Guardians of the gut: harnessing bioinformatics to study the gut microbiome and faecal microbiota transplantation in intestinal disorders

Nooij, S. (2025)

Doctoral Thesis

Intestinal disorders are often related to the bacteria that live there: the gut microbiome. Gut diseases associated with the microbiome may be treated with microbiota-focused treatment such as faecal microbiota transplantation (FMT). This thesis describes microbiome changes in patients with recurrent infections or ulcerative colitis who are treated with FMT. By comparing their gut bacteria to those from healthy donors or controls we find bacteria that appear associated with disease and recovery, and that FMT may reduce the risk of developing colorectal cancer and infections by multidrug resistant bacteria. The thesis continues with a genomic study of the gut bacterium Ruminococcus gnavus, that is highly prevalent in humans and is associated with various diseases. This bacterium has distinct genetic variants that indicate possible disease-causing genetic differences. The results contribute to an improved understanding of interactions between humans and bacteria that can help in maintaining a healthy gut or develop new microbiota-based therapies.

• Human gut
• Bacterial genomics
• Metagenomics
• Clostridioides difficile infection
• Inflammatory bowel diseases
• Colorectal cancer
• Antimicrobial resistance
• Next-generation sequencing

• All authors: Nooij, S.
• Supervisor: Kroes, A.C.M.
• Co-supervisor: Terveer, E.M.; Ducarmon, Q.R.
• Committee: Kuijper, E.J.; Zeller, G.F.; Schürch, A.C.; Schaik, W. van
• Qualification: Doctor (dr.)
• Awarding Institution: Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University
• Date: 2025-10-10
• ISBN (print): 9789465224701