Identification of microbial diversity of fermented pickled vegetable with tomato juice using Next-Generation Sequencing technique

A total of 58 bacteria fromthree fermented vegetables samples were isolated. These isolates were identified as 64% Lactobacillus, 5% Pediococcus, 4.5% Leuconostoc and 26.5% unclassified bacteria based on phenotypic characterizations using morphological and biochemical tests. This identification was completed by culture-independent molecular method based on next-generation sequencing of 16S ribosomal RNA gene amplicons. The V3 and V4 regions of 16S rRNA gene were amplified and sequenced using IlluminaMiSeq platform. These data were analyzed employingBaseSpace software andGreengenes database. The analysis revealed 77.12% Lactobacillus, 7.51% Pediococcus, 5.61% Leuconostoc, 1.20% Acinetobacter, 1.00% Enterobacter, 0.35% Erwinia, 0.35% Dickeyaas the predominant genera and 2.79% unclassified bacteria. At species level, 19.32% Lactobacillus brevis, 15.71% Lactobacillus japonicus, 13.25% Lactobacillus pentosus, 10.26% Lactobacillus senmaizukei, 4.6% Lactobacillus plantarum, 2.65% Leuconostocmesenteroides and 2.32% Lactobacillus acidifarinaeand 17.26% unclassified bacteria were identified. The same identification resultswereobtainedby both phenotypic andNext- generation sequencing assays at genus level.In this study, application of next generation sequencing in identification of whole microbial community of this fermented product revealed that lactic acid bacteria include Lactobacillus, Pediococcusand Leuconostoc as dominant flora, were involved in fermentation process. Non-lactic acid bacteria such as Acinetobacter,Enterobacter,Erwinia and Dickeyageneramayplay important role in fermented pickled vegetable with tomato juice ripening. Moreover, probiotic bacteria such as Lactobacillus plantarum,Lactobacilluspentosus,Leuconostocmesenteroides and Lactobacillus breviswere identified in this fermented product.