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Enrico Sandro Colizzi

@escolizzi.bsky.social
1.4K followers 837 following 42 posts

Tenured scientist @INRIA, Lyon. Studying how microbes evolve new stuff with computer simulations.

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Reposted by Enrico Sandro Colizzi
Archaea Biology Vienna @archaea-vienna.bsky.social · 01/10/2026
Our paper on the dynamics of Asgard archaea (Promethearchaeota) is now out in Nature! Huge thanks to the reviewers for helping make the manuscript stronger. www.nature.com/articles/s41... Two “Lokis” stained for Lokiactin (FastAct, magenta), reaching toward each other to celebrate 🎉 #archaea
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Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 01/10/2026
#Evolution can innovate without inventing. Cell type families can retain ancient regulatory “vocabularies”, while individual cell types evolve by reshuffling how those motifs are combined. @natecoevo.nature.com New cell types from old regulatory words. We like this! doi.org/10.1038/s415...
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Sara Mitri @saramitri.bsky.social · 22/09/2026
Check out @sulheim.bsky.social's paper! The latest from our lab showing that some species do actually coexist robustly, no matter what or how much you feed them, whether the environment around them is constant, and whether or not they depend on each other metabolically for amino acids and vitamins.
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Kelley Gallagher @kelleygallagher.bsky.social · 07/08/2026
Excited to share our lab's first paper on the evolution of a c-di-GMP-controlled sigma factor: journals.asm.org/doi/10.1128/...
journals.asm.org
Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota | mSystems
Mounting global responses to dynamic environmental conditions is a crucial function that bacterial cells must perform. Global regulatory networks are most often studied in individual species, however,...
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 22/09/2026
This is very cool @kelleygallagher.bsky.social et al Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota doi.org/10.1128/msys...
doi.org
Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota | mSystems
Mounting global responses to dynamic environmental conditions is a crucial function that bacterial cells must perform. Global regulatory networks are most often studied in individual species, however,...
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Reposted by Enrico Sandro Colizzi
Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect
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Christian Kost @kostchristian.bsky.social · 24/08/2026
Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb
nature.com
Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology
Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...
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Enrico Sandro Colizzi @escolizzi.bsky.social · 21/08/2026
Super interesting! the biorxiv link does not work though.
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Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect
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Enrico Sandro Colizzi @escolizzi.bsky.social · 08/07/2026
Nice piece! Congrats @kostchristian.bsky.social and collaborators.
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Christian Kost @kostchristian.bsky.social · 08/07/2026
Happy to announce that a new opinion paper of our group just came out: A conceptual framework to dissect emergent functions in microbial communities with @swagatika.bsky.social @sharvari27.bsky.social @anjanaprasad.bsky.social @palshubharthi.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A conceptual framework to dissect emergent functions in microbial communities
Microbial communities play vital roles in diverse ecosystems and are key drivers of numerous industrial or health-related applications. In many cases,…
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Cameron Thrash @jcamthrash.bsky.social · 29/06/2026
Cyanobacterial flocculation as a defence against bacterial predation academic.oup.com/ismej/advanc... #jcampubs
academic.oup.com
Cyanobacterial flocculation as a defence against bacterial predation
Abstract. Many cyanobacteria are capable of flocculation: the formation of floating linked assemblages of many thousands of cells. Flocculation is a highly
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🍁 Alex Smith 🍁 @alexsmithants.bsky.social · 07/07/2026
🧪 Physiology is a hidden dimension of diversity in the radiation of woodland salamanders | PNAS www.pnas.org/doi/10.1073/...
pnas.org
Physiology is a hidden dimension of diversity in the radiation of woodland salamanders | PNAS
Morphological evolution can be explosive, producing visually spectacular adaptive radiations like Caribbean anoles, Malagasy vangas, and African Ri...
