S’Wipe: User-Friendly Stool Collection for High-Throughput Gut Metabolomics

ABSTRACT Microbiome is increasingly recognized as a key factor in health. Intestinal microbiota modulates gut homeostasis via a range of diverse metabolites. For example, molecules such as short chain fatty acids (SCFAs), the microbial fermentation products of dietary fiber, have been established to be reflective of microbiome and/or dietary shifts and SCFAs alterations have been linked to multiple gastrointestinal disorders from cancer to colitis. Despite their potential as biomarkers, technical challenges in stool collection have limited clinical translation. Here we present Stool Wipe (S’Wipe), an ultra-low-cost fecal collection method using lint-free, mass spectrometry-compatible cellulose wipes as toilet paper. Specimens are preserved in ethanol without refrigeration and can be shipped via regular mail. Mass spectrometry analysis demonstrated that S’Wipe captures both volatile and non-volatile metabolites with reproducibility and stability validated for diagnostically relevant molecules. We show that S’Wipe performs equivalently to direct stool collection, enabling interchangeable use and comparison with existing studies. This methodology is ideally suited for large-scale population studies, longitudinal tracking, and personalized medicine applications. IMPORTANCE Gut microbiome and intestinal metabolome present invaluable diagnostic and therapeutic targets. However, conventional stool testing has several barriers limiting bioassessment from populations. Routine, high temporal resolution monitoring of stool metabolome, including extensively validated and broadly informative biomarkers such as short chain fatty acids (SCFAs), is not implemented due to relatively high cost and inconvenience of sampling, possible need for clinical setting for sample collection, difficulty to collect samples reproducibly, especially due to potential for user errors, requirement for freezer storage and maintaining cold chain during shipment. We present a sampling strategy specifically designed to overcome these obstacles. We demonstrate how this method can enable capturing accurate molecular snapshots at massive scales, at ultra low cost. The approach collapses complex medical-grade collection into easy self-administration. Individuals can thereby self-monitor therapeutic responses through routine metabolome tracking, including the volatilome, otherwise hindered by infrastructure restrictions. Ultimately, this sampling approach is intended to enable participatory wellness transformation through practical high frequency self-sampling.