Resource allocation models: theory and applications in microbial biotechnology doi.org/10.1016/j.co...
Pierre Millard
@pierremillard.bsky.social
Systems biologist at Toulouse Biotechnology Institute, INRAE, France Member of MetaboHub consortium ❓️ Focus on microbial metabolism for biotechnology and health 🛠 Main tools: modeling, fluxomics, metabolomics, isotope-based approaches
Why fundamental research is fundamental to progress, seeding major breakthroughs Editorial @nature.com this week And 7 basic science discoveries that changed the world nature.com/articles/d41... nature.com/articles/d41...
Cool enzyme specificity predictor🦠✨! Build on >300k enzyme-substrate pairs (UniProt, BRENDA, literature), combining ESM-2 embeddings and GNNs to model atom–residue interactions. In one test (34 E. coli metabolites × 860 enzymes), it correctly matched 10! #microsky 🧪 www.nature.com/articles/s41...
Enzyme specificity prediction using cross attention graph neural networks - Nature
Nature - Enzyme specificity prediction using cross attention graph neural networks
nature.com
Domesticated animals have pulled our heavy carts and turned our large mills for centuries. But what about the opposite end of the spectrum—what if the wheel you want to turn is so small you can’t see it? Turns out we can harness the power of bacteria to power the world’s smallest machines. 1/7 ⚛️🧪
How can we design complex computational systems using synthetic biology? Check our paper, where we use space as a computational element, dramatically reducing communication requirements while allowing modularity, reusability, scalability & minimal cell engineering. journals.plos.org/ploscompbiol...
Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks doi.org/10.1021/acss...
Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks
Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO2 as a sustainable feedstock. Formate-fixing path...
doi.org
How can biological systems anticipate future events? In our new paper with @jordiplam.bsky.social, we show how a simple genetic circuit can predict future trends through a simple (and perhaps widespread) mechanism @drmichaellevin.bsky.social @koseskalab.bsky.social www.biorxiv.org/content/10.1...
🚀 Thrilled to share our new Nature Communications article: “A blueprint for designing the next-generation of synthetic C1 microbes” We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts. 🔗 www.nature.com/articles/s41... A short 🧵1/4
A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications
Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.
nature.com
For 25 years, the Chair of the @laskerfdn.bsky.social Jury has reflected on the intersection of science and art in an annual essay. This year, Joseph L. Goldstein explores “From simplicity to complexity: A path to innovation in science and art.” Read now: www.pnas.org/doi/10.1073/...
Suite à la migration de scientifiques et d'universitaires de X, Bluesky est devenue une l'une des alternatives. Afin d'évaluer sa viabilité/pertinence pour la communication scientifique, cette étude présente une analyse à grande échelle de la diffusion d'articles scientifiques sur Bluesky. 1/5
Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests www.biorxiv.org/content/10.1...
Cool! Some gut microbes make 2-MiCit from propionate. In vitro, it inhibits 3D colon tumor growth (and normal cells at high dose). Just a 'lucky' one among millions of microbial by-products? I haven't thought of any selective advantage 🤔 Thoughts? 🦠🧪 #microsky #microbiomesky doi.org/10.1016/j.ce...
Chemotherapy modulation by a cancer-associated microbiota metabolite
Martinez-Martinez et al. combine a host-microbe-drug-nutrient screen with multi-omics to reveal how the cancer-associated microbiota modulates chemotherapy. They identify 2-methylisocitrate, a microbi...
cell.com
Helena Cocheme@cochemelab.bsky.social · 11mo ago"Microbial allies: bacteria help fight against cancer" ✨ News story from #LMS @mrc-lms.bsky.social, covering the beautiful study led by #postdoc Daniel Martinez @dmartimarti.bsky.social - congrats! ✨ #PostdocAppreciationWeek #PAW2025 #Cancer #Microbiome #Chemotherapy lms.mrc.ac.uk/microbial-al...
🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳 📖 Preprint: www.biorxiv.org/content/10.1... 🔍 Explorer: explore.omnipathdb.org OmniPath integrates 160+ resources for multi-omics analysis & modeling. 🧶⬇️
Thrilled to share our new paper in @science.org describing our discovery that bacteria can switch from competitors to bonafide predators when resources run dry—arming nanoscale “spears” (T6SS) to stab & consume neighbours. www.science.org/doi/10.1126/... #MicroSKy #Microbiology
Antagonism as a foraging strategy in microbial communities
In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependen...
science.org
Congrats Snorre!!! 👏 It's great to see this coming out 🎉 and thank you for giving the chance to be a (small) part of this very cool work! "Microbes release lower-value metabolites at higher rates" 🦠
Snorre Sulheim@sulheim.bsky.social · 12mo agoExcited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social www.biorxiv.org/content/10.1...
