Effects of Probiotic–Phytonutrient Blends on Defecation, Intestinal Barrier Function, and Gut Microbiota: A Randomized, Placebo-Controlled Trial

Background/Objectives: Probiotic interventions are widely used to improve intestinal health; however, comparative evidence on multi-strain formulations with different potencies, particularly when combined with plant-based complexes, remains limited. This study evaluated the effects of two probiotic blends containing phytonutrients: PBP1, comprising Lacticaseibacillus strains, and PBP2, comprising Lacticaseibacillus, Lactobacillus, and Bifidobacterium strains. The effects on bowel function, microbial metabolites, and gut barrier-related markers were investigated. Methods: In this randomized, double-blind, placebo-controlled trial, participants received PBP1, PBP2, or placebo for 8 weeks. Stool patterns (7-day Bristol Stool Form Scale (BSFS) diary), fecal short-chain fatty acids (SCFAs), tryptophan metabolites, zonulin, and gut microbiota were assessed at baseline and Week 8. Efficacy was evaluated by comparing each intervention group with the placebo group. Results: Both PBP1 and PBP2 significantly increased the proportion of normal stool types (BSFS types 3–5) compared with placebo (p < 0.05). Fecal SCFA levels, including acetate, propionate, and butyrate, were significantly increased in both intervention groups. Notably, butyrate levels were significantly elevated compared with placebo. Fecal tryptophan levels decreased, while indole metabolites showed increasing trends, with an inverse correlation observed between tryptophan and indole, particularly in the PBP2 group. Fecal zonulin showed a decreasing trend, with significant reductions in participants with 25.0 ≤ BMI < 30.0 kg/m2. Microbiome analysis revealed preserved alpha diversity with selective compositional shifts, including enrichment of Lactobacillus-related taxa. Conclusions: Supplementation with PBP1 and PBP2 improved bowel function and was associated with changes in microbiome-derived metabolites, including SCFAs and tryptophan–indole metabolism, with BMI-dependent changes in barrier markers. These findings suggest a potential role of microbiome-mediated metabolic modulation in intestinal health.