Fast evaluation by quantitative PCR of microbial diversity and safety of Chinese Paocai inoculated with Lactobacillus plantarum NCU116 as the culture starter

A rapid and reliable method for the determination of Lactiplantibacillus plantarum during wine fermentation based on PMA-CELL-qPCR

Real-time monitoring of microbial dynamics during fermentation is essential for wine quality control. This study developed a method that combines the fluorescent dye propidium monoazide (PMA) with CELL-qPCR, which can distinguish between dead and live microbes for Lactiplantibacillus plantarum. This method could detect the quantity of microbes efficiently and rapidly without DNA extraction during wine fermentation. The results showed that (1) the PMA-CELL-qPCR enumeration method developed for L. plantarum was optimized for PMA treatment concentration, PMA detection sensitivity and multiple conditions of sample pretreatment in wine environment, and the optimized method can accurately quantify 10⁴-10⁸ CFU/mL of the target strain (L. plantarum) in multiple matrices; (2) when the concentration of dead bacteria in the system is 10⁴ times higher than the concentration of live bacteria, there is an error of 0.5-1 lg CFU/mL in the detection results. The optimized sample pretreatment method in wine can effectively reduce the inhibitory components in the qPCR reaction system; (3) the optimized PMA-CELL-qPCR method was used to monitor the dynamic changes of L. plantarum during the fermentation of Cabernet Sauvignon wine, and the results were consistent with the plate counting method. In conclusion, the live bacteria quantification method developed in this study for PMA-CELL-qPCR in L. plantarum wines is accurate in quantification and simple in operation, and can be used as a means to accurately monitor microbial dynamics in wine and other fruit wines.

Effect of Levilactobacillus brevis as a starter on the flavor quality of radish paocai

The aim of this study was to investigate the effectiveness of Levilactobacillus brevis on the fermentation kinetics and flavor quality of radish paocai. Compared with spontaneous fermentation (SF), the radish paocai of inoculated fermentation (IF) using Levilactobacillus brevis PL6-1 as a starter could rapidly utilize sugar to produce acid, thus accelerating the fermentation process. The texture including hardness, chewiness, and springiness of the IF were all higher than that of the SF, and the IF paocai showed higher L value in color. L. brevis PL6-1 as a starter could increase the final levels of metabolites of mannitol (5.43 mg/g), lactic acid (543.44 mg/100 g) and acetic acid (87.79 mg/100 g). Fifteen volatile organic compounds (VOCs) were identified as key aroma-active compounds in radish paocai and 8 differential VOCs were considered as the potential markers. L. brevis PL6-1 could improve the levels of 1,8-cineole, 1-hexanol, hexanoic acid, 2-methoxy-4-vinylphenol, and eugenol, giving the radish paocai floral, sweet, and sour aroma, and reduce the unpleasant odor of garlic, onion, and pungent, contributed by erucin, diallyl disulfide, and allyl trisulfide. Sensory evaluation results showed that the appearance, taste, texture, and overall acceptability of IF paocai were all better than the SF group. Therefore, L. brevis PL6-1 could be a potential starter to improve the flavor and sensory quality for radish paocai fermentation.

Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.

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.

Natural Environmental Variation Determines Microbial Diversity Patterns in Serofluid Dish, a Traditional Chinese Fermented Vegetable Food

Serofluid dish is a traditional fermented food that contains rich microbial populations. To gain insight into the environmental variables shaping the microbial diversity patterns, serofluid dish samples were collected from different areas, and 16S rRNA sequencing was performed. Analyses revealed both species and community diversity, including phylotype richness, Shannon index and phylogenetic diversity, were mostly influenced by pH. Additionally, such effects were corroborated by the Mantel test of pairwise UniFrac distances and variable selection of multiple linear regression models. Eventually, correlations between dominant lineages and the pH of serofluid dish other than geographical distance explained a large portion of the changes in microbial composition and diversity. Lactobacillus and related genera, Pediococcus and Acetobacter were largely driven by the variability of pH, and higher richness was observed under moderate pH ranges. Collectively, the results demonstrated that a microbial diversity pattern in serofluid dish is predictable by natural environmental variation and can be better understood through pH conditions.

