1 PhD project offered in the IPP winter call 2023/2024

Scientific background

The gut microbiome is by far the densest and metabolically most active human-associated microbial community and performs essential functions for health. The metagenomic sequencing-based profiling of the human gut microbiota has linked microbial compositional and functional shifts to suboptimal health and disease, but also the efficacy therapeutic interventions. In the past,  we used microbiome monitoring efforts in large populations to characterise normal ecosystem (eubiosis) variation as necessary step towards studying aberrant states of the microbiota (dysbiosis). We studied which environmental parameters drive human gut microbiome composition in health (Falony et al., Science, 2016; Falony et al., Nat. Microbiol., 2018), how alterations contribute to patho-mechanisms (Vieira-Silva et al., Nature, 2020), and how drugs can modify expected host- interactions (Vieira-Silva et al., Nature, 2020).

PhD project: Characterisation of microbiome-drug interactions and prediction of therapeutic response

This project aims to investigate how the human gut microbiota modulates therapeutic response in inflammatory disorders. The project will exploit multi-omics datasets of drug intervention trials (longitudinal datasets) in order to characterise the functional or compositional properties linked to therapeutic success or failure. Microbiome features will be combined with clinical features, including inflammatory parameters, to predict therapeutic outcome using machine learning methods. We aim not only to predict the best therapeutic choice but to identify the key determinants of therapy success to unravel potential mechanisms contributing to remission.

The project will target the study of microbial metabolism and microbiome-immunity interactions, using computational biology for -omics exploration and machine learning for prediction. We are looking for candidates interested in interdisciplinary research for which openness and flexibility are essential. Experience in statistics, coding (R/Python/other), and/or -omics data analysis, is a plus.

If you are interested in this project, please select Vieira-Silva as your group preference in the IPP application platform.

Publications relevant for this project

Vieira-Silva S*, Falony G*, Belda E*, [MetaCardis Consortium], Clément K, Raes J. (2020) Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature (581), 310–315 Link

Falony G, Vieira-Silva S & Raes J. (2018) Richness and ecosystem development across faecal snapshots of the gut microbiota. Nat. Microbiol. 3, 526–528 Link

Falony G*, Joossens M*, Vieira-Silva S*, Wang J*, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonckheere K, et al. (2016) Population-level analysis of gut microbiome variation. Science 352, 560–4 Link

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