The gut microbiota-metabolite-target axis in insomnia: network pharmacology and gut microbiota profiling insights into pathogenesis and intervention with Cinnamomi Cortex-Gardeniae Fructus.

OBJECTIVE

To investigate the mechanism underlying the association between gut microbiota metabolites and insomnia, focusing on the "gut microbiota-metabolite-target" axis. The Cinnamomi Cortex-Gardeniae Fructus (CC-GF) combination was used as an intervention.

METHODS

Network pharmacology was applied to predict insomnia-related gut microbiota metabolites and their targets. A PCPA-induced rat insomnia model was established, and gut microbiota dysbiosis was validated using 16S rRNA sequencing. Core gut microbiota were identified, and core targets were screened via protein-protein interaction (PPI) network analysis and multi-algorithm ranking. A "core microbiota-metabolite-core target" network was constructed, and binding affinities were verified using molecular docking and molecular dynamics simulations.

RESULTS

Twenty-eight targets were predicted, and CASP3, NFE2L2, HDAC1, and CCND1 were identified as core targets related to oxidative stress, apoptosis, epigenetic regulation, and circadian disturbance. In the insomnia model, the beneficial genera Bifidobacterium and Bacteroides were decreased, whereas the harmful genera Ruminococcus and Blautia were increased. Nine key metabolites were identified; folic acid exhibited the strongest binding affinity to the core targets (average -8.83 kcal/mol) and was defined as the core metabolite. CC-GF reversed these microbiota alterations, confirming the regulatory role of this axis.

CONCLUSION

This study elucidates the "gut microbiota-metabolite-target" axis in insomnia and highlights the "Bifidobacterium-folic acid-target" pathway as a core mechanism. CC-GF intervention provides experimental evidence supporting this axis as a target for insomnia treatment.