Summer School: Design and Control of Microbial Communities

11 - 13th Sep 2023
Leuven, Belgium
max 35
Places
3
Days
12+
Speakers

About

In this summer school, we want to introduce students at the Master and PhD level to different computational methods to manipulate microbial communities to shift them towards a desired composition or function. In addition, we want to broaden the horizon of our students with a couple of research talks on the latest developments in the field. Beyond the educational purposes, we also hope to initiate a scientific exchange between speakers and students.

The organizing team

Karoline Faust, Leo Lahti & Didier Gonze

Event Starts In:

Previously

Speakers

Didier Gonze
Unit of Theoretical Chronobiology
Université Libre de Bruxelles
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Frank Delvigne
Gembloux Agro-Bio Tech - Uliège
Microbial Processes and Interactions (MiPI)
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Hidde de Jong
INRIA
Université Grenoble Alpes
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Alex Fedorec
University College London
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Karoline Faust
Department of Microbiology, Immunology and Transplantation
KU Leuven
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Shiri Freilich
Agricultural Research Organization
Newe Ya'ar Research Center
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Ophelia Venturelli
University of Wisconsin-Madison
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Beatriz García Jiménez
Biome Makers Inc.
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Steffen Waldherr
University of Vienna
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Leo Lahti
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Teppo Hiltunen
University of Turku
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Lutz Becks
Universität Konstanz
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Ville Mustonen
University of Helsinki
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Aura Raulo
University of Turku
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Schedule

8:45 - 9:00

Opening of the school

9:00 - 10:00

Didier Gonze

Introductory talk: How to model microbial communities with differential equations?

The time evolution of microbial communities can be described by ordinary differential equations (ODE). In this lecture I will show how such ODE-based models are build and analyzed, and I will illustrate the role of these mathematical models in the design and control of bacterial communities with selected examples from the literature.

10:00 - 11:00

Hidde de Jong

Enhanced production of heterologous proteins in synthetic microbial consortia: conditions and trade-offs

Synthetic microbial consortia have been increasingly utilized in biotechnology. Experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, a quantitative understanding of the conditions that make stable coexistence and higher productivity possible is still limited. I present a coarse-grained mathematical model of a prototypical synthetic consortium consisting of two E. coli strains. A first strain produces a heterologous protein, while a second strain is engineered to scavenge toxic byproducts, thus favoring growth of the producer at the expense of diverting part of the resources to growth of the cleaner. The simplicity of the consortium is ideal to perform an in-depth analysis of conditions enabling stable coexistence of the strains. Moreover, it allows an analysis of the trade-offs involved in heterologous protein production by a consortium as compared to a mono-culture. I also present some initial experimental results on the growth of the E. coli consortium in a computer-controlled mini-bioreactor system.

11:00 - 11:30

Coffee Break

Entrance Van Den Heuvel Institute

11:30 - 12:30

Frank Delvigne

A general framework for controlling the composition of microbial co-cultures based on reactive flow cytometry





12:30 - 13:30

Lunch Break

Entrance Van Den Heuvel Institute

13:30 - 14:30

Alex Fedorec

Two different approaches to community control

In this talk, I will detail how we have tackled two distinct questions that have fascinated us over the past few years: do we have to understand a community to control it, and can we design a community to (robustly) control itself? I will cover the computational and mathematical approaches used and demonstrate how we can validate some of our theoretical results in the lab with synthetic biology.

14:30 - 17:00

Hidde de Jong

Tutorial: Dynamic models integrating metabolism and gene expression

We will step-by-step build quantitative ODE models of a metabolic network integrating regulation on both the metabolic and gene expression level, and investigate the effect of these layers of regulation on the networks dynamics. The course will be structured around the case of carbon catabolite repression in bacteria, using simple kinetic models. All simulations will be carried out by means of Matlab (no toolboxes needed). The hand-out and the models and simulation code are available from the instructor.

