Metagenomic analysis reveals functional potential and storage-driven dynamics of the Kalamata olive microbiome

Abstract

Background Fermented olives are a staple of the Mediterranean diet due to their nutritional value. Despite advances in olive microbiome research, published research on the functional contributions of fermented food-associated microbiota and the impact of storage on these microbial communities remains limited. Methods We studied the bacterial communities of ready-to-eat Kalamata olives, stored in glass jars or vacuum-sealed bags at various temperatures (4°C, 8°C and 15°C) for 55-day period. The bacterial abundance, taxonomical composition and functional potential were analyzed by quantitative PCR and amplicon sequencing of 16 rRNA gene, and metagenome sequencing. Results The microbiota was dominated by Lactobacillaceae (94.6%), a family of lactic acid bacteria (LAB), with dominant genera such as Pediococcus, Lactiplantibacillus and Secundilactobacillus. At the functional level, bacterial genes involved in the biosynthesis of vitamins B1, B2, B5, B7, B9, B12, and vitamin K, as well as short-chain fatty acid metabolism, were observed. Importantly, those functions were not restricted to LAB, underscoring the potential functional contribution of non-LAB taxa to the olive microbiome. Despite conservation, post-fermentation storage, especially the incubation time, temperature, and packaging, influenced the bacterial communities. Lactic acid bacteria were enriched in olives stored at 15°C, whereas non-LAB taxa proliferated more at lower temperatures. Conclusion Our study showed that Kalamata olives contain a highly abundant and diverse microbiota that responds to storage practices and carries genes encoding functions that may contribute to the characteristics and quality of the fermented product.