Molecular identification of microbial community in surface and undersurface douchi during postfermentation

Microbiology of fermented soy foods in Asia: Can we learn lessons for production of plant cheese analogues?

The food industry is facing the challenge of creating innovative, nutritious, and flavored plant-based products, due to consumer's increasing demand for the health and environmental sustainability. Fermentation as a unique and effective tool plays an important role in the innovation of food products. Traditional fermented soy foods are popular in many Asian and African countries as nutritious, digestible and flavorful daily staples or condiments. They are produced by specific microorganisms with the unique fermentation process in which microorganisms convert the ingredients of whole soybean or soybean curd to flavorful and functional molecules. This review provides an overview on traditional fermented food produced from soy, including douchi, natto, tempeh, and sufu as well as stinky tofu, including the background of these products, the manufacturing process, and the microbial diversity involved in fermentation procedures as well as flavor volatiles that were identified in the final products. The contribution of microbes to the quality of these five fermented soy foods is discussed, with the comparison to the role of cheese ripening microorganisms in cheese flavor formation. This communication aims to summarize the microbiology of fermented soy foods in Asia, evoking innovative ideas for the development of new plant-based fermented foods especially plant-based cheese analogues.

Fermented soybean foods and diabetes

The number of patients with type 2 diabetes mellitus is increasing, and its prevention and management are important. One of the factors contributing to the increased incidence of type 2 diabetes mellitus is the change in dietary habits, including a Westernized diet. Fermented foods are foods that are transformed by the action of microorganisms to produce beneficial effects in humans and have been consumed for thousands of years. The production and consumption of fermented soy foods, including natto, miso, douchi, cheonggukjang, doenjang, tempeh, and fermented soy milk, are widespread in Asian countries. This review focuses on fermented soybean foods and summarizes their effects on diabetes. Fermentation increases the content of ingredients originally contained in soybeans and adds new ingredients that are not present in the original soybeans. Recent studies have revealed that fermented soybean food modifies the gut microbiota-related metabolites by modifying dysbiosis. Furthermore, it has been reported that fermented soybean foods have antioxidant, anti-inflammatory, and anti-diabetic effects. In recent years, fermented foods, including fermented soybeans, have shown various beneficial effects. Therefore, it is necessary to continue focusing on the benefits and mechanisms of action of fermented foods.

Comparison of four multilocus sequence typing schemes and amino acid biosynthesis based on genomic analysis of Bacillus subtilis

Bacillus subtilis, a valuable industrial microorganism used in starter cultures in soybean fermentation, is a species of bacteria with interspecies diversity. Here, four multilocus sequence typing (MLST) schemes developed to assess the diversity of B. subtilis or Bacillus spp. were applied and compared to confirm the interspecies diversity of B. subtilis. In addition, we analyzed correlations between amino acid biosynthesis genes and sequence types (STs); this is important because amino acids are key taste components in fermented foods. On applying the four MLST methods to 38 strains and the type strain of B. subtilis, 30 to 32 STs were identified. The discriminatory power was 0.362-0.964 for the genes used in the MLST methods; the larger the gene, the greater the number of alleles and polymorphic sites. All four MLST methods showed a correlation between STs and strains that do not possess the hutHUIG operon (which contains genes required for the production of glutamate from histidine). This correlation was verified using 168 further genome-sequence strains.

Discrimination of Bacillus subtilis from Other Bacillus Species Using Specific Oligonucleotide Primers for the Pyruvate Carboxylase and Shikimate Dehydrogenase Genes

Bacillus subtilis is a useful bacterium in the food industry with applications as a starter strain for fermented food and as a probiotic. However, it is difficult to discriminate B. subtilis from other Bacillus species because of high phenotypic and genetic similarity. In this study, we employed five previously constructed multilocus sequence typing (MLST) methods for the discrimination of B. subtilis from other Bacillus species and all five MLST assays clearly distinguished B. subtilis. Additionally, the 17 housekeeping genes used in the five MLST assays also clearly distinguished B. subtilis. The pyruvate carboxylase (pyrA) and shikimate dehydrogenase (aroE) genes were selected for the discrimination of B. subtilis because of their high number of polymorphic sites and the fact that they displayed the lowest homology among the 17 housekeeping genes. Specific primer sets for the pyrA and aroE genes were designed and PCR products were specifically amplified from B. subtilis, demonstrating the high specificity of the two housekeeping genes for B. subtilis. This species-specific PCR method provides a quick, simple, powerful, and reliable alternative to conventional methods in the detection and identification of B. subtilis.

