Clemente lab

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

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...

This Research Experiences for Undergraduates (REU) program is funded by the National Science Foundation to create "points of entry" for students interested in research. Students apply from across the country to spend 10 weeks in Bozeman, Montana this summer (May 26, 2026 - August 1, 2026). Admitted students are paired with a faculty mentor, who serves as an advisor for a student's summer project. Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Our program leverages MSU’s unique microbiology expertise, focusing specifically on microbes living with little or no oxygen (like those in the hot springs of nearby Yellowstone). Low oxygen microbes are essential to human and ecosystem health. They influence (or control) such processes as the breakdown of food in the GI tract, removal of toxins from our bodies and the environment, and production of greenhouse gases. They are also models for understanding the origins of life on this planet, and the potential for life on other planets. A key goal of our program is to recruit students from schools with limited research infrastructure. Being in Montana, a state with a vibrant Native American community, we are particularly interested in applications from students at tribal colleges. However, ANYONE with an interest in microbiology - or biology/science in general - can and should apply. If willing and able, please share/tweet/spread the word far and wide. Applications are due February 14, 2026. Full details can be found through our website http://www.montana.edu/mbi/reu/

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/...

photograph of mountain scenery overlaid with save-the-date information for the Having IMPACTT 6 Symposium in Canmore, AB

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.

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

🥁 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!

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.

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

The Bryson Lab | Vaccine Development & Research at MIT Developing effective accessible vaccines to end tuberculosis worldwide. Combining immunoengineering, molecular microbiology & systems biology at MIT.

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!

Gut microbiota promotes immune tolerance at the maternal-fetal interface Microbiota-dependent tryptophan-derived indole deficiency is linked to mouse fetal resorption and human recurrent miscarriage. Tryptophan-derived indoles prime MDSCs and RORγt+ Tregs to suppress IFN-γ+ or IL-17A+ T cells at the maternal-fetal interface, respectively, thereby promoting maternal-fetal immune tolerance.

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

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

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.

Inhibition of IRAK4 by microbial trimethylamine blunts metabolic inflammation and ameliorates glycemic control - Nature Metabolism The microbial metabolite trimethylamine (TMA), the precursor of TMAO, which is associated with adverse cardiometabolic outcomes, is shown to have beneficial metabolic and anti-inflammatory effects in ...

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 the Petition Support a New York State Biomedical Institute for a Healthier, More Affordable Future

📢 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

🚨⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️🚨

PhyloWeaver – Interactive phylogenetic tree editor Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.

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.

This has been known for some time, although it's a good reminder. A previous study that comes to mind (www.nature.com/articles/nbt...) found most of the variation was due to extraction methods, while the bioinformatics analysis had a smaller effect.

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

a man wearing glasses says i very much need your help ALT: a man wearing glasses says i very much need your help

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

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

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

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

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. 🧬🔑

Long-read metagenomics for strain tracking after faecal microbiota transplant Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

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

Kudos to everybody in the papers for their hard work and contributions. We are so fortunate to work with such an outstanding group of colleagues and friends!

The second study was an anti-inflammatory dietary intervention in osteoarthritis. Responders had significant differences in microbiome and metabolome, and taxa within the Lachnospiraceae were associated with pain reduction and anti-inflammatory metabolite production.

www.mdpi.com/2072-6643/17...