SeppeKuehnLab
@seppekuehnlab.bsky.social
Physics and biology of microbial communities. Structure, function, evolution. Center for the Physics of Evolving Systems. Dept. of Ecology and Evolution. UChicago. @NITMB, @CLS. kuehnlab.org
Pinned
SeppeKuehnLab
@seppekuehnlab.bsky.social
· Jul 17
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
We're hiring faculty at the interface of climate systems engineering and ecology -- climateengineering.uchicago.edu/opportunitie...
Assistant Professors - Ecological Consequences of Climate Engineering
Salary Range: $140,000 – $180,000 a year The University of Chicago’s Department of Ecology & Evolution in the Biological Sciences Division and the Climate Systems Engineering Initiative (CSEi) are sea...
climateengineering.uchicago.edu
November 12, 2025 at 4:08 AM
We're hiring faculty at the interface of climate systems engineering and ecology -- climateengineering.uchicago.edu/opportunitie...
Reposted by SeppeKuehnLab
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 12, 2025 at 3:43 AM
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
I'm attending No Kings's event, “NO KINGS in Chicago” - sign up here www.mobilize.us/nokings/even...
NO KINGS in Chicago · No Kings
**In America, we don’t put up with would-be kings.**
Here in Chicago we know how to rise up, fight back, and support each other. It is more important than ever that we do that together on October 18t...
www.mobilize.us
October 17, 2025 at 11:16 PM
I'm attending No Kings's event, “NO KINGS in Chicago” - sign up here www.mobilize.us/nokings/even...
Schmidt AI + Science. Amazing fellowship opportunity at UChicago! apply.interfolio.com/173322
Apply - Interfolio
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apply.interfolio.com
September 26, 2025 at 9:47 PM
Schmidt AI + Science. Amazing fellowship opportunity at UChicago! apply.interfolio.com/173322
Great new paper from Kyle Crocker -- a talented postdoc in the group who is ** on the job market now ** !! @kylecrocker.bsky.social bsky.app/profile/kyle...
New paper out (doi.org/10.1093/isme...) with fantastic grad students Abby Skwara and Rathi Kannan! Advised by the excellent @seppekuehnlab.bsky.social and @amurugan.bsky.social. Overview in the thread below.
Timescale of environmental change modulates metabolic guild cohesion in microbial communities
Abstract. Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to lon
doi.org
September 16, 2025 at 3:06 PM
Great new paper from Kyle Crocker -- a talented postdoc in the group who is ** on the job market now ** !! @kylecrocker.bsky.social bsky.app/profile/kyle...
Center for Living Systems -- seeking strong post docs at the interface of physics and biology. Consider applying by Oct. 13! docs.google.com/forms/d/e/1F...
docs.google.com
September 4, 2025 at 2:06 AM
Center for Living Systems -- seeking strong post docs at the interface of physics and biology. Consider applying by Oct. 13! docs.google.com/forms/d/e/1F...
This important contribution sharpens the ill-defined concept of functional redundancy in microbial communities. It's a term we use a lot, but the exact meaning is elusive, and this paper is the first to sharpen it via proper null models. @ po-yi ho and KC Huang. www.sciencedirect.com/science/arti...
Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities
Microbiomes often show similar functional profiles despite highly variable taxonomic compositions, a phenomenon attributed to “functional redundancy” …
www.sciencedirect.com
August 10, 2025 at 3:32 PM
This important contribution sharpens the ill-defined concept of functional redundancy in microbial communities. It's a term we use a lot, but the exact meaning is elusive, and this paper is the first to sharpen it via proper null models. @ po-yi ho and KC Huang. www.sciencedirect.com/science/arti...
