Background <p>Obesity, characterized by excess body fat accumulation, is closely linked to the alteration of gut microbiota, which contribute to systemic inflammation. Probiotics intervention has emerged as a promising strategy favorably modulating gut microbiota composition in obese individuals accompanied by improvements in metabolic parameters. The objective of this study was to evaluate whether supplementation with <i>Bifidobacterium bifidum</i> BGN4 alters gut microbiota composition and to assess its associated effects on circulating zonulin, a marker of intestinal permeability, as well as metabolic parameters in individuals with excess adiposity.</p> Methods <p>This randomized, double-blind, placebo-controlled trial involved 60 adults with excess body fat (body fat percentage ≥ 20% for males and ≥ 28% for females). A total of 60 adults were enrolled, and sex- and age-stratified randomization allocated 30 participants to each group. Participants received one capsule of <i>B. bifidum</i> BGN4 (9 × 10⁹ colony forming unit) or matched placebo for 8&#xa0;weeks. Blood samples were analyzed for zonulin, TNFα, hs-CRP, glucose, insulin, lipid profiles, and total antioxidant capacity. Fecal samples were analyzed to determine alterations in gut microbiota composition.</p> Results <p>A total of 58 participants, with 29 individuals in each group, successfully completed the 8-week intervention. Supplementation with <i>B. bifidum</i> BGN4 did not result in significant changes in BMI, body fat percentage, or the primary outcome, hs-CRP. In contrast, significant improvements were observed in serum zonulin (between-group differences: -1.61 ± 2.69&#xa0;ng/mL), TNFα (between-group differences: -0.17 ± 0.26&#xa0;pg/mL), and fasting insulin (between-group differences: -3.52 ± 10.25 μIU/mL). The probiotic intervention modulated the enrichment of several taxa, including <i>Bacteroides coprocola, Bifidobacterium catenulatum</i> group, <i>Lactiplantibacillus plantarum</i> group, and <i>Prevotella stercorea</i>. In addition, several microbial taxa demonstrated correlations with metabolic and inflammatory parameters. No adverse effects were observed, as indicated by stable liver enzyme concentrations, blood pressure, and gastrointestinal symptoms.</p> Conclusion <p>The results indicate that <i>B. bifidum</i> BGN4 may serve as a preventive strategy for metabolic disorders in individuals with excess adiposity through the maintenance of gut microbial balance and intestinal barrier integrity thereby potentially mitigating inflammation and metabolic stress.</p> Trial registration <p>Clinical trial registration number: KCT0010817. Date of registration: July 28, 2025.</p>