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Pawel Burkhardt @pawelburkhardt.bsky.social · 16/06/2026
How ancient are the building blocks of animal sensory systems? Key components of animal sensory systems evolved before animals. We find that choanoflagellates possess diverse & spatially segregated TRP channels, pointing to ancient origins of sensory specialization. doi.org/10.64898/202...
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Leah McPhillips @leahmcphillips.bsky.social · 09/06/2026
Excited to share this is now published in @narjournal.bsky.social 🎉 see the preprint thread below for a summary of our findings on plasmids with multiple partition systems using the Streptomyces plasmid SCP1 as a model! academic.oup.com/nar/article/...
academic.oup.com
Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems
Abstract. Low-copy-number plasmids often rely on dedicated maintenance mechanisms, such as partitioning systems, to ensure stable inheritance across genera
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Tung Le @tunglejic.bsky.social · 08/06/2026
now published!!! @johninnescentre.bsky.social @leahmcphillips.bsky.social academic.oup.com/nar/article/...
academic.oup.com
Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems
Abstract. Low-copy-number plasmids often rely on dedicated maintenance mechanisms, such as partitioning systems, to ensure stable inheritance across genera
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Enrico Sandro Colizzi @escolizzi.bsky.social · 01/06/2026
Congratulations @jeroenmeijer.bsky.social !
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Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
science.org
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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Sarah Robinson @robinsonsci.bsky.social · 28/05/2026
www.cam.ac.uk/jobs/researc...
cam.ac.uk
Research Assistant - Robinson Group
Applications are invited for a Research Assistant position in the group of Dr Sarah Robinson at the Sainsbury Laboratory Cambridge University. The successful applicant will be part of a group that inv...
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Enrico Sandro Colizzi @escolizzi.bsky.social · 22/05/2026
This, of course, without taking anything away from the great recent preprint of @wcratcliff.bsky.social - of whom I remain a big fan :) 3/3
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Enrico Sandro Colizzi @escolizzi.bsky.social · 22/05/2026
I often feel that if we embraced biological specificity (and complexity) in modelling, and made a lot of different detailed models, we would be able to identify novel common patterns that we did not pre-conceive. 2/3
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Enrico Sandro Colizzi @escolizzi.bsky.social · 22/05/2026
I really resonate with this take @multicellgenome.bsky.social. I'd add that the problem of collapsing the diversity of multicellularity onto simple pre-determined narratives is even more acute in the computational/mathematical modelling world. 1/3
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Drew Bridges @bridgesbio.bsky.social · 29/04/2026
New preprint: "A branching cell-fate decision in biofilm dispersal enables long-term surface persistence." When V. cholerae biofilms disperse, it isn’t a uniform exit, rather, an opportunity to bet-hedge. A subpopulation of cells stay behind, primed for biofilm regrowth. doi.org/10.64898/202...
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Paula García-Galindo @ggalindopaula.bsky.social · 22/04/2026
Phenotypic cliffs paper is out! We observe in RNA that phenotypic sites which typically keep the phenotype unchanged through mutation (robust), are also the ones which lead to the most change when they do. royalsocietypublishing.org/rsif/article...
royalsocietypublishing.org
Phenotypic cliffs in the RNA genotype–phenotype map
Abstract. Point mutations of a genotype can leave the phenotype unchanged, or change it, in some cases radically. The extent of this phenotypic change can
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Reposted by Enrico Sandro Colizzi
Theory of Living Matter Group @tlmcambridge.bsky.social · 14/04/2026
New lineup of exciting speakers for the Easter term. Sign up to our mailing list for updated zoom links 📝📩
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Sam von der Dunk @derdunk.bsky.social · 09/04/2026
Very excited with the online publication of our modeling work on the evolution of sexual reproduction during obligate endosymbiosis: doi.org/10.1098/rstb.... The first publication of Alkmini Zania 🎉; together with Paulien Hogeweg.
doi.org
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Christian Kost @kostchristian.bsky.social · 14/04/2026
@shrylishreekar.bsky.social and me wrote a commentary on Chunhui Hao's and @stuwest.bsky.social et al.'s recent paper "Cooperation and the evolution of bacterial niche breadth" in PNAS. Please find our commentary here: www.pnas.org/doi/10.1073/...
