Data integration with Microbial Networks and Community Models

24th - 25th Sep 2025
Leuven, Belgium
max 40
Places
2
Days
8
Speakers

About

Data integration is a challenging but necessary step to derive hypotheses and insights from meta-omics data of microbial communities. In this summer school, we want to introduce students at the Master and PhD level to black-box and white-box data integration methods, i.e. approaches that do not require a mechanistic understanding (e.g. association networks, prediction of species distributions with machine learning) and those that do (mechanistic models). For this, we plan to combine introductory talks with 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,

Haris Zafeiropoulos & Karoline Faust

Event Starts In:

Previously

Speakers

Karoline Faust
Department of Microbiology, Immunology and Transplantation
KU Leuven
Read more →
Mani Arumugam
Novo Nordisk Foundation Center for Basic Metabolic Research
University of Copenhagen
Read more →
Antton Alberdi
Center for Evolutionary Hologenomics / GLOBE Institute
University of Copenhagen
Read more →
Haris Zafeiropoulos
Department of Microbiology, Immunology and Transplantation
KU Leuven
Read more →
Didier Gonze
Unit of Theoretical Chronobiology
Université Libre de Bruxelles
Read more →
Rosalind Jane Allen
Institute of Microbiology
Universität Jena
Read more →
Djordje Bajić
Department of Biotechnology
TU Delft
Read more →
Andreas Ulmer
Institute of Microbiology
Universität Jena
Read more →

Schedule

8:50 - 9:00

Opening of the school

9:00 - 10:00

Karoline Faust

Introductory talk: microbial network inference and analysis


Microbial network inference is a popular exploratory data analysis technique for microbial sequencing data. In a microbial network, edges connect taxa (and also metadata) that are significantly associated across samples. Microbial networks can in some cases identify ecological interactions or biologically informative taxon groups. However, there are several pitfalls both in their construction and interpretation. Here, I will discuss the challenges of microbial network construction and analysis, present inference algorithms and introduce tools that help make sense of the hairballs.

10:00 - 11:00

Mani Arumugam

TBA


TBA


11:00 - 11:30

Coffee Break

Cafeteria Rega Institute (06.B213)

11:30 - 12:30

Antton Alberdi

Unveiling microbial interactions through micro-scale spatial metagenomics

Microbial genomics and metagenomics are powerful tools for uncovering potential microbial interactions from molecular data. However, these approaches treat complex microbial communities as homogeneous samples, overlooking the spatial organisation of microorganisms. Micro-scale spatial metagenomics now enables the analysis of microbial communities at the scale at which interactions occur, providing new opportunities to explore community structures and microbiome functions.




12:30 - 13:30

Lunch Break

Cafeteria Rega Institute (06.B213)

13:30 - 15:00

Haris Zafeiropoulos

Tutorial: microbetag: metabolic secrets behind microbial co-occurrence

Microbial co-occurrence network inference is often limited by low accuracy and tool dependency, while interpreting the usually resulting 'hairball' and extracting biological insights remain challenging. In this workshop, we will investigate how reverse-ecology based methods can be used to annotate nodes and edges of such networks and how those methods, combined with network clustering and enrichment analysis, can address this challenge. More specifically, microbial taxa in a co-occurrence network will be annotated with phenotypic traits, while their edges with metabolic complementarities, i.e. potential cross-feeding interactions where missing metabolites and/or enzymes required by a species can be supplied by co-occurring taxa. For most steps of this pipeline, we will use microbetag (https://microbetag.readthedocs.io), a recently developed software suite supporting these tasks.

15:00 - 15:30

Coffee break

Cafeteria Rega Institute (06.B213)

15:30 - 17:00

Haris Zafeiropoulos

Tutorial: microbetag continued






19:00

Restaurant

9:00 - 10:00

Didier Gonze

Introductory talk: Modelling of microbial communities

Natural microbial communities are continuously subject to changes in the environment and dynamically respond to these perturbations. Mathematical models, often based on ordinary differential equations (ODE), are invaluable for understanding the stability and resilience of the communities and to predict their time evolution. In this lecture I will show how such ODE-based models are build and analyzed, from the growth of monocultures to systems of interacting microbial communities. I will also show how these models can be extended to account for the spatial patterns.


