New preprint from the lab is out! 🥳 We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions. www.biorxiv.org/content/10.6... 👇

This is really cool and important.

📍Our paper is out!📍 Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. Check it out! link.springer.com/article/10.1...

Highly interesting work identifying commonly targeted enzymes for production improvement of target compounds across literature by dan1elmachado.bsky.social: www.biorxiv.org/content/10.6...

A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products https://www.biorxiv.org/content/10.64898/2025.12.15.694291v1

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...

"One small molecule for man, one giant leap for mankind with obesity" sciencedirect.com/science/arti... But the very high amounts of drug in pills relative to injectable peptides, due to such poor bioavailability, means we need to be watchful for new side effects when these pills get widely used

Denmark just mapped its entire environmental microbiome. More than 10,000 samples revealing hidden, dominant nitrifiers that shape fertilizer use, water quality, and climate impact. A national microbiome atlas could transform sustainable agriculture across Europe. #AMR www.nature.com/articles/s41...

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.

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

Controlled settings may offer limited insight into the complexities of ageing in natural and variable ecosystems, and why (and how) ageing patterns vary so widely across individuals, populations, and species. We call for more research on ecology of ageing! onlinelibrary.wiley.com/doi/10.1111/...

New preprint: www.biorxiv.org/content/10.6...

💬 Beim zweiten Research Festival der Medizinischen Fakultät der #UniKiel standen der interdisziplinäre Austausch und die Forschung des wissenschaftlichen Nachwuchses im Mittelpunkt: 🔗: https://www.uni-kiel.de/de/detailansicht/news/206-researchfestival#UniKiel 📷: Kerstin Nees/Felix Lürssen, Uni Kiel

Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani

Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes go.nature.com/4azJDF8

1/3 We're hiring! Join us as a PhD student in metabolic microbiome modeling within @spp2474.bsky.social — help uncover the microbiome’s dark matter alongside top microbiome labs across Germany! @uni-kiel.de jobs.uksh.de/job/Kiel-PhD...

Looks interesting: “A host-centric view of the microbiota metabolome” www.cell.com/immunity/abs...

Excited to see our work published. Thanks for the support, Johannes Zimmermann, Jan Taubenheim, @kaletalab.bsky.social and our funding bodies.

Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome. By integrating faecal metabolomics, metagenomics, and dietary data Falchi et al. show that faecal metabolites capture mediations between diet and the gut microbiome www.nature.com/articles/s41...

Excited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...

(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....

HGMT: a database of human gut microbiota for tumors and immunotherapy response. #GutMicrobiota #TumorSample #Metagenomics #ImmunotherapyTreated #GenomeBiology 🧪🧬 🖥️ link.springer.com/article/10.1...

👇Three days left to apply👇

1/4 🌍 We are looking for a passionate #PhD student in #Metabolic #Microbiome #Modeling in the Marie Skłodowska-Curie Doctoral Network MenoBrain. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @uni-kiel.de 🔗 www.uniklinikum-jena.de/menobrain/en...

New data that supports metformin as a potential intervention to reduce #LongCovid www.authorea.com/users/100423...

Highly interesting note of caution about research on the link between autism and the microbiome. Summary adapted from the article: Across many fields, we’ve learned that a lot of smoke doesn’t necessarily mean there’s any real fire. www.sciencedirect.com/science/arti...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field open.substack.com/pub/blekhman...

Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host. Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social) Registrants will receive free memberships to Applied Microbiology International. Details below 👇

How can gut microbes modulate host lifespan? @jogender-singh.bsky.social & coworkers show that in C. elegans, lifespan extension arises from microbial perturbation of iron homeostasis and oxidative stress response activation #RefereedPreprint c/o @reviewcommons.org www.embopress.org/doi/full/10....

1/4 🌍 We are looking for a passionate #PhD student in #Metabolic #Microbiome #Modeling in the Marie Skłodowska-Curie Doctoral Network MenoBrain. Join us at one of Europe’s microbiome research hubs and push the boundaries of microbiome science! @uni-kiel.de 🔗 www.uniklinikum-jena.de/menobrain/en...

Excited to share a review on metabolic modelling of host-microbiome-interactions by Natchapon Srinak (@snatchapon.bsky.social) and Jan Taubenheim from the lab: www.sciencedirect.com/science/arti...

Excellent article on quantitative production of fermentation products by the microbiota. Key takeaway: microbial fermentation products may be more important in mice than humans, amplifying microbiome effects in mice. www.cell.com/cell/fulltex...

🕰️ Is aging driven by a programmed/programmatic mechanism, or by the unavoidable burden of imperfect maintenance? Our perspective argues that aging reflects finite maintenance and reduced evolutionary pressure🧵🧪 www.nature.com/articles/s43... @bjornschumacher.bsky.social @alexeimaklakov.bsky.social

Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...

So, is this bacterial metabolite relevant in humans? With help from @kaletalab.bsky.social we predicted its production is significantly higher in the gut microbiomes of colorectal cancer patients. It is also present in cancer-associated microbiomes. What does it actually do to cancer cells?

Happy to have contributed!

Excited to share our latest work at Cabreiro lab! Chemotherapy modulation by a cancer-associated microbiota metabolite www.cell.com/cell-systems... Here's what we discovered 🧵

🚨New paper published today on cancer bugs and drugs!🚨 “Chemotherapy modulation by a cancer-associated microbiota metabolite” Congrats to the Cabreiro lab on this exciting study! #Cancer #Microbiome #Metabolism #Chemotherapy #MRC_LMS #ImperialCollege #CECAD_Cologne www.cell.com/cell-systems...

Delighted to share: "Metatranscriptomics-based Metabolic Modeling of Patient-Specific Urinary Microbiomes during Infection". Great work led by Jonathan Josephs-Spaulding, in collaboration with the Rupp lab. @uni-kiel.de @crc1182.bsky.social @uniluebeck.bsky.social (1/7) rdcu.be/eFnXZ

Only 10 days left to apply: We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥 I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com @cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social www.cell.com/cell-systems... 🧵...

Out stody Is now on National Geographic!!! www.nationalgeographic.com/animals/arti...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵

(1/5) 🧠 Excited to share our new preprint on molecular drivers of cognitive function in aging mice! Led by Stefano Flor & @sciwitch.bsky.social, with the Frahm lab @uni-kiel.de @crc1182.bsky.social 📄 www.biorxiv.org/content/10.1...

Interesting perspective calling into question the hologenome/holobiont concept. They argue that the holobiont does not qualify as a unit of selection and rather traditional approaches from genetics and ecology are more suitable to study host-microbiome-interactions: journals.asm.org/doi/10.1128/...

www.nature.com/articles/s41... The role of metabolism in shaping enzyme structures over 400 million years