Effects of Japanese pepper and red pepper on the microbial community during nukadoko fermentation

Nukadoko is a fermented rice bran bed traditionally used for pickling vegetables in Japan. To date, the production of both homemade and commercial nukadoko has depended on natural fermentation without using starter cultures. Spices, Japanese pepper, and red pepper, are added to nukadoko empirically, but the functions of spices in nukadoko have not been fully elucidated. To investigate the effects of Japanese pepper and red pepper on nukadoko fermentation, we compared the chemical and microbiological changes during 2 months of fermentation of a laboratory model nukadoko with or without spices. The successive pH values and colony counts in the first 10 days showed that the spices promoted lactic acid bacteria (LAB) growth and fermentation in the nukadoko niche. The successive bacterial communities during natural fermentation of nukadoko were carefully monitored by pyrotag 16S rRNA analysis, and the effect of spices on the development and maintenance of the nukadoko microbiota was investigated. It was shown that addition of Japanese peppers and red peppers shortened the pre-lactic acid fermentation phase, during which Staphylococcus saprophyticus grew dominantly, and promoted the development of a microbiota that LAB dominated. Notably, the growth of the dominant LAB, Pediococcus pentosaceus, was improved by adding either Japanese pepper or red pepper. The differences in the LAB species, which were associated with the differences in chemical composition of the nukadoko, were dependent on the type of pepper used. We conclude that the spices used can affect the bacterial community and modulate its metabolic profile in nukadoko.