Molecular Monitoring of Bacterial Community Structure in Long-Aged Nukadoko: Pickling Bed of Fermented Rice Bran Dominated by Slow-Growing Lactobacilli

Jiro Nakayama, Hiroyuki Hoshiko, Mizuki Fukuda, Hidetoshi Tanaka, Naoshige Sakamoto, Shigemitsu Tanaka, Kazutoshi Ohue, Kenji Sakai, Kenji Sonomoto

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)481-489
Number of pages9
JournalJournal of Bioscience and Bioengineering
Volume104
Issue number6
DOIs
Publication statusPublished - Dec 1 2007

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Bacterial Structures
Pickling
Lactobacillus
Bacteria
Fermentation
Monitoring
Polymerase chain reaction
Denaturing Gradient Gel Electrophoresis
Microbiota
Vegetables
Transcription
Lactic acid
Ribosomal DNA
Electrophoresis
Fluorescence In Situ Hybridization
rRNA Genes
Reverse Transcription
Sequence Analysis
Real-Time Polymerase Chain Reaction
Lactic Acid

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

Cite this

Molecular Monitoring of Bacterial Community Structure in Long-Aged Nukadoko : Pickling Bed of Fermented Rice Bran Dominated by Slow-Growing Lactobacilli. / Nakayama, Jiro; Hoshiko, Hiroyuki; Fukuda, Mizuki; Tanaka, Hidetoshi; Sakamoto, Naoshige; Tanaka, Shigemitsu; Ohue, Kazutoshi; Sakai, Kenji; Sonomoto, Kenji.

In: Journal of Bioscience and Bioengineering, Vol. 104, No. 6, 01.12.2007, p. 481-489.

Research output: Contribution to journalArticle

Nakayama, Jiro ; Hoshiko, Hiroyuki ; Fukuda, Mizuki ; Tanaka, Hidetoshi ; Sakamoto, Naoshige ; Tanaka, Shigemitsu ; Ohue, Kazutoshi ; Sakai, Kenji ; Sonomoto, Kenji. / Molecular Monitoring of Bacterial Community Structure in Long-Aged Nukadoko : Pickling Bed of Fermented Rice Bran Dominated by Slow-Growing Lactobacilli. In: Journal of Bioscience and Bioengineering. 2007 ; Vol. 104, No. 6. pp. 481-489.
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