Background/objectives: The mode of athletic training exerts a profound influence on both physiological parameters and gut microbiota composition; yet, comprehensive integrative analyses in elite athletes are scarce. This study systematically profiled and contrasted body composition, bone health, resting metabolic rate (RMR), fasting respiratory quotient (RQ), hematological indices, dietary intake, and key gut bacterial taxa among elite Indian endurance athletes, strength athletes, and sedentary controls. Methods: Male participants were classified as endurance athletes (n = 27), strength athletes (n = 29), or sedentary controls (n = 24). Body composition and bone mineral density were measured by dual-energy X-ray absorptiometry (DEXA); RMR and RQ were measured via indirect calorimetry; hematological parameters and inflammatory markers were measured from fasting blood samples; dietary intake was assessed via 24-h recalls; and gut microbiota abundance was assessed using quantitative real-time polymerase chain reaction (qPCR). Results: Strength athletes had significantly greater body weight, lean mass, bone mineral density, and absolute RMR than both endurance athletes and controls. Endurance athletes exhibited lower body fat, elevated fasting fat oxidation, and hematological profiles indicative of enhanced oxygen transport. Athletes showed higher relative abundances of bile-tolerant and proteolytic taxa, including Bacteroides spp., Prevotella, and Streptococcus spp., compared with controls. Endurance athletes had higher relative abundance of Methanobrevibacter, whereas strength athletes exhibited higher abundance of Desulphovibrio spp. The relative abundance of Lactobacillus spp. was highest in controls, while Fecalibacterium, Enterobacteriaceae, Bifidobacterium spp., and Akkermansia did not differ between groups. Conclusions: Elite Indian endurance and strength athletes present distinctive, sport-specific physiological and gut microbial signatures. This integrative approach uncovers novel associations and underscores the complex interplay between training modality, nutrition, and the host-microbiome axis in elite athletic populations.
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