Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl

Authors: Perez Diaz, Ilenys; Hayes, Janet; MEDINA, EDUARDO - North Carolina State University; WEBBER, ASHLEE - Former ARS Employee; BUTZ, NATASHA - University Of North Carolina; DICKEY, ALLISON - North Carolina State University; LU, ZHONGJING - Kennesaw State University; AZCARATE-PERIL, MARIA - University Of North Carolina

Submitted to: Food Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2018
Publication Date: 2/1/2019
Publication URL: https://handle.nal.usda.gov/10113/6111375
Citation: Perez Diaz, I.M., Hayes, J.S., Medina, E., Webber, A., Butz, N., Dickey, A., Lu, Z., Azcarate-Peril, M.A. 2019. Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl. Food Microbiology. 77:10-20. https://doi.org/10.1016/j.fm.2018.08.003.
DOI: https://doi.org/10.1016/j.fm.2018.08.003

Interpretive Summary: The fermentation of cucumbers, a centuries-old process to extent the shelf-life of such fruit, is known to improve sensorial characteristics as compared to the fresh produce and popularly believe to enhance beneficial microbes content and bioactivity. The properly preserved product enjoys a good safety record as defined by the incidence of a limited number of outbreaks in which pickles have been implicated. Although, various scientific reports have demonstrated that fermented vegetables support a quick die off of microbes of public health significance, there is limited knowledge of the microbiome of such fermentations, in particular to the population of oxygen-dependent microbes. This research focused in defining the microbiome of fresh and fermented cucumbers to fill the knowledge gap and determine if the indigenous microbial population could play a role in the quality of the finished fermented products. It was learned that three taxonomical families dominate in the fresh cucumbers, including Rhizobiales, Enterobacteriales and Pseudomonadales. While Rhizobiales are excluded from cucumber fermentations very early in the process; Enterobacteriales and Pseudomonadales appear to persist in low densities as long as oxygen is present in the system. As anticipated, Lactobacillales take over in cucumber fermentations in a relative abundance of more than 90 %. We aim at elucidating if a low incidence of Enterobacteriales and Pseudomonadales influence the quality of finished fermented cucumbers.

Technical Abstract: Limited documentation of the cucumber fermentation microbiome has impeded the understanding of the role of microbes on the quality of finished products. We characterized the microbiome of fresh and fermented cucumber samples using culture dependent and independent techniques, with an emphasis on the non-lactic acid bacteria (non-LAB) population. Insubstantial microbiome variations were observed among fresh cucumber types with Rhizobium (31.04%), Pseudomonas (14.08%), Pantoea (9.25%), Stenotrophomonas (6.83%), and Acinetobacter (6.5%) prevailing. The relative abundance of LAB remained below 0.4% and 4.0% on fresh cucumbers and day 3 of the fermentations brined with 6% sodium chloride, respectively. Fermentation cover brine samples collected on day 1 harbored Pseudomonas, Pantoea, Stenotrophomonas, Acinetobacter, Comamonas, Wautersiella, Microbacterium, Flavobacterium, Ochrobactrum and the Enterobacteriaceae, Citrobacter, Enterobacter and Kluyvera. Plate counts for presumptive Klebsiella and Pseudomonas from fermentation cover brine samples reached 2.80 ± 0.36 and 2.78 ± 0.83 log of CFU/mL, respectively, in 30% and 60% of the nine tanks scrutinized with selective media. Both genera were found in cover brine samples with pH values at 4.04 ± 0.15. We aim at elucidating whether the low relative abundance of non-LAB in commercial cucumber fermentations, in particular Pseudomonas and Enterobacteriaceae, impacts the quality of fermented cucumbers.