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

• Published in: PloS one Vol. 11; no. 12; p. e0168166
• Main Authors: Yang, Lin, Yang, Hui-Lin, Tu, Zong-Cai, Wang, Xiao-Lan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19-12-2016; Public Library of Science (PLoS)
• Subjects: Actinobacteria; Analysis; Ascomycota; Aspergillus; Bacillus; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacterial genetics; Beans; Biodiversity; Biology and Life Sciences; Communities; Corynebacterium; Deoxyribonucleic acid; DNA; DNA sequencing; Ecology and Environmental Sciences; Enzymes; Fermentation; Fermented food; Firmicutes; Food Microbiology; Food production; Food science; Fungi; Fungi - classification; Fungi - genetics; Fungi - isolation & purification; Genera; High-Throughput Nucleotide Sequencing - methods; Koji; Lichtheimia; Medicine and Health Sciences; Microbiomes; Microbiota; Microorganisms; Multivariate analysis; Next-generation sequencing; Phylogeny; Physiological aspects; Polymerase chain reaction; Principal Component Analysis; Probiotics; Protein sources; Proteobacteria; Redundancy; Research and Analysis Methods; RNA, Ribosomal, 16S - analysis; rRNA 16S; Separation; Sequence Analysis, RNA - methods; Soybeans; Spacer; Staphylococcus; Studies; Variance analysis; Weissella; Zygomycota; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0168166

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.