High-throughput sequencing and culture-based approaches to analyze microbial diversity associated with chemical changes in naturally fermented tofu whey, a traditional Chinese tofu-coagulant

Characterization and correlations of dominant microorganisms and volatile compounds in fermentation process of Yangjiang douchi

BACKGROUND

Yangjiang douchi (YD) is a traditional fermented soybean product, which is popular in Chinese cuisine for its unique flavor. However, due to its high salt content and unstable flavor, its competitiveness in the international market is gradually weakening. Microorganisms have a key role in the production process of YD because it is a fermented food but the effect of microorganisms on the volatile compounds of YD is also not currently clear.

RESULTS

In this paper, aroma compounds and microbial diversity in different fermentation stages of YD were analyzed using gas chromatography-mass spectrometry/olfactometry (GC-MS/O) and IlluminaMiseq system sequencing. A total of 78 aroma-active compounds were detected throughout the fermentation process and they influenced the formation of flavor in YD. Fungi flora were relatively single in YD, and bacteria were rich and varied. A total of 418 species of bacteria were present during fermentation, with unclassified_Staphylococcus, Staphylococcus_kloosii, and Bacillus_velezensis_Bacillus predominating. There were 25 species of fungi at the species level, and Aspergillus minisclerotigenes (OTU 4) played a dominant role in the whole fermentation process.

CONCLUSION

Staphylococcus and Bacillus in the bacterial genus were strongly correlated with most flavor compounds detected, and A. minisclerotigenes in the fungi were more relevant to flavor compounds. This research provides a theoretical basis for the enhancement of the flavor of traditional fermented douchi in China. © 2024 Society of Chemical Industry.

Soybean fermentation: Microbial ecology and starter culture technology

Fermented soybean products, including Soya sauce, Tempeh, Miso, and Natto have been consumed for decades, mainly in Asian countries. Beans are processed using either solid-state fermentation, submerged fermentation, or a sequential of both methods. Traditional ways are still used to conduct the fermentation processes, which, depending on the fermented products, might take a few days or even years to complete. Diverse microorganisms were detected during fermentation in various processes with Bacillus species or filamentous fungi being the two main dominant functional groups. Microbial activities were essential to increase the bean's digestibility, nutritional value, and sensory quality, as well as lower its antinutritive factors. The scientific understanding of fermentation microbial communities, their enzymes, and their metabolic activities, however, still requires further development. The use of a starter culture is crucial, to control the fermentation process and ensure product consistency. A broad understanding of the spontaneous fermentation ecology, biochemistry, and the current starter culture technology is essential to facilitate further improvement and meet the needs of the current extending and sustainable economy. This review covers what is currently known about these aspects and reveals the limited available information, along with the possible directions for future starter culture design in soybean fermentation.

Enhancement of the organic acid content and antioxidant capacity of yellow whey through fermentation with Lacticaseibacillus casei YQ336

Fermentation is considered an effective tool for improving the functional characteristics of food. In this study, Lacticaseibacillus casei YQ336 was used to ferment yellow whey, and physical and chemical analysis was performed to identify the changes in the nutritional components and antioxidant activity of the fermented yellow whey. Non-targeted metabolomics was used to study the transformation of small molecular substances in the fermented yellow whey. After 48 h of pure culture fermentation with L. casei YQ336, the pH of yellow whey decreased significantly (p < 0.05). Meanwhile, the content of total acids, organic acids, sugars, total phenols, and total flavonoids and the antioxidant activity showed a significant increase (p < 0.05). A total of 628 differential metabolites were identified between fermented and unfermented yellow whey samples, of which 293 were upregulated and 335 were downregulated. After fermentation, due to the growth and metabolic activity of L. casei YQ336, meaningful metabolites such as homovanillic acid, lactic acid, oxalic acid, L-glutamic acid, and phenylalanine, as well as phenyllactic acid, gallic acid, and genistein were produced. This increased the organic acid content and antioxidant activity of yellow whey. The findings provide a theoretical and practical basis for further research on the bio-functional activity of yellow whey and the recycling and utilization of food by-products.

