Dissertation

Metabolomics Insights into the Gut Microbiome and Infants with Cow’s Milk Allergy

The rapid expansion of research on human gut microbiome in recent decades has highlighted its role in human metabolism, immune regulation, and behavior.

Author: P. Zhu
Date: 13 January 2026
Links: Thesis in Leiden Repository

Despite significant progress in deciphering how the gut microbiome affects human health and disease, a long journey lies ahead to fully solve the puzzle. Combining multi-omics analyses has become a trend to unravel the intricate relationship between the gut microbiome and the human host. Among the omics techniques, as a direct readout of phenotypes, metabolomics provides a snapshot reflecting the functional properties of the gut microbiome at the molecular level. This emphasizes the crucial role of metabolomics in revealing this complex relationship and underscores the needs for advances in metabolomics techniques. In this thesis, by proposing strategies to address the matrix effect in LC-ESI-MS-based analytical method, we advanced untargeted metabolomics towards quantitative analysis. The focus then shifted to deepening our understanding of the interactions between the gut microbiome and CMA in early life from a metabolomics perspective. Overall, the research in this thesis suggested that several gut microbiome-involved metabolic pathways may play a role in the acquisition of CM tolerance, and provided evidence that the fecal metabolome can serve as a potential readout to reflect the impact of early synbiotic supplementation in infants. These findings offered valuable insights into the relationship between the gut microbiome and CMA, aiding future research in developing microbiome-targeted strategies for the prevention and management of CMA in early life.