Magliulo, Raffaele (2026) Exploiting fermented foods microbiome to improve food quality and human health. [Tesi di dottorato]

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Abstract

Fermented foods are among the oldest biotechnologies used by humans, yet only recently we have started to examine them with the tools of contemporary microbiome science, multiomics, and artificial intelligence. This thesis sits at the intersection of food microbiology, bioinformatics, and data science. Its overarching aim is to characterise the microbiomes of fermented foods in a systematic, genome-resolved way, and to explore how these communities contribute to food quality, safety, and potential health-relevant functions. The work focuses primarily on traditional cheeses and kombucha, using shotgun metagenomics, complementary ‘omics, and explainable machine learning to move from descriptive catalogues of microbes towards predictive insights. The thesis is organised into five main chapters, followed by a general discussion that integrates the findings and outlines future directions. Each chapter builds on the previous ones, moving from a broad conceptual framework to detailed case studies, then to large-scale resources and finally to a potential model system for precision fermentation.

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