Functional and metabolomic profiling supports rational selection of probiotic strains for the gut - skin axis

Abstract The gut–skin axis is a promising target for oral probiotics, yet strain choice is often empirical, rather than aligned to defined, skin-relevant functional readouts. Here, we applied a multi-criterion screening pipeline to prioritize lactobacilli and bifidobacteria candidates by integrating antagonism against skin-associated pathobionts, targeted LC-MS/MS metabolite profiling of cell-free spent media, a simple adhesion proxy (polystyrene binding), and assessment of intestinal epithelial resistance during Caco-2 monolayer maturation. Antimicrobial activity was strongly strain dependent and most pronounced against Staphylococcus aureus and Cutibacterium spp., with Lacticaseibacillus rhamnosus SCN01 and Limosilactobacillus fermentum LF160 showing the broadest inhibition profiles. Replicated metabolomics revealed distinct, reproducible extracellular signatures: lactate dominated across lactobacilli, B. breve SCN03 showed the clearest acetate increase, and L. fermentum LF160 displayed a coordinated arginine-to-ornithine/citrulline shift with high succinate. Nicotinic acid (vitamin B3) accumulated most in L. acidophilus LA120 and B. breve SCN03, whereas pyridoxal (vitamin B6) and GABA were most enriched in L. plantarum SCN02; biogenic amines remained low in all replicated assays. Functionally, L. rhamnosus SCN01 produced the strongest sustained TEER increase without detectable changes in cellular metabolic activity. Collectively, integrated functional and metabolomic profiling enables transparent prioritization of oral probiotic strains with mechanistically plausible gut–skin-relevant modes of action and supports evidence-based formulation rather multi-strain than single strain strategies for downstream preclinical and clinical evaluation.