Multi-omics integration of gut-skin axis in probiotic-treated dermatological conditions

The gut-skin axis is an integrated biological communication network linking gut microbial metabolites, immune regulation, oxidative stress responses and skin barrier function. Dysregulation of inflammatory and metabolic pathways has been associated with dermatological disorders including psoriasis, eczema and atopic dermatitis. Postbiotic metabolites derived from probiotics are increasingly recognized for their anti-inflammatory, antioxidant and immunomodulatory activities that may contribute to skin homeostasis. Here, we aimed to investigate the multi-omics effects of probiotic metabolite extracts (PMEs) in an in vitro inflammatory keratinocyte model relevant to gut-skin axis-associated signaling pathways.

HaCaT keratinocytes and Human Dermal Fibroblast (HDF) cells were employed as complementary in vitro skin models and stimulated with lipopolysaccharide (LPS) to induce an inflammatory microenvironment. The inclusion of HDF cells enabled assessment of probiotic metabolite effects on both epidermal and dermal cellular responses relevant to skin homeostasis and repair. For each experiment, triplicate biological replicates (n = 3) were used. The multi-omics profiling included LC-MS/MS-based metabolomics, RNA-seq transcriptomics, qRT-PCR validation, ELISA-based cytokine quantification, oxidative stress assays and integrated correlation network analysis using weighted gene co-expression network analysis (WGCNA).

After PME treatment, keratinocyte viability was significantly higher (95.4%) compared with the inflammatory control group (62.4%). Pro-inflammatory cytokine levels were significantly decreased (TNF-α: 86.7 to 28.9 pg/mL; IL-6: 79.5 to 25.7 pg/mL), intracellular ROS decreased from 248 RFU to 116 RFU, and antioxidant enzyme activities were restored. Metabolomic profiling showed increased levels of short-chain fatty acids (SCFAs) such as butyrate (1.24 to 3.02 µmol/g), which are beneficial to the skin. Transcriptomic and qRT-PCR analyses showed upregulation of genes associated with the skin barrier, such as FLG (1.28-fold), LOR (1.31-fold) and IVL (1.29-fold).

Integrated multi-omics analysis suggested that PMEs may modulate inflammatory signaling and enhance epidermal barrier-related gene expression through coordinated metabolic and transcriptional regulation, which may validate the therapeutic potential of probiotic-derived metabolites as candidate adjunctive strategies for inflammatory skin disorders.