Fermented Soy Products and Their Potential Health Benefits: A Review

In the growing search for therapeutic strategies, there is an interest in foods containing natural antioxidants and other bioactive compounds capable of preventing or reversing pathogenic processes associated with metabolic disease. Fermentation has been used as a potent way of improving the properties of soybean and their components. Microbial metabolism is responsible for producing the β-glucosidase enzyme that converts glycosidic isoflavones into aglycones with higher biological activity in fermented soy products, in addition to several end-metabolites associated with human health development, including peptides, phenolic acids, fatty acids, vitamins, flavonoids, minerals, and organic acids. Thus, several products have emerged from soybean fermentation by fungi, bacteria, or a combination of both. This review covers the key biological characteristics of soy and fermented soy products, including natto, miso, tofu, douchi, sufu, cheonggukjang, doenjang, kanjang, meju, tempeh, thua-nao, kinema, hawaijar, and tungrymbai. The inclusion of these foods in the diet has been associated with the reduction of chronic diseases, with potential anticancer, anti-obesity, antidiabetic, anticholesterol, anti-inflammatory, and neuroprotective effects. These biological activities and the recently studied potential of fermented soybean molecules against SARS-CoV-2 are discussed. Finally, a patent landscape is presented to provide the state-of-the-art of the transfer of knowledge from the scientific sphere to the industrial application.

Correlation Analysis of Microbiota and Volatile Flavor Compounds of Caishiji Soybean Paste

Microbial diversity plays a crucial part in the fermentation of Caishiji soybean paste (CSP). In the current study, the microbiota and volatile flavor compounds (VFCs) in CSP were identified through Illumina MiSeq sequencing and headspace gas chromatography–mass spectrometry. Five bacterial (Bacillus, Tetragenococcus, Salinivibrio, Halomonas, and Staphylococcus) and four fungal genera (Aspergillus, Debaryomyces, Nigrospora, and Curvularia) were revealed as dominant among the entire microbiome of CSP. More than 70 VFCs, including 8 acids, 15 esters, 8 alcohols, 14 aldehydes, 4 ketones, 5 phenols, and 20 miscellaneous VFCs were detected during the fermentation process. A total of 12 kinds of VFCs were identified in the odor activity value (OAV) analysis. The results of the correlation analysis between microbiota and VFCs indicated that Bacillus, Tetragenococcus, Staphylococcus, and Aspergillus were the main microbiota affecting the flavor of CSP. These results may serve as a reference for enhancing the quality of CSP.

High-throughput sequencing-based analysis of fungal diversity and taste quality evaluation of Douchi, a traditional fermented food

Douchi, a popular traditional fermented soybean product, is mainly made by natural fermentation. However, its taste quality is affected by specific fungal communities which vary greatly according to fermentation conditions and production technologies used in different regions. Therefore, the taste quality of Douchi samples from different regions was digitally evaluated using electronic tongue technology. In addition, the fungal community structures and its association of them were also identified using high-throughput sequencing technology. Results showed that there were obvious differences in the taste quality of samples from different regions, while the tastes of different types of samples from the same region were similar. Sourness, umami, richness, and saltiness were the main reasons for regional differences in taste. Similarly, the results of high-throughput sequencing indicated that samples from different regions displayed important differences in dominant fungal genus, among which Debaryomyces, Fusarium, Pichia, Aspergillus, and Saccharomyces were the main dominant fungi. Debaryomyces and Trichosporon were conducive to the formation of taste qualities of Douchi, while Cladosporium and Candida have a negative impact on the taste quality of Douchi var correlation analysis. This study indicated the effects of dominant fungi on the formation of Douchi taste quality, allowing a deeper understanding of the role of microbial species in generating fermented soybean products in China. Our work provides theoretical support to guide the improvement of the industrial production process of Douchi.

Variations in Fungal Community and Diversity in Doushen With Different Flavors

Doushen, a traditional Chinese fermented soybean product, may be spiced or spicy depending on whether pepper powder is added. While numerous studies have investigated the microbial communities of other fermented foods, little is known on the fungal diversity of Doushen. Therefore, in this study, we investigated the fungal community and diversity in both spiced and spicy Doushen. Our results revealed that fungal species richness significantly differed between the samples with different flavors. A total of nine phyla and 188 fungal genera were identified, and Ascomycota and Aspergillus were predominant in all samples. Based on linear discriminant analysis, a total of 57 OTUs were significantly different between the two samples. Results of non-metric multidimensional scaling and unweighted pair-group analysis suggested that the presence of pepper powder affects the microbial community in Doushen. Network analysis showed that microbial interactions between fungal communities in Doushen with different flavors were significantly different. The results on the enumeration and identification of fungi were consistent with the composition of the dominant genera in the samples with different flavors. This study provides a theoretical basis for future research on food ecology in Doushen.

