Exploring Microbial Diversity and Yeast Typing in Traditional Sourdoughs from Villaurbana (Sardinia, Italy) Using an Integrated Approach

Sourdoughs are complex microbial ecosystems fundamental to traditional breadmaking. Despite extensive research, variability among traditional sourdough ecosystems remains a key area of investigation. In this context, 13 type I sourdough starters from Villaurbana (Sardinia, Italy) were characterised combining molecular and biochemical techniques. Bacterial and fungal communities were identified by NGS-based amplicon sequencing, while lactic and acetic acid, and residual sugars were quantified. The bacterial population was dominated by the genus Fructilactobacillus, whereas the fungal community spanned multiple genera. To explore the mycobiota, 130 yeast isolates were identified sequencing D1–D2 domain and through MALDI-TOF mass spectrometry. Six yeast species were detected: Saccharomyces cerevisiae was the dominant species (58.46%), followed by non-Saccharomyces yeasts (41.54%), including Torulaspora delbrueckii, Pichia fermentans, Wickerhamomyces anomalus, Maudiozyma humilis, and Monosporozyma unispora. Strain-level typing via microsatellite analysis revealed high intraspecific diversity among S. cerevisiae and T. delbrueckii isolates. S. cerevisiae strains were distributed across distinct genetic lineages, with some clustering alongside industrial reference strains and others displaying unique evolutionary trajectories. T. delbrueckii strains formed two clonal groups substantially divergent from reference strains. This study supports the restitution of characterized yeast strains to the community as a resource for establishing a new microbial consortium representative of Villaurbana sourdough tradition.