Impact of vegetables on the microbiota of the rice bran pickling bed Nukadoko

Abstract

Nukadoko, a fermented rice bran bed for pickling vegetables called nukazuke, has a complex microbiota. Within it, deep interactions between the microbiota of the pickled vegetables and nukadoko characterize and control the qualities of both products. To address this notion, we monitored the changes in the microbiota of nukadoko and nukazuke while pickling different vegetables. Raw or roasted rice bran was mixed with salted water and fermented at 24°C for 40 days, following which different species of vegetable, Cucumis sativus var. sativus, Brassica oleracea var. capitata, or Raphanus sativus var. hortensis, were pickled. The microbial composition of the washing solution of fresh vegetables, as well as that of the nukadoko and nukazuke for each vegetable, was analyzed by amplicon sequencing of 16S rRNA genes. Although the microbiota of nukadoko varied depending on the species of pickled vegetables, no transcolonization of any species of bacteria from fresh vegetables to nukadoko was observed. However, some lactic acid bacterium (LAB) species eventually dominated the microbiota of both nukazuke and matured nukadoko, although they were not detected in either the fresh vegetables or rice bran. Particularly, Lactiplantibacillus plantarum was dominant among all pairs of pickled vegetables and matured nukadoko, whereas the transcolonization of some other LAB species was observed in a pickled vegetable-specific manner. Staphylococcus xylosus was observed to some extent in each nukadoko, yet it was not detected in any nukazuke. Overall, a LAB-dominant microbiota was established in both nukadoko and nukazuke in an underlying process that was different but partly common among vegetables.