Dynamics of microbial communities, flavor, and physicochemical properties of pickled chayote during an industrial-scale natural fermentation: Correlation between microorganisms and metabolites

Pickled chayote is a Chinese fermented vegetable with unique flavors and is favored by local consumers. However, little is known about its quality changes and microbial community succession during fermentation and the relationship between microbes and quality. In the work, the physicochemical quality attributes (pH, acidity, nitrite, texture, and color) and flavor properties (sugars, organic acids, free amino acid [FAA], and volatiles) were investigated. The results revealed that organic acids, FAAs, and key volatiles (esters, terpenes, alcohols, and phenols) significantly increased during fermentation. Lactobacillus was the dominant bacterial genus with Lactobacillus alimentarius being the prevalent species; Kazachstania and Pichia were dominant fungal genera with Kazachstania humilis and Pichia membranifaciens being the prevalent species. The microbial metabolic network found that bacteria (L. alimentarius, L. futsaii, and L. paralimentarius) and fungi (K. humilis and P. membranifaciens) played significant roles in the physicochemical changes and flavor production of pickled chayote.

Microbial composition and correlation between microbiota and quality-related physiochemical characteristics in chongqing radish paocai

Chongqing radish paocai (paocai) is produced by fermentation of fresh vegetables. It gained attention for its non-negligible contribution in Sichuan cuisine and potential health benefits. This study explored microbial structures in six home-made paocai using high through-put sequencing. Key microbial communities were identified based on significant correlations with quality-related physiochemical attributes. Results suggest bacterial diversity level significantly decreased during fermentation, while fungal diversity level were inconsistent across different alpha-diversity indexes. Firmicutes and Proteobacteria were the predominant bacterial phylum in all samples. Lactic acid bacteria, namely Lactobacillus and L. plantarum were the predominant bacteria at genus and species levels. Fungi had overall weak correlations with physiochemical attributes, several bacterial species significantly correlated with physiochemical attributes, including Lactobacillus plantarum, Lactobacillus acetotolerans, and Weissella cibaria. Overall, this study identified key microbial communities and discussed their functional roles that could contribute to consistent production of high-quality Chongqing radish paocai.

Improving the quality of Suancai by inoculating with Lactobacillus plantarum and Pediococcus pentosaceus

The quality characteristics of Suancai fermented with Lactobacillus plantarum CGMCC No.20193 (Lb. plantarum) and Pediococcus pentosaceus CGMCC No. 20192 (P. pentosaceus) were investigated. Their inoculation affected the bacterial communities revealed by Pacbio Sequel platform. After fermentation, the dominant phylum and genus in inoculation and spontaneous fermented Suancai were Firmicutes and Lactobacillus. Compared with single inoculation, the co-inoculation of Lb. plantarum and P. pentosaceus had a higher bacterial diversity. The Suancai co-inoculated with Lb. plantarum and P. pentosaceus had a more similar VCs profile with spontaneous fermented Suancai. The inoculation of Lb. plantarum and P. pentosaceus increased the content of organic acids, such as lactate, acetate, citrate, succinate, malate and tartrate. The most amino acids content in Suancai fermented with Lb. plantarum and P. pentosaceus were higher than that in spontaneous fermented Suancai. Compared single inoculation, the Suancai co-inoculated with Lb. plantarum and P. pentosaceus had a higher similarity of organoleptic tastes with spontaneous fermented Suancai. These results may facilitate the understanding of the starters' effects on the Suancai fermentation and the selection of applicable starters to manipulate the flavor.

Culture-independent analysis of the bacterial community in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial community using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from 6 samples. Firmicutes and Proteobacteria were the main phyla in all of the samples. Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated clear differences were there between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole-genome analysis of Levilactobacillus suantsaii, Latilactobacillus sakei subsp. sakei, and Weissella cibaria showed that they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

Purification of Crude Fructo-Oligosaccharide Preparations Using Probiotic Bacteria for the Selective Fermentation of Monosaccharide Byproducts

Probiotics are microbes that promote health when consumed in sufficient amounts. They are present in many fermented foods or can be provided directly as supplements. Probiotics utilize non-digestible prebiotic oligosaccharides for growth in the intestinal tract, contributing to a healthy microbiome. The oligosaccharides favored by probiotics are species-dependent, as shown by the selective utilization of substrates in mixed sugar solutions such as crude fructo-oligosaccharides (FOS). Enzymatically produced crude FOS preparations contain abundant monosaccharide byproducts, residual sucrose, and FOS varying in chain length. Here we investigated the metabolic profiles of four probiotic bacteria during the batch fermentation of crude FOS under controlled conditions. We found that Bacillus subtilis rapidly utilized most of the monosaccharides but little sucrose or FOS. We therefore tested the feasibility of a microbial fed-batch fermentation process for the purification of FOS from crude preparations, which increased the purity of FOS from 59.2 to 82.5% with a final concentration of 140 g·l-1. We also tested cell immobilization in alginate beads as a means to remove monosaccharides from crude FOS. This encapsulation concept establishes the basis for new synbiotic formulations that combine probiotic microbes and prebiotic oligosaccharides.