Diversifying the Flavor of Black Rice Wines through Three Different Regional Xiaoqus in China and Unraveling Their Core Functional Microorganisms

The flavor of black rice wine (BRW) can be diversified by the Xiaoqus, from different regions; however, the functional microbiota that contributes to its flavor remains unclear. Accordingly, this study selected three regional Xiaoqus from Sichuan Dazhu (Q1), Jiangxi Yingtan (Q2), and Hubei Fangxian (Q3) as starters to investigate flavor compounds and microbial communities during BRW brewing. Results indicated that altogether 61 flavor substances were identified, 16 of which were common characteristic flavor compounds (odor activity value > 0.1). Each BRW possessed unique characteristic flavor compounds. O2PLS and Spearman's correlation analysis determined that characteristic flavor compounds of BRW were mainly produced by Saccharomyces cerevisiae, non-Saccharomyces yeasts, and lactic acid bacteria, with the common core functional strains being Wickerhamomyces and Pediococcus, and with their unique core functional strain likely causing a unique characteristic flavor. This study could promote the high-quality development of the black rice wine industry.

Lacticaseibacillus rhamnosus C1 effectively inhibits Penicillium roqueforti: Effects of antimycotic culture supernatant on toxin synthesis and corresponding gene expression

Recently, consumers are increasingly concerned about the contamination of food by molds and the addition of chemical preservatives. As natural and beneficial bacteria, probiotics are a prospective alternative in food conservation because of their antimycotic activities, although the mechanism has not been explained fully at the level of metabolites. This study aimed at investigating the antifungal activities and their mechanisms of five potential probiotic strains (Lacticaseibacillus rhamnosus C1, Lacticaseibacillus casei M8, Lactobacillus amylolyticus L6, Schleiferilactobacillus harbinensis M1, and Limosilactobacillus fermentum M4) against Penicillium roqueforti, the common type of mold growth on the bread. Results showed that C1 emerged the strongest effectiveness at blocking mycelium growth, damaging the morphology of hyphae and microconidia, decreasing DNA content and interfering in the synthesis of the fungal toxins patulin, roquefortine C and PR-toxin, as well as downregulating the expression of key genes associated with the toxin biosynthesis pathways. Further metabonomic investigation revealed that protocatechuic acid with the minimum inhibitory concentration of 0.40 mg/mL, may be most likely responsible for positively correlated with the antimycotic effects of C1. Thus, C1 is expected to be both a potentially greatly efficient and environmental antimycotic for controlling P. roqueforti contamination in foods.

Tofu Whey Wastewater as a Beneficial Supplement to Poultry Farming: Improving Production Performance and Protecting against Salmonella Infection

Tofu whey wastewater (TWW) is a by-product of the tofu production process, and contains high amounts of organic products and Lactobacillus ap. However, no studies have been reported on whether naturally fermented TWW can be used as a beneficial additive for poultry production. This study analyzed the main nutritional components and microbial flora of naturally fermented TWW from rural tofu processing plants and their effect on chick production performance, role in modulating the biochemical and immune parameters, and protection against Salmonella enteritidis (S. enteritidis) infection. It was observed that the average pH of TWW was 4.08; therefore, the total viable count was 3.00 × 10⁹ CFU/mL and the abundance of Lactobacillus was 92.50%. Moreover, TWW supplementation increased the total weight gain and feed intake, reduced the feed/gain ratio, increased the length and relative weight of the gut, and reduced the colonization and excretion of S. enteritidis in chickens. Additionally, TWW decreased oxidative damage and pro-inflammatory cytokine secretion caused by S. enteritidis infection. In addition, TWW supplementation ensured the structure of the intestine remained relatively intact in S. enteritidis-infected chicken. Furthermore, TWW markedly promoted the intestinal barrier integrity and up-regulated the relative abundance of Lactobacillus, counteracting the changes in gut microbiota caused by S. enteritidis infection in chicken. In conclusion, our data demonstrated that TWW could be used as a beneficial addition to poultry production, providing a research basis for the further development of TWW as a health care application in in food-producing animal.

