A millet alcoholic beverage that is made primarily from glutinous rice or millet is a traditional drink of indigenous Taiwanese tribes. In this study, we used both culture-dependent and culture-independent methods to analyse the diversity of the lactic acid bacteria (LAB) that are present during the process of millet alcohol fermentation, including during starter preparation and brewing. Based on random amplified polymorphic DNA (RAPD)-PCR fingerprinting profiles, 147 LAB isolates were identified and categorised into 38 groups. Phylogenetic analyses of 16S rRNA, phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA) gene sequences identified representative strains from each of the 38 groups as belonging to the following ten species: Enterococcus faecium group, Lactobacillus brevis, Lactococcus garvieae, Lactococcus lactis, Leuconostoc carnosum, Leuconostoc (Leu.) mesenteroides, Pediococcus pentosaceus, Pediococcus stilesii, Weissella cibaria and Weissella soli. The results of the LAB species diversity studies were confirmed using 16S rRNA gene-based denaturing gradient gel electrophoresis (PCR-DGGE), which showed that P. pentosaceus was mainly involved in the fermentation in both the starter preparation and at the brewing stage. However, L. brevis, Leu. mesenteroides and P. stilesii were the predominant LAB strains found during the brewing stage.
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