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

Nukadoko, a fermented rice bran bed for pickling vegetables called nukazuke, comprises of complex microbiota. Therein, deep interaction between microbiota of the pickled vegetables and nukadoko presents and controls 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 degree centigrade 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 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, transcolonization of any species of bacteria from fresh vegetables to nukadoko was not 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 vegetable 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, the LAB-dominant microbiota were established in both nukadoko and nukazuke in an underlying process different and partly common among vegetables.

糠床（Nukadoko）是用于制作糠渍菜（nukazuke）的发酵米糠基质，其内部包含复杂的微生物群落。腌制蔬菜与糠床的微生物群落之间存在深度互作，这种互作共同调控两者的产品品质。为探究这一科学问题，本研究监测了不同蔬菜腌制过程中糠床与糠渍菜的微生物群落变化。将生米糠或焙炒米糠与盐水混合，于24℃下发酵40天；随后分别以三种蔬菜——黄瓜（Cucumis sativus var. sativus）、结球甘蓝（Brassica oleracea var. capitata）、水萝卜（Raphanus sativus var. hortensis）进行腌制。通过16S rRNA基因扩增子测序技术，对每种蔬菜的新鲜蔬菜清洗液、对应腌制用糠床及成品糠渍菜的微生物群落组成进行分析。尽管糠床的微生物群落组成因腌制蔬菜种类不同而存在差异，但并未观测到新鲜蔬菜中的任何细菌类群向糠床发生跨定殖。然而，部分乳酸菌（LAB）类群最终成为糠渍菜与成熟糠床微生物群落的优势类群，尽管这类群在新鲜蔬菜及米糠中均未被检测到。具体而言，植物乳杆菌（Lactiplantibacillus plantarum）在所有蔬菜组合与成熟糠床的微生物群落中均为优势类群；而部分其他乳酸菌类群的跨定殖则呈现蔬菜种类特异性。木糖葡萄球菌（Staphylococcus xylosus）在所有糠床样本中均有一定程度的检出，但在所有糠渍菜样本中均未被检测到。总体而言，乳酸菌主导的微生物群落在糠床与糠渍菜中均得以形成，其形成过程因蔬菜种类而异，但部分路径存在共性。