Jose Clemente

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

Hi folks, we had a last minute cancellation at MBL STAMPS, the microbiome data analysis course in Woods Hole that runs from July 14th to July 24th. We can provide housing space for a woman. If you or anyone you know is interested, pls drop me an e-mail at ctbrown@ucdavis.edu. Thx!

Our lab is hiring!

Based out of @rcsi.bsky.social Beaumont Hospital we are looking for a research assistant to work on an exciting project looking at early signatures associated with early stage #lungcancer.

Feel free to share/reach out.

#microbiome #cancer #omics

my.corehr.com/pls/rcsirecr...

Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial. Synbiotic interventions show variable effects across individuals, likely driven by ecological interactions with the endogenous microbiota and the host diet. Rationally predicting individual-specific s...

Our latest preprint is online @medrxivpreprint.bsky.social:

"‪Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial." www.medrxiv.org/content/10.1...

Amazing work here by postdoc Nick Quinn-Bohmann @isbscience.org

🧵...

Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemo...

I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published.

www.tandfonline.com/doi/full/10....

Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social

Postdoctoral Associate MIT - Postdoctoral Associate - Cambridge MA 02139

‼️I'm looking for a postdoc‼️ Come join effort in using metagenomes to quantify microbial catabolic potential and carbon substrate availability at the ecosystem level. We seek to understand evolutionary forces shaping the carbon cycle. Part of ccomp-stc.org

careers.peopleclick.com/careerscp/cl...

Apply now! Applications will be closing soon.

The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...

If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...

We are recruiting a tenure-track assistant professor in molecular microbiology in our department in Lausanne! Do consider appyling!!

We have two new positions, a PhD and a Post doc at #InstituteofBiologyLeiden within our @microclockerc.bsky.social #ERCSyG project to discover interaction of #circadianclocks between Bacillus subtilis and Arabidopsis

please share these with your network! 🙏

links below👇
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Probiotics in pregnancy: Where do we stand?

Our new Gut Microbes review zooms in on the real-world potential of probiotics to support maternal health. #Spoiler: there’s promise—but also plenty of caveats.

www.tandfonline.com/doi/full/10....

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

www.nature.com/articles/s41...

🧵⬇️

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I interviewed for a postdoc position in Howard's lab many eons ago. Although I ended up working in another (fantastic) lab, I always felt working with Howard & Nancy would have been an incredible opportunity. Highly recommended.

Howard's: evolution of microbial genes, genomes and communities. Can be experimental or computational. If interested, contact Howard Ochman, howard.ochman@austin.utexas.edu
Homepage: web.biosci.utexas.edu/ochman/index...

An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky

Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...

So sorry to hear, Sean. Disheartening.

🟠 SCIENCE |

Extra Seminar: "Development of the microbiome in early life: role in disease risk and therapeutic interventions"

👤: Jose C. Clemente
🗓️: 26-05 | 12:30 h.
📍: IBiS Assembly Hall

+ info ➡️ www.ibis-sevilla.es/es/eventos/2...

@csic.es @unisevilla.bsky.social @csicandalextrem.bsky.social

The Brain-Body Research Institute @IcahnMountSinai is hiring an Associate Director to build clinical and translational research in brain-body sciences. See ad here: neuroscience.mssm.edu/pdf/Brain-Bo.... @sinaibrain.bsky.social @sinaiimmuno.bsky.social @brainbodylab.bsky.social

My job at the Univ. of Arizona has been funded by the NSF and NIH. The money runs out pretty soon, so I’m seeking a new role. #Python #Rust #Elm #Bioinformatics

We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com

Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable

OPEN CALL for PhD positions in our lab through the semm_it program:

1️⃣ Microbiome signatures of early on-set colorectal cancer
2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission

More info: www.semm.it/education/op...

Apply by June 9!

Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties Abstract. Metagenomic classifiers are widely used for the taxonomic profiling of metagenomics data and estimation of taxa relative abundance. Small subunit

I haven't used it, but I've heard RiboTaxa has good overall performance: academic.oup.com/nargab/artic...

Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice - Nature Microbiology A multi-omics approach reveals host–microbiome interactions in aging in mice.

1/12 Thrilled to share our latest paper on host-microbiome-interactions in aging out in Nature Microbiology @naturemicrobiol.bsky.social, great work led by Lena Best @sci-witch.bsky.social with the Frahm lab within the ITN SmartAge. @crc1182.bsky.social @uni-kiel.de
www.nature.com/articles/s41...

Sketch, capture and layout phylogenies www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/husonlab/phy...

Introducing our latest preprint which discovered Clostridium sp. grow on HMOs. Using computational and experimental approaches we show this has beneficial consequences for the developing microbiome and the host. But there is nuance.

A 🧵...

www.biorxiv.org/content/10.1...

Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models - Nature Microbiology DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generali...

Happy to share DEBIAS-M, our new method for domain adaptation and bias correction in #microbiome data.🧬🖥️

Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...

🌊 Save the Date! 🌍
#SAME18 — Aquatic Microbiomes on a Changing Planet
📍 Barcelona, Spain | 🗓️ Sept 28 – Oct 3, 2025
At the iconic PRBB 🧬🌿
Join us to explore the frontiers of aquatic microbial ecology.

📢 Stay tuned for more info and follow us on Bluesky!

#MicrobialEcology #MarineMicrobiology #SAME18

Interesting new work on marker gene selection from whole genomes and incomplete MAGs.