New preprint! A monumental four year effort by Vaibhhav Sinha: when a bacterium eats organic carbon, how much becomes biomass and how much comes back out as CO₂? The answer is structured hierarchically by substrate and taxonomy. 🧵 www.biorxiv.org/content/10.6...

Hierarchical control of bacterial growth efficiency by substrate and taxonomy

Heterotrophic bacteria utilize organic carbon as a source of energy and material for growth. The balanced allocation of carbon between these two processes, termed growth efficiency, is a key physiolog...

biorxiv.org

Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...

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...

Just quit

Quitting projects in science is hard, but we should be doing a lot more of it.

open.substack.com

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...

Predicting drug inactivation by changes in bacterial growth dynamics - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - Predicting drug inactivation by changes in bacterial growth dynamics

nature.com

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!

Sophie Jean Walton@sophiejwalton.bsky.social · 9mo ago

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...

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...

mobilize.us

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...

Kyle Crocker@kylecrocker.bsky.social · 11mo ago

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.

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” …

sciencedirect.com

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...

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.

nature.com

📢 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...

Evolutionary Games: Mathematical Theory and Biological Insights

nitmb.org

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

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

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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

This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...

SeppeKuehnLab@seppekuehnlab.bsky.social · last yr.

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...

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...