شناسایی تنوع میکروبی سبزیجات شور تخمیر شده با آب گوجه فرنگی با استفاده از تکنیک نسل جدید توالی یابی

A total of 58 bacteria from three 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 Illumina MiSeq platform. These data were analyzed with BaseSpace software and Greengenes database. The analysis revealed 77.12% Lactobacillus, 7.51% Pediococcus, 5.61% Leuconostoc, 1.20% Acinetobacter, 1.00% Enterobacter, 0.35% Erwinia, 0.35% Dickeya as 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% Leuconostoc mesenteroides and 2.32% Lactobacillus acidifarinae and 17.26% unclassified bacteria were identified. The same identification results were obtained by both phenotypic and Next- 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, Pediococcus and Leuconostoc as dominant flora, were involved in fermentation process. Non-lactic acid bacteria such as Acinetobacter, Enterobacter, Erwinia and Dickeya genera also play important role in fermented pickled vegetable with tomato juice ripening. Moreover, probiotic bacteria such as Lactobacillus plantarum, Lactobacillus pentosus, Leuconostoc mesenteroides and Lactobacillus brevis were identified in this fermented product.