Large-scale multi-omics survey unveils microbial drivers of fermentation and flavor development across Mediterranean table olives

Table olives are a traditional fermented food typical of the Mediterranean countries. To become edible, they undergo diverse processes that shape their microbiome composition and flavor profile. By integrating shotgun metagenomics and volatilomics on 271 table olive samples from across the Mediterranean basin, we investigated how the technological process influences microbial communities and, in turn, the volatile organic compounds profiles. Indeed, naturally fermented olives showed enrichment of heterofermentative Lactic Acid Bacteria such as Lentilactobacillus buchneri , Lentilactobacillus rapi , and Pediococcus parvulus upon fermentation, that were highlighted as the main contributors to flavor development. We also highlighted the presence of bacteriophages targeting Lactiplantibacillus plantarum , providing novel insights into the modulatory role of the viral community, as well as the volatile organic compounds varietal fingerprints. This large‑scale multi‑omics investigation of table olives proposes new perspectives into microbial drivers of table olive quality, with potential implications for fermentation biocontrol and development of targeted starter cultures.