Identification of Microbial Profile of Koji Using Single Molecule, Real‐Time Sequencing Technology

Abstract

Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively. At the genus level, Ochrobactrum and Wickerhamomyces were the most abundant bacterial and fungal genera, respectively. The predominant bacterial and fungal species were Ochrobactrum lupini and Wickerhamomyces anomalus, respectively. Our study profiled the microbiota composition of 3 Japanese koji samples to the species level precision. The results may be useful for further development of traditional fermented products, especially optimization of koji preparation. Meanwhile, this study has demonstrated that SMRT is a robust tool for analyzing the microbial composition in food samples.

Fermentation and the microbial community of Japanese koji and miso: A review

“…SMRT technology sequences individual unamplified molecules in real time (Roberts et al., 2013). Testing of three samples of rice koji purchased from Japanese supermarkets found a diverse range of microorganisms (Hui et al., 2017). The predominant bacterial and fungal species found in the samples had a very high relative abundance, averaging over 93% of the microorganisms identified in the samples.…”

“…The microbial community of koji and miso during fermentation is considered essential to the development of its unique flavor, texture, and nutritional profile (Hui et al., 2017; Onda, Yanagida, Uchimura, et al., 2003). Despite the importance of microorganisms in the production of miso , limited research is documented characterizing such microbial populations and processes.…”

Microbiota in milk from healthy and mastitis cows varies greatly in diversity, species richness and composition, as revealed by PacBio sequencing

“…Furthermore, changes in susceptibility to mastitis might be coupled with changes in community composition of the milk microbiota, such as increases in B. dorei and La. lactis (Xu et al, 2017).…”

“…Third-generation sequencing technology, such as the PacBio single-molecule real-time (SMRT) sequencing platform, is increasingly being used to characterize the microbiota of environmental samples (e.g. dairy products (Hui et al, 2017), milk (Hou et al, 2015) and food (Nakano et al, 2016) etc. In contrast to the older sequencing technologies, PacBio SMRT sequencing is high throughput and produces long reads capable of microbial identification to species level when used in conjunction with polymerase chain reaction (PCR) of full-length 16S rRNA genes (Mosher et al, 2014).…”

Community structure and metabolic potentials for biofuel production of an ancient beer starter ‘emao' revealed by a whole-metagenome study

“…Usually, 3-5 herbs are used in emao preparation, sometimes alternatively based on availability at the time of its preparation. Researchers studied the microbial diversity on several such traditional starters across the world using both culture-dependent [10][11][12][13][14][15][16] and culture-independent methods [14,[17][18][19][20][21][22][23]. Nonetheless, the microbial study on emao is limited, and only four fungal species (one mould and three non-Saccharomyces yeasts) have been reported to date using culture-dependent methods .…”