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laurenmlui.bsky.social @laurenmlui.bsky.social · 08/04/2026
With a 135 complete, circular Pelagibacter genomes, we have answered some of the most outstanding questions about what is often considered the most abundant organism on the planet, with roughly 10 million times more individuals in the ocean than stars in the universe. Check out our preprint.
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Vaughn Cooper @vscooper.micropopbio.org · 30/03/2026
Now out in AEM @asm.org! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy journals.asm.org/eprint/FBU9M...
journals.asm.org
Genetic diversification of Pseudomonas fluorescens maintained by multi-niche selection within biofilms | Applied and Environmental Microbiology
Bacterial biofilms dominate microbial life; however, their evolutionary genetics remain incompletely understood. Extensive replication of biofilm selection experiments by secondary school students can...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 29/03/2026
On the architecture and evolution of prokaryotic multicellularity Preprint from @escolizzi.bsky.social www.authorea.com/doi/full/10....
authorea.com
On the architecture and evolution of prokaryotic multicellularity
AbstractProkaryotes form multicellular structures under both natural and experimental conditions, based on developmental programs that sometimes echo those known from eukaryotes. Recent research has i...
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SPP2389 - Emergent Functions of Bacterial Multicellularity @spp2389.bsky.social · 26/03/2026
What started out as a student project has grown over the last 2 years into a full-fledged review! So many thanks to @escolizzi.bsky.social for leading this multicellular effort and sharing your evolutionary wisdom with us 🫶🏻🦠
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Enrico Sandro Colizzi @escolizzi.bsky.social · 26/03/2026
Phd students Genna Sohl and Arthur Schubert led this work, which began over a year ago at the @spp2389.bsky.social meeting, when Thorsten Mascher asked me to work with them. Link: bit.ly/4ta06Gq 4/4
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Enrico Sandro Colizzi @escolizzi.bsky.social · 26/03/2026
We hope this review helps conceptualise multicellularity on prokaryotic terms - and highlights just how much remains to understand about its evolution (which is a lot!). 3/4
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Enrico Sandro Colizzi @escolizzi.bsky.social · 26/03/2026
Spoiler: Prokaryotic multicellularity is pervasive and incredibly diverse. Filaments, floating aggregates, motile collectives, biofilms... we have barely scratched the surface (pun intended) of how they organise multicellular life. And that organisation is intimately tied to how they evolve. 2/4
tree of bacterial and archaeal life, showing that each major clade has reported examples of multicellular organisations, including biofilms, filaments, fruiting bodies, motile aggregates, etc.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 26/03/2026
How common is multicellularity in bacteria? And archaea? And how does it evolve? We wrote a short review "On the architecture and evolution of prokaryotic multicellularity". Preprint link: bit.ly/4ta06Gq Sharing and comments are much appreciated. 1/4
An overview of bacterial multicellular formations: biofilms, filaments, free-floating aggregates, motile collectives and fruiting bodies. For each form, we mention an analogous eukaryotic multicellular form (respectively animal epitelia, filaments in fungi, Volvox, Dictyostelium/social animals, Dictyostelium and other slime moulds)
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Megan Bergkessel @slowgoing.bsky.social · 24/03/2026
Now out in its final form, our investigation of how Pseudomonas aeruginosa manages resources to permit ongoing adaptations to environment during starvation: journals.asm.org/doi/10.1128/... Congrats to first author @findunmun1.bsky.social, and co-authors Claudia Hemsley and Elize Ambulte.
