Dr. ir. Kim De Paepe

Telephone number: 
+32 9/264 59 76
Postdoctoral staff

Kim De Paepe is a postdoctoral researcher at the Center for Microbial Ecology and Technology (CMET, Ghent University). As a Bioscience Engineer, she applies and continues to engineer advanced human gut in vitro models to address fundamental questions in gut microbial ecology. Her research approach is functionality-driven and heavily relies on bioinformatics and statistics tools.

She holds a 50% permanent scientific staff position as bioinformatician/statistician at CMET, which allows her to apply and transfer her knowledge and skills in a broader context. She supports fellow researchers exploring diverse research
lines in microbial ecology and takes great pleasure in teaching courses and supervising bachelor, master and PhD students.

She followed several bioinformatics and statistics courses and was recently (2022) admitted to a course in bioinformatics of Microbial Single Cells (Single-amplified genomes/SAGs), held at the Single Cell Genomics Center at Bigelow Laboratory for Ocean Sciences, Maine, USA.

She gained experience with several cutting-edge single-cell, function-based labelling and sorting techniques during a long research stay abroad (2019-2020) at the Division of Microbial Ecology (research group of Prof. D. Berry) at the University of Vienna.

Her current research projects focus on:

  1. single-cell analysis to probe necrotrophy by the human gut microbiome
  2. quantitative microbiome profiling to identify the environmental and physiological drivers of gut microbial load and community composition
  3. development of an in vitro model to simulate the ileum microbiome
  4. development of a postbiotic enriched sourdough bread
  5. function-targeted single-cell analysis of gut microbe-fibre interactions to enable the rational design of synbiotics to restore human gut microbiome homeostasis
  6. tryptophan metabolism and its impact on host-microbe crosstalk in irritable bowel syndrome


During her PhD research, under supervision of Prof. dr. ir. T. Van de Wiele, she identified wheat bran as a driver of gut microbiota niche diversification and spatial organization.