In our new review, we revisit overflow #metabolism across living organisms and propose universal principles of its functioning, integrating insights from studies on yeast, bacterial, and mammalian cells 🦠✨ First first-author paper of Thomas Gosselin-Monplaisir 🥳 👉 Read it here: urlr.me/82Zspc
Overflow metabolism in bacterial, yeast, and mammalian cells: different names, same game | Molecular Systems Biology
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
urlr.me
Pierre Millard@pierremillard.bsky.social · 11mo agoOverflow metabolism: Why cells waste nutrients—and why it’s not really waste go.nature.com/4n39Ijw
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm
Gade et al. report that polysomes and mRNA levels impact the biophysical properties of the cytoplasm. Using passive rheology probes and single-particle tracking, they demonstrate that intracellular diffusion is enhanced when polysomes are disassembled or when mRNA levels are reduced in eukaryotic cells.
dlvr.it
A plasmid golden ratio? 🧬 Plasmid copy number ≈ 2.5% of chromosome size—consistent across bacterial species! pmc.ncbi.nlm.nih.gov/articles/PMC... @jerorb.bsky.social 🧪 #microbesky
Jerónimo Rodríguez-Beltrán@jerorb.bsky.social · last yr.🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...
Overflow metabolism: Why cells waste nutrients—and why it’s not really waste go.nature.com/4n39Ijw
Overflow metabolism: Why cells waste nutrients—and why it’s not really waste
Cells often appear to waste nutrients by releasing them as useless, and sometimes toxic, by-products—a phenomenon known as overflow metabolism. Far from being mere waste, these molecules also play vit...
go.nature.com
Can a single cell learn? Even without a brain, some microbes show simple forms of cognition. Can this basal cognition be engineered? Check our new paper with @jordiplam.bsky.social on the minimal synthetic circuits & their cognitive limits. @drmichaellevin.bsky.social www.biorxiv.org/content/10.1...
I'm going to be advertising for a few positions in my group in the next couple of months for a big project on synthetic microbial communities. I would love to hear from you if you are interested and I'd also appreciate if everyone could share this far and wide!
Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging Congrats Hannah Ochner and authors on this important paper! Strong collaboration with @kiranrpatil.bsky.social www.biorxiv.org/cgi/content/... @mrclmb.bsky.social @wellcometrust.bsky.social
Please repost! Postdoc in adaptive laboratory evolution and C1 synthetic metabolism! Location: DTU Biosustain 🦠🧬🔬 Starting in 01/2026! Fell free to reach out if you have questions! efzu.fa.em2.oraclecloud.com/hcmUI/Candid...
efzu.fa.em2.oraclecloud.com
Je pense à ce fil depuis hier, et je me posais la question de ce que ça implique pour les efforts d'apprendre la programmation et ou l'algorithmique aux non spécialistes.
Julien Gossa@juliengossa.cpesr.fr · 11mo agoMy two cents after two months of AI-assisted programming. Agile methods are going to lose ground, and we’ll go back to requirement documents and specifications/designs carefully tied up in advance. And this poses an educational challenge.
Regulation by RNAs might be even more extensive than we thought. Many enzymes and other proteins not previously considered as RNA-binding proteins do seem to fall into this class & might have their activity regulated by RNA. www.cell.com/cell/fulltex...
Rethinking RNA-binding proteins: Riboregulation challenges prevailing views
The advent of system-wide proteomic approaches has largely expanded the number of RNA-binding proteins (RBPs). This review discusses how recent discoveries are transforming our understanding of biolog...
cell.com
Strategies and applications of synthetic cell communication doi.org/10.1038/s415...
Strategies and applications of synthetic cell communication - Nature Chemical Biology
Recent advances in engineering bottom-up synthetic cells have created powerful compartmentalized biochemical reactors with cell-like abilities. To push the boundaries of the collective capabilities of...
doi.org
big one! a decade in the making. nadler & team develop tools to track lipid transport in living cells at single-species resolution. turns out non-vesicular, asymmetry-driven transport is the main architect of organelle identity. feels like the dawn of a golden era for lipid biology. rdcu.be/eBGJv
Quantitative imaging of lipid transport in mammalian cells
Nature - Directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting into organelle membranes.
rdcu.be
For life to emerge on Earth, peptides must first have formed without the aid of enzymes — but how? Reactions of sulfur-containing molecules might have been key go.nature.com/4oX04jC
Origins of life: the molecules that could have unlocked peptide synthesis
For life to emerge on Earth, peptides must first have formed without the aid of enzymes — but how? Reactions of sulfur-containing molecules might have been key.
go.nature.com
Aggresomes protect mRNA under stress in Escherichia coli www.nature.com/articles/s41... "prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, compaction and selective mRNA enrichment within these aggresomes" 🦠 #microsky #rnasky
Aggresomes protect mRNA under stress in Escherichia coli - Nature Microbiology
Ribonucleoprotein aggresomes exclude ribonucleases and protect mRNA to promote rapid translation reactivation and cellular recovery after stress alleviation in Escherichia coli.
nature.com