Kiseok (Keith) Lee
@kiseokmicro.bsky.social
380 followers 620 following 33 posts
How can we understand & design robust community functions? Postdoc: UDel, Aditya Kunjapur lab PhD: UChicago, Seppe Kuehn lab Scholar: https://scholar.google.com/citations?user=&user=UcMtC88AAAAJ Linkedin: https://www.linkedin.com/in/kiseokkeithlee/
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kiseokmicro.bsky.social
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...
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...
www.nature.com
kiseokmicro.bsky.social
It was one of the most interactive departmental seminar I've given. Thank you @xinsun-putiger.bsky.social for hosting this seminar in the beautiful campus of Penn, Department of Biology! Astounded by a full room of people studying soil, marine ecology, plant biology, and earth/environmental science.
Reposted by Kiseok (Keith) Lee
seppekuehnlab.bsky.social
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...
kiseokmicro.bsky.social
News article covering our story/research here from Matt Wood!
biologicalsciences.uchicago.edu/news/soil-mi...
kiseokmicro.bsky.social
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...
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...
www.nature.com
kiseokmicro.bsky.social
Woohoo!! Starting Gordon Research Seminar (Microbial population biology) at Andover, NH. Thank you GRC GRS organizers!! @mikeblazanin.bsky.social @lcatherines.bsky.social
kiseokmicro.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
mikeblazanin.bsky.social
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC
kiseokmicro.bsky.social

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!
kiseokmicro.bsky.social
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!
kiseokmicro.bsky.social
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...
kunjapur.bsky.social
It seems there are no free-living organisms known to rely exclusively on one other organism for their survival

Until perhaps now

Check out our latest publication in @natmicrobiol.nature.com to see how we designed an exclusive microbial reliance using GCE

rdcu.be/ekepI
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Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid
Nature Microbiology - A genetically engineered microbial symbiosis based on synthetic auxotrophy is created, with potential implications as a biocontainment strategy.
rdcu.be
kiseokmicro.bsky.social
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!!
kiseokmicro.bsky.social
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!!
kiseokmicro.bsky.social

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!
GPS Event Calendar
From the Caltech Division of Geological and Planetary Sciences
www.gps.caltech.edu
kiseokmicro.bsky.social
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/...
kiseokmicro.bsky.social
So great to be breathing the same air with the great minds in the same room! Simons foundation NITMB annual meeting in NY!
Reposted by Kiseok (Keith) Lee
seppekuehnlab.bsky.social
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?
kiseokmicro.bsky.social
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...
www.biorxiv.org
Reposted by Kiseok (Keith) Lee
uncultured.carinilab.com
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...
Beyond Official Advisors: The Power of Shadow Mentors
Build a Cabinet of "Shadow Mentors"
uncultured.carinilab.com
kiseokmicro.bsky.social
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!