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

Abstract

Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.

Microbial community diversity of Jinghong laying hens at peak production based on 16S rRNA sequencing

“…During the recent years, Illumina MiSeq has been widely applied in many fields to investigate several microbial ecosystems and provide a comprehensive insight into microbial community diversity. Furthermore, Illumina MiSeq has the benefit of easy miniaturization and parallelization, which could dramatically decrease the cost of microbial community diversity analysis (Yang et al 2016). Studies integrating the V3-V4 region (Klindworth et al 2013) and longer MiSeq read chemistry may provide a better resolution in microbial diversity and operational taxonomic units (OTU) classification (Ong et al 2013), and consequently, may resolve or validate some of the potential discrepancies between culture-based and culture-independent assessment of the chicken microbiota (Shaufi et al 2015).…”

Variations in Fungal Community and Diversity in Doushen With Different Flavors

“…exogenous microorganisms involved in the fermentation process. Therefore, there is a variety of microorganisms present in the fermented soybean products (Chen et al, 2011;Yang et al, 2016).…”

“…Environmental factors might shape the microbial communities Chen et al, 2012;Chen et al, 2014). Over the last four decades, several studies have analyzed the fungal community of traditional fermented soybean products using culture-dependent or cultureindependent methods Chen et al, 2011;Chen et al, 2012;Nam et al, 2012;Chen et al, 2014;Ji et al, 2014;Yang et al, 2016;Zhang et al, 2018). To date however, no studies have evaluated the microbial community in Doushen.…”

“…This technology circumvents the limitations associated with culture-dependent methods and, consequently, has been widely applied to analyze the microbial diversity in various natural environments such as soil, air, water, plants, and various human microbiota (Arumugam et al, 2011;Fu et al, 2015;Helena et al, 2016;Qin et al, 2016;Kozyaeva et al, 2017). Recently, numerous traditional fermented foods such as douchi (Yang et al, 2016;Zhang et al, 2018), soybean paste (Nam et al, 2012), cheese (Ahram et al, 2018), yogurt (Lisa et al, 2013), Qula , and Pu-er tea (Zhang et al, 2016) have been analyzed using high-throughput sequencing In this study, we used high-throughput sequencing to evaluate the fungal community diversity in Doushen with different flavors obtained from Henan province. Our findings may assist in understanding the complex fungal community structure in Doushen, thereby providing a solid theoretical basis to select appropriate strains suitable for high-quality Doushen.…”

Suitability of various DNA extraction methods for a traditional Chinese paocai system

“…In preliminary experiment, the efficiency of the popular DNA extraction kits including QlAamp Ò DNA Stool Mini Kit 24,25 the E.Z.N.A. Ò Soil DNA Kit, [26][27][28] and FastDNA Ò SPIN Kit (method 4) was investigated, and FastDNA Ò SPIN Kit (method 4), the widely used in DNA extraction from kimchi (a fermented vegetable from Korean), 2,[29][30][31] presented the most efficient performance among these commercial kits. Hence, method 4 was used as a positive control in the present study.…”