A Multi-Omics Approach to Investigating the Role of Fecal miRNAs in the Gut Microbiota in Response to Physical Exercise: A Pilot Study

Introduction:
Regular physical activity improves overall health and reduces the risk of non-communicable diseases. These benefits have been linked to positive shifts in gut microbiota composition; however, the molecular mechanisms driving these adaptations remain unclear. Fecal microRNAs (miRNAs) may serve as mediators connecting exercise, inflammation, and microbial regulation.

Objective:

This pilot study aimed to evaluate the effects of physical exercise on fecal miRNA expression and explore its relationship with gut microbiota composition and inflammatory profiles.

Methods:

A total of 27 healthy adults (aged 20–45) were recruited and classified according to their physical activity level, including trained individuals (≥3 sessions/week, 60–90 min, moderate–high intensity). Participants were clustered by IL-6 and LPS plasma levels into three inflammatory profiles (low, moderate, high). From these, six trained subjects (two per cluster) were selected and compared with one sedentary participant (<1 session/week). Fecal miRNAs were quantified using TaqMan Array Cards (ThermoFisher) assessing 386 miRNA, while gut microbiota composition was determined by 16S rRNA sequencing. Microbial associations with IL-6 and LPS were analyzed via MaAsLin2.

Results:
The clustering approach identified three distinct inflammatory groups. MaAsLin2 analysis showed that Christensenellaceae R-7 group and Lachnospiraceae NK4A136 group were positively associated with lower IL-6 and LPS levels, suggesting an anti-inflammatory microbial signature in trained individuals. Conversely, Bifidobacterium, Collinsella, and Solobacterium were negatively correlated with these markers. Exercise-modulated miRNAs, including hsa-miR-1-3p and hsa-miR-92a-3p, were related to cardiac function, angiogenesis, and endothelial regulation. The integration of miRNA and microbiota datasets is currently ongoing to identify shared mechanistic pathways.

Conclusions:
These preliminary findings suggest that regular exercise modulates the expression of specific fecal miRNAs, potentially influencing host–microbiota interactions. Integration of demographic, inflammatory, microbiota, and transcriptomic data in larger cohorts is required to further elucidate the mechanisms underlying the interplay between physical activity, fecal miRNAs, and gut microbial dynamics.