Bioinformatic Insights into the Carotenoids’ Role in Gut Microbiota Dynamics

<b>Background/Objectives:</b> Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. <b>Methods:</b> Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. <b>Results:</b> β-carotene and lycopene promoted acid-tolerant taxa such as <i>Escherichia-Shigella</i>, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including <i>Bifidobacterium</i> and <i>Bacteroides</i> and promoting structured ecological trajectories. <b>Conclusions:</b> These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.