15:00 - 15:15

Coffee Break

Summer school room

9:00 - 10:00

Karoline Faust

Introductory talk: Metabolic modelling of microbial communities

In this talk, I will give an introduction to metabolic reconstruction, topological metabolic modelling and metabolic modelling of communities with flux balance analysis. In particular, I will emphasise the assumptions and challenges of flux balance analysis applied to microbial communities.

10:00 - 11:00

Shiri Freilich

Community modelling: using genomics for management of the microbiome in natural and agricultural ecosystems

Microbial function can be potentially harnessed for the service of ecology & agriculture through the educated design of communities. To this end, as part of the research in my group, we apply and develop computational models for predicting and understanding the networks of interactions formed within microbial communities by analyzing meta/genomics data. The processing of genomic data can lead to the delineation of trophic dependencies, exchanges, competitive and cooperative interactions within natural microbial communities. Simulations can further serve the prediction of potential routes for the optimization of predefined functions.

11:00 - 11:30

Coffee Break

Entrance Van Den Heuvel Institute

11:30 - 12:30

Beatriz García Jiménez

Metabolic Modeling and AI: Unlocking the Potential in Shaping Microbial Communities

Genome-Scale Metabolic modeling is a powerful tool for understanding microbial communities and their interactions. I will discuss my work on designing and engineering these communities, often using Artificial Intelligence. This involves simulating community growth and metabolite exchange in different environments, like the human gut, bioremediation, and synthetic biology. I will share my experiences about the challenges and opportunities for real-world applications of metabolic modeling in microbial communities.

12:30 - 13:30

Lunch Break

Entrance Van Den Heuvel Institute

13:30 - 14:30

Ophelia Venturelli

Decoding microbiome interaction networks in the human gut microbiome

Online presentation.




14:30 - 17:00

Steffen Waldherr
Local support: Haris Zafeiropoulos

Tutorial

We discuss specific steps and software tools for metabolic network reconstruction, as well as how to use the reconstructed networks for microbial community modelling and control using dynamic flux balance analysis. Participants will go through the main steps of the reconstruction process and community modelling in Jupyter notebooks. Code templates and instructions will be available through a github repository.





15:00 - 15:15

Coffee Break

Summer school room

19:00

Restaurant De Werf

If you want to join for the summer school restaurant, please register here.

9:00 - 10:00

Leo Lahti

Introductory talk






10:00 - 11:00

Teppo Hiltunen

Using synthetic microbial communities to study eco-evolutionary dynamics





11:00 - 11:30

Coffee Break

Summer school room

11:30 - 12:30

Lutz Becks

Are there simple rules for predicting the composition of phytoplankton communities?

The consequences of species interactions for community dynamics are a cornerstone of ecological and evolutionary research, and the mechanisms identified and their understanding are key to answering core questions in biology. Current approaches and theories often fail to describe observed community changes over time, such as changes in community composition, resilience to disturbance, and the effects of evolution within communities. This mismatch between theory and observation prevents us from predicting the general conditions for community stability and community responses to anthropogenic pressures, and from developing appropriate mitigation measures. I will discuss results from experiments with microbial phytoplankton communities where we have dissected the interactions between community members using phenomenological, trait-based and mechanistic approaches. I will also briefly touch on ecological theory and experimental results on how consumers can control the coexistence of competitors.



12:30 - 13:30

Lunch Break

Summer school room

13:30 - 14:30

Ville Mustonen

Eco-evolutionary control theory

Quantitative understanding of microbial growth and how to manipulate it by the means of human induced control is a prerequisite to successfully combat pathogens and develop biotechnology applications. However, the task is complex as growth is the result of genotypic composition of the microbial population and the surrounding environment and their interactions, leading to complex dynamical scenarios, which are presently understood only in a limited way. Here I will first discuss an emerging theoretical framework of eco-evolutionary control. Then I present a computational approach, that that can convert massively parallel growth curve data, which suffer from various biases, to estimates of genotype dependent growth laws.



