Analysis of Pickled Cucumber Products, Based on Microbial Diversity and Flavor Substance Detection

Changes to the microbial community during pickled cucumber fermentation were studied using the 16S rDNA technique. The changes of volatile organic compounds (VOCs) during pickled cucumber fermentation were studied by gas chromatograph-ion mobility spectrometry. At the phylum level, Cyanophyta and Proteobacteria were the dominant flora in the natural fermentation group, and Firmicutes were the dominant flora in the added-bacteria fermentation group. At the generic level, the addition of Lactobacillus led to changes in the community of the bacteria in the added-bacterial fermentation group and decreased the species abundance of other bacteria. In total, 75 volatile organic compounds were identified from naturally fermented pickled cucumber, and 60 volatile organic compounds were identified from fermented pickled cucumber with bacterial addition. The main metabolites were esters, aldehydes, acids, alcohols, ketones, alkanes, nitriles, and alkenes. These metabolites will bring their unique aroma components to the pickled cucumber. Metabolomic analysis of the O2PLS model showed that Weissella and Lactobacillus were closely and positively correlated with nine alcohols, six esters, five aldehydes, four acids, three ketones, and one pyrazine. Pseudomonas and norank_f_Mitochondria show a close positive correlation with four kinds of alcohols, two kinds of esters, one kind of aldehyde, and one kind of nitrile.

Exploring potential correlations between bacterial communities, organic acids, and volatile metabolites of traditional fermented sauerkraut collected from different regions of Heilongjiang Province in Northeast China

In this study, the bacterial communities and flavor metabolites of 27 traditional naturally fermented sauerkraut samples collected from nine regions of Heilongjiang Province in Northeast China were investigated. The dominant genera were Lactobacillus, Pseudomonas, Alcaligenes, Arcobacter, Pseudarcobacter, Lactococcus, Comamonas, Pediococcus, Prevotella, and Insolitispirillum. A total of 148 volatile compounds were detected in seven categories; esters and acids were the most abundant volatiles. Additionally, the highest content (15.96 mg/g) of lactic acid was detected in YC1. Acetic acid, oleic acid, palmitic acid, elaidic acid, and dehydroacetic acid were the key differential volatile compounds, which may be related to the bacterial communities. Spearman's correlation analysis revealed that Lactococcus and Lactobacillus were significantly positively correlated with flavor metabolites, suggesting that they may play a more significant role in flavor formation. The results of this study can help in the development of better quality of fermented vegetables.

Diurnal Variation of Epiphytic Microbiota: an Unignorable Factor Affecting the Anaerobic Fermentation Characteristics of Sorghum-Sudangrass Hybrid Silage

Forage epiphytic microbiota exhibits pronounced changes in composition and function throughout the day. However, the effects of these changes on silage fermentation are rarely explored. Here, we transplanted the epiphytic microbiota of sorghum-sudangrass hybrid (SSG) harvested at 7:00 h (AM), 12:00 h (M), and 17:00 h (PM) to sterilized SSG to evaluate the effects of diurnal variation of epiphytic microbiota on fermentation characteristics. During fermentation, remarkable differences in bacterial community successions were observed between silages inoculated with AM and M microbiota. Compared to AM microbiota, M microbiota inoculation increased the proportions of Pantoea dispersa, Leuconostoc lactis, Enterobacter, and Klebsiella variicola, whereas it decreased the proportions of Weissella cibaria and Lactobacillus plantarum during fermentation. This led to the most rapid pH declines and organic acid production in AM silage and the slowest in M silage. Both M and PM microbiota affected the bacterial cooccurrence patterns, indicated by decreased complexity and stability in the community structures of M and PM silages compared to that of AM silage. The predicted functions indicated that some key carbohydrate metabolism pathways related to lactic acid synthesis were downregulated, while some competing pathways (ascorbate and aldarate metabolism and C5-branched dibasic acid metabolism) were upregulated in M silage compared to AM silage after 3 days of fermentation. Correlation analysis revealed positive correlations between competing pathways and enterobacterial species. The current study highlights the importance of diurnal variation of epiphytic microbiota in affecting the silage bacterial community, potentially providing an effective strategy to improve silage quality by optimizing harvest time. IMPORTANCE Ensiling is a way to preserve wet biomass for animal and bioenergy production worldwide. The fermentation quality of silage is largely dependent on the epiphytic microbiota of the material. Plant epiphytic microbiota exhibit diurnal changes in composition and function. However, the effects of these changes on silage fermentation are rarely explored. The results presented here demonstrated that diurnal variation of epiphytic microbiota could affect the fermentation characteristics and bacterial community during SSG fermentation. Marked bacterial community differences were observed between AM and M silages during the initial 3 days of fermentation. The dominance rate of Lactobacillus plantarum was highest in AM silage, whereas enterobacterial species were more abundant in M silage. The predicted function revealed downregulated lactic acid synthesis pathways and upregulated competing pathways in M silage compared to those in AM silage. This study provides clues for technological-parameter optimization of the fermentation process by the selection of harvest time.

