Monahan, H. | Search bioRxiv

bioRxiv2025

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

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 (SWipe), 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 SWipe captures both volatile and non-volatile metabolites with reproducibility and stability validated for diagnostically relevant molecules. We show that SWipe 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. IMPORTANCEGut 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.

biochemistry↗

bioRxiv2024

S-Wipe: stool sample collection for metabolomic gut health tracking

Microbiome is increasingly recognized as a key factor in health. Intestinal microbiota modulates gut homeostasis via a range of diverse metabolites. 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 have been linked to multiple gastrointestinal disorders from cancer to colitis, and thus present an excellent diagnostic target. Yet, technical bottlenecks preclude broad translation of such established biomarkers into routine medical practice. In particular, easily accessible, reproducible and robust sampling of stool remains challenging. Here we present Stool Wipe (S-Wipe), an ultra low cost, simplified fecal specimen collection approach designed to overcome key translational barriers without compromising analytical rigor. This sampling approach harnesses lint-free mass spectrometry-compatible cellulose wipes used as a regular toilet paper. The collected stool specimens are then preserved in ethanol solution, do not require refrigeration and can be shipped via regular mail. Using mass spectrometry, we have demonstrated a broad range of captured metabolites, both volatile and non-volatile. The reproducibility and stability of the method was validated for a panel of molecules of particular diagnostic interest, including SCFAs and p-cresol. We demonstrate sensitivity as well as stability and reproducibility of various metabolites collected with S-Wipe. We further demonstrate that S-Wipe is equivalent to the direct stool collection and thus could be used interchangeably and compared to other studies where stool is collected directly. This methodology is ideally suited and is scalable for broad population-based studies, longitudinal tracking such as therapeutic interventions and personalized medicine. IMPORTANCEGut 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 validated biomarkers such as 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 possible user errors, requirement for freezer storage and maintaining cold chain during shipment. We present a sampling strategy specifically designed to overcome these obstacles. 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.

biochemistry↗