journals.asm.org
Pseudomonas aeruginosa dynamically prioritizes motility and resource recycling during prolonged starvation | mSystems
Molecular microbiology has traditionally focused on exponential growth in model organisms as the preferred context in which to study bacterial physiology, especially the regulation of new protein synt...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 16/03/2026
Do you know a paper describing evolution of (enhanced) biofilm formation upon phage exposure? Thus not an experiment where biofilm is used for EE, but EE of a bacterial population leading to protection against phage via biofilm matrix/aggregation/etc Asking for a friend's teaching lecture
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 23/03/2026
Phd Position alert 🚨 Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. It’s not going to be just regular fun. It’s going to ASTRAfun. 🤓 www.uu.nl/en/organisat...
uu.nl
PhD Position in Computational Modelling of Fungal Evolution
How do giant mobile elements called ‘Starships’ reshape fungal plant pathogens? Help us computationally model their spread and impact in nature and agriculture!
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
The take-home message is: Multicellular reproduction can be a rewired unicellular program. Please see the pre-print: bit.ly/4rr2mHU Plenty more detail in the paper, plus some nice extra results. End.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
So to recap: ➡️ Early developmental programs evolve from the ecological dynamics of the unicellular ancestor. ➡️ Depending on resource distribution, our model yields different multicellular life cycles, including some that reproduce via unicellular propagules.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
Why this matters: it suggests a general route to early development. New multicellular traits can appear by co-opting existing regulation, repurposing when/where effector genes act. In our model, the coupling of cell state (behaviour) and adhesion is what gets co-opted to generate propagules.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
Answer: co-option is pervasive. The mechanism that makes propagules in the multicellular state—low adhesion during the dividing state—is co-opted from the ancestral unicellular life cycle, and repurposed during the transition to multicellularity to make offspring.
Re-playing the evolutionary steps from the unicellular ancestors to a multicellular group that reproduces through propagules: the adhesion mechanism of the ancestor becomes co-opted (incorporated) in the multicellular life-cycle.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
We then wondered how propagules evolved. Are they constructed from scratch? Do they co-opt pieces of the unicellular ancestor? Because it’s a computational model, we have the full fossil record. We can literally rewind evolution and watch the steps, generation by generation.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
Mechanistically, propagule formation is driven by a regulatory switch: cells stick strongly while migrating, but once fed they reduce adhesion and switch into division. Dividing cells then peel off as propagules (follow the white border cell).
Following a single cell within a cluster - as it transition from high adhesion and migratory to down-regulating adhesion and dividing - thus forming a propagule. The cell then divides and the two offspring adhere to each other and migrate as a small offspring cluster.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
When food patches are near, only unicellular solutions evolve: by not sticking cells disperse better and reach resources faster. At intermediate patchiness, multicellular groups produce propagules. The group migrates rapidly towards food, and propagules colonise new patches—best of both worlds.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
Why do different life cycles evolve? Well, cells survive if they eat. So resource distribution is the key parameter. When food is far apart, adhesion enables collective migration (see: bit.ly/4s9YIUa). So selection favours groups that reproduce by splitting—each daughter already functional.
When resources are more homogeneously distributed, the system evolves unicellular solutions, when resources are patchy and far apart, multicellular life cycles evolve, including propagules and for high resource heterogeneity group splitting.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
And it’s not just this outcome. From the same ingredients, we get a whole zoo of possible solutions: unicellular life cycles, single-cell and multicellular propagules (in the video), and large groups that split by tearing themselves apart.
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
Over generations, cells evolve adhesion and form multicellular groups. But then: how does a group reproduce? In many runs, groups release single-cell propagules that detach and grow into new groups. Single-cell propagules are everywhere in multicellular life—and here they evolve spontaneously 😎
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Enrico Sandro Colizzi @escolizzi.bsky.social · 10/03/2026
In the model, each cell carries a gene regulatory network: a small circuit controlling when to forage, divide, and stick to other cells. Mutations during division rewire the network, so these behaviours evolve. Cells that do not eat die. That’s it! Mutation + selection. Can development evolve?
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