First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study

Introduction The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population. Methods We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19–69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age. Results We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19–29 years, n = 33; 22.7%), G2 (30–39 years, n = 30; 20.7%), G3 (40–49 years, n = 27; 18.6%), G4 (50–59 years, n = 31; 21.4%), and G5 (60–69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R 2 = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age. Conclusion In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.