Exploring functional core bacteria in fermentation of a traditional Chinese food, Aspergillus-type douchi

Douchi is a type of traditional Chinese flavoring food that has been used for thousands of years and is produced by multispecies solid-state fermentation. However, the correlation between the flavor, the microbiota, and the functional core microbiota in Aspergillus-type douchi fermentation remains unclear. In this study, Illumina MiSeq sequencing and chromatography were used to investigate the bacterial community and flavor components in Aspergillus-type douchi fermentation. The dominant phyla were Firmicutes, Proteobacteria, and Actinobacteria, and the dominant genera were Weissella, Bacillus, Anaerosalibacter, Lactobacillus, Staphylococcus, and Enterococcus. A total of 58 flavor components were detected during fermentation, including two alcohols, 14 esters, five pyrazines, three alkanes, four aldehydes, three phenols, six acids, and five other compounds. Bidirectional orthogonal partial least square modeling showed that Corynebacterium_1, Lactococcus, Atopostipes, Peptostreptococcus, norank_o__AKYG1722, Truepera, Gulosibacter, norank_f__Actinomycetaceae, and unclassified_f__Rhodobacteraceae are the functional core microbiota responsible for the formation of the flavor components during douchi fermentation. This is the first study to investigate the functional core microbiota in douchi fermentation using Illumina MiSeq sequencing and chromatographic techniques. Our findings extend our understanding of the relationships between flavor, the microbiota, and the functional core microbiota during Aspergillus-type douchi fermentation.

Difference in microbial community and taste compounds between Mucor-type and Aspergillus-type Douchi during koji-making

Douchi has attracted people's attention because of its unique taste and rich health function. The microbes participated in the koji-making process contribute to taste compounds of Douchi. However, the majority of studies on Douchi focused on their functional components and the microbial community in single type of Douchi during koji-making so far. In the present study, the taste components of Mucor-type and Aspergillus-type Douchi were measured initially and the results showed that the amino acid and organic acid levels as well as the percentage of unsaturated fatty acids in Mucor-type Douchi were significantly higher than those in Aspergillus-type. The investigation of the microbial composition in two types of Douchi showed that Aspergillus, Candida, Meyerozyma and Lecanicillium were shared by >50% of samples during koji-making. Comparison of the microbial community between the two types of Douchi revealed that Meyerozyma and Lecanicillium were the main microbial community with significant difference during the initial stage of koji-making, while Candida was significantly different during the later stage of koji-making. When supplemented with Meyerozyma and Candida in Aspergillus-type Douchi, the level of all amino acid and organic acids as well as the percentage of unsaturated fatty acid was significant improved, which further validated the importance roles of the two microorganisms in enhancing the taste components of Douchi during koji-making. The results provide useful information on optimizing the microbial community structure of Douchi during the process of koji-making and improving the product quality.

Isolation of nitrite-degrading strains from Douchi and their application to degrade high nitrite in Jiangshui

BACKGROUND

Excessive nitrite in food is potentially harmful to human health because of carcinogenic effects caused by its nitroso-derivatives. Douchi, which widely distributed throughout the country, is a traditional solid fermented soybean food with low nitrite content.

RESULTS

In this study, bacteria which can degrade nitrite were isolated from Douchi and identified from their 16S rDNA sequences. Acinetobacter guillouiae, Acinetobacter bereziniae, Bacillus subtilis, Bacillus tequilensis, Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus aryabhattai and Bacillus methylotrophicus were selected. It was shown that all strains were able to degrade nitrite to some extent, including Bacillus subtilis NDS1, which was able to degrade 99.41% of nitrite. The enzyme activities of these strains were determined at 24 and 48 h and were shown to correspond with their nitrite degradation rates. The strains were used to inoculate Jiangshui, a kind of traditional fermented vegetable from northwest China that often has a high nitrite content. Of the strains tested, Bacillus subtilis NDS1, Bacillus tequilensis NDS3, Acinetobacter bereziniae NDS4, Bacillus subtilis NDS6, and Bacillus subtilis NDS12 were able to degrade nitrite in Jiangshui more rapidly, with Acinetobacter bereziniae NDS4 degrading almost all nitrite in 48 h compared with 180 h of control.

