Transcriptomic and metabolomic profiling reveals media- and host-dependent responses to Staphylococcus hominis in cell models

Background/aims Host-microbiota co-evolution maintains homeostasis via metabolic, immune, and neuroendocrine pathways. Diverse culture media and host cell models are widely used in microbiota research, but how these variables shape host transcriptional responses remains unclear. This study combined metabolomic, transcriptomic, and functional analyses to investigate how microbial culture medium and host cell type influence responses to a gut-derived Staphylococcus hominis isolate. Methods S. hominis was cultured for 96 h in Brain Heart Infusion (BHI) or Gifu Anaerobic Medium (GAM). Culture supernatants were collected for untargeted metabolomics and epithelial cell stimulation. Metabolomic profiling identified differentially expressed metabolites (—log 2 FC— >0, p < 0.05, variable importance in projection, VIP >1). RNA sequencing assessed transcriptional responses in four cell lines (MODE-K, NCM460, Henle-407, HEK-293T) treated with BHI- or GAM-derived supernatants. Differentially expressed genes (DEGs; —log 2 FC— >1, adjusted p < 0.05) were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and principal component and correlation analyses were used to characterize transcriptional changes under different treatments. Functional assays quantified interleukin-6 (IL-6) and interleukin-8 (IL-8) secretion, intracellular triglyceride levels, and the lactate/pyruvate ratio. Results Metabolomics revealed medium-dependent remodeling of the exometabolome: BHI-derived supernatants were enriched in fatty acyls, glycerophospholipids, and pathways related to carbohydrate, energy, and lipid metabolism, whereas GAM-derived supernatants contained higher levels of sphingolipids and organic carbonic acids linked to purine and polyunsaturated fatty acid metabolism. Across four cell lines, DEGs induced by BHI-derived supernatants were mainly enriched in metabolic pathways, while GAM-derived supernatants more often engaged immune- and inflammation-related pathways. DEG overlap between cell types was limited, and KEGG enrichment and multivariate analyses supported cell type-specific transcriptional patterns. Functionally, GAM-derived supernatants significantly increased IL-6 and IL-8 secretion, whereas BHI-derived supernatants were more closely associated with changes in intracellular triglycerides and the lactate/pyruvate ratio in a cell-dependent manner ( p < 0.05). Conclusion Metabolomic, transcriptomic, and functional data demonstrate that microbial culture conditions and host cell identity critically shape in vitro readouts of host–microbe interactions and should therefore be carefully considered when designing and interpreting microbiota-host interaction studies.