Today’s children are increasingly facing metabolic-related health issues, among which the worldwide prevalence of overweight and obesity is rising at an alarming pace. Childhood obesity is associated with the early onset of chronic diseases including an emergence of prediabetes and diabetes mellitus type 2. The decline of insulin sensitivity already years before puberty, exposes children to long-term complications prior the appearance of clinical symptoms and time of diagnosis. The shortened life expectancy and large economic burden imposed underlines the need for the identification of metabotypes at risk at an early stage. One’s genetics, microbial gut composition and every aspect of the environment in which children are raised have been implicated in diet-related obesity rendering metabolomics a very powerful tool towards precision medicine. Yet, the excellence of stool in reflecting the intertwining thereof is completely unexplored for pediatric purposes, whereas blood sampling causing pain and stress for child and parent only captures a narrow fraction of the metabolome. As such, I propose rectal sampling using a medical swab tailored with electrospun nanofibers for optimal gut metabolome coverage. Ambient laser desorption ionization will be hyphenated to high-resolution mass spectrometry-based metabolomics to provide a framework for elucidating predictive and/or prognostic biomarkers for ever-increasing pediatric metabolic diseases such as obesity and (pre)diabetes.