Stability of potential prophages in commercial strain Lactobacillus plantarum NCU116 under various stressors

Genetic stability of bacterium as a starter culture is vital for product quality in fermentation industry. The commercial strain Lactobacillus plantarum NCU116 widely used in fruit and vegetable fermentation was induced with various stressors to investigate the stability of potential prophages. PHAge Search Tool (PHAST) identified three potential prophages in bacterial genome. By spectrophotometric analysis, mitomycin C (MMC), lactic acid, and bile salt were found to inhibit the growth of L. plantarum NCU116 while ethanol and hydrogen peroxide had no notable impacts. Transcriptions of four phage-synthesizing genes (phaR, phacap, phaada, phatail) and four phage-resistant genes (cas116, helR, hsd1, hsd2) under stressors were investigated by quantitative reverse transcription PCR. MMC was found to most significantly upregulated transcriptions of phage-synthesizing genes, followed by lactic acid and bile salt. By transmission electron microscopy, no virus particles from the lysates of strain NCU116 treated by MMC were observed, corresponding to the result that no phage nucleic acids could be extracted from the supernatants of strain NCU116 treated by MMC. This study suggested that no prophages could be induced from L. plantarum NCU116 by strong inducer MMC, indicating its genetic stability, which supports the comprehensive application of strain NCU116 in industry without causing fermentation failure.

Removal of Small-Molecular Byproducts from Crude Fructo-Oligosaccharide Preparations by Fermentation Using the Endospore-Forming Probiotic Bacillus coagulans

Short-chain prebiotic fructo-oligosaccharides (FOS) produced by enzymatic conversion from sucrose often contains high concentration of monosaccharides as byproducts. In addition to conventional physical/chemical purification processes, microbial treatment is an alternative method to remove these byproducts. We used Bacillus coagulans to reduce the abundance of byproducts during the enzymatic production of FOS. It is a promising probiotic because this thermophilic and spore-forming bacterium remains viable and stable during food processing and storage. B. coagulans also produces lactic acid during the carbohydrate metabolism and is used industrially to produce lactic acid for medical and food/feed applications. We aimed to establish an evaluation system to screen different strains of B. coagulans for their performance and selected B. coagulans Thorne for the treatment of crude FOS due to its high growth rate, high sporulation rate, and low nutrient requirements. B. coagulans preferentially utilized monosaccharides over other sugar components of the FOS mixture. Glucose and fructose were completely consumed during the fermentation but 85% (w/w) of the total FOS remained. At the end of the fermentation, the total viable cell count of B. coagulans Thorne was 9.9 × 108 cfu·mL−1 and the maximum endospore count was 2.42 × 104 cfu·mL−1.

A comparative study of the effects of microbial agents and anaerobic sludge on microalgal biotransformation into organic fertilizer

The effects of Lactobacillus bulgaricus, Rhodopseudomonas palustris, Issatchenkia orientalis and anaerobic sludge on anaerobic digestion of microalgae to organic fertilizer were studied. High-throughput sequencing was used to analyze characteristics of microbial community structure during anaerobic digestion of microalgae using different inocula. Lactobacillales and Saccharomycetales were more likely to become dominant bacteria and eukaryotes. The relative abundance of Lactobacillales was 98.15%, 88.61% and 81.73% of total bacteria at the beginning, middle and end of the experiment, respectively. Meanwhile, the relative abundance of Saccharomycetales was 90.91%, 98.41% and 98.8% of eukaryotes at the beginning, middle and end of the experiment, respectively. At the end of digestion, the microcystin content in the reactor inoculated with Issatchenkia orientalis decreased to 0.71 μg/kg, which met drinking water standards. Rhodopseudomonas palustris did not become a dominant microorganism and had the most negative impact on the atmosphere. Volatile organic compounds were 11.92 mg/kg while the odor concentration reached 97,724 ou/m³. The organic matter content in reactors inoculated with specific groups of microbial agents, which was higher than the standard required for bio-organic fertilizer, occupying over 96% dry weight. In addition, the effective microorganism counts of Issatchenkia orientalis and Lactobacillus bulgaricus in fermentation products reached 1.8E+09 colony-forming units (cfu)/g and 1.6E+09 cfu/g, respectively, which are suitable values for microbial fertilizer.