New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

Looking for a #postdoc outside the US, focusing on gut microbiome, AMR dynamics & phage-bacteria interactions. Bridging wet lab and computational approaches🦠👩‍💻. Hartmann Lab, Northwestern University, defending late 2026. Boosts appreciated 🙏🧫🧪 #microbiome #metagenomics #MicroSky

REMINDER 🚨 Harvard Chan Microbiome in Public Health Center (co-directed by Wendy Garrett & Curtis) will host its annual symposium on May 18 at Harvard T.H. Chan School @hsph.harvard.edu. The theme will be 'Translating the Microbiome'. Poster abstracts are due April 1. Register : hsph.me/hcmph2026

📣 We’re hiring! Our lab at Mount Sinai is looking for an experienced clinical coordinator to contribute to our #IBD translational studies. If you’d like to expand your translational research skills with a dynamic team, apply below. @sinaiimmuno.bsky.social careers.mountsinai.org/jobs/3037038...

Naama does amazing work and she is a terrific person to work with. Highly recommended!

Here we show that buildup of uremic toxins during CKD generates nitrate in the colon. Nitrate supports expansion of Enterobacteriaceae, turning them into a major source of uremic toxins. Inhibiting nitrate production (iNOS inhibition) mitigates disease progression. www.science.org/eprint/YGNMK...

Nature research paper: Microbiota-mediated induction of beige adipocytes in response to dietary cues go.nature.com/4rdQ8Cq

A new probiotic in development? 🦠👶 Clostridium perfringens isolated from preterm infants metabolizes human milk oligosaccharide to promote commensal Bifidobacteria, inhibit pathogens and suppress inflammation in organoids Interesting work from @stewartlab.bsky.social www.nature.com/articles/s41...

Out Now! Spatial transcriptomics maps host–gut microbiome biogeography at high resolution #MicroSky

Results and health assessments from gut microbiome home-testing kits vary whether they are produced by the same or different manufacturers. The findings, published in Communications Biology, highlight the need for caution when interpreting or acting on test results, according to the authors. 🧪

Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...

Friends, please help spread the word about our microbiology REU program at Montana State University. www.montana.edu/mbi/reu/ Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Details in the attached pic--Feb 14 deadline 🧫🧪🦠#microsky

New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...

Please save the date! We are excited to announce that our "Having IMPACTT" Symposium will be back for another engaging event! More details will be sent out in the coming weeks. Subscribe to updates at the link in our profile.

🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10

Excited to announce the re-establishment of the Central New York Branch of the American Society for Microbiology (CNY ASM)! Founded in 1921, revived in 2025 to support collaboration, inclusive programming, and microbiologists at all career stages! This is our official BlueSky account!

This is such hard news to process. Such an amazing scientist and inspiration for so many of us. www.embl.org/news/embl-an...

Please share and distribute ILC6 in Vancouver Abstract submission and registration are open: ilc6vancouver.com #immunosky #ILC6vancouver #ILC6 Lots of presenter spots available Secure your spot and discounted fees during early bird registration and come visit beautiful Vancouver.

🟡CONVOCATORIAS DE EMPLEO | 👉 ibis-sevilla.es/es/ofertas-e... 👉 ibis-sevilla.es/es/ofertas-e... @csic.es @csicandalextrem.bsky.social @unisevilla.bsky.social

Two pieces of fun news: 1. We've launched a new website for our lab: www.brysonlab.org 2. With some new funding, we are recruiting for new postdocs and graduate students. The projects build upon our previous studies of antigen presentation and phagosome biology and go into new exciting dimensions!

Now online! Gut microbiota promotes immune tolerance at the maternal-fetal interface

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

I'm very happy to share our latest manuscript published today in @nature.com !! ➡️ doi.org/10.1038/s415... We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.

Our study, now out in Nature Metabolism: 🔥 Microbial trimethylamine inhibits IRAK4, a key kinase in inflammation ➡ This blunts TLR-driven inflammation and decouples metabolic dysfunction from obesity ✅ This casts IRAK4 as a therapeutic target for metabolic diseases. Meet TMA, our unexpected hero ⬇️

📢 SIGN & SHARE THE PETITION! 📢 New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW

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I’ve released a tool to sketch and edit phylogenetic trees! yawak.jp/PhyloWeaver/ Load a Newick file and intuitively add/remove/resize branches. Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

Proud to share that three Sinai Genetics and Genomics faculty have been named Clarivate Highly Cited Researchers 2025: • José Clemente, PhD • Guo-Cheng Yuan, PhD • Bin Zhang, PhD Their work spans #microbiome science, systems #genomics, single-cell biology, and AI-enabled disease modeling.

My lab is recruiting a post-doc ! please share ! emploi.cnrs.fr/Offres/CDD/U...

Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4

🟠 SCIENCE | Don't forget it‼️ 6th IBiS-Winter International Symposium of External Young Investigators 2025! #IBiSWISE 🗓️10-11/12 ONLINE for PhD students & postdocs researching abroad, especially if consider joining Spanish research system. ⏳Deadline for abstracts 14/11! @unisevilla.bsky.social

Hi #GIsky and #GIresearch friends, who has had success culturing mouse small intestinal enteroid monolayers? We could use some wisdom!

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs. @quadraminstitute.bsky.social rdcu.be/eMmcT

NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data! www.nature.com/articles/s41... 🧵⬇️ 1/8

1/5 Today we are introducing the Key-Cutting Machine (KCM) for protein and peptide design. Like cutting a key to fit a lock, KCM sculpts sequences to match a target backbone—on a single GPU. No retraining. No clusters. 🧬🔑

Excited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/ 📄 rdcu.be/eL8mR

🟠SCIENCE | 6th IBiS-Winter International Symposium of External Young Investigators 2025 is coming! #IBiSWISE 10th-11th December ONLINE, for PhD students & postdocs researching abroad, especially if consider joining Spanish research system Deadline: 14th November @unisevilla.bsky.social

We recently got two papers published on the relation between microbiome and arthritis, in collaboration with the groups of Jose Scher (NYU), Frances Williams (King's College) and Monica Guma (UCSD). In both papers with Kevin Bu, postdoc extraordinaire in my lab, as first co-author!

Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...

New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium) academic.oup.com/ismej/advanc...

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers. 🚨 Submit your abstracts now! 🚨 Please RT coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org

Dear #microbiology and #immunology community- I took a break from social media after I deleted my Twitter account, but am back here. Please help me rebuild my community by following me and amplifying this message- I will follow you back. Thank you and I look forward to our many interactions!

📚🩺Nuestro académico y virólogo Luis Enjuanes ha colaborado en este libro "La expedición Balmis. Primer modelo de lucha global contra las pandemias" 🦠 [...] Hoy podemos afirmar que el modelo de lucha contra la covid-19 tiene su germen en esta epopeya médica pionera @cnb-csic.bsky.social #geoplaneta

The gut microbiota is essential for maintaining female fertility go.nature.com/46OM03J

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine. 1) MMG (my dept): fundamental research in med micro 2) Peds ID / I4Kids institute 3) Center for Vaccine Research 🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

If you made it this far, thanks for reading. I hope you enjoyed it. I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.

Re-upping this: For those of you having new students in the lab, I have curated a YouTube playlist on molecular biology: www.youtube.com/playlist?lis... I usually have my students watch it before I show them how to do it in the lab.

Tenure-track Assistant Professor in Computational Ecology and/or Evolution @columbiauniversity.bsky.social. Deadline to apply September 30. Reach out if you have questions. apply.interfolio.com/172496

Now online! Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition