Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods

Abstract

Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria (4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion, this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.

Pyrosequencing Analysis of Microbiota inKaburazushi, a Traditional Medieval Sushi in Japan

“…In this study, we analyzed the microbiota of kaburazushi in detail using the 16S rDNA-based pyrosequencing approach. Pyrosequencing is a common technique for clarifying natural fermentation processes [6][7][8][9][10][11][12] or elucidating the influence of a starter inoculation on the ultimate microbial composition. 13,14) The data obtained revealed the microbial dynamics of kaburazushi fermentation and the differences and similarities as between the microbial compositions of medieval and ancient sushi.…”

Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing

“…A number of studies analyzing the microorganisms during vinegar fermentation by culture-dependent methods have been published, providing a partial picture of the microbial community [9,10,26,33]. However, culture-dependent approach is deficient for understanding the microflora comprehensively since the obtained results covered only microorganisms that could be easily cultivated [14]. Novel approaches are still needed to provide a better understanding of the complex microbial communities in the process of vinegar production.…”

“…Compared with culture and nonculture methods mentioned above, the result obtained by pyrosequencing could provide more comprehensive microbial information of the samples. For example, Kim et al [14] applied both pyrosequencing and cultivation-based approaches to explore the bacterial communities in Meju (a Korean traditional fermented soybean brick). The bacterial genera varied from 23 to 561 in different samples using pyrosequencing method, while only 11 genera detected in all samples by cultivation-based approach.…”

Next-generation approaches to the microbial ecology of food fermentations

“…It has been used to study the bacterial diversity of a number of fermented foods, including narezushi (fermented fish and rice) (62,63), nukadoko (fermented rice bran) (64), Chinese liquor fermentations (65), Danish raw milk cheeses (66), Polish Oscypek cheese (66), and pearl millet fermentations (67). It has been remarkably well-utilized for studying Korean fermented foods, including bacteria and archaea of fermented seafood (68), bacterial and fungal communities of Makgeolli (rice beer) (69), meju (70) and doenjang (soybean pastes) (71), kochujang (fermented red pepper condiment) (72), and kimchi (73). It has also been used to study the viral communities inhabiting a range of Korean fermented food products (74).…”