14:30 - 17:00

Aura Raulo

Tutorial: Metacommunity theory for microbiome design – manipulation of microbial communities through transmission networks

Host-associated microbiomes develop like all ecological communities, following four main forces of (meta)community assembly: 1) species interactions, 2) local selection, 3) chance effects and 4) dispersal = movement of microbes between communities. Accumulating understanding of the ecology of microbiomes have led to ecologically informed interventions that aim at manipulating microbiomes to have more beneficial effects for their host, such as probiotics to enhance human health. However, even ecologically informed microbiome interventions usually focus on manipulating microbiomes using knowledge on the first two forces of community assembly: local selection and microbial interactions. But could host-associated microbial communities be modified by manipulating the latter force of community assembly: the transmission network of microbes among hosts? This workshops focuses on the lesser-studied theory of how microbial communities could be manipulated by manipulating their transmission network. Focusing on the metacommunity theory and other fields of network theory, we will review the theoretical basis of how we expect different transmission network structures to influence microbial communities. We will learn a few analytical methods for a) describing social contact networks and microbiome compositions in a population of hosts, b) summarising different network structures and positions within a transmission network, c) exploring statistical effects of network position on important microbiome properties, such as alpha diversity and d) building a predictive model to explore optimal network positions for important microbiome properties, such as alpha diversity All analyses are done in R, using packages rstan, brms and igraph. Workshop material will be provided in advance.

15:00 - 15:15

Coffee Break

Summer school room

17:00 - 17:15

Closing

Download Schedule

Registration

There are places for maximal 35 participants. The registration fee is 175 Euro. Please click here to register.

Important payment information

If you require an invoice, please select 'invoice' in the final step of your online registration and contact chantal.biernaux@kuleuven.be. The invoice will be sent to you by email, including corresponding payment instructions. Please do not pay before receiving the invoice. If you have already paid your registration by credit card or bank transfer, you will still be able to receive a proof of payment, indicating the amount, however, it will no longer be possible to receive an official invoice. Therefore if you require an invoice, please contact us first and wait with your payment until you receive our invoice!

What's included?

  • Talks and tutorials
  • Drinks, refreshments, and lunch

Venue

Location

The venue is located in the center of Leuven, in the Van Den Heuvel Institute.


Address

Room 02.40, Van Den Heuvel Institute
Dekenstraat 2
3000, Leuven

How to get there

Leuven is a very well connected city and easily reachable by train. If you come by plane, you can go by bus from Brussels airport to Leuven with lines 616, 651 or 652.
The next bus stops to the venue are at Leuven Campus Vesalius and Rustoord Remy (bus lines 1, 4, 5, 6 and 597). You can plan bus trips with De Lijn.

For more information about Leuven, please check out Wikitravel's helpful Leuven guide.

Accommodations

Please be aware that the registration to the summer school does not cover accommodation. Below, we list a couple of low-budget hotels (with prices below 100 Euro per night, prices as of November 2022) in walking distance to the summer school.

  • Leuven City Hostel A youth hostel well located in the city center. Dorms from 22 Euro per night.
  • De Blauwput A youth hostel located at the edge of the city, at the railway station, outside the city ring. Dorms from 30 Euro per night.
  • Ibis Budget Hotel Leuven A hotel located at the railway station outside the city ring. Rooms from 70 Euro per night.
  • Park Inn A hotel located at the railway station outside the city ring. Rooms from 85 Euro per night.
  • La Royale A hotel located at the railway station inside the city ring. Rooms from 89 Euro per night.

More hotels are listed in Wikitravel's helpful Leuven guide.

Information

Structure of the summer school
The summer school consists of research talk and teaching (hands-on) sessions. Each day is focused on a particular topic, which is introduced by an overview talk on the morning of that day. The afternoons are dedicated to hands-on sessions on the computer.
Preparation for tutorials
The summer school will take place in a class-room style lecture hall. Participants are required to bring their own laptop. To be able to follow the hands-on sessions, participants should install the following software beforehand:
Tutorial day 1: Please install Octave
Tutorial day 2: No installations required (Jupyter notebooks planned)
Tutorial day 3: R packages rstan, brms and igraph. We recommend to work with RStudio available here. You can install packages in R using command: install.packages("name")

Contact

Scientific Organizers
Karoline Faust
Didier Gonze
Leo Lahti

Administrative support
Chantal Biernaux