Background <p>Yeast mannans are microbial-available substrates that may improve laxation and specifically modulate gut microbiota composition. The aim of this study is to determine the effect of yeast mannan supplementation on stool frequency in adults. Secondary aims will assess gastrointestinal tolerance and quality of life, whole gut transit time, fecal microbiota composition, and fecal and urinary levels of microbial-generated metabolites.</p> Methods <p>A 6-week, double-blinded, parallel, randomized trial will evaluate the effect of 12&#xa0;g of yeast mannan (<i>Saccharomyces cerevisiae</i> cell wall fraction containing mannan-oligosaccharides and mannoproteins) or control (maltodextrin and yeast protein) supplementation on mean daily stool frequency in adults (<i>n</i> = 60). Participants will complete a daily survey of stool frequency, gastrointestinal symptoms, and quality of life, any adverse events, and compliance with supplement intake during the 2-week baseline and 4-week intervention periods; gastrointestinal tolerance will be assessed weekly. Capsules containing radiopaque markers will be administered, and all stools will be collected during the last 3&#xa0;days of baseline and intervention. Whole gut transit time will be estimated using the 80% recovery of radiopaque markers method. Per period, 24-h urine will be collected, and metabolomics will be determined by LC–MS/MS.&#xa0;For the primary outcome, change from baseline daily stool frequency between groups will be compared, and between-group comparisons of secondary outcomes using appropriate generalized linear regression models, and for those outcomes with repeated measures, linear mixed effect models. Fecal microbiome using whole metagenome sequencing data will be processed using metaphlan4, Braken, or another tool appropriate for estimating the relative abundance of microbial species. Additional analysis using tools such as humann3 will enable functional assignment of reads. Resulting relative abundance and normalized functional data will be further analyzed using a combination of tools in R software, including phyloseq and vegan packages.</p> Discussion <p>In accordance with our pilot open-label study, the hypothesis is that yeast mannans will increase daily stool frequency, be highly tolerable, and demonstrate specific modulation of the microbiota, supporting its prebiotic properties. Additionally, yeast mannan supplementation may decrease whole gut transit time and mitigate the microbial production of inflammatory microbial-generated metabolites.</p> Trial registration <p>NCT ID NCT06911177. Registered on 04 April 2025.</p>