Growth costs of suboptimal protein allocation in nonlinear models of growing cells doi.org/10.64898/202...

"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule! Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other. www.nature.com/articles/s41...

share.google/vZAlQNIFbeN1... !!!!

Excited to see this work out! 💩🍨🐁 "If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice" www.frontiersin.org/journals/imm... @isbscience.org @uwnews.uw.edu 🧵...

We've known the gut-brain axis is a key underpinning of Parkinson's disease. Today, for the 1st time, a gut microbiome signature denoting risk found in healthy individuals with genetic predisposition nature.com/articles/s41...

🧵 Our new paper is out today in molecularcell.bsky.social! After 7 years of a truly intriguing discovery journey, we can finally share what controls how molecules move inside living E. coli cells. Spoiler: it's not what the field thought. A thread 👇 📄 doi.org/10.1016/j.molcel.2026.03.018

The lab of Johannes Zimmermann at Jena University has an opening for a PhD position - exciting research in a highly innovative group: www.jsmc-phd.de/admission/va...

All currently approved antibiotics inhibit essential cellular processes. Ever wonder if we could kill bacteria using the opposite strategy? Here, we demonstrate an alternative antibacterial strategy: lethality through pathway over-activation. www.nature.com/articles/s41... (1 out of 3)

Cool new study in Nat Comm by Amanda Dugan, Deepsing Syangtan, et al that identifies INTELECTIN-2 as a broad-spectrum antimicrobial operating right at mucosal surfaces INTELECTIN-2 not only senses microbes, it actively shapes which microbes gets to stay 🧵 (1/5) @natcomms.nature.com

You can also find the full paper here: rdcu.be/e74Ou 📄 As my first study as a senior author, this marks an important milestone—and the starting point for many new projects, directions, and ideas 🚀

Can diet shape your microbiome’s ability to produce neuroactive compounds? Our latest study shows dietary patterns influence in silico GABA production capability by Bifidobacterium adolescentis and other gut bacteria. Led by Ann Homscheid and @maringos.bsky.social. doi.org/10.1038/s415...

Dogs evolved to eat your leftovers! Comparing dog & wolf genomes revealed dogs have up to 30 EXTRA copies of the amylase gene (AMY2B) that helps digest starch. This is a key genomic signature of living alongside humans & table scraps for thousands of years 🐕 www.nature.com/articles/nat... #2026MMM

Looks interesting! Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals www.nature.com/articles/s41...

A single course of antibiotics can have lasting effects on your gut microbiome, with changes that last well beyond 4 years. Three types of antibiotics stood out for their long term disruptive impact (3 at left, Figure) nature.com/articles/s41...

Predicting Alzheimer's disease up to 25 years in advance of any symptoms with the p-tau217 biomarker blood test, among 2,766 women mean age 70 jamanetwork.com/journals/jam...

Our work with Lena Takayasu and @dwmckellar.bsky.social in Iwijn De Vlaminck's lab is now out in @natmicrobiol.nature.com ! 🎉 Spatial transcriptomics maps host–gut microbiome biogeography at high resolution rdcu.be/e7i7o

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