Objectives: This study aimed to investigate the therapeutic effects and potential mechanisms of Lonicerae japonicae Flos (Jinyinhua, JYH) against respiratory syncytial virus (RSV)-induced pneumonia by integrating lung tissue metabolomics with gut microbiota analysis. Methods: An RSV-infected mouse model was established through intranasal inoculation. Lung pathological changes, viral RNA levels, lung index, and inflammatory cytokine levels were evaluated. Untargeted metabolomics and 16S rRNA gene amplicon sequencing were performed to characterize JYH-mediated alterations in pulmonary metabolites and the gut microbiota. Spearman correlation analysis was conducted to assess associations between differentially abundant bacterial genera and significantly altered metabolites. Results: JYH alleviated RSV-induced pulmonary histopathological injury, reduced viral RNA levels, decreased lung index and interleukin-6 (IL-6) levels, and increased interferon-γ (IFN-γ) levels. Metabolomic profiling identified 46 differential metabolites, among which 26 showed a reversal trend following JYH administration. These metabolites were mainly enriched in pathways associated with the synaptic vesicle cycle, lysosomal function, and Forkhead box O (FoxO) signaling. Gut microbiota analysis showed that JYH increased microbial richness and diversity, whereas KEGG-based functional prediction indicated that the differentially abundant taxa were primarily involved in amino acid, carbohydrate, and nucleotide metabolism. Moreover, correlation analysis revealed significant associations between key bacterial genera, including Gemella, Sutterella, and CC_115, and differential metabolites such as pyridoxamine, uridine monophosphate (UMP), and argininosuccinic acid. Conclusions: JYH may protect against RSV-induced pneumonia by restoring pulmonary metabolic homeostasis and modulating gut microbiota composition. These findings provide new insights into metabolite–microbiota interactions underlying the anti-RSV activity of JYH.

Lonicerae japonicae Flos (LJF) is a medicinal and edible herbal material whose chemical characteristics and biological activity may vary with geographical origin. In this study, 27 LJF batches from Shandong, Henan, and Hebei Provinces were evaluated using headspace gas chromatography–ion mobility spectrometry (HS–GC–IMS), multivariate analysis, and a mouse model of Staphylococcus aureus superinfection following influenza A (H1N1) virus infection. HS–GC–IMS detected 62 volatile ion signals; 49 were tentatively assigned to 36 unique volatile organic compounds (VOCs), while 13 remained unidentified. Fingerprint analysis revealed distinct origin-associated differences in volatile profiles, and OPLS–DA showed the clearest separation of Shandong samples from those from Henan and Hebei (R²Y = 0.898; Q² = 0.844). Thirty-two VIP-ranked signals were identified as candidate discriminant variables. In vivo, LJF aqueous extracts reduced the lung index, pulmonary bacterial burden, and relative NP RNA expression. Samples from Shandong and Henan generally showed greater improvements than those from Hebei across the evaluated endpoints. Overall, both the chemical and pharmacodynamic datasets indicated origin-associated variation in LJF. Direct relationships between specific volatile constituents and pharmacodynamic effects, however, were not established. These findings support the integration of HS–GC–IMS profiling with pharmacodynamic assessment as a practical framework for origin-related quality evaluation of LJF, while targeted confirmation of key discriminatory VOCs and further chemical–efficacy analyses remain warranted.