Effects of post-fermentation on the flavor compounds formation in red sour soup

Red Sour Soup (RSS) is a traditional fermented food in China. After two rounds of fermentation, sour soup has a mellow flavor. However, the microbial composition and flavor formation processes in post-fermentation in RSS are unclear. This study investigates the bacteria composition of RSS during the post-fermentation stage (0–180 days) using high-throughput sequencing. The results show that lactic acid bacteria (LAB) are dominant during the post-fermentation process, and their abundance gradually increases with fermentation time. Additionally, gas chromatography-mass spectrometry was used to detect volatile flavor compounds in the post-fermentation process. Seventy-seven volatile flavor compounds were identified, including 24 esters, 14 terpenes, 9 aromatic hydrocarbons, 9 alkanes, 6 heterocyclic compounds, 3 alcohols, 3 acids, 3 ketones, 2 phenols, 2 aldehydes, 1 amine, and 1 other. Esters and aromatic hydrocarbons are the main volatile compounds in RSS during the post-fermentation process. Orthogonal partial least squares screening and correlation analysis derived several significant correlations, including 48 pairs of positive correlations and 19 pairs of negative correlations. Among them, Acetobacter spp., Clostridium spp. and Sporolactobacillus spp. have 15, 14, 20 significant correlation pairs, respectively, and are considered the most important bacterial genera post-fermentation. Volatile substances become abundant with increasing fermentation time. LAB are excessive after more than 120 days but cause a drastic reduction in volatile ester levels. Thus, the post-fermentation time should be restricted to 120 days, which retains the highest concentrations of volatile esters in RSS. Overall, these findings provide a theoretical basis to determine an optimal post-fermentation time duration, and identify essential bacteria for manufacturing high-quality starter material to shorten the RSS post-fermentation processing time.

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.

Adaptive mechanism of Lactobacillus amylolyticus L6 in soymilk environment based on metabolism of nutrients and related gene-expression profiles

Lactobacillus amylolyticus L6 isolated from naturally fermented tofu-whey was characterized as potential probiotics. To give insight into the adaptive mechanism of L. amylolyticus L6 in soymilk, the gene-expression profiles of this strain and changes of chemical components in fermented soymilk were investigated. The viable counts of L. amylolyticus L6 in soymilk reached 10¹² CFU/mL in the stationary phase (10 hr). The main sugars reduced gradually while the acidity value significantly increased from 45.33° to 95.88° during fermentation. About 50 genes involved in sugar metabolization and lactic acid production were highly induced during soymilk fermentation. The concentration of total amino acid increased to 668.38 mg/L in the logarithmic phase, and 45 differentially expressed genes (DEGs) in terms of nitrogen metabolism and biosynthesis of amino acid were detected. Other genes related to lipid metabolism, inorganic ion transport, and stress response were also highly induced. Besides, the concentration of isoflavone aglycones with high bioactivity increased from 14.51 mg/L to 36.09 mg/L during the fermentation, and the expression of 6-phospho-β-glucosidase gene was also synchronously induced. This study revealed the adaptive mechanism of L. amylolyticus L6 in the soymilk-based ecosystem, which gives the theoretical guidance for the application of this strain in other soybean-derived products.

Culture media based on effluent derived from soy protein concentrate production for Lacticaseibacillus paracasei 90 biomass production: statistical optimisation, mineral characterization, and metabolic activities

The waste and by-products of the soybean industry could be an economic source of nutrients to satisfy the high nutritional demands for the cultivation of lactic acid bacteria. The aims of this work were to maximize the biomass production of Lacticaseibacillus paracasei 90 (L90) in three culture media formulated from an effluent derived from soy protein concentrate production and to assess the effects these media have on the enzymatic activity of L90, together with their influence on its fermentation profile in milk. The presence of essential minerals and fermentable carbohydrates (sucrose, raffinose, and stachyose) in the effluent was verified. L90 reached high levels of microbiological counts (∼ 9 log cfu mL^-1) and dry weight (> 1 g L^-1) on the three optimized media. Enzymatic activities (lactate dehydrogenase and β-galactosidase) of L90, and its metabolism of lactose and citric acid, as well as lactic acid and pyruvic acid production in milk, were modified depending on the growth media. The ability of the L90 to produce the key flavour compounds (diacetyl and acetoin) was maintained or improved by growing in the optimized media in comparison with MRS.

Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing

Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00963-3.

