Individualized and temporally stable gut microbiota across training and peak- performance phases in elite Polish athletes: a case-series pilot study

Abstract Introduction: The gut microbiota of elite athletes has been characterized largely through cross-sectional, athlete-versus-control comparisons, leaving open whether microbiota features are stable or fluctuate within individuals across a competitive season. We performed a repeated-measures, within-athlete longitudinal characterization of 11 elite Polish track-and-field athletes (national-team members; endurance and strength/speed-power disciplines), collecting repeated fecal samples aligned to athlete-specific training-period blocks (preparatory, competition, and peak-performance) rather than to fixed calendar dates. Methods: Gut microbiota composition was profiled by 16S rRNA (V3–V4) sequencing, yielding 1,438 ASVs, with inferred functional potential from PICRUSt2. Because the design targets within-athlete dynamics, analyses used linear mixed-effects models with athlete as a random effect. Results: Alpha diversity was dominated by stable, athlete-specific signatures: between-athlete variation accounted for over 40% of the total variance (intraclass correlation = 0.43), and Shannon and Simpson indices did not differ significantly across training periods, sport types, or their interaction. Beta-diversity analyses reinforced this individuality: athlete identity explained 59% of the variation in community composition (PERMANOVA on Bray-Curtis distances, R² = 0.585, P = 0.0001), within-athlete dissimilarities were consistently lower than between-athlete dissimilarities, and neither training period nor any transition category (direction, or entering/leaving peak performance) was significantly associated with community structure or turnover. Against this stable background, exploratory analyses identified a nominal decrease in Shannon diversity on leaving the peak-performance phase and candidate genus- and pathway-level shifts that differed by sport type but did not survive multiple-testing correction. Conclusions: Collectively, the elite-athlete gut microbiota appears strongly individualized and globally resilient across a periodized season, with any phase-related responses emerging as selective, athlete-specific changes rather than community-wide restructuring. Larger longitudinal studies using shotgun metagenomics, metabolomics, and more detailed performance and recovery measures are warranted.