We study the structure and dynamics of microbial communities with systems biology methods.
Contact


Funding sources:

Research

The main interest of this lab is to explore microbial community structure and dynamics in silico and in vitro. We therefore work at the boundary of microbial ecology, systems biology and bioinformatics. If you are interested, please have a look at our ERC project.

People

Karoline Faust

Karoline Faust

PI
Haris Zafeiropoulos

Haris Zafeiropoulos

Postdoc
Charlotte van de Velde

Charlotte van de Velde

Research associate
Anna Krzynowek

Anna Krzynowek

PhD student
Co-supervisors: Ellen Decaestecker
and Dirk Springael
Pallabita Saha

Pallabita Saha

PhD student

Co-supervisor: Kristel Bernaerts
Xingjian Zhou

Xingjian Zhou

PhD student
Adedamola Daodu

Adedamola Daodu

PhD student

Involved in HoloGen Doctoral Network
Wannes Nauwynck

Wannes Nauwynck

Co-supervised PhD student

Main supervisor: Nico Boon


Master students/Visitors

  • Sotiris Touliopoulos (Erasmus student, Spring 2025)
  • Xi Peng (Visiting PhD student, 2024/2025)
  • Andrew Radev (Master student, 2024/2025)

Alumni

  • Ermis Ioannis Michail Delopoulos (Master student, 2023/204)
  • Sofia Monsalve Duarte (Master student, 2023/204)
  • Jasper Snoeks (Master student, 2023/2024)
  • Bin Liu (Postdoc, 2021-2024, now at the Chinese Academy of Sciences)
  • Eliseo Molina (Visiting PhD student, Autumn/Winter 2023)
  • Tinh Van Nguyen (Co-supervised PhD student, 2019-2023, main supervisor: Dirk Springael)
  • Mathias Bonal (Co-supervised PhD student, 2017-2023, main supervisor: Isabelle George)
  • Daniel Rios Garza (Postdoc, 2020-2023, now at INRAE)
  • Clémence Joseph (PhD student, 2019-2023)
  • Julia Casado Gomez-Pallete (Master student, 2023)
  • Vladislav Vlasov (Master student, 2022)
  • Helena Santiago Lima (Visiting PhD student, Autumn/Winter 2022)
  • Manuel Anguita Maeso (Visiting PhD student, Autumn 2022)
  • Yu Gao (Visiting PhD student, 2021/2022)
  • Sam Röttjers (PhD student, 2017-2021, now at Biome Makers)
  • Emma Gheysen (Master student, 2021)
  • Tine Logghe (Master student, 2021)
  • William Roberts-Sengier (Master student, 2020)
  • Xinyi Cao (Visiting PhD student, 2020)
  • Jule Freudenthal (Online visiting PhD student, Spring 2020)
  • Susana Martinez Arbas (Visiting PhD student, Autumn 2017)
  • Leandro Nascimento Lemos (Visiting PhD student, Autumn 2017)
  • Lyu Su (Visiting PhD student, Autumn 2017)
  • Ina Deutschmann (Visiting PhD student, Spring 2017)
  • Hajar Fauzan Ahmad (Visiting PhD student, Spring 2017)
  • Nguyen Thi Loan Anh (Visiting Postdoc, 2017)
  • Eduardo Pérez Valera (Visiting PhD student, 2014/2015)
  • Aria Hahn (Visiting PhD student, 2014/2015)

Publications

See top publications.

Tool Development

If these tools are of use to you, please consider supporting our research.

microbetag

Microbial network annotation
microbetag

miaSim

Simulation of microbial community dynamics (R package in the miaverse)
miaSim

CellScanner

Flow cytometry data analysis
CellScanner

Mako

Network meta-analysis
Mako

Anuran

Network comparison
Anuran

Manta

Network clustering
Manta

seqgroup

Microbial sequencing data analysis
seqgroup

seqtime

Microbial community simulation and time series analysis
seqtime

CoNet

Microbial network inference
CoNet

Teaching

Events

Upcoming events



Past events

Below are pictures from our lab events and our participation at ISME18.

Guest speakers

  • Clémence Frioux "Exploration of microbial ecosystems: from compositional patterns to metabolic models" (4th July 2023, defence Clémence)
  • Adama Ouattara "Democratizing Biotech 4.0 using Constellab™: From global data federation to bioprocess optimization using digital twins" (4th July 2023, defence Clémence)
  • Almut Heinken "The AGORA2 resource and its applications for modeling the human microbiome" (21st June 2023)
  • Research seminar by Aurore Woller (4th May 2023)
  • Susann Müller "Stabilising microbial communities by looped mass transfer" (27th February 2023, defence Charlotte)
  • Gail Rosen "Discovery of Microbial Community Structure and Interactions through Machine Learning" (29th June 2022)
  • Christian von Mering "STRING and MicrobeAtlas - new developments for microbiologists" (26th October 2021, defence Sam)
  • Modeling microbial ecology series - Hilje Doekes (17th August 2021)
  • Modeling microbial ecology series - Veronika Dubinkina (6th April 2021)
  • Research seminar by Christoph Ratzke (15th December 2020)
  • Maxime Fajgenblat "Modelling adaptational regime shifts in populations using spatially and genetically explicit Lotka-Volterra models" (6th October 2020)
  • Bin Ma "Exploring Soil Microbiomes from a Network Perspective" (17th June 2019)
  • Hein Sprong "Eco-epidemiology of Lyme borreliosis" (29th June 2018)

Support our research

Team
You can support our research through a donation to the KU Leuven account number BE45 7340 1941 7789, BIC code KREDBEBB with structured transfer number +++400/0026/88555+++. If you donate at least 40 euros annually, you are entitled to a tax certificate and tax reduction of 45% on the donated amount in Belgium.
Please click here for more information or scan the QR code below to make a donation. QR code


Help us better understand our gut microbes

Our gut is home to an intricate ecosystem of trillions of microbes, known as the gut microbiome. These microbes play essential roles in our health - helping to digest food, producing essential vitamins, and protecting us from pathogens. The composition of the gut microbiome often changes in gastrointestinal diseases such as inflammatory bowel disease (IBD). This has inspired researchers to explore whether treating these microbes directly could help manage or even cure some of these gut-related diseases. But despite intensive research efforts, only very few microbiome-based treatments have been officially approved as drugs to date. One major challenge is that we still don’t know much about these microbes - what they eat, which conditions they thrive in, how they interact with one another, and how they coexist in our bodies. Studying them is challenging, since gut microbes don't like oxygen and thus have to be grown in a special environment with a controlled atmosphere. In our lab, we combine microbiology with systems biology and bioinformatics to understand how gut microbes make a living, how they interact and how they respond to antibiotics and probiotic species. Such fundamental research is essential but notoriously difficult to fund, making every contribution valuable to advancing our understanding.

Vacancies

Spontaneous applications

If you are interested to join the lab as a PhD student or postdoctoral researcher or as a visiting student, please send your CV and motivation letter to: karoline.faust(at)kuleuven.be


Available positions

    Currently no position available.

Contact

Address

Laboratory of Molecular Bacteriology
Department of Microbiology, Immunology and Transplantation (Rega Institute)
KU Leuven
Rega institute, 7th floor (Room 7.B142)
Bus: 1028
Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium

Email

karoline.faust(at)kuleuven.be

Phone

+32-16-322698