Single-cell phenotypes revealed as a key biomarker in bacterial-fungal interactions: a case study of Staphylococcus and Malassezia

Microbial interactions are determined by competition, cooperation, and inaction, depending on the transcriptional response to the metabolites secreted by each other. The consequence of these interactions is reflected in the cell phenotype by the composition of cell materials, including lipids, nucleotides, and proteins. We studied the phenotypic plasticity of single cells involved in microbial interactions using Raman spectroscopy and evaluated the types of interactions by linking phenotypes to transcriptional profiles. We used a membrane-based co-culture system to induce chemical interactions between skin-dominant bacteria and fungi, Staphylococcus and Malassezia. Staphylococcus species exhibited an amensalism interaction with Malassezia based on growth and cell viability. Malassezia co-cultured with S. epidermidis and S. aureus resulted in significant changes in the Raman spectra of nucleic acids and proteins in the Raman phenotypes, respectively. The observed differences in phenotypes during co-culture with Malassezia were significantly associated with changes in transcriptomic profiles, which demonstrated variations in the defense/resistance and biofilm-formation mechanisms of S. epidermidis, whereas no meaningful changes were observed for the transcriptome of S. aureus. These approaches provide a robust, simple, and reproducible method for comprehending bacterial-fungal interactions.