Differences in the microbiome composition of the traditional fermented rice beverage Miki from Amami Island

Abstract

Miki, a traditional fermented rice beverage from Amami Oshima, Japan, is produced by spontaneous fermentation of porridge after saccharification using amylase of raw mashed sweet potatoes. Considering the health benefits of endogenous lactic acid bacteria (LAB) and the lack of comprehensive information on Miki, the microbiota characteristics and diversity of Miki were examined. In total, 15 products from four factories in Amami Oshima and one product each from two other regions were subjected to both culture-dependent and 16S rDNA (V4) amplicon sequencing analyses. The total, LAB, and yeast viable counts were 6.9–9.2, 6.8–9.2, and 2.0–5.8 log CFU/g, respectively. The Leuconostoccaceae family was present in all Miki products. In samples from two Amami factories, Leuconostoc and Lactococcus were the dominant LABs. Streptococcus and Bacillus were the dominant genera in samples from one Amami factory, while Geobacillus and Anoxybacillus were the dominant genera in samples from the fourth Amami factory. In samples from other regions, lactobacilli were dominant. Among the 14 typical LAB isolates obtained from the agar plate used to determine viable counts, 10 were identified as Leuconostoc lactis. Other isolates were identified as Leuconostoc holzapfelii, Lactoccus raffinolactis, Streptococcus thermophilus, and Limosilactobacillus fermentum. Saccharomyces cerevisiae and Candida lusitaniae isolated as typical yeasts. Geobacillus stearothermophilus and Anoxybacillus sp. were isolated from samples incubated at 60 °C. Differences in the microbiota composition of different processors are attributed to different microorganisms from each factory and the application of heat processing.