Effects of Protein Intake on Gut Microbiota in Physically Active Individuals: A Systematic Review and Meta-Analysis

Context Protein (PRO) intake supports exercise adaptation and recovery, but its effects on gut microbiota (GM) in physically active individuals remain inconsistent across doses, PRO sources, and exercise conditions. Objective To systematically evaluate and meta-analyze the effects of PRO intake on GM in physically active individuals. Data Sources The PubMed, EBSCOhost, the Cochrane Library, and Web of Science databases were searched through June 2026. Reference lists of relevant studies and reviews were also examined. Data Extraction Two reviewers independently screened records and extracted study, participant, intervention, and outcome data. Eligible studies quantified PRO intake, included an exercise or physical-activity component, and reported extractable GM outcomes. Risk of bias and evidence certainty were assessed using the Cochrane Risk of Bias 2.0 tool and Grading of Recommendations, Assessment, Development and Evaluation approach, respectively. Data Analysis Random-effects meta-analyses using Hedges’ g, subgroup analyses, and meta-regression were performed. Eighteen studies (n = 819 participants) were included. Protein intake significantly increased the Shannon and Chao1 indices but not the Simpson index or observed operational taxonomic units (OTUs). A significant U-shaped association was observed between PRO dose and the α-diversity effect size, with the fitted curve reaching its lowest point at 1.5-2.0 g kg−1 d−1. Protein intake significantly decreased populations of Actinobacteria, Bifidobacterium, and Firmicutes, and the Firmicutes to Bacteroidetes ratio, and increased Bacteroidetes numbers. Subgroup findings suggested that age, body mass index, intervention duration, PRO dose, and exercise modality and intensity moderated the effects on Shannon diversity and Bifidobacterium abundance. Conclusions Protein intake appears to improve gut microbial diversity in physically active individuals but may also induce notable shifts in beneficial taxa, particularly reductions in Bifidobacterium. Future studies should prioritize individualized microbiome-informed strategies, evaluate long-term safety, and clarify the ecological impact of different PRO sources to optimize exercise nutrition interventions. Systematic Review Registration PROSPERO registration No. CRD420261288197.