This is a complete microbiota and primary outcomes analysis pipeline. To reproduce all results and figures, first use the bash script to generate the ASV table and associated objects with the qiime2. Then, use qiime2 artifacts to make a phyloseq object and run the script in order.
Intestinal microbiota interacts with its host through metabolite production. Individual variability in intestinal microbiota highlights the need for personalized dietary interventions to optimize health benefits. This study explores effects of personalized prebiotics consumption on endurance exercise performance and gut microbiome modulation in vivo in humans. In a randomized, placebo-controlled trial with 34 healthy, recreationally active participants (BMI 18.5–25 kg/m², 18-40 years), a time-to-exhaustion (TTE) cycling test was performed before and after six weeks of 15 g/day supplementation with one of five preselected prebiotics: galacto-oligosaccharides (GOS), fructo-oligosaccharides (FOS), arabinoxylo-oligosaccharides, inulin, or resistant starch, selected based on individuals’ fecal microbiome composition. Fecal microbiota were analyzed using 16S rRNA gene profiling, and fasted blood samples were collected to measure short-chain fatty acids, insulin, glucose, and cytokines. After six weeks, the prebiotics group showed a trend towards improved TTE exercise performance compared to the control group (p=0.074). Pairwise comparison revealed improvement in TTE within the prebiotics group (p=0.004), while the control group showed no change (p=0.547). The intervention led to small but consistent shifts in microbiota composition (Bray-Curtis; R²=0.006; p=0.025), with increased abundance of ASVs belonging to genera Christensenellaceae R_7, Bifidobacterium , Butyricicoccus, Lachnospiraceae UCG_010, and Collinsella aerofaciens sp. in the prebiotics group but not in the control group. Blood parameters remained unaffected between groups. The study showed that personalized prebiotic intake improved endurance performance within the prebiotics group. Further research with larger sample sizes is needed to confirm these findings and their implications for skeletal muscle health in clinical and athletic settings.