Functional Soy and Lupin Protein-Based Beverages Modulate Gut Microbiome and Attenuate Metabolic Dysregulation in Adolescent Boys with Overweight and Obesity

Background/Objectives: Given the rising prevalence of overweight and obesity in pediatric populations, identifying effective nutritional interventions for metabolic management is crucial. Beyond their nutritional value, soy and lupin proteins are recognized for their bioactive properties. We formulated two protein-enriched functional beverages and evaluated their impact on the metabolic profile and gut microbiota of adolescent boys with overweight or obesity. Methods: A randomized, double-blind clinical trial was conducted with 30 Mexican male adolescents (12–16 years old). Participants were randomly assigned to consume a functional beverage providing a daily 10 g portion of either soy or lupin protein for 5 weeks. Results: Following the intervention, both groups exhibited significantly attenuated fasting glucose (soy: 93.1 vs. 99.5 mg/dL; lupin: 92.3 vs. 97.9 mg/dL) and C-peptide levels. Consequently, insulin sensitivity, assessed via the HOMA2 index, improved significantly in both cohorts. The soy protein group showed a marked reduction in total cholesterol (–10.4%) and triglycerides (–17.1%). Furthermore, serum levels of plasminogen activator inhibitor-1 (PAI-1) and visfatin were decreased after both interventions. A post-treatment reduction in glucose-dependent insulinotropic polypeptide (GIP) was specifically observed in the lupin group. Regarding the gut microbiota, both protein-based beverage interventions correlated with enhanced 16S rDNA diversity and increased the abundance of the Bacillota phylum and butyryl-CoA transferase-positive bacteria. Conclusions: Our data suggests that the daily consumption of soy or lupin protein-based beverages could exert beneficial metabolic and endocrine effects in adolescent boys with overweight and obesity, potentially mediated by the modulation of the gut microbiome.