The challenge of microbiome preservation from fermented food: the successful story of preserving the microbial consortia associated with Italian table olives

Microbial biodiversity in fermented foods is a valuable source of functional traits with important applications for human health. However, its exploitation is strictly linked to preservation methods that need to maintain the viability, structure, and metabolic activity of complex microbial communities over time. While single-strain preservation is well established, maintaining the viability, structure, metabolic activity, and functionality of entire microbiomes remains a significant challenge for Culture Collections. This gap has been addressed by focusing on the microbiomes associated with table olives, a globally significant fermented plant-based food that is central to the Mediterranean diet (Gialluisi et al., 2026). Naturally fermented olives microbiomes from two typical Italian region cultivars, Leccino and Bella di Cerignola, were conserved for long-term by cryopreservation and freeze-drying, respectively. To ensure a comprehensive assessment of preservation success, the microbial community was characterized before and during storage using culture-dependent methods, metabarcoding, and metabolic profiling. The results showed that, after long-term storage using both cryopreservation and freeze-drying approaches, there was a high retention of microbial viability regardless of the cryoprotectant used. Metabarcoding analysis confirmed the stability of relative abundances across preservation methods. Furthermore, no significant alterations were detected in the metabolic profiles, indicating that the functional potential of the consortia was fully maintained during storage. Overall, our findings demonstrate the effectiveness of both cryopreservation and the newly developed freeze-drying protocol as robust tools for the long-term conservation of olive-associated microbiomes. The viability, structure, and functionality of olive-associated microbial consortia provide valuable tools for their long-term conservation, scientific valorisation and future biotechnological exploitation.