Gut Microbiota and Dietary Intake Across Training Phases in Competitive Long-Distance Runners: An Exploratory Longitudinal Study

Background/Objectives: In this exploratory longitudinal study, we examined dietary intake and gut microbiota across preparation, competition, and transition phases in competitive long-distance runners and explored microbial patterns associated with phase-specific dietary intake. Methods: Seven competitive long-distance runners were assessed across three training phases. At each phase, dietary intake and body composition were assessed, and fecal samples were collected. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Phase-related taxonomic differences were evaluated using repeated-measures approaches with multiple-testing correction, and differential abundance analysis was performed using DESeq2 with participant identity included as a blocking factor. Additionally, exploratory k-means clustering based on energy, carbohydrate, and protein intake was used to characterize dietary intake patterns. Results: Energy, protein, and fat intake differed significantly across training phases, whereas carbohydrate intake did not reach statistical significance. Exploratory alpha- and beta-diversity analyses yielded no statistically detectable differences across phases. At the phylum level, Synergistetes showed an overall phase effect after FDR correction, although no pairwise comparison remained significant after Bonferroni adjustment. In the DESeq2 analysis, Haemophilus was more abundant during the transition than preparation phase, Enterococcus was more abundant during preparation than transition, and Cronobacter was more abundant during preparation than competition (all adjusted p < 0.05). Exploratory dietary clustering identified additional cluster-associated microbial differences, but cluster membership substantially overlapped with the training phase. Conclusions: Dietary intake varied across the competitive training cycle. Community-level diversity results were presented for exploratory purposes only in this small cohort. A limited number of taxa showed phase-related differences after multiple-testing correction. Because dietary intake and training phase changed concurrently, the cluster-associated microbial findings should be interpreted as exploratory patterns within the combined nutritional and training context rather than as independent dietary effects.