Reposted by SeppeKuehnLab
Mathematical Frameworks for Stability, Evolution, and Control in Microbial Communities
Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!
tinyurl.com/378ua7ws
Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!
tinyurl.com/378ua7ws
August 6, 2025 at 8:42 PM
Mathematical Frameworks for Stability, Evolution, and Control in Microbial Communities
Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!
tinyurl.com/378ua7ws
Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!
tinyurl.com/378ua7ws
Reposted by SeppeKuehnLab
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by SeppeKuehnLab
🥂This was the highlight of my year. The "instigators", led by local master of the ceremony @svobodalab.bsky.social will never forget the privilege of organizing it and i think every participant will treasure the experience forever ❤️ @nature.com @josiegz.bsky.social www.nature.com/articles/d41...
Scientific bedlam at the world’s weirdest and wildest research conference
Woodstock Bio2 + Night Science aimed to encourage collaborations through creativity. The walk-on music for presentations was fun, too.
www.nature.com
July 31, 2025 at 4:22 AM
🥂This was the highlight of my year. The "instigators", led by local master of the ceremony @svobodalab.bsky.social will never forget the privilege of organizing it and i think every participant will treasure the experience forever ❤️ @nature.com @josiegz.bsky.social www.nature.com/articles/d41...
Reposted by SeppeKuehnLab
📢 We're seeking a postdoc to work on a project funded by HFSP @hfspo.bsky.social at the intersection of bacterial physiology, ecology and evolution. You can find more details about the project, the position, and how to apply here www.dalbellolab.com/hfsp-project! #bacteria #ecosky #MevoSky #microSky
HFSP project — dal bello lab
www.dalbellolab.com
July 23, 2025 at 6:41 PM
📢 We're seeking a postdoc to work on a project funded by HFSP @hfspo.bsky.social at the intersection of bacterial physiology, ecology and evolution. You can find more details about the project, the position, and how to apply here www.dalbellolab.com/hfsp-project! #bacteria #ecosky #MevoSky #microSky
Reposted by SeppeKuehnLab
Excited to report that Joy Bergelson (bergelsonlab.org) and I will be running a brand new GRC conference on the Function of Evolving Systems in the summer of 2026. The 2028 one will be chaired by Mikhail Tikhonov (physics.wustl.edu/people/mikha...) and @asanchezlab.bsky.social! Stay tuned!
Faculty
physics.wustl.edu
December 30, 2024 at 7:43 PM
Excited to report that Joy Bergelson (bergelsonlab.org) and I will be running a brand new GRC conference on the Function of Evolving Systems in the summer of 2026. The 2028 one will be chaired by Mikhail Tikhonov (physics.wustl.edu/people/mikha...) and @asanchezlab.bsky.social! Stay tuned!
Reposted by SeppeKuehnLab
I am really happy to share that there will be a @nitmb.bsky.social workshop next year on mathematical and biological features of evolutionary game theory.
It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.
www.nitmb.org/evolutionary...
It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.
www.nitmb.org/evolutionary...
Evolutionary Games: Mathematical Theory and Biological Insights
www.nitmb.org
July 18, 2025 at 1:57 PM
I am really happy to share that there will be a @nitmb.bsky.social workshop next year on mathematical and biological features of evolutionary game theory.
It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.
www.nitmb.org/evolutionary...
It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.
www.nitmb.org/evolutionary...
Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...
Simple rules govern soil microbiome responses to environmental change
Research from UChicago shows how environmental changes lead to predictable responses in soil microbiome metabolism.
biologicalsciences.uchicago.edu
July 18, 2025 at 11:01 AM
Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...
Reposted by SeppeKuehnLab
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
July 17, 2025 at 8:32 PM
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
recruit.ap.uci.edu/JPF09601
Reposted by SeppeKuehnLab
Nature research paper: Functional regimes define soil microbiome response to environmental change
go.nature.com/3IqdJzd
go.nature.com/3IqdJzd
Functional regimes define soil microbiome response to environmental change - Nature
Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynamics.
go.nature.com
July 17, 2025 at 9:47 AM
Nature research paper: Functional regimes define soil microbiome response to environmental change
go.nature.com/3IqdJzd
go.nature.com/3IqdJzd
This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
July 17, 2025 at 7:07 AM
This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
July 17, 2025 at 6:36 AM
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
First paper we've found that validates auxotrophy predictions from genomes. in non-host associated communities (e.g. soils) auxotrophy is rare. I believe the assumption of prevalent auxotrophies emerging out of pervasive cross-feeding needs to be reconsidered.. www.nature.com/articles/s41...
