Comparative microbial metabarcoding and metabolomics of naturally fermented Chondrolia Chalkidiki table olives

Abstract

Naturally fermented green Chondrolia Chalkidiki table olives were assessed using a culture independent study and 16S metabarcoding to monitor the bacterial community evolution and its effect on their metabolome. Samples, ranging from raw olives after harvest to brine and olive samples up to 150 days post fermentation were subjected to Ion Torrent 16s rRNA sequencing. Gas Chromatography Mass Spectrophotometry was performed for metabolite identification. A comparative analysis was carried out with table olives of the same cultivar, harvested in another area, year (2018) and fermented under slightly different conditions. Considerably different characteristics were observed between olives harvested in year 2019 to 2018. In year 2019, the dominating family at the end of fermentation was Pseudomonadaceae, followed by Enterobacteriaceae. Targeted PCR amplification additionally revealed a large abundance of yeast DNA. The fermentation from year 2018 exhibited a dominance of L. parafarraginis, a member of Lactic Acid Bacteria, as well as a lower amount of yeast DNA. This difference was highly reflected in their metabolic profile. The 2019 fermentations contained a high percentage of alcohol, notably 2-Butanol-1-methyl, 3-Butanol-1-methyl and Phenylethyl alcohol, all of which are related to yeast fermentation pathways. This corresponded to the observation of higher yeast counts. The 2018 fermentations were characterized by a very high percentage of esters, notably ethyl acetate, which is related to high abundance of bacteria. Overall it was estimated that the slightly different fermentation conditions had a strong effect on microbial dynamics, metabolite production and the outcome of fermentation. The combination of 16S metagenomics with GCMS metabolomics is a powerful approach to uncover the relationship between microbiota evolution and biochemical and organoleptic profile in fermented table olives.