Marine Actinomycetes, New Sources of Biotechnological Products

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis

To identify the microbial community and origin of the spoilage flora of bacon, the changes in microbial population numbers and community structure were followed along the processing line, using culture-independent and culture-dependent methods. 16S rRNA gene amplicon sequencing (16S-seq) analysis showed that community complexity and structure significantly differed at different processing stages. Some 428 bacterial groups were ascertained at genus level, and Acinetobacter, Pseudomonas, Psychrobacter, and Brochothrix were the predominant bacteria on raw meats. After curing specimens dominated by Psychrobacter, Weissella, Vibrio, Leuconostoc, Myroides, Acinetobacter, and Lactobacillus, a total of 33 species were identified by traditional microbiological analyses and direct sequence determination methods. Our results indicated that curing should be considered one of the primary factors during various processing steps, presumably contaminating the products directly or indirectly.

Cloning and expression of a novel α-galactosidase from Lactobacillus amylolyticus L6 with hydrolytic and transgalactosyl properties

Lactobacillus amylolyticus L6, a gram-positive amylolytic bacterium isolated from naturally fermented tofu whey (NFTW), was able to hydrolyze raffinose and stachyose for the production of α-galactosidase. The cell-free extract of L. amylolyticus L6 was found to exhibit glycosyltransferase activity to synthesize α-galacto-oligosaccharides (GOS) with melibiose as substrate. The coding genes of α-galactosidase were identified in the genome of L. amylolyticus L6. The α-galactosidase (AglB) was placed into GH36 family by amino acid sequence alignments with other α-galactosidases from lactobacilli. The optimal reaction conditions of pH and temperature for AglB were pH 6.0 and 37°C, respectively. Besides, potassium ion was found to improve the activity of AglB while divalent mercury ion, copper ion and zinc ion displayed different degrees of inhibition effect. Under the optimum reaction condition, AglB could catalyze the synthesis of GOS with degree of polymerization (DP) ≥5 by using 300 mM melibiose concentration as substrate. The maximum yield of GOS with (DP) ≥3 could reach 31.56% (w/w). Transgalactosyl properties made AglB a potential candidate for application in the production of GOS.

The effects of CS@Fe3O4 nanoparticles combined with microwave or far infrared thawing on microbial diversity of red seabream (Pagrus major) fillets based on high-throughput sequencing

The present study investigated the effects of CS@Fe₃O₄ nanoparticles combined with microwave or far infrared thawing on microbial diversity of red seabream (Pagrus major) fillets in terms of thawing loss, pH, TVB-N, classical microbiological enumeration and high-throughput sequencing, and the same parameters were also studied for 24 h after thawing. Four thawing methods were used: microwave thawing (MT), far-infrared thawing (FT), CS@Fe₃O₄ nanoparticles combined with microwave thawing (CMT) and CS@Fe₃O₄ nanoparticles combined with far-infrared thawing (CFT). The results showed that CFT and CMT had lower values of pH and TVB-N compared to the FT and MT. Based on conventional microbial count analysis, CFT and CMT samples also maintained lower TVC, pseudomonas and LAB counts. Using high-throughput sequencing analysis, Compared with FT and MT, CFT and CMT samples showed a significant decrease in the proportion of the Pseudomonadaceae flora. However, the proportion of Pseudomonas, Bacillaceae and Thermaceae also increased significantly after 24 h of storage, which indicated that become the predominant microbiota in red seabream (Pagrus major) fillets.

Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd

BACKGROUND

Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter. In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation.

RESULTS

During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>10⁵  CFU g^-1 ) indicate a potential hazard to consumers.

CONCLUSION

The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products. © 2019 Society of Chemical Industry.

Physicochemical properties and microbial community dynamics during Chinese horse bean-chili-paste fermentation, revealed by culture-dependent and culture-independent approaches

The production of Chinese horse bean-chili-paste (CHCP) involves three fermentation phases: chili-to-moromi fermentation (CF) phase, horse bean-to-meju fermentation (HF) phase and moromi-meju mixed fermentation (MF) phase. To understand the microbial dynamics among these three phases and the potential roles of viable microbes for fermentation, microbial community dynamics was investigated by using culture-dependent and culture-independent methods. Furthermore, the capacities of enzyme-producing of the isolates were determined. During the CF phase, reducing sugar content increased from 3.1% to 3.49%, while pH declined from 4.85 to 4.5. The protein content in the HF phase and MF phase reduced sharply from 22.23% to 10.29% and 4.39%-1.19%, respectively. Bacillus sp., Staphylococcus sp., Oceanobacillus sp., Candida sp., Zygosaccharomyces sp. and Aspergillus sp. dominated the CF phase, while Bacillus sp., Candida sp. and Zygosaccharomyces sp. were the dominant microorganisms in both the HF and MF phases. B. amyloliquefaciens, B. methylotrophicus, B. subtilis, B. licheniformis and A. oryzae possessed strong capacities of producing enzymes, i.e. α-amylase, cellulase and xylanase, acid protease and leucine aminopeptidase, and could make a great contribution to CHCP fermentation.