Taxonomic and environmental distribution of bacterial amino acid auxotrophies - Nature Communications
Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial ge...
www.nature.com
July 10, 2025 at 8:49 AM
First paper we've found that validates auxotrophy predictions from genomes. in non-host associated communities (e.g. soils) auxotrophy is rare. I believe the assumption of prevalent auxotrophies emerging out of pervasive cross-feeding needs to be reconsidered.. www.nature.com/articles/s41...
Reposted by SeppeKuehnLab
The Regular Registration deadline for the NITMB MathBio Converge Conference is Monday, July 14th
Register today to secure your spot at the conference!
www.nitmb.org/nitmb-mathbi...
Register today to secure your spot at the conference!
www.nitmb.org/nitmb-mathbi...
June 30, 2025 at 6:51 PM
The Regular Registration deadline for the NITMB MathBio Converge Conference is Monday, July 14th
Register today to secure your spot at the conference!
www.nitmb.org/nitmb-mathbi...
Register today to secure your spot at the conference!
www.nitmb.org/nitmb-mathbi...
Being rich doesn’t make you smart or ethical. When will science contend with these fools? www.nytimes.com/2025/06/28/t...
The Narrowing of Mark Zuckerberg and Priscilla Chan’s Philanthropy
www.nytimes.com
June 28, 2025 at 4:31 PM
Being rich doesn’t make you smart or ethical. When will science contend with these fools? www.nytimes.com/2025/06/28/t...
Reposted by SeppeKuehnLab
Very much enjoyed yesterday's Physics of Life community event in Utrecht! @seppekuehnlab.bsky.social: microbial communities, #PhilippSavakis: yeast glycolysis, @janniharju.bsky.social: DNA organization in bacteria, #ArthurHernandez: axis formation in hydra, and #LouiseJawerth: protein condensates
June 19, 2025 at 6:37 AM
Very much enjoyed yesterday's Physics of Life community event in Utrecht! @seppekuehnlab.bsky.social: microbial communities, #PhilippSavakis: yeast glycolysis, @janniharju.bsky.social: DNA organization in bacteria, #ArthurHernandez: axis formation in hydra, and #LouiseJawerth: protein condensates
Reposted by SeppeKuehnLab
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
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...
www.science.org
June 13, 2025 at 5:39 AM
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
www.science.org/doi/10.1126/...
#MicroSKy #Microbiology
I can't say I agree with everything here, especially as I think it overstates how much evolutionary theory can explain about what we observe in Nature. However, I very much appreciate the perspective and a bit of muckraking. www.pnas.org/doi/10.1073/...
Complexity myths and the misappropriation of evolutionary theory | PNAS
Recent papers by physicists, chemists, and geologists lay claim to the discovery of
new principles of evolution that have somehow eluded over a cen...
www.pnas.org
June 10, 2025 at 7:14 PM
I can't say I agree with everything here, especially as I think it overstates how much evolutionary theory can explain about what we observe in Nature. However, I very much appreciate the perspective and a bit of muckraking. www.pnas.org/doi/10.1073/...
PhD students interested in ecology and evolution -- consider applying. Reach out to me if you are interested in discussing. www.simonsfoundation.org/grant/simons...
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
www.simonsfoundation.org
June 2, 2025 at 9:14 PM
PhD students interested in ecology and evolution -- consider applying. Reach out to me if you are interested in discussing. www.simonsfoundation.org/grant/simons...