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. 2016 Dec 19;11(12):e0168166.
doi: 10.1371/journal.pone.0168166. eCollection 2016.

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

Lin Yang  1 , Hui-Lin Yang  1 , Zong-Cai Tu  1 , Xiao-Lan Wang  1
Affiliations

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

Lin Yang et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Relative abundance of bacteria at phyla (a) and genus (b) levels during koji making and fermentation.
Fig 2
Fig 2. Heatmap and dendrogram of abundant bacterial (a) and fungal (b) genera present in the microbial community of 10 samples from koji making and fermentation.
The heatmap plot indicates the relative abundance of genera in different samples (variables clustered on the vertical axis). The phylogenetic tree was calculated using the neighbour-joining method. The colour intensity is proportional to the relative abundance of bacterial and fungal genera.
Fig 3
Fig 3. Principal coordinate analysis of microbial communities based on (a) weighted and (b) unweighted UniFrac metrics of samples from koji making and fermentation.
Red and blue symbols represent samples from fermentation and koji making, respectively.
Fig 4
Fig 4. Cluster analysis of the bacterial microbiota in koji making and fermentation based on unweighted UniFrac distances.
Fig 5
Fig 5. Bioplot of redundancy analysis of bacteria in koji making and fermentation.
F represents fermentation and K represents koji making.
Fig 6
Fig 6. Relative abundance of fungi at phyla (a) and genus (b) levels during koji making and fermentation.
Fig 7
Fig 7. Principal coordinate analysis of microbial communities based on (a) weighted and (b) unweighted UniFrac metrics of samples from koji making and fermentation.
Red and blue symbols represent samples from fermentation and koji making, respectively.
Fig 8
Fig 8. Cluster analysis of fungal microbiota in koji making and fermentation based on unweighted UniFrac distances.
See this image and copyright information in PMC

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