Investigation of the microbial changes during koji‐making process of Douchi by culture‐dependent techniques and PCR‐DGGE

Abstract

Douchi as a traditional fermentation soyfood with an acquired taste had been appreciated by consumers for thousands of years in China and few Asian countries. Unfortunately, few studies had been conducted on the changes of microbial community during the koji-making process, and whether the pathogenic microorganisms involving the fermentation process is still unclear. Therefore, the PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S and 18S rRNA genes was applied to characterise the dynamic changes of Bacteria, Bacilli and Fungi during koji-making process. The results of DGGE showed that eleven species of bacteria, nine species of bacilli and seven species of Fungi had been detected during the kojimaking progress, of which the Bacillus subtilis and Aspergillus oryzae belonged to the dominant microorganisms. Also, eleven strains were isolated from Koji-making samples and were identified as B. subtilis, Bacillus amyloliquefaciens, A. oryzae, Brachybacterium sp., Aspergillus niger, Staphylococcus saprophyticus, Micrococcus sp., Staphylococcus gallinarum, Absidia corymbifera, Saccharomyces cerevisiae, Malassezia sp.; Our results revealed that pathogenic microorganisms were involved in the koji-making process, but the probiotic microorganisms occupied the dominant position of community in the koji-making process.

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

“…Diversity indices indicated that the diversity of the bacterial community increased as the koji making stage progressed, consistent with a previous report [25]. However, bacterial diversity then declined during the early stages of fermentation, before gradually recovering.…”

“…Traditional Chinese medicine also uses douchi for treating dyspepsia, restlessness, asthma, and to increase sweating [2,3]. Recent studies indicated that douchi can inhibit prostate and breast cancer [4], and it also displays anti-diabetic activity [5] and protects against osteoporosis and cardiovascular diseases [6].…”

“…Illumina MiSeq has been used to investigate many microbial ecosystems, including milk [17,18], landfill leachate treatment [19], Italian salami [20], gut [21], and cheese [22–24]. Such high-throughput sequencing approaches can provide a more comprehensive insight into microbial community diversity without the bias associated with some of the other techniques [25]. Furthermore, Illumina MiSeq has the benefit of easy miniaturization and parallelization, which dramatically decreases the cost of microbial community diversity analysis.…”

The Effects of Rebaudioside A on Microbial Diversity in Mouse Intestine

“…Total bacteria -ATTACCGCGGCTGCTGG- (Chen et al, 2011a;Chen et al, 2011b;Jeyaram et al, 2008;Wang and Lee, 1997) 518…”

“…During processing, the background was subtracted, differences in the intensity of the lanes were compensated during normalization and the correlation matrix was calculated. Clustering was done with Pearson correlation and the un-weighted pair group method with arithmetic mean (UPGMA) method (Chen et al, 2011a). When analyzing genetic diversity, Richness (S), ShannonWiener indices (H') and Evenness (E) were used according to the following equations (Luo et al, 2004):…”