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



News


Our research is supported by an

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
Daniel Rios Garza

Daniel Rios Garza

Postdoc
Bin Liu

Bin Liu

Postdoc
Sam Roettjers

Sam Röttjers

PhD student
Charlotte van de Velde

Charlotte van de Velde

PhD student
Clemence Joseph

Clémence Joseph

PhD student
Anna Krzynowek

Anna Krzynowek

PhD student

Co-supervisors: Ellen Decaestecker
and Dirk Springael
Mathias Bonal

Mathias Bonal

Co-supervised PhD student

Main supervisor: Isabelle George
Wannes Nauwynck

Wannes Nauwynck

Co-supervised PhD student

Main supervisor: Nico Boon
Tinh Van Nguyen

Tinh Van Nguyen

Co-supervised PhD student

Main supervisor: Dirk Springael


Master students/Visitors

  • Yu Gao
  • Felix Anto Ophelia Eusebious Rajan

Alumni

  • 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 PĂ©rez Valera (Visiting PhD student, 2014/2015)
  • Aria Hahn (Visiting PhD student, 2014/2015)

Publications

Find publications on Google Scholar.

Selected Publications

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

K. D'hoe*, S. Vet*, K. Faust* et al. (2018) eLife e37090.

The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than those in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depends on the initial conditions. Our work has important implications for gut microbial community modeling as well as for ecological interaction detection from batch cultures.

Determinants of community structure in the global plankton interactome

G. Lima-Mendez*, K. Faust*, N. Henry* et al. (2015) Science 348, 6237.

Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed in the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

Microbial interactions: from networks to models

K. Faust and J. Raes (2012) Nature Reviews Microbiology 10, 538-550.

Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.

Tool Development

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
seqtime

CoNet

Microbial network inference
CoNet

Events

Upcoming events



Past events

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.A130)
Bus: 1028
Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium

Email

karoline.faust(at)kuleuven.be

Phone

+32-16-322698