Characterization of the dominant bacterial communities of traditional fermentation starters for Hong Qu glutinous rice wine by means of MALDI-TOF mass spectrometry fingerprinting, 16S rRNA gene sequencing and species-specific PCRs

Abstract

The main goal of this work was to investigate the bacterial flora present in the traditional fermentation starters using matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometry fingerprinting combined with 16S rRNA gene sequencing and species-specific PCRs. A total of 1314 bacterial strains were obtained from ten kinds of representative wine fermentation starters (5 Hong Qu and 5 Yao Qu) and classified by MALDI-TOF mass spectrometry. Sixteen different bacterial species belonging to six different genera (Bacillus, Staphylococcus, Leuconostoc, Pediococcus, Lactobacillus and Lactococcus) were identified with high accuracy by comparing them with generated spectra of MALDI Biotyper database. Comparison of 16S rRNA gene phylogeny and MALDI-TOF mass spectrometry analysis showed that MALDI-TOF mass spectrometry fingerprinting was a good complementary approach to 16S rRNA sequencing and even a more powerful tool in the accurate differentiation and classification of Bacillus species, especially for differentiating between Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus methylotrophicus. MALDI-TOF mass spectrometry was also found to provide valuable information at species levels for the genus of Lactobacillus. The identification revealed that most strains isolated from traditional fermentation starters were B. amyloliquefaciens (31.81%), followed by Bacillus megaterium (16.89%), Lc. lactis subsp. lactis (8.60%) and B. subtilis (8.14%). In the culture-dependent quantitative analysis, 69.01% of the detected isolates were Bacillus species, and 30.44% of the detected isolates belonged to the class of lactic acid bacteria (LAB), including Leu. mesenteroides, Pediococcus pentosaceus, Lactobacillus plantarum, Lactobacillus paracasei, Lactobacillus brevis, Pediococcus acidilactici, Lactobacillus coryniformis and Lc. lactis subsp. lactis. This study provides detailed evaluation of bacterial communities in the traditional fermentation starters for Hong Qu glutinous rice wine using a fast and cost-effective technique—MALDI-TOF mass spectrometry fingerprinting. Information provided by this study is fundamental and useful to develop effective strategies for the selection of beneficial bacterial strains and improve of quality of Hong Qu glutinous rice wine.