Koji-making is a key process for production of high quality soy sauce. The microbial composition during
koji-making was investigated by culture-dependent and culture-independent methods to determine
predominant bacterial and fungal populations. The culture-dependent methods used were direct culture
and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by
sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone
libraries. There were differences between the results obtained by different methods. However, sufficient
overlap existed between the different methods to identify potentially significant microbial groups. 16 and
20 different bacterial species were identified using culture-dependent and culture-independent
methods, respectively. 7 species could be identified by both methods. The most predominant bacterial
genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culturedependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition duringsoy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product.