Genetic Characteristics Associated with Probiotic Functions in Four Indonesian Skin Microbiome-Derived Bacterial Strains

The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their "generally recognized as safe" (GRAS) status remains challenging. Here, we have subjected the annotated draft genome sequences of four human skin-derived bacterial strains, namely <i>Bacillus subtilis</i> MBF10-19J, <i>Micrococcus luteus</i> MBF05-19J, <i>Staphylococcus hominis</i> MBF12-19J, and <i>Staphylococcus warneri</i> MBF02-19J, to bioinformatic analyses to detect the genes associated with important probiotic traits, as well as undesirable characteristics such as antibiotic resistance, virulence factors, and toxic metabolites. Each bacterium harbors at least one type of adhesin-encoding gene, while only <i>S. hominis</i> MBF12-19J and <i>S. warneri</i> MBF02-19J contain the putative genes encoding enzymes for metabolism improvement. In vitro assays, including antibiotic susceptibility and antimicrobial activity testing, revealed strain-specific safety characteristics that complement the genomic findings. With regard to antibiotic resistance determinants, <i>S. hominis</i> MBF12-19J showed the most favorable profile, <i>S. warneri</i> MBF02-19J and <i>M. luteus</i> MBF05-19J appeared suitable when used with appropriate caution, and <i>B. subtilis</i> MBF10-19J exhibited amoxicillin resistance, i.e., warrants careful evaluation. Further in vivo validation is needed to determine whether these strains do indeed comply with GRAS evaluation frameworks.