Jose Clemente

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...

Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygo…

The first work studied two different cohorts (US, UK) of monozygotic twins who were discordant for rheumatoid arthritis. Affected twins had a decrease in SCFA producers in both populations, and lower concentration of butyrate, propionate and acetate.

www.sciencedirect.com/science/arti...

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...

Very nice paper Noah, congratulations. Hope all is well in Boulder!

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

Gut microbiota keeps watch over future egg cells Certain gut bacteria help to extend the reproductive lifespan of female mice, experiments show.

The gut microbiota is essential for maintaining female fertility

go.nature.com/46OM03J

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 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...

At Handan campus, Fudan University, Shanghai.

Exploring the Great Wall near Beijing

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.

Molecular_Bio - YouTube

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

Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition Minich et al. hypothesized that complete metagenome-assembled genomes, recovered through long-read DNA sequencing, would enable pangenome and microbial genome-wide association analyses to identify microbial genetic associations with child linear growth. This cross-platform, long-read resource demonstrates the power of comparing cMAGs with health trajectories, establishing a new standard for microbiome research.

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

🚀 NY-CURES Launch — Championing State-Wide Investment in Science! 🚀

Our new coalition advocates for sustained public support of New York’s vibrant biomedical research ecosystem — creating cures, economic gains & strengthening communities.

Sign up. Stay informed. Join the movement: www.nycures.org/

The landscape of microbial associations in human cancer Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.

A new paper is out from our research team at the @ueamedical.bsky.social at @uniofeastanglia.bsky.social titled "The landscape of microbial associations in human cancer" available from doi.org/10.1126/scit....

Led by @abrahamgihawi.bsky.social

🧬🖥️ @cancerinnorwich.bsky.social

Commensal yeast promotes Salmonella Typhimurium virulence - Nature Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

Excited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.

Now online! Ancient host-associated microbes obtained from mammoth remains

Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology The microbial composition of metagenomes is identified in seconds by profiling against large databases.

The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4

Non-antibiotics disrupt colonization resistance against enteropathogens Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

Finally online!
Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections.
rdcu.be/ewwrG

🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics