
October 27 - 31, 2025
Microbial Communities: Energetics and Dynamics Across Space and Time

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Location
Workshop Organizers
NITMB
Overview
Research on microbial communities presents fundamental questions about how microbes come
together and co-exist in Nature and what “community-level” functions they display. This
workshop will explore these open questions in the context of energetics and spatio-temporal
dynamics.
As dynamic ecosystems, microbial communities exhibit energy and material fluxes and adhere
to thermodynamic laws. The quantitative measurement of these fluxes and their evaluation in a
thermodynamically correct manner has been lacking. The application of concepts from
nonlinear, nonequilibrium thermodynamics to communities is still largely unexplored, and their
relevance to understanding community dynamics remains unknown.
Interlinked with this energetic view of microbial communities is the fact that microbial
communities are temporally dynamic and almost always spatially structured. This gives rise to
spatiotemporal dynamics in both species (consumers) and chemical (resources, metabolites)
abundances, which are rarely quantified or modelled.
This one-week workshop aims to develop an integrated theoretical and experimental framework
that accounts for the energetics of microbial communities and their spatiotemporal dynamics.
The key areas of discussion will be centered around:
-
Energy balances and quantitative measurement of metabolic fluxes in microbial communities
-
Thermodynamic and physiological constraints at the community and species levels
-
Spatial and temporal dynamics of species and metabolites
In each area, we will examine the experimental challenges and explore possible theoretical
approaches that can be applied. On the experimental side, we are particularly interested in
exploring model systems and under-represented measurement approaches, such as calorimetry
and spatially resolved methods. These approaches are needed to understand how energy
fluxes operate at the community-level, as well as how they vary in space and time.
Participants
Speaker
Attendee
Organizers
Jonas Cremer - Stanford University (Organizer)
Akshit Goyal - Int. Centre for Theoretical Sciences (Organizer)
Seppe Kuehn - University of Chicago (Organizer)
Arvind Murugan - University of Chicago (Organizer)
Samraat Pawar - Imperial College (Organizer)
Wenying Shou - University College London (Organizer)
Orkun Soyer - University of Warwick (Organizer)​
Invited Speakers
Martina D Bello - Yale University (Speaker)
Rebeca González Cabaleiro - Delft University (Speaker)
Paul Falkowski - Rutgers University (Speaker)
Avi Flamholz - Rockefeller University (Speaker)
William Harcombe - University of Minnnesota (Speaker)
Kabir Husain - University College London (Speaker)
Kerwyn Huang - Stanford University (Speaker)
Eric Jones - University of Colorado, Colorado Springs (Speaker)
Michael Kuehl - University of Copenhagen (Speaker)
Elena Litchman - Michigan State University (Speaker)
Sergei Maslov - University of Illinois Urbana-Champaign (Speaker)
Babak Momeni - Boston College (Speaker)
Daniel Rothman - Massachusetts Institute of Technology (Speaker)
David Russell Johnson - Swiss Federal Institute of Aquatic Science and Technology (Speaker)
Pablo Sartori - Gulbenkian Institute for Molecular Medicine (Speaker)
Daniel Segre - Boston University (Speaker)
Mary Silber - University of Chicago (Speaker)
Eric Smith - Santa Fe Institute (Speaker)
Alfred Sporman - Stanford University (Speaker)
Chris Thompson - University College London (Speaker)
Ophelia Venturelli - Duke University (Speaker)
Participants
Farah Abdul-Rahman - Yale University
Achuthan Ambat - Stanford University
Daniel Amor - École normale supérieure - PSL University
Ratul Biswas - NITMB
Theodore Bouchez - INRAE PROSE
Douglas Brumley - The University of Melbourne
Maryn Carlson - NITMB
Tristan Caro - California Institute of Technology
Milena Chakraverti-Wuerthwein - University of Chicago
Aniruddha Chattaraj - Harvard University
Ikchang Cho - University of Chicago
Kyle Crocker - University of Chicago
Ankit Dhanuka - NCBS-TIFR
Purushottam Dixit - Yale University
Quqiming Duan - Imperial College London
Song Feng - Pacific Northwest National Laboratory
Federica Ferritti - NITMB
Peter Foster - University of Southern California
Andrew Freiburger - Northwestern University
Stephen Lindemann - Purdue University
Giulia Garcia Lorenzana - NITMB
Emily Gracie - Newcastle University
Doruk Efe Gokmen - NITMB
Karna Gowda - The Ohio State University
Shin Haruta - Tokyo Metropolitan University
Alasdair Hastewell - NITMB
Elizabeth Heidrich - Newcastle University
Toko Hisano - Purdue University
Sergei Katsev - University of Minnesota Duluth
Hannah Dion-Kirschner - University of Chicago
Christopher Klausmeier - Michigan State University
Kasturi Lele - Tufts University
Jay Lennon - Indiana University
Milton Lin - NITMB
Aditya Mahadevan - NITMB
Madhav Mani - Northwestern University
Yoshiya Matusbara - University of Chicago
Matteo Mori - University of California, San Diego
Rintaro Niimi - The University of Tokyo
Rachel Porter - Stanford University
Steven Redford - University College London
Maria Rebolleda-Gomez - University of California, Irvine
Forest Rohwer - San Diego State University
Jamila Rowland-Chandler - University College London
Gabriel Salmon - NITMB
Mariya Savinov - NITMB
Alberto Scarampi - University of Warwick
Daniel Segre - Boston University
Li Shen - NITMB
Farshad Shirani - Emory University
Sergei Shmakov - University of Chicago
Vaibhhav Sinha - University of Chicago
Matteo Sireci - CNRS-Laboratory of physics of ENS
Abigail Skwara - Yale University
David Smith - Earth-Life Science Institute, Institute of Science Tokyo, and iCOOL Center, Georgia Institute of Technology
Chuliang Song - University of California, Los Angeles
Emina Stojkovic - Northeastern Illinois University
Jinyun Tang - Lawrence Berkeley National Laboratory
Pankaj Trivedi - Texas Tech University
Andreas Ulmer - Friedrich Schiller University Jena, Germany
Dervis Vural - University of Notre Dame
Xueying Wang - NITMB
Zihan Wang - University of Illinois Urbana-Champaign
Guan'ao Yan - NITMB
Jumpei Yamagishi - Center for Biosystems Dynamics Research, RIKEN
Gabriel Yvon-Durocher - University of Exeter
Adrianne Zhong - NITMB
Yan Zhu - Imperial College London
Agustina Ziliani - ETH Zürich/Eawag
Oct
27
2025
Monday
Overview & Perspectives: Meeting introduction, Earth Systems & Microbial Ecology, Community Assembly & Dynamics, Metabolism & Thermodynamics, Modeling & Theory
Speakers: Akshit Goyal, William Harcombe, Michael Kuehl, Jay Lennon, Samraat Pawar, Maria Rebolleda-Gomez, Daniel Rothman, Alberto Scarampi, Wenying Shou, Orkun Soyer & Ophelia Venturelli
8:30 am - 9:30 am
Light Breakfast
9:30 am - 10:00 am
Welcome, Housekeeping & Introduction to NITMB
10:00 am - 10:20 am
Introduction to Workshop: Why this meeting? – Orkun Soyer
10:20 am - 10:50 am
Introduction to Workshop: Measurement challenges – Wenying Shou
10:50 am - 11:20 am
Introduction to Workshop: Modeling challenges – Akshit Goyal & Samraat
Pawar
11:30 am - 12:00 pm
Ice Breaker
12:00 pm - 1:00 pm
Lunch
1:00 pm - 1:20 pm
“Mapping the microenvironmental landscape in microbial communities” - Michael Kuehl
Abstract: The interaction of microbes (with other microbes or hosts) takes place in a dynamic microenvironment characterized by spatio-temporal gradients and structural complexity, which modulate microbial life but also are a result of their metabolic and behavioral activity. I present a brief overview of tools that enable minimally invasive characterization of physico-chemical microenvironments and microbial activity along with some examples of their application in microbial communities.