Metagenomic Insights Into the Taxonomic and Functional Features of Kinema, a Traditional Fermented Soybean Product of Sikkim Himalaya

Kinema is an ethnic, naturally fermented soybean product consumed in the Sikkim Himalayan region of India. In the present study, the whole metagenome sequencing approach was adopted to examine the microbial diversity and related functional potential of Kinema, consumed in different seasons. Firmicutes was the abundant phylum in Kinema, ranging from 82.31 to 93.99% in different seasons, followed by Actinobacteria and Proteobacteria. At the species level, the prevalent microorganisms were Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, Corynebacterium glutamicum, Bacillus pumilus, and Lactococcus lactis. The abundance of microbial species varied significantly in different seasons. Further, the genomic presence of some undesirable microbes like Bacillus cereus, Proteus mirabilis, Staphylococcus aureus, Proteus penneri, Enterococcus faecalis, and Staphylococcus saprophyticus, were also detected in the specific season. The metagenomic analysis also revealed the existence of bacteriophages belonging to the family Siphoviridae, Myoviridae, and Podoviridae. Examination of the metabolic potential of the Kinema metagenome depicted information about the biocatalysts, presumably involved in the transformation of protein and carbohydrate polymers into bioactive molecules of health-beneficial effects. The genomic resource of several desirable enzymes was identified, such as β-galactosidase, β-glucosidase, β-xylosidase, and glutamate decarboxylase, etc. The catalytic function of a novel glutamate decarboxylase gene was validated for the biosynthesis of γ-aminobutyric acid (GABA). The results of the present study highlight the microbial and genomic resources associated with Kinema, and its importance in functional food industry.

Naturally Fermented Acid Slurry of Soy Whey: High-Throughput Sequencing-Based Characterization of Microbial Flora and Mechanism of Tofu Coagulation

Tofu processing generates large quantities of whey as waste water. Although naturally fermented whey serves as a coagulant, the critical constituents remain unknown. High-throughput sequencing identified predominant Lactobacillus in the naturally fermented acid slurry. Lactobacillus casei YQ336 with high coagulating ability and lactic acid production was isolated and its soy protein coagulating mechanism was determined. The acid in YQ336 fermented acid slurry lowered soy milk pH and reduced negatively charged groups of denatured soy protein, leading to coagulation. Acid slurry metal ions also promoted pH decline; moreover, YQ336-produced protease might partially hydrolyse soy protein, further promoting coagulation. Thus, organic acids, metal ions, and enzymes together promote coagulation, with the former acting as the main contributing factor. This study will pave the way for future industrial application of L. casei YQ336 in acid slurry tofu processing and food manufacturing, thereby potentially reducing resource waste and environmental pollution.

Microbial Profile and Genetic Polymorphism of Predominant Species in Some Traditional Fermented Seafoods of the Hainan Area in China

Fermented fish, fermented shrimp and fermented crab are traditionally prepared seafoods that are commonly consumed in the Hainan area in China. We studied the microbial diversity and metabolic pathways in traditional fermented seafoods using high-throughput sequencing technology, and based on our previous research, we also compared the differences between fermented seafood and fermented vegetables. The alpha diversity of fermented seafood was higher than that of fermented vegetables and attained the highest level in fermented shrimp. The dominant genera in fermented seafood were different from those of fermented vegetables. Furthermore, we analyzed the 16S rDNA gene polymorphisms (SNPs) of the same dominant species (Lactobacillus plantarum and Lactobacillus fermentum) in two fermented environments, which showed that most of the mutations occurred in fermented vegetables and that fermenting environment might be the major factor for these mutations. This research provides us with new insights into beneficial microbial resources in regard to microbial diversity and genetic polymorphisms and lays a foundation for the subsequent development and utilization of beneficial microorganisms.