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/
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...
I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...
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!
Erik Bakkeren@erikbakkeren.bsky.social · 9mo agoCan 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...
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...
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 agoNew 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.
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.
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...
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
Kiseok (Keith) Lee@kiseokmicro.bsky.social · last yr.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...
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...
nature.com
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
Mike Blazanin@mikeblazanin.bsky.social · last yr.Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days! go.bsky.app/GGxRjzC
<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!
When is microbial cross-feeding evolutionarily stable? 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,...
biorxiv.org
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...
Aditya Kunjapur@kunjapur.bsky.social · last yr.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
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!!
<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!
GPS Event Calendar
From the Caltech Division of Geological and Planetary Sciences
gps.caltech.edu
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!!
SeppeKuehnLab@seppekuehnlab.bsky.social · last yr.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?
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...
biorxiv.org
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
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!
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...
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.
nature.com
"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...
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...
journals.plos.org