1:30 pm - 1:50 pm
“Fluctuation-limited dynamics of microbial starvation” – Daniel Rothman
2:00 pm - 2:30 pm
Coffee break
2:30 pm - 2:50 pm
“Design of multi-scale dynamics and functions of microbial communities” –
Ophelia Venturelli
3:00 pm - 3:20 pm
“Media composition determines outcome of microbial community assembly” - Alberto Scarampi
3:30 pm - 3:50 pm
“Ecological and evolutionary consequences of carbon preferences in bacteria” - Maria Rebolleda-Gomez
4:00 pm - 4:30 pm
Coffee Break
4:30 pm - 4:50 pm
“Evolutionary bioenergetics of sporulation” - Jay Lennon
5:00 pm - 5:20 pm
“The effect of species interactions on stress response” - William Harcombe
Oct
28
2025
Tuesday
Overview & Perspectives: Spatial Dynamics, Phage & Virus Ecology, Thermodynamics & Applications, Metabolism & Thermodynamics
Speakers: Jonas Cremer, Eric Jones, Kerwyn Huang, S. Redford, J. Chandler, David R. Johnson, Forest Rohwer, Rebeca González Cabaleiro, Elizabeth Heidrich, Akshit Goyal, Peter Foster, Sergei Maslov
8:30 am - 9:00 am
Light Breakfast
9:00 am - 9:20 am
“Quantifying the metabolic fluxes that govern the gut microbiota” – Jonas Cremer
9:30 am - 9:50 am
Spatial niches in the fruit fly microbiome” – Eric Jones
10:00 am - 10:20 am
“Ecology and evolution of the gut microbiome” – Kerwyn Huang
10:30 am - 10:40 am
"Towards an understanding of metabolically driven spatial architecture in microbial communities" - S. Redford
10:45 am - 10:55 am
"Resource diversity begets stability in complex ecosystems" - J. Chandler
11:00 am - 11:30 am
Group Photo and Coffee break
11:30 am - 11:50 am
“Phage predation, pattern formation, and the spread of costly traits” – David
Russell Johnson
12:00 pm - 12:20 pm
“Flux of energy and metabolic speciation” – Alfred Sporman
12:30 pm - 1:30 pm
Lunch
1:30 pm - 2:30 pm
Free time – optional walk
2:30 pm - 2:50 pm
“Glycolysis in anaerobic fermentation: how nature efficiently resolves the
electron puzzle.” – Rebeca González Cabaleiro
3:00 pm - 3:20 pm
"Microbial electrochemistry: a window into understanding microbial formation, behaviour and energetics” - Elizabeth Heidrich
3:30 pm - 4:00 pm
Coffee break
4:00 pm - 4:20 pm
“Energetics drive the sustenance and collapse of microbial ecosystems” – Akshit Goyal
4:30 pm - 4:50 pm
“Physical Bioenergetics” – Peter Foster
5:00 pm - 5:20 pm
“Models of Essential Resource Exchange and Thermodynamic Dissipation in Slow-Growing Microbial Ecosystems” – Sergei Maslov
5:30 pm - 7:00 pm
Poster session & snacks
Oct
29
2025
Wednesday
Overview & Perspectives: Physiology & Biogeochemistry, Macroecology & Theory, Metabolic Theory & Systems Biology
Speakers: Purushottam Dixit, Tristan Caro, Avi Flamholz, Seppe Kuehn, Elena Litchman, Mary Silber, Eric Smith, Jinyun Tang & Jumpei Yamagishi
8:30 am - 9:00 am
Light Breakfast
9:00 am - 9:20 am
"Metabolic niche dimensionality drives microbial community structure" - Purushottam Dixit
9:30 am - 9:50 am
“From soils to single cells: probing microbial growth across scales” – Tristan Caro
10:00 am - 10:20 am
“Learning microbiome design principles from natural variation” – Seppe Kuehn
10:30 am - 10:50 am
“Using physical rules to scale from genomes to microbial communities” – Jinyun Tang
11:00 am - 11:30 am
Coffee break
11:30 am - 11:50 am
“Landscape-scale self-organized dryland vegetation patterns” – Mary Silber
12:00 pm - 12:20 pm
“A mechanistic framework for understanding host-associated microbiota dynamics” – Elena Litchman
12:30 pm - 1:30 pm
Lunch
1:30 pm - 2:30 pm
Free time – optional walk
2:30 pm - 2:50 pm
“The proteome is a terminal electron acceptor” – Avi Flamholz
3:00 pm - 3:20 pm
“Microeconomics of Cellular Metabolism” – Jumpei Yamagishi
3:30 pm - 3:50 pm
“The (thermodynamic) cost of not doing things” – Eric Smith
4:00 pm - 4:30 pm
Coffee break
4:30 pm - 6:00 pm
Structured Discussion / Open time for one-to-one's
6:00 pm - 7:00 pm
Poster session
Oct
30
2025
Thursday
Overview & Perspectives: Synthetic & Systems Microbiology, Thermodynamics & Energetics, Modeling & Theory
​
Speakers: Douglas Brumley, Martina Dal Bello, Aniruddha Chattaraj, Quqiming Duan, Shin Haruta, Milena Chakrawerti-Wurthwein, Babak Momeni, Matteo Mori & Farshad Shirani
8:30 am - 9:30 am
Light Breakfast
9:30 am - 9:50 am
“Microbial ecosystem metabolism in physical and functional space” – Daniel Segrè
10:00 am - 10:20 am
“Energy Balance and Protein Turnover: The Physiological Role of ATP Synthase” – Matteo Mori
10:30 am - 10:50 am
“Decoding the evolution of anticipation and decision making in uncertain
environments” – Martina Dal Bello
11:00 am - 11:30 am
