Use of Fecal Sampling for Assessing Probiotic Effects on the Gut Microbiome: A Focused Narrative Review

Most clinical studies investigating the effects of probiotics on the gut microbiota rely on fecal samples, which are generally assumed to reflect the gut microbial environment. However, growing evidence indicates that fecal samples do not always accurately represent the gastrointestinal microbiota, particularly the mucosa-adherent microbiome. This focused narrative review examines the limitations of fecal sampling in probiotic research while acknowledging contexts where this approach remains informative. It also discusses methodological strategies that may improve the reliability of microbiome studies, including multi-day sample collection, optimized DNA extraction incorporating bead beating, quantitative microbiome profiling, and ingestible capsule-based sampling. Together, these approaches may provide a more comprehensive assessment of the gut microbiome and improve our understanding of how probiotics influence microbial communities throughout the gastrointestinal tract.