Kiseok (Keith) Lee

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...

News article covering our story/research here from Matt Wood!
biologicalsciences.uchicago.edu/news/soil-mi...

Thank you!

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 dynami...

Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change.
www.nature.com/articles/s41...

Woohoo!! Starting Gordon Research Seminar (Microbial population biology) at Andover, NH. Thank you GRC GRS organizers!! @mikeblazanin.bsky.social @lcatherines.bsky.social

Let's connect soon at GRC / GRS Microbial Population Biology!!! I have a very late night talk on Saturday around 9pm in the GRS hahaha...!! I am super excited to (re)connect with old/new friends/colleagues! So many talks I am looking forward to 😀 #grc2025 #microbialpopulationbiology

<End of the PhD chapter>
Graduation happened last week! So grateful for all the relationships I nurtured at uchicago. I will miss this place! Thank you Cathy for hooding me! Also, I am very excited to start postdoc tomorrow in Aditya Kunjapur @kunjapur.bsky.social lab in University of Delaware!

So happy to see this paper finally out! A fun project with collaborators Emily Zakem, @jlw-ecoevo.bsky.social and Yubin Raut!

Congrats on this work being published Harish!!

When is microbial cross-feeding evolutionarily stable? Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding,...

When is microbial cross-feeding evolutionarily stable?
www.biorxiv.org/content/10.1...

Thank you everyone for coming to my PhD defense today in person and on zoom. Really can't thank everyone enough. Special thanks to Seppe Kuehn @seppekuehnlab.bsky.social and Madhav Mani for supporting me throughout the PhD journey.

Thanks Hyunkyung for the beautiful cake resembling the soil!

Congratulations for this work seeing the light after many years of hard incredible work!! Go go Forti (Mandy) et al. and Aditya (soon to be postdoc advisor).
Commensalism engineered with non-standard amino acid:
www.nature.com/articles/s41...

Such a great conference! @recombconf.bsky.social RECOMB-Microbiome. Learned so much and asked a lot! Was able to catch up with many colleagues/professors and met amazing people doing great science!!

@hdkgeo.bsky.social Thanks again!!

Caltech is such a research paradise! The resource, the people... just in awe. Thanks for hosting me Hannah!! Made so many amazing scientist friends/colleagues!!

GPS Event Calendar From the Caltech Division of Geological and Planetary Sciences

<Shameless seminar self-promotion>
I'll be giving a talk at Caltech in the Geoclub Seminar Series (www.gps.caltech.edu/news-and-eve...) this Thursday (4/10 4pm, Buwalda Rm). Join us if you are interested in hearing about the functional response of the soil microbiome to environmental perturbations!

My good friend Dr. Myeonghwan Kim et al. figured out the molecular mechanism of how lipid nanoparticle encapsulated mRNA uptake happens in the cellular level! Today in Science!
www.science.org/doi/10.1126/...

So great to be breathing the same air with the great minds in the same room! Simons foundation NITMB annual meeting in NY!

Seppe's thread!!

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?

Excited to share our new paper!🎉 We (the amazing Mahmoud Yousef et al.) learn the functional landscape from designing synthetic communities🧫 to degrade plastic-derived pollutant BPA in soils. As we increase BPA concentration, epistatic effects dominate!
www.biorxiv.org/content/10.1...

Beyond Official Advisors: The Power of Shadow Mentors Build a Cabinet of "Shadow Mentors"

In our latest blog post we discuss why "Shadow Mentors" are important in careers. I've been fortunate to have many—too many to list here.

Check it out below and please share with someone who might find it useful.

uncultured.carinilab.com/p/beyond-off...

It was amazing to connect with Dr. Otto Cordero again! His talk at UChicago was intellectually very satisfying!! I knew Xiaoyu's great coarse-graining work but Dr. Stefany Moreno Gamez's work on the molecular mechanism of niche partitioning was super stimulating...!! Thanks Otto!

Microbes can capture carbon and degrade plastic — why aren’t we using them more? Interventions involving bacteria or fungi could help to sequester greenhouse gases, create more sustainable products and clean up pollution — in ways that are economically viable and safe.

How can we leverage microbes to address the climate crisis? The @asm.org & IUMS Scientific Advisory Group introduces a new framework in Nature for assessing microbial solutions, focusing on economic returns, safety and societal impact. Read more @nature.com: www.nature.com/articles/d41...

Understanding climate change from a global analysis of city analogues Combating climate change requires unified action across all sectors of society. However, this collective action is precluded by the ‘consensus gap’ between scientific knowledge and public opinion. Her...

"We notably predict that Madrid’s climate in 2050 will resemble Marrakech’s climate today, Stockholm will resemble Budapest, London to Barcelona, Moscow to Sofia, Seattle to San Francisco, Tokyo to Changsha"

By 2050!

journals.plos.org/plosone/arti...

If you are interested in environmental microbiology and the intersection of ecology and physiology, join this wonderful group of scientists in Karna Gowda lab at Ohio State University!! I guarantee great mentorship and fascinating science!

Happy to be reunited with Professor Yong-Hwan Lee (SNU) at his RR Nelson memorial lecture at Penn State! He is a living history with ~40 years of ground-breaking forward/reverse genetics and bioinformatics on rice blast. He had a profound influence on me.

Glad this paper is out. The review was quite an adventure.

<Shameless seminar promotion at Ohio State>
Please join us at the QMicro seminar, where I will delve into soil microbial ecology and how metabolic functions change in varying environments!

- When: Tuesday, March 18, 2025, 3:00 PM EST
- Where: Pomerene Hall, Rm 150, Ohio State University

First post: 🦠🌊Denitrification is the main nitrogen loss process, but how do microbes performing different steps coexist? We outline the rules governing this coexistence and explain why some denitrifiers are more abundant than others in the ocean. Check it out here: www.pnas.org/doi/10.1073/...