Coffee break
11:30 am - 11:50 am
“Community structure and stability shaped by energy quantity and quality” – Shin Haruta
12:00 pm - 12:20 pm
“Bacterial foraging in dynamic nutrient landscapes” – Douglas Brumley
12:30 pm - 1:30 pm
Lunch & Questionnaire
1:30 pm - 2:30 pm
Free time – optional walk
2:30 pm - 2:50 pm
"Designing combination therapy using kinetic models of bacterial metabolism" - Aniruddha Chattaraj
3:00 pm - 3:20 pm
“A General Framework for Predicting the Temperature-Dependence of Microbial Interactions” – Quqiming Duan
3:30 pm - 4:00 pm
Survey & Coffee break
4:00 pm - 4:20 pm
“Coexistence and colonization resistance in a spatially structured microbial
community” – Babak Momeni
4:30 pm - 4:50 pm
“Minimizing co-growth as a unifying principle for robust communities” – Milena Chakrawerti-Wurthwein
5:00 pm - 5:30 pm
“The Coevolution of Species’ Borders: Mathematical Modeling and Numerical Analysis” – Farshad Shirani
Oct
31
2025
Friday
Overview & Perspectives: Synthetic & Systems Microbiology, closing discussion
Speakers: Daniel Amor, Pablo Sartori, Matteo Sireci, Dervis Can Vural, Emina Stojkovic & Christopher Klausmeier
8:30 am - 9:00 am
Light Breakfast
9:00 am - 9:20 am
“The fire within cells: dissipation and versatility of microbial metabolism” – Pablo Sartori
9:30 am - 9:50 am
“Metabolic states shape ecological interactions in the Drosophila gut microbiomes,” – Matteo Sireci
10:00 am - 10:30 am
Coffee break
10:30 am - 10:40 am
"Social Evolution in Dynamic Fluids” - Dervis Can Vural
10:40 am - 10:50 am
"Photomorphogenesis of Myxobacteria: New Insights for Light Regulation of Cell Development” - Emina Stojkovic
10:50 am - 11:00 am
"Microbial cross-feeding: coexistence and collapse, spatial patterns and population cycles” - Christopher Klausmeier
11:00 am - 11:20 am
“Alternative stable states and low variance modes in microbial community structure” – Daniel Amor
11:30 am - 12:30 pm
Closing discussion
12:30 pm - 1:30 pm
Lunch
Wenying Shou
Recorded on 10/27/2025
Title: Introduction to Workshop: Measurement challenges
Akshit Goyal
Recorded on 10/27/2025
Title: Introduction to Workshop: Modeling challenges
Michael Kuehl
Recorded on 10/27/2025
Title: Mapping the microenvironmental landscape in microbial communities
Abstract: The interaction of microbes (with other microbes or hosts) takes place in a dynamic microenvironment characterized by spatio-temporal gradients and structural complexity, which modulate microbial life but also are a result of their metabolic and behavioral activity. I present a brief overview of tools that enable minimally invasive characterization of physico-chemical microenvironments and microbial activity along with some examples of their application in microbial communities.
Ophelia Venturelli
Recorded on 10/27/2025
Title: Design of multi-scale dynamics and functions of microbial communities
Alberto Scarampi
Recorded on 10/27/2025
Title: Media composition determines outcome of microbial community assembly
Maria Rebolleda-Gomez
Recorded on 10/27/2025
Title: Ecological and evolutionary consequences of carbon preferences in bacteria
Jay Lennon
Recorded on 10/27/2025
Title: Evolutionary bioenergetics of sporulation
William Harcombe
Recorded on 10/27/2025
Title: The effect of species interactions on stress response
Aniruddha Chattaraj
Recorded on 10/30/2025
Title: Designing combination therapy using kinetic models of bacterial metabolism
Quqiming Duan
Recorded on 10/30/2025
Title: A General Framework for Predicting the Temperature-Dependence of Microbial Interactions
Babak Momeni
Recorded on 10/30/2025
Title: Coexistence and colonization resistance in a spatially structured microbial community
Milena Chakrawerti-Wurthwein
Recorded on 10/30/2025
Title: Minimizing co-growth as a unifying principle for robust communities
Farshad Shirani
Recorded on 10/30/2025
Title: The Coevolution of Species’ Borders: Mathematical Modeling and Numerical Analysis
Pablo Sartori
Recorded on 10/31/2025
Title: The fire within cells: dissipation and versatility of microbial metabolism
Matteo Sireci
Recorded on 10/31/2025
Title: Metabolic states shape ecological interactions in the Drosophila gut microbiomes
Emina Stojkovic
Recorded on 10/31/2025
Title: Photomorphogenesis of Myxobacteria: New Insights for Light Regulation of Cell Development
Christopher Klausmeier
Recorded on 10/31/2025
Title: Microbial cross-feeding: coexistence and collapse, spatial patterns and population cycles
Daniel Amor
Recorded on 10/31/2025
Title: Alternative stable states and low variance modes in microbial community structure