New paper out today in Nature Microbiology: "Epistatic interactions inform rational design of synthetic microbial communities for bioremediation." 🧵https://www.nature.com/articles/s41564-026-02386-4 @kiseokmicro.bsky.social @nitmb.bsky.social

New preprint w/Milena Chakraverti-Wuerthwein with Alissa Domenig. “Everything is everywhere; the environment selects.” But which traits does the environment select on? Is there a relationship between evolutionary conservation of traits and variation in community composition? doi.org/10.64898/202...

New preprint! www.biorxiv.org/content/10.6... A theory to explain global epistasis in microbial communities

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

The Abreu lab at NYU is hiring another postdoc! We study microbial ecology and evolution, using yeast/bacteria microcosms, DNA barcoding for evolutionary lineage tracking, and simple mathematical modeling. Apply here: apply.interfolio.com/179949

It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027! See you there!! @wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social #microsky #mevosky

Hello, Chicago! I'll be giving a public talk on Wednesday about reporting on science in these rocky times. events.uchicago.edu/event/259056...

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪 www.nature.com/articles/s44...

Have a research group you’d love to bring to NITMB? Apply for an NITMB Focused Research Group Award, welcoming small groups of participants from multiple institutions to gather at NITMB to focus intently on independent, ambitions joint research projects www.nitmb.org/research/foc...

We're hiring faculty at the interface of climate systems engineering and ecology -- climateengineering.uchicago.edu/opportunitie...

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...

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...

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...

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

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! 🧵

🥂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...

📢 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

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!

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...

Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...

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

Nature research paper: Functional regimes define soil microbiome response to environmental change 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...

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...

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...

Being rich doesn’t make you smart or ethical. When will science contend with these fools? www.nytimes.com/2025/06/28/t...

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

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

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...

Are you interested in the math-bio interface? Secure your place at the NITMB MathBio Convergence Conference! www.nitmb.org/nitmb-mathbi...

ACTION ITEM-----ACTION ITEM Implementation of Schedule F This is what a lot of us have been worried about. This allows for many civil service positions to replaced with political appointees. This could include NIH institute directors and even POs. BUT THERE IS A COMMENT PERIOD... 1/n

Northwestern has not received any NIH funds since March. No written communication about why or what can be done. Thank you Ben Singer for raising awareness at #ATS2025

This is the best tool I've seen for rapidly writing your reps. DO IT! www.aps.org/initiatives/...

It is a great pleasure to listen to @seppekuehnlab.bsky.social His talk is about ´Learning microbiome design principles from natural variation ´. Below, the #liveSketch painting during the seminar and given at the end! #ArtAndScience #MediationScientifique

SaveNSF is a coalition of concerned scientists and allies who are working to save funding for scientific grants through the NSF. The mission is to support and advocate for the continuation of vital research and innovation. Join: www.savensf.com

Third preprint! – We use community-function landscapes to rationally design communities for bioremediation in soils! Spoiler - it works! Led by Mahmoud Yousef, with @kiseokmicro.bsky.social, J. Tang, V. Charisopoulos, B Willett. @nitmb.bsky.social, NSF, MSTP UChicago. www.biorxiv.org/content/10.1...

Another preprint! Microbiomes are often structured in guilds, or groups of taxa that use similar resources - wastewater, fermentation, human gut. How do these guilds respond to environmental fluctuations? Can we learn these guilds from time series in the wild?

It’s increasingly clear that the language of microbial communities is one of resources. Conserved metabolism leads to regular, reliable resource flows across ecosystems—from the gut to wastewater. In complex communities, one serious challenge is: who is eating what?

My lab at NYU is hiring a postdoc in microbial ecology and evolution! We are looking for someone interested in both wet and dry lab techniques, including experimental evolution, genome editing, bioinformatics, and some modeling. Apply here: apply.interfolio.com/164683

🚨🧪 Are you a researcher affected by the recent cancellation of federal grants and contracts at Columbia University? I'm working on a story for @Nature.com. If you want to chat, your identity will be kept private. Signal: humbertobasilio.24 Email: [email protected] Repost please!

Deactivated my twitter/X. You should do the same.

Amazing — www.nature.com/articles/s41...