Ecology meets human health: studies on human gut microbiota in health and disease

Pinto, S. (2025)

Doctoral Thesis

The bacteria in the human intestine form a complex ecosystem that contributes to health. Disturbances in this ecosystem, the gut microbiota, are associated with several diseases. Within the Ecology meets human health project, we examined the gut microbiota from an ecological perspective, focusing on how bacterial communities coexist and respond to environmental change. Our work aimed to understand how the composition and stability of the gut microbiota relate to health and disease, and how ecological principles can inform research on intestinal disorders and their treatment.

We first investigated bacterial interactions and evaluated the reliability of a commonly used analytical method: correlation analysis. Using a computational model, we simulated how bacteria influence each other and under which conditions ecological interactions can be identified in data. Time series from two individuals who collected stool samples almost daily were then analyzed. The application of wavelet clustering revealed temporal patterns in the microbiota that were not detectable with conventional methods. 

Subsequently, we studied the gut microbiota of patients with inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis. The microbiota composition varied strongly between patients, indicating that no single microbial profile characterizes these conditions. Finally, we examined fecal microbiota transplantation (FMT) and found that treatment outcomes depend on both donor composition and the resilience of the recipient’s microbiota.

• Gut microbiota
• Microbiome ecology
• Inflammatory bowel disease
• Fecal microbiota transplantation
• Microbial dynamics
• Microbial interactions
• Longitudinal data
• Dysbiosis
• Crohn’s disease
• Ulcerative colitis

• All authors: Pinto, S.
• Supervisor: Steyerberg, E.W.
• Co-supervisor: Bogaards, J.A.; Benincà, E.
• Committee: Putter, H.; Smits, W.K.; Faust, K.; Wijgert, J.H.H.M. van de
• Qualification: Doctor (dr.)
• Awarding Institution: Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University
• Date: 2025-11-20
• Sponsorship: The work in this thesis was financially supported by the Dutch Research Council (NWO) through the program Complexity in Health and Nutrition (NWO grant 645.001.002; www⁠.nwo.nl/onderzoeksprogrammas/complexiteit), with co-funding by the National Institute for Public Health and the Environment (RIVM), the Netherlands.