Daniel Rios GarzaPostdoc
Sam RöttjersPhD student
Charlotte van de VeldePhD student
Clémence JosephPhD student
- Yu Gao
- Felix Anto Ophelia Eusebious Rajan
- 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)
Find publications on Google Scholar.
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.
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.
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.
Microbial community modelling talk series
Organizer: Daniel Rios Garza
- School on the Analysis of Microbial Time Series Data (2-4 Nov 2021)
- Summer School on Microbial Community Modeling (16-18 Sep 2019)
- Dynamics of Biological Systems (2-4 May 2018)
Session on Microbial Systems Biology
- Netherlands Annual Ecology Meeting (13-14 Feb 2018)
Session on Microbial Ecology: Community composition and dynamics
- Summer School on Ecological Network Inference And Analysis (11-13 Sep 2017)
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
Currently no position available.
Laboratory of Molecular Bacteriology
Department of Microbiology, Immunology and Transplantation (Rega Institute)
Rega institute, 7th floor (Room 7.A130)