Integration of MALDI-TOF MS and 16S rRNA Analysis for Identification of Plant-Based Fermentation-Associated Microbiota

Abstract

The specific fermented matrices influence microbial diversity and proteomic adaptations being crucial for optimising fermentation efficiency and effective microbial identification. Therefore, the study aimed to investigate the impact of plant-based fermentation matrices and their physicochemical composition on microbial diversity and MS-protein profiles. Microbial communities were characterised using MALDI-TOF MS and 16S rRNA sequencing. Physicochemical analyses were conducted on the 10 fermentation matrices. The sequencing verified low-confidence MALDI identifications and assessed species-level microbial diversity. Combined MALDI-TOF MS and 16S rRNA gene sequencing confirmed the presence of 24 species across five taxonomic classes and revealed strong matrix-dependent variation in the lactic acid bacteria composition. A significant positive correlation was observed between Lactiplantibacillus pentosus abundance and pH, with the presence being negatively associated with Ca and Mg levels in the fermented products. Furthermore, the concentration of carbohydrates and Fe was positively correlated with Corynebacterium amycolatum and Micrococcus luteus. MALDI−TOF MS spectra obtained for the key lactic acid bacteria species revealed differences in protein profiles depending on the type of fermented matrices. The study provides new insights into the interactions between microbial communities and fermentation substrates, emphasising the role of physicochemical properties of plant-based matrices in shaping microbial diversity and proteomic adaptations.