The Metabolite Profiling and Microbial Community Dynamics during Pineapple By-Product Fermentation Using Co-Inoculation of Lactic Acid Bacteria and Yeast

Value-added utilization of pineapple waste is very import for the food industry and environmental protection. In this study, whey protein (2.6%, w/w) was added to pineapple waste in order to make up for the protein deficiency of the raw material and give the final products better flavor characteristics. Autochthonous Lactococcus lactis LA5 and Hanseniaspora opuntiae SA2 were used for the co-inoculation of pineapple by-products; during fermentation, the metabolite profiling and microbial community dynamics were investigated. Results showed that the contents of organic acids, total FAAs, total phenolic compounds and flavonoids significantly increased with fermentation, and 152 kinds of peptides were identified in the final products. Relevant analyses demonstrated that dominant strains including Lactococcus lactis, Hanseniaspora and Saccharomyces not only significantly promoted the accumulation of organic acids, total phenols and other active substances, but also inhibited the growth of pathogenic bacteria and further influenced the fermentation process of pineapple waste.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Exploring Core Microbiota Based on Characteristic Flavor Compounds in Different Fermentation Phases of Sufu

Sufu, a Chinese traditional fermented soybean product, has a characteristic foul smell but a pleasant taste. We determined the core functional microbiota and their metabolic mechanisms during sufu fermentation by examining relationships among bacteria, characteristic flavor compounds, and physicochemical factors. Flavor compounds in sufu were detected through headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry, and the microbial community structure was determined through high-throughput 16S rRNA sequencing. The results showed that the fermentation process of sufu could be divided into early and late stages. The early stage was critical for flavor development. Seven microbiota were screened based on their abundance, microbial relevance, and flavor production capacity. Five microbes were screened in the early stage: Pseudomonas, Tetragenococcus, Lysinibacillus, Pantoea, and Burkholderia–Caballeronia–Paraburkholderia. Three microbes were screened in the late stage: Exiguobacterium, Bacillus, and Pseudomonas. Their metabolic profiles were predicted. The results provided a reference for the selection of enriched bacterial genera in the fermentation process and controlling applicable process conditions to improve the flavor of sufu.

Determination of the microbial communities of Guizhou Suantang, a traditional Chinese fermented sour soup, and correlation between the identified microorganisms and volatile compounds

Guizhou Suantang (GZST), a type of sour soup, is a traditional fermented food that can be classified into Hong Suantang (HST) and Bai Suantang (BST). GZST possesses unique flavors arising from various microbiota in fermentation ecosystems. However, the association between these microbiota and flavors remains poorly understood. Accordingly, this study analyzed the volatile components and microbial communities of GZST via headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry and high-throughput 16S rRNA and internal transcribed spacer sequencing techniques. Results showed that 133 compounds, including alcohols, esters, phenols, hydrocarbons, ketones, aldehydes, nitriles, acids, and sulfides, were identified from GZST. Moreover, principal component analysis found significant variances in the composition of volatile compounds among different samples. The bacterial genus level indicated that all GZST samples were dominated by Lactobacillus. At the fungal genus level, BST was dominated by Pichia, Debaryomyces, Mortierella, unclassified, Meyerozyma, and Dipodascus. Meanwhile, HST was dominated by Pichia, Candida, Kazachstania, Debaryomyces, Archaeorhizomyces, and Verticillium. The potential correlations between microbiota and volatile components were also explored through bidirectional orthogonal partial least squares-based correlation analysis. Nine bacterial genera and eight fungal taxa were identified as functional core microbiota for flavor production on the basis of their dominance and functionality in the microbial community. In addition, excessive Lactobacillus inhibited the formation of certain flavor substances. These findings provided basic data for the isolation, screening, and fermentation regulation of functional microorganisms in GZST. The information provided in this study is valuable for the development of effective strategies for selecting beneficial bacterial and fungal strains to improve the quality of GZST.

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

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.

Bacterial diversity and community structure in Chongqing radish paocai brines revealed using PacBio single-molecule real-time sequencing technology

BACKGROUND

Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight 'Yanzhi' (red, RRPB group) and 'Chunbulao' (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in these brines were determined using PacBio single-molecule real-time sequencing of their full-length 16S rRNA genes.

RESULTS

In total, 30 phyla, 218 genera, and 306 species were identified from the RRPB group, with 20 phyla, 261 genera, and 420 species present in the WRPB group. Obvious differences in bacterial profiles between the RRPB and WRPB groups were found, with the bacterial diversity of the WRPB group shown to be greater than that of the RRPB group. This study revealed several characteristics of the bacteria composition, including the predominance of heterofermentative lactic acid bacteria, the species diversity of genus Pseudomonas, and the presence of three opportunistic pathogenic species.

CONCLUSION

This study provides detailed information on the bacterial diversity and community structure of Chongqing radish paocai brine samples, and suggests it may be necessary to analyze paocai brine for potential sources of bacterial contamination and take appropriate measures to exclude any pathogenic species. © 2018 Society of Chemical Industry.