CONCLUSION

These results indicate that the selected strains have potential to be used as nitrite-degrading agents in food. © 2018 Society of Chemical Industry.

Biogenic amines analysis and microbial contribution in traditional fermented food of Douchi

Biogenic amines (BAs) have been reported to threaten the Douchi safety, while the BAs formation mechanism and corresponding control method have not been clarified for Douchi. The present study aims to investigate the microbial contribution to BAs in Douchi, and to find the beneficial strain for BAs control. Firstly, the BAs profiles of 15 Douchi samples were analyzed, and common 6 kinds of BAs were detected from different samples. All the samples showed the total BAs contents within the safe dosage range, while the histamine concentrations in 2 samples and β-phenethylamine in 6 samples were above the toxic level. Then, the bacterial and fungal communities were investigated by high-throughput sequencing analysis, and Bacillus and Candida were identified as the dominant bacteria and fungi genus, respectively. Furthermore, nineteen strains were selected from the dominant species of Douchi samples, including 14 Bacillus strains, 2 Staphylococcus strains, 1 Enterococcus strain and 2 Candida strains, and their BAs formation and degradation abilities were evaluated. B. subtilis HB-1 and S. pasteuri JX-2 showed no BAs producing ability, and B. subtilis GD-4 and Candida sp. JX-3 exhibited high BAs degradation ability. Finally, fermented soybean model analysis further verified that B. subtilis HB-1 and S. pasteuri JX-2 could significantly reduce BAs. This study not only contributed to understanding the BAs formation mechanism in Douchi, but also provided potential candidates to control the BAs in fermented soybean products.

Comprehensive Secondary Metabolite Profiling Toward Delineating the Solid and Submerged-State Fermentation of Aspergillus oryzae KCCM 12698

Aspergillus oryzae has been commonly used to make koji, meju, and soy sauce in traditional food fermentation industries. However, the metabolic behaviors of A. oryzae during fermentation in various culture environments are largely uncharacterized. Thus, we performed time resolved (0, 4, 8, 12, 16 day) secondary metabolite profiling for A. oryzae KCCM 12698 cultivated on malt extract agar and broth (MEA and MEB) under solid-state fermentation (SSF) and submerged fermentation (SmF) conditions using the ultrahigh performance liquid chromatography-linear trap quadrupole-ion trap-mass spectrometry (UHPLC-LTQ-IT-MS/MS) followed by multivariate analyses. We observed the relatively higher proportions of coumarins and oxylipins in SSF, whereas the terpenoids were abundant in SmF. Moreover, we investigated the antimicrobial efficacy of metabolites that were extracted from SSF and SmF. The SSF extracts showed higher antimicrobial activities as compared to SmF, with higher production rates of bioactive secondary metabolites viz., ketone-citreoisocoumarin, pentahydroxy-anthraquinone, hexylitaconic acid, oxylipins, and saturated fatty acids. The current study provides the underpinnings of a metabolomic framework regarding the growth and bioactive compound production for A. oryzae under the primarily employed industrial cultivation states. Furthermore, the study holds the potentials for rapid screening and MS-characterization of metabolites helpful in determining the consumer safety implications of fermented foods involving Koji mold.

Reclamation of Herb Residues Using Probiotics and Their Therapeutic Effect on Diarrhea

Residues from herbal medicine processing in pharmaceutical plants create a large amount of waste (herb residues), which consists mainly of environmental pollution and medicinal waste. In order to resolve this problem, probiotics of Bacillus (B.) subtilis, Aspergillus (A.) oryzae, and Lactobacillus (L.) plantarum M3 are selected to reuse herb residue of Jianweixiaoshi tablets (JT), and an antibiotic-associated diarrhea (AAD) mouse model was established to evaluate the therapeutic effects of the herb residue fermentation supernatant. Our results indicated that the fermentation supernatant had scavenged 77.8% of 2,2-diphenyl-1-picrylhydrazyl (DPPH), 78% of O₂^•−, 36.7% of ^•OH, 39% of Fe²⁺ chelation, and 716 mg/L reducing power. The inhibition zones for Salmonella (S.) typhimurium, S. enteritidis, Shigella (Sh.) flexneri, Escherichia (E.) coli, Listeria (L.) monocytogenes, Sh. dysenteriae 301, and Staphylococcus (S.) aureus were 17, 14, 19, 18, 20, 19, and 20 mm, respectively. The in vivo results indicated that the fermentation supernatant resulted in a high diarrhea inhibition rate (56%, p < 0.05), greatly enhanced the disruption of bacterial diversity caused by antibiotics, and restored the dominant position of L. johnsonii in the treatment and recovery stages. Therefore, the combination of the herb residue and probiotics suggests a potential to explore conversion of these materials for the possible development of therapies for AAD.

