com/articles/s41...

Factors shaping #vaginal #microbiota long-term community dynamics in young adult women #microbiome peercommunityjournal.org/articles/10....

The DOMINO project held its second annual meeting from 26 to 28 March in the city of Cork. It was an intense and warm moment thanks to the efficient and very friendly organisation of Teagasc and its incredible team coordinated by Orla O’Sullivan and John Kenny. fme.micalis.fr/meeting/2025...

Thank you @teagasc.bsky.social and @ucc.ie for hosting the #dominoEU annual meeting in lovely Cork city #food #gut #microbiome

What a place to do #microbiome science for #dominoEU project. Thank you UCC & Teagasc Cork for hosting this event.

One week left to apply! If you're looking for a postdoc in analyzing environmental microbiome data in beautiful Heidelberg, this is your chance!

...Abelardo Margolles, Hindrek Teder, @raj09.bsky.social Jekaterina Kazantseva, @julientap.bsky.social, Katie Fala, @orlaos.bsky.social, @pauldcotter.bsky.social, Stephane Chaillou, @vloux.bsky.social, Niccolò Carlino, @vheidrich.bsky.social, Federica Pinto, Nicola Segata, @epasolli.bsky.social 5/5

🥁 We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD) 🔗 Get it here: github.com/SegataLab/cFMD 🧵👇 1/5

I receive 3 to 4 peer review invitations per day from various journals. This volume is simply unmanageable. At some point, it starts feeling like spam rather than genuine academic engagement. Am I alone? Is it a share feeling?

🧪✊ Science thrives on free inquiry, yet researchers worldwide face persecution—even now in the USA, where academic freedom is under attack. We stand in solidarity: science must serve progress, not oppression. #StandUpForScience2025 #AcademicFreedom

No significant differences in gut #microbiome composition or function were observed in relation to fitness, training volume www.nature.com/articles/s41...

Glad to share our work about the comparison between clinical metagenomics (CMg) and the good old 16S rDNA Sanger sequencing for bacteriological diagnosis. Our work shows that they are rather complementary.

🚀 Last chance to join our 2025 mixOmics online workshop! 🚀 Learn omics data integration with mixOmics through hands-on training & expert guidance. 📅 Closes soon! 🔗 Sign up: mixomics.org/2024/12/onli... We can’t wait to welcome our new cohort! 🎉 #mixOmics #bioinformatics #RStats

Though it's already a weeks ago, the newest paper from the (old) lab came out. We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and diet peerj.com/articles/186...

Looking forward to presenting at the 2nd #Fermented #Foods forum in Malaga next week Happy to chat on Wed or Thurs with anyone else who’s going to be there @seqbiome.bsky.social @apcmicrobiomeirel.bsky.social

New paper out today from the lab on Akkermansia muciniphila 🦠and how it breaks down host glycans! Very proud of my group, especially @cassiebakshani.bsky.social who did an amazing job. @naturemicrobiol.bsky.social www.nature.com/articles/s41...

Nice one about of Akkermansia CAZy very useful ressources #microbiome www.nature.com/articles/s41...

Landmark publication of a reference catalogue of the gut #microbiome in Africa www.nature.com/articles/s41...

Microbiome science needs more microbiologists www.nature.com/articles/s41...

#microbiome "Here we showed that seasonal shifts between the Prevotella- and Bifidobacterium/Ruminococcus-driven community types, or ecological states [...] particularly in fermented milk consumers." in Indian agrarian individuals. www.nature.com/articles/s41...

I like to use last Pat Schloss tool Phylotypr journals.asm.org/doi/epdf/10....

Is it the future of protein functional annotation? #IA #protein #llm www.marktechpost.com/2025/01/09/e...

Fibre is good for health, fibre is good for the gut microbiota. Yes but which fiber? All types? Mixtures of types? That's what they looked at there, showing that (perhaps unsurprisingly) a mixture of fibres could enhance SCFA production better than single sources. www.tandfonline.com/doi/full/10....

The nightmare of every microbiology lab manager, freezer failures! For taxonomic composition analyses, storing samples at -80C is shown here to be better than storing DNA at -20C in case of freezer failure. Fungal richness also seems more resilient than bacterial. 🔗 journals.asm.org/doi/full/10....