Kiseok (Keith) Lee
@kiseokmicro.bsky.social
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/
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/
Pinned
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
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...
www.nature.com/articles/s41...
Wow wow wow. As soon as I saw this paper, I dropped everything I was doing and read it. Brilliant simple model and experiment to validate synergistic effect of toxin & private nutrient for strain displacement. My research directions greatly impacted. Amazing work Erik and the Foster lab!
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 11:24 PM
Wow wow wow. As soon as I saw this paper, I dropped everything I was doing and read it. Brilliant simple model and experiment to validate synergistic effect of toxin & private nutrient for strain displacement. My research directions greatly impacted. Amazing work Erik and the Foster lab!
It was eye opening to listen to Sara Molinari (University of Maryland)'s fascinating talk on engineering protein secretion to create cell aggregates/living materials. Asked so many questions and learned so much! @saramol.bsky.social
October 11, 2025 at 3:40 AM
It was eye opening to listen to Sara Molinari (University of Maryland)'s fascinating talk on engineering protein secretion to create cell aggregates/living materials. Asked so many questions and learned so much! @saramol.bsky.social
Ohio State microbiology department is hiring assistant professor of Microbiome science (due Nov 6). It's an amazing department please apply!! (I would apply if I had more pubs haha...)
jobs.sciencecareers.org/job/675478/a...
jobs.sciencecareers.org/job/675478/a...
October 9, 2025 at 1:49 AM
Ohio State microbiology department is hiring assistant professor of Microbiome science (due Nov 6). It's an amazing department please apply!! (I would apply if I had more pubs haha...)
jobs.sciencecareers.org/job/675478/a...
jobs.sciencecareers.org/job/675478/a...
Reposted by Kiseok (Keith) Lee
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...
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.
August 30, 2025 at 5:18 AM
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
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...
News article covering our story/research here from Matt Wood!
biologicalsciences.uchicago.edu/news/soil-mi...
biologicalsciences.uchicago.edu/news/soil-mi...
July 16, 2025 at 4:25 PM
News article covering our story/research here from Matt Wood!
biologicalsciences.uchicago.edu/news/soil-mi...
biologicalsciences.uchicago.edu/news/soil-mi...
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...
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
July 16, 2025 at 3:19 PM
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...
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
July 5, 2025 at 7:54 PM
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
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
July 4, 2025 at 5:38 PM
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
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!
June 15, 2025 at 4:37 PM
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!
Reposted by Kiseok (Keith) Lee
So happy to see this paper finally out! A fun project with collaborators Emily Zakem, @jlw-ecoevo.bsky.social and Yubin Raut!
Functional biogeography of marine microbial heterotrophs #USC_MEB #ResearchAtUSC www.science.org/doi/abs/10.1... #jcampubs 🌊
Functional biogeography of marine microbial heterotrophs
Heterotrophic bacteria and archaea (“heteroprokaryotes”) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale unders...
www.science.org
May 26, 2025 at 8:55 PM
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!!
Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients | Nature Communications https://www.nature.com/articles/s41467-025-60004-z
Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients - Nature Communications
Bacterial colonies growing on solid surfaces can exhibit robust expansion kinetics, with constant radial growth and saturating vertical expansion. Here, the authors use modeling and experiments to show that colony growth dynamics are driven by an interplay of mechanical constraints and nutrient gradients arising from obligatory metabolic processes.
www.nature.com
May 27, 2025 at 4:54 AM
Congrats on this work being published Harish!!
Reposted by Kiseok (Keith) Lee
When is microbial cross-feeding evolutionarily stable?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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,...
www.biorxiv.org
May 20, 2025 at 2:19 PM
When is microbial cross-feeding evolutionarily stable?
www.biorxiv.org/content/10.1...
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!
Thanks Hyunkyung for the beautiful cake resembling the soil!
May 17, 2025 at 8:15 AM
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!
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...
Commensalism engineered with non-standard amino acid:
www.nature.com/articles/s41...
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
1/2
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
1/2
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
May 2, 2025 at 2:26 PM
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...
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!!
April 25, 2025 at 9:04 AM
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!!
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!!
April 11, 2025 at 6:08 AM
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!!
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
April 8, 2025 at 1:10 AM
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/...
www.science.org/doi/10.1126/...
April 5, 2025 at 12:16 AM
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/...
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!
April 3, 2025 at 10:27 PM
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!!
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...
Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design
The metabolic activity of microbial communities is essential for host and environmental health, influencing processes from immune regulation to bioremediation. Given this importance, the rational desi...
www.biorxiv.org
March 31, 2025 at 1:36 PM
Seppe's thread!!
Reposted by Kiseok (Keith) Lee
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?
March 26, 2025 at 12:07 PM
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
March 29, 2025 at 9:35 PM
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/content/10.1...
Reposted by Kiseok (Keith) Lee
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...
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
March 29, 2025 at 1:24 PM
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...
Check it out below and please share with someone who might find it useful.
uncultured.carinilab.com/p/beyond-off...