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




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
Wannes Nauwynck

Wannes Nauwynck

Co-supervised PhD student

Main supervisor: Nico Boon


Master students/Visitors

  • Andrew Radev

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

miaSim

R package in the miaverse for the simulation of microbial community dynamics
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)

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