Assessment of the bacterial community in directly brined Aloreña de Málaga table olive fermentations by metagenetic analysis

Abstract This study uses an “omics” approach to evaluate the bacterial biodiversity changes during fermentation process of natural green cracked Alorena de Malaga table olives, from raw material to fermented fruit. For this purpose, two industries separated by almost 20 km in Guadalhorce Valley (Malaga, Spain) were analysed for obtaining both brines and fruit samples at different moments of fermentation (0, 7, 30 and 120 days). Physicochemical and microbial counts during fermentation showed the typical evolution of this type of processes, apparently dominated by yeasts. However, high-throughput barcoded pyrosequencing analysis of V2–V3 hypervariable region of the bacterial 16S rRNA gene showed at 97% identity the presence of 131 bacterial genera included in 357 operational taxonomic units, not detected by the conventional approach. The bacterial biodiversity was clearly higher in the olives at the moment of reception in the industry and during the first days of fermentation, while decreased considerably as elapse the fermentation process. The presence of Enterobacteriaceae and Lactobacillaceae species was scarce during the four months of study. On the contrary, the most important genus at the end of fermentation was Celerinatantimonas in both brine (95.3% of frequency) and fruit (89.4%) samples, while the presence of well-known spoilage microorganisms ( Pseudomonas and Propionibacterium ) and halophilic bacteria ( Modestobacter , Rhodovibrio , Salinibacter ) was also common during the course of fermentation. Among the most important bacterial pathogens related to food, only Staphylococcus genus was found at low frequencies (