Therapeutic effect of herb residue fermentation supernatant on spleen‑deficient mice

To minimize the waste of active ingredients present in herb residues, in the present study, probiotics of Bacillus subtilis, Aspergillus oryzae and Lactobacillus plantarum M3 were selected to reuse herb residues from Jianweixiaoshi tablets, and the therapeutic effects of the herb residue fermentation supernatant were evaluated using a spleen‑deficient mouse model. The results of the present study indicated that the fermentation supernatant may effectively improve the immunity of mice, as measured by body weight, spleen and thymus index, and inflammatory cytokines, including interleukin (IL)‑2, IL‑4 and interferon‑γ. The viable cell count and denaturing gradient gel electrophoresis results indicated that the fermentation supernatant markedly enhanced bacterial diversity and the number of lactobacilli in mouse intestines. Therefore, the combination of the Jianweixiaoshi herb residue and probiotics provided a novel method to reuse herb residues and may in the future contribute to the treatment of spleen deficiency.

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.

Efficacy of oral Bifidobacterium bifidum ATCC 29521 on microflora and antioxidant in mice

This study aimed to examine whether Bifidobacterium bifidum ATCC 29521, a species of colonic microflora in humans, is involved in the intestinal tract of mice. This study was also conducted to determine the antioxidant activity of this species by evaluating different microbial populations and reactive oxygen species isolated from feces and intestinal contents for 28 days of oral administration. Microbial diversities were assessed through bacterial culture techniques, PCR–DGGE, and real-time PCR. This study showed that the intake of B. bifidum ATCC 29521 significantly (p < 0.05) improved the ecosystem of the intestinal tract of BALB/c mice by increasing the amount of probiotics (Lactobacillus intestinalis and Lactobacillus crispatus) and by reducing unwanted bacterial populations (Enterobacter, Escherichia coli). Antioxidative activities of incubated cell-free extracts were evaluated through various assays, including the scavenging ability of DPPH radical (64.5% and 67.54% (p < 0.05), respectively, at 21 days in nutrients and 28 days in MRS broth), superoxide anion, and hydroxyl radical (85% and 61.5% (p < 0.05), respectively, at intestinal contents in nutrients and 21 days in MRS broth). Total reducing power (231.5 μmol/L (p < 0.05), 14 days in MRS broth) and mRNA level of genes related to oxidative stress were also determined. Results indicated that B. bifidum ATCC 29521 elicits a beneficial effect on murine gut microbiota and antioxidant activities compared with the control samples. This species can be considered as a potential bioresource antioxidant to promote health. Bifidobacterium bifidum ATCC 29521 may also be used as a promising material in microbiological and food applications.

Identification of key micro-organisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation

AIMS

To screen and identify safe micro-organisms used during Douchi fermentation, and verify the feasibility of producing high-quality Douchi using these identified micro-organisms.

METHODS AND RESULTS

PCR-denaturing gradient gel electrophoresis (DGGE) and automatic amino-acid analyser were used to investigate the microbial diversity and free amino acids (FAAs) content of 10 commercial Douchi samples. The correlations between microbial communities and FAAs were analysed by statistical analysis. Ten strains with significant positive correlation were identified. Then an experiment on Douchi fermentation by identified strains was carried out, and the nutritional composition in Douchi was analysed. Results showed that FAAs and relative content of isoflavone aglycones in verification Douchi samples were generally higher than those in commercial Douchi samples.

CONCLUSIONS

Our study indicated that fungi, yeasts, Bacillus and lactic acid bacteria were the key players in Douchi fermentation, and with identified probiotic micro-organisms participating in fermentation, a higher quality Douchi product was produced.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report to analyse and confirm the key micro-organisms during Douchi fermentation by statistical analysis. This work proves fermentation micro-organisms to be the key influencing factor of Douchi quality, and demonstrates the feasibility of fermenting Douchi using identified starter micro-organisms.