Probiotic Supplementation Induces a Partial Shift Toward an Active-Like Gut Microbiome in Physically Inactive Young Adults

Sedentary behavior is associated with gut microbiota dysbiosis and increased metabolic risk, yet effective microbiome-modulating strategies for individuals who cannot engage in sufficient physical activity remain underexplored. Probiotics may modulate sedentary-associated microbial alterations. We conducted a cross-sectional multi-omics comparison of physically active (PA, <em>n</em> = 65) and physically inactive (PI, <em>n</em> = 90) young adults, followed by a 6-week randomized, double-blind, placebo-controlled trial in the PI cohort (probiotic: PIP, <em>n</em> = 45; placebo: PIC, <em>n</em> = 45). At baseline, PA individuals exhibited higher α-diversity and a more favorable microbial community structure than PI participants, enriched in <em>Bifidobacterium adolescentis</em>, <em>B. bifidum</em>, <em>Anaerostipes hadrus</em>, and associated metabolites. A random forest classifier distinguished PA from PI with high accuracy (96.1%; area under the curve, AUC = 0.993). Following intervention, PIP subjects showed a modest shift toward an active-like microbiome: root Jensen-Shannon similarity between PIP and PA (69.3%) was significantly higher than between PIC and PA (67.8%; <em>P</em> &lt; 0.001), and levels of key taxa (<em>A. hadrus</em>, <em>B.</em> <em>bifidum</em>) and metabolites (vanillic acid, prolylglycine) moved closer to PA. Consistently, classifier performance decreased for PIP vs. PA (AUC 0.690; accuracy 68.2%) but remained higher for PIC vs. PA (AUC 0.843; accuracy 80.0%), indicating a probiotic-associated reduction in microbiome dissimilarity. These findings suggest that probiotic supplementation induces a partial, ecologically measurable shift toward an active-like gut microbiome configuration in inactive individuals, without replicating the full physiological benefits of regular physical activity, highlighting its potential as a scalable, adjunctive strategy for microbiome health in sedentary populations.