Longitudinal integration of microbiota and metabolomics reveals (poly)phenols-driven gut ecosystem dynamics

The gut microbiota and its "theatre of activity" (the collective pool of metabolites and signaling molecules) function as a plastic interface that responds to nutritional inputs. Dietary (poly)phenols are key bioactive components of berries and are increasingly recognized for their capacity to modulate gut microbiota composition and metabolic activity while being biotransformed by microbiota. However, the temporal dynamics of this interaction remain poorly resolved, as most studies rely on cross-sectional or endpoint-only designs. Here, we conducted a longitudinal multi-omic study to map the co-evolution of the fecal microbiota and the metabolome during a sustained consumption of a berry-enriched diet. Using a murine model, fecal samples were collected at baseline, mid-intervention (day 21) and endpoint (day 42). These samples were analyzed by 16S rRNA gene sequencing and untargeted metabolomics to distinguish transient perturbations from stabilized ecosystem reorganization. Two-stage ecosystem reconfiguration was observed concurrent with the intervention: an early, high-magnitude reconfiguration phase (D0 - D21), followed by a period of stabilization (D21 - D42). The initial phase was characterized by the enrichment of the tryptophan metabolic pathway and significant taxonomic shifts, including the proliferation of Lachnospiraceae and Oscillospiraceae alongside the depletion of Prevotellaceae and Akkermansiaceae. Conversely, the stabilization phase was defined by the emergence of tyrosine-derived aromatic signatures and the recovery of Muribaculaceae. Integrated Procrustes analysis confirmed that the strongest coordination between the microbiota and metabolome occurred during the first 21 days, suggesting that microbial composition and metabolic output co-evolve most dynamically during the initial exposure to berry (poly)phenols. We conclude that dietary exposure to berries is associated with a rapid, coordinated restructuring of the gut ecosystem that stabilizes over time, emphasizing that longitudinal multi-omic designs are essential to capture the transient metabolic nodes and stable configurations that define the diet-microbe-metabolite loop.