Exploitation of the Functional Potential of Autochthonous Microorganisms from Fermented Foods

Protein valorization represents a significant challenge in the transition toward more sustainable and health-oriented food systems. Fermentation by autochthonous lactic acid bacteria (LAB) offers a promising approach to enhance the nutritional and functional potential of animal and plant pro-teins. Through their metabolic activity, LAB can drive the biotransformation of proteins into health-promoting compounds, while contributing to the sustainable use of underexploited protein sources. Based on this rationale, this PhD project explored the potential of autochthonous LAB to generate health-promoting properties from food proteins through fermentation. Two protein mod-els were studied, representing animal (whey) and plant (pea) sources. After isolating and identifying wild LAB strains from dairy and plant-based fermented foods (FFs), dairy isolates were screened for their ability to hydrolyze whey proteins and release low-molecular-weight peptides, which are most frequently reported to exert bioactive properties. In contrast, plant-derived isolates were tested on pea proteins. The selected strains, twelve from dairy and seven from plant-based FFs, were used in fermentation trials in whey and pea protein media. The composition of the resulting microbial fermentates was characterized, and their biologically active properties were evaluated. Across all experimental con-ditions, LAB strains exhibited a strain-dependent behavior in terms of proteolytic activity and func-tional outcomes. Several strains were able to generate fermentates displaying antioxidant, ACE-inhibitory, and antimicrobial properties. Moreover, some fermentates modulated intestinal micro-bial communities, promoting beneficial taxa and supporting metabolic functions associated with gut health. A promising strain, Lacticaseibacillus paracasei AF43, was selected for in-depth analysis and was used to ferment media containing whey protein, pea protein, or a mixture of both. Integrated pro-teomics, metabolite profiling, and functional assays revealed that the growth medium strongly shaped the metabolism of the strain and the bioactivity of the fermentates. Depending on the substrate, differences were observed in carbohydrate metabolism, with the strain shifting between homo- and heterofermentative routes. These adaptations affected growth efficiency and were ac-companied by variations in metabolite utilization and accumulation, ultimately influencing the functional output of the fermentates. Additionally, the strain’s tolerance to digestive transit was found to be markedly affected by the cultivation environment preceding gastrointestinal exposure, suggesting that specific nutritional contexts can pre-adapt LAB for enhanced survival during gas-trointestinal transit. Together, these findings contribute to a deeper understanding of the interplay between microbial metabolism, protein substrates, and health-related functionalities, offering per-spectives for the sustainable valorization of protein sources.