Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

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

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉 How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬 www.nature.com/articles/s41...

I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...

V. interesting work from @gibbological.bsky.social et al showing that metabolic modeling can predict probiotic engraftment & SCFA production across human intervention trials w/ ~75-80% accuracy. Great argument for model-informed personalised probiotic interventions. journals.plos.org/plosbiology/...

#NatMicroPicks A microbial signature of health! 🦠⚕️ A large meta-analysis highlights the importance of previously unknown and uncultured gut bacteria in maintaining human health #MicroSky www.cell.com/cell-host-mi...

Here is a robust biochemical & functional difference between young and old mammalian cells: - The fraction of new amino acids incorporated into proteins. The difference is consistent, quantitative, cell-type specific, and deeply intriguing. What aging mechanisms cause it ? 1/

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself. www.science.org/doi/10.1126/...

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia A nice demonstration of how cross-feeding shapes small microbial community compositions From Segré lab @dsegre.bsky.social www.biorxiv.org/content/10.6...

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

3 recent trials in Nature Medicine test FMT as an ICI add-on (renal+lung cancers). Early efficacy signals + mechanistic hints that taxa/function shifts may matter more than donor similarity + toxicity effects mixed. Promising, but prob need larger trials and more standardisation. Links to studies 👇

What causes tipping points in complex microbial ecosystems? Check this @pnas.org paper by @thilogross.bsky.social showing that cross-feeding networks create strong interdependencies & small structural changes can trigger abrupt collapses. @akhilesh-nandan.bsky.social www.pnas.org/doi/epdf/10....

The immune systems paradox Some widespread prokaryotic immune systems are absent in eukaryotes, whereas relatively rare ones became central to eukaryotic innate immunity @audeber.bsky.social & E. Koonin hypothesize the answer is #HGT shareable link: rdcu.be/e2EmD www.nature.com/articles/s41...

Comparative genomics of Bifidobacterium adolescentis (n=1.6k genomes, mostly MAGs from 44 countries) for adult-gut adaptation signatures: 203 soft-core host-interaction genes (incl adhesion/pili) +7 clades w/ some geographic structure + co-occur w/ butyrate producers journals.asm.org/doi/full/10....

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

Out Now! Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function #MicroSky

An “extraordinary” brain network discovery shows that Parkinson’s disease may not be a movement disorder after all

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer www.biorxiv.org/content/10.6...

A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia "This genome falls outside of known T. pallidum lineages today, but it has many genetic hallmarks associated with virulence in modern pathogens of these subspecies" Science pubmed.ncbi.nlm.nih.gov/41570125/ #MicroSky

Mega-journal Heliyon retracts hundreds of papers after internal audit  @retractionwatch.com retractionwatch.com/2026/02/03/m...

What drives immunosenescence—the degradation of function our immune system with aging that increases the risk of age-related diseases? Today's report: B cells are identified as the bad actors because they induce T cell (CD4) dysfunction and inflammaging science.org/doi/10.1126/...

🆕 @science.org Revising the heritability of lifespan, from 25% to ~50%, by correcting for extrinsic factors science.org/doi/10.1126/...

Intriguing work showing that essential amino acids in metazoans have considerable higher biosynthetic costs, potentially explaining the loss of their biosynthetic pathways: rdcu.be/e09J7

Out Now! Genomic features associated with sustained mammalian transmission of avian influenza A viruses #MicroSky

Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky

Single #gene found to influence #gut #bacteria balance and #IBD susceptibility ... | #PTPN2 | #infection | #microbiome | #microbes | Via @sciencex.bsky.social

#NatMicroPicks Baby-to-baby strain transmission shapes the developing gut microbiome - out now in Nature! 👶🦠👶 #microsky #microbiome @nature.com @cibiocm.bsky.social www.nature.com/articles/s41...

#NatMicroPicks bacterial amino acid metabolism affects cancer progression 🦠🦀🐁 Bacteroides asparaginase lowers intestinal asparagine levels and drives colorectal tumor progression #MicroSky www.cell.com/cell-host-mi...

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....