10:00 - 11:00

Rosalind Allen

Tracking microbial community resilience at the species level

Ecological resilience describes the ability of a community to return to its original state following a perturbation. To probe the meaning of this concept for a microbial community, we analyse in detail the response of soil microbial microcosms to a temperature perturbation, using data collected by Sorensen and Shade (2020, Phil. Trans. R. Soc. B). In this dataset, active vs dormant taxa can be identified. Tracking the response of individual OTUs to the temperature shift we characterise different microbial strategies in response to the temperature shift. We discuss how these individual strategies combine to produce emergent community resilience.

11:00 - 11:30

Coffee Break

Cafeteria Rega Institute (06.B213)

11:30 - 12:30

Djordje Bajić

Modeling microbial communities in time and space using COMETS

Stoichiometric modeling of microbial metabolism has proven a powerful tool for predicting the behavior and physiology of microorganisms from their genomic data. Metabolic models also hold great potential as a tool for predicting the composition and function of multi-species microbial communities. In this workshop, we will explore the application of metabolic models to microbiomes using COMETS, a tool that incorporates dynamic as well as spatial components in the simulation of multispecies communities.

12:30 - 13:30

Lunch Break

Cafeteria Rega Institute (06.B213)

13:30 - 15:00

Andreas Ulmer

Tutorial: Analysing microbial growth curves with GrowthAnalysisToolbox

Growth curves for mono- and co-cultures provide a simple yet effective way to characterize microbial populations and communities. However, to accurately compare microbial behavior and to explain their ecological relevance, we need to extract growth and interaction parameters from growth curve data, by fitting to mathematical models. We will demonstrate the use of our new GrowthAnalysisToolbox web-based software, that enables the easy fitting of growth curves to extract key growth and interaction parameters.

15:00 - 15:30

Coffee Break

Cafeteria Rega Institute (06.B213)

15:30 - 16:50

Andreas Ulmer

Tutorial continued

16:50 - 17:00

Closure of the school

Registration

There are places for maximal 40 participants. The registration fee is 100 Euro. To register, please click here.

Important payment information


Payment by invoice (recommended for corporate/institutional payment)
1. Fill in your institute's invoicing address and institutional VAT number (mandatory) in the profile details
2. Select "invoice" in the final step of your online registration
3. An invoice will be sent to you or your invoicing team by email, including corresponding payment instructions.
Please do not pay before receiving the invoice!

Payment with VGS (KU Leuven students and staff only)
1. If you are a student or staff member of the KU Leuven or it's Association please select Online Payment
2. Provide your local finance officer with the VGS code mentioned in the payment options and the amount due and ask him/her to settle the payment.

Payment by credit card or bank transfer (recommended for private payment)
1. Fill in your private address in the profile details for payments with private credit card or bank transfer
2. Upon receipt of your payment, you will receive a proof of payment (mentioning your name, address, amount and payment date)
Please notice that no invoice can be issued when this type of payment is selected!

Questions? Please don’t hesitate to reach out to Mrs. Chantal Biernaux (Chantal.Biernaux@kuleuven.be).

What's included?

  • Talks and tutorials
  • Drinks, refreshments, and lunch

Venue

Location

The venue is the Rega institute, located in Gasthuisberg near Leuven.


Address

Seminar room 1, Rega Institute
Herestraat 49
3000 Leuven
Link to map

How to get there

For participants arriving by plane, Leuven is connected to Brussels airport by train or bus.
The closest bus stop to the venue is Gasthuisberg Campus (line 43). Station 'Gasthuisberg Kliniek' is served more regularly by different bus lines but entails a long walk to the Rega. More details can be found here. You can plan bus trips with De Lijn.

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

Accommodation

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 January 2025).

  • 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.
  • Leuven City Hostel A youth hostel well located in the city center. Dorms from 32 Euro per night.
  • La Royale A hotel located at the railway station inside the city ring. Rooms from 54 Euro per night.
  • Ibis Budget Hotel Leuven A hotel located at the railway station outside the city ring. Rooms from 73 Euro per night.
  • Hotel Industry A hotel located at the railway station inside the city ring. Rooms from 90 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 Cytoscape and the MGG Cytoscape app
Tutorial day 2: TODO

Contact

Scientific Organizers
Karoline Faust
Haris Zafeiropoulos

Administrative support
Chantal Biernaux