Monitoring of the microbiota profile in nukadoko, a naturally fermented rice bran bed for pickling vegetables.

Nukadoko is a fermented rice bran mash traditionally used for pickling vegetables in Japan. To date, the production of both homemade and commercial nukadoko depends on natural fermentation without using starter cultures. Here, we monitored chemical and microbiological changes in the initial batch fermentation of nukadoko. Nukadoko samples were prepared by spontaneous fermentation of four different brands of rice bran, and microbiome dynamics were analyzed for 2 months. In the first week, non-Lactobacillales lactic acid bacteria (LAB) species, which differed among the samples, grew proportionally to pH decrease and lactate increase. Thereafter, Lactobacillus plantarum started growing and consumed residual sugars, causing further lactate increase in nukadoko. Finally, microbial communities in all tested nukadoko samples were dominated by L. plantarum. Taken together, our results suggest that the mixture of the fast-growing LAB species and slow-growing L. plantarum may be used as a suitable starter culture to promote the initial fermentation of nukadoko.