Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing

Cheonggukjang is a traditional fermented soybean food product manufactured using steamed soybeans and natural starter microorganisms originating from jip (dried rice straws). The nutritional accessibility of cheonggukjang is largely improved by microbial reaction but our knowledge about the microorganisms in cheonggukjang is still limited. Therefore, in the current study, bacterial communities of eight local and one commercial brand of cheonggukjang were analyzed with two molecular analysis methods, barcoded pyrosequencing and denaturant gradient gel electrophoresis (DGGE). After analyzing 12,697 bacterial pyrosequences, we found that almost all the bacteria were members of the phylum Firmicutes (>95%), with only a small portion belonging to Proteobacteria (<5%). Among the 79 identified bacterial species, Bacillus species were the dominant type, but, contrary to previous reports, the levels of Bacillus subtilis (1.1–45.2%), Bacillus licheniformis (3.2–33.6%) and Bacillus amyloliquefaciens (0.2–9.2%) varied between samples and were not even the dominant microbes in some samples. In various samples, specific unclassified Bacillus species and Lactic acid bacteria existed as the dominant microbes of cheonggukjang. Compared to pyrosequencing analysis, DGGE method only revealed some of the major bacterial species such as Bacillus thermoamylovorans and B. licheniformis, and could not detect a large number of predominant or diverse rare bacterial species identified in pyrosequencing analysis. Community comparison analysis of both two molecular methods suggested cheonggukjang samples collected from similar regions exhibited a similar bacterial composition, but the regional differences of bacterial community were more clearly represented in pyrosequencing method than DGGE analysis.