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...
Huge thanks to Seppe Kuehn @seppekuehnlab.bsky.social, Vincenzo Vitelli, and all the funding sources (NITMB, NSF, Simons, CZI).
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!
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...
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...
Thank you!
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!!
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!!
<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...
