Dynamic and Functional Characteristics of Predominant Species in Industrial Paocai as Revealed by Combined DGGE and Metagenomic Sequencing

Abstract

The microbial community during the fermentation of industrial paocai, a lactic acid fermented vegetable food, was investigated via combined denaturing gradient gel electrophoresis (DGGE) and metagenomic sequencing. Firmicutes and Proteobacteria were identified as the dominant phyla during the fermentation. DGGE results of the bacterial community analysis showed that many genera were observed during the fermentation of industrial paocai, but the same predominant genus and species were observed: Lactobacillus and Lactobacillus (L.) alimentarius/L. paralimentarius. The abundance of L. alimentarius/L. paralimentarius increased fast during the initial stage of fermentation and approximately remained constant during the later stage. Metagenomic sequencing was used to finally identify the predominant species and their genetic functions. Metabolism was the primary functions of the microbial community in industrial paocai fermentation, including carbohydrate metabolism (CM), overview (OV), amino acid metabolism (AAM), nucleotide metabolism (NM), energy metabolism (EM), etc. The predominant species L. alimentarius and L. paralimentarius were involved in plenty of pathways in metabolism and played different roles in the metabolism of carbohydrate, amino acid, lipid to form flavor compounds during industrial paocai fermentation. This study provided valuable information about the predominant species in industrial paocai and its functional properties, which could enable us to advance our understanding of the fermentation mechanism during fermentation of industrial paocai. Our results will advance the understanding of the microbial roles in the industrial paocai fermentation and provide a theoretical basis for improving the quality of industrial paocai products.

Keywords: DGGE; dominant species; functional characteristics; industrial paocai; metagenomic sequencing.

FIGURE 1

Changes in pH, total titratable acidity (TTA), salinity, and nitrite during industrial paocai fermentation. Panels (A,B) represent industrial ZP and QP, respectively.

FIGURE 2

DGGE profile of microbiota from microbial DNA extracted from industrial ZP (A) and QP (B) samples collected over fermentation process. The denaturing gradient was 30–55%. The bands indicated by the arrows and numbers were sequenced and the alignment results are listed in Table 1.

FIGURE 3

Microbial distributions in industrial paocai during fermentation. Panels (A–F) represent the heatmaps of bacterial community in industrial ZP (QP) at phylum, genus, and species level.

FIGURE 4

PCA of bacterial distribution in the industrial ZP and QP during fermentation based on the DGGE data of bacterial community. Samples are displayed by circles. The directions of the curved arrows indicate the routes of data points on the score plots during fermentation. The elliptical area represents 95% confidence intervals.

FIGURE 5

Taxonomy of the microbial community in matured industrial ZP and QP using metagenomic sequencing. The phylum with abundance ≥0.1% (A) and the genus with abundance ≥0.1% (B) in at least one sample were presented. Only the species affiliated with Lactobacillus with abundance ≥0.5% (C) in at least one sample was presented. L, Lactobacillus.

FIGURE 6

Gene functional annotation (A) of microbial community, KEGG pathways of metabolism (B), and functional roles of L. alimentarius and L. paralimentarius in metabolism (C) in industrial ZP and QP. (C) The pathways with abundance ≥0.1% in at least one sample were presented. The black box represented genes encoding related enzymes in the pathway were detected while white box represented not. LA, L. alimentarius and LPA, L. paralimentarius.