Molecular monitoring of bacterial community structure in long-aged nukadoko: pickling bed of fermented rice bran dominated by slow-growing lactobacilli

Journal Article

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Journal of bioscience and bioengineering

J.Biosci.Bioeng.

Dec

104

481

489

LR: 20151119; JID: 100888800; 2007/05/28 [received]; 2007/09/18 [accepted]; ppublish

Japan

1389-1723; 1347-4421

PMID: 18215635

eng

Journal Article; IM

10.1263/jbb.104.481 [doi]

Unknown(0)

18215635

Nukadoko is the fermented rice bran bed traditionally used for pickling vegetables in Japan. Here, we investigate the bacterial community structure of nukadoko using several culture-independent methods. Denaturing gradient gel electrophoresis (DGGE) and sequence analysis of V2-V3 16S rRNA gene (16S rDNA) fragments amplified from a long-aged nukadoko bacterial community indicated seven predominant operational taxonomic units (OTUs) closely related to known Lactobacillus species. Phylogenetic analysis of these OTUs indicated a major cluster consisting of six OTUs including a dominant OTU closely related to Lactobacillus acidifarinae and one distinct OTU corresponding to Lactobacillus acetotolerans. L. acetotolerans was commonly detected as a dominant species in samples from different seasons. The succession of microbial community structure in the fermentation and ripening processes was investigated using a laboratory model nukadoko. The L. acidifarinae-like bacteria grew rapidly with a pH decrease in the first few days after inoculation, whereas L. acetotolerans grew slowly and became dominant after one week. Real-time quantitative polymerase chain reaction (Q-PCR) showed that the doubling time of L. acetotolerans was 12 h, while that of total bacteria was 4 h. Real-time quantitative reverse transcription polymerase chain reaction (Q-RT-PCR) targeting 16S rRNA showed a low metabolic activity of L. acetotolerans throughout the fermentation and ripening processes. Fluorescence in situ hybridization (FISH) showed that L. acetotolerans was a dominant bacterium in the ripening period and had a low metabolic activity. These results indicate that the slow-growing L. acetotolerans stably dominated nukadoko microbiota after the L. acidifarinae-like bacteria mainly contributed to the lactic acid fermentation of the rice bran.

Colony Count, Microbial/methods, Fermentation, Lactobacillus/classification/genetics/isolation & purification, Oryza/microbiology, Reverse Transcriptase Polymerase Chain Reaction/methods

Nakayama,J., Hoshiko,H., Fukuda,M., Tanaka,H., Sakamoto,N., Tanaka,S., Ohue,K., Sakai,K., Sonomoto,K.

Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan. nakayama@agr.kyushu-u.ac.jp

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2007