Characterization and comparison of metaproteomes in traditional and commercial dajiang, a fermented soybean paste in northeast China

Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production

Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.

The quality of beef-soybean paste and the relationship between microbial composition and flavor changes during fermentation

Compound fermented seasonings were increasingly favored by consumers. This study using Aspergillus oryzae and soybeans as raw materials to make koji. Lactobacillus plantarum and Pediococcus pentosaceus were used as starters for common fermentation with mature koji and beef to obtain a fermented beef-soybean paste. The physicochemical parameters, volatile flavor compounds, and microbial community of beef-soybean paste during fermentation were determined, and the relationship between flavor changes and microbial community changes was analyzed. Compared to the soybean paste, the addition of beef for fermentation can significantly enhanced the content of protein, amino acid nitrogen, and free amino acids in the compound fermented soybean paste, improved the nutritional and health value of the product. The addition of beef also caused a decrease in pH and total acid content in the compound soybean paste. The flavor changed during the fermentation process of beef-soybean paste were related to the changed in its microbial community.

Potential Role of Lauric Acid in Milk Fat Synthesis in Chinese Holstein Cows Based on Integrated Analysis of Ruminal Microbiome and Metabolome

The composition and metabolic profile of the ruminal microbiome have an impact on milk composition. To unravel the ruminal microbiome and metabolome affecting milk fat synthesis in dairy cows, 16S rRNA and internal transcribed spacer (ITS) gene sequencing, as well as ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) methods were used to investigate the significant differences in ruminal bacterial and fungal communities as well as metabolome among Chinese Holstein cows with contrasting milk fat contents under the same diet (H-MF 5.82 ± 0.41% vs. L-MF 3.60 ± 0.12%). Another objective was to culture bovine mammary epithelial cells (BMECs) to assess the effect of metabolites on lipid metabolism. Results showed that the acetate-to-propionate ratio and xylanase activity in ruminal fluid were both higher in H-MF. Microbiome sequencing identified 10 types of bacteria and four types of fungi differently abundant at the genus level. Metabolomics analysis indicated 11 different ruminal metabolites between the two groups, the majority of which were lipids and organic acids. Among these, lauric acid (LA) was enriched in fatty acid biosynthesis with its concentration in milk fat of H-MF cows being greater (217 vs. 156 mg per 100 g milk), thus, it was selected for an in vitro study with BMECs. Exogenous LA led to a marked increase in intracellular triglyceride (TG) content and lipid droplet formation, and it upregulated the mRNA abundance of fatty acid uptake and activation (CD36 and ACSL1), TG synthesis (DGAT1, DGAT2 and GPAM), and transcriptional regulation (SREBP1) genes. Taken together, the greater relative abundance of xylan-fermenting bacteria and fungi, and lower abundance of bacteria suppressing short-chain fatty acid-producing bacteria or participating in fatty acid hydrogenation altered lipids and organic acids in the rumen of dairy cows. In BMECs, LA altered the expression of genes involved in lipid metabolism in mammary cells, ultimately promoting milk fat synthesis. Thus, it appears that this fatty acid plays a key role in milk fat synthesis.

A comparative study on the nutritional composition, protein structure and effects on gut microbiota of 5 fermented soybean products (FSPs)

In this study, we conducted an analysis of the differences in nutrient composition and protein structure among various fermented soybean products and their impacts on the gut microbiota of rats. Conventional physicochemical analysis was employed to analyze the fundamental physicochemical composition of the samples. Additionally, we utilized high-performance liquid chromatography and ELISA techniques to quantify the presence of antinutritional compounds. Fourier infrared spectroscopy was applied to delineate the protein structure, while 16 s rRNA gene sequencing was conducted to evaluate alterations in gut microbiota abundance. Subsequently, KEGG was utilized for metabolic pathway analysis. Our findings revealed that fermented soybean products improved the nutritional profile of soybeans. Notably, Douchi exhibited the highest protein content at 52.18 g/100 g, denoting a 26.58 % increase, whereas natto showed a 24.98 % increase. Douchi and natto demonstrated the most substantial relative amino acid content, comprising 50.86 % and 49.04 % of the total samples, respectively. Moreover, the levels of antinutritional factors markedly decreased post-fermentation. Specifically, the α-helix content in doujiang decreased by 13.87 %, while the random coil content in soybean yogurt surged by 132.39 %. Rats that were fed FSP showcased notable enhancements in gut microbiota and associated metabolic pathways. A strong correlation was observed between nutrient composition, protein structure, and gut microbiota abundance. This study furnishes empirical evidence supporting the heightened nutritional attributes of FSPs.

Ultrasound-assisted fermentation for antioxidant peptides preparation from okara: Optimization, stability, and functional analyses

This study investigated the effects of ultrasound-assisted fermentation (UAF) on the preparation of antioxidant peptides (UAFP) from okara and examined their content, chemical structures, and antioxidant activity. After the optimal ultrasonic processing (time, 20 min; frequency, 45 KHz; power, 120 W/L), the peptide content yield reached the maximum of 12.36 ± 0.02 mg/mL, and their DPPH free radical scavenging rate was 65.15 ± 0.32 %. UAF increased the number of globular aggregates with deeper gullies, a looser structure, and higher porosity. The experiments conducted using the oxidative stress injury model of HepG2 cells showed that okara UAFP promoted cell growth and exerted a protective effect. Moreover, ultrasonic treatment remarkably improved the environmental stability (NaCl, glucose, sodium benzoate, temperature, pH, metal ions) and antioxidant activity of UAFP. Concisely, optimal ultrasonic processing can aid the fermentation of agroindustrial by-products to prepare antioxidant peptides, such as natural food antioxidant peptides from soybean waste.

Metaproteomics revealing microbial diversity and activity in the spontaneous fermentation of maize dough

Maize was spontaneously fermented and metaproteomic analysis was performed on the maize dough to investigate the profile of microbial communities. pH decreased (5.36, 4.44, and 4.42 after 24, 72, and 12 h), while lactic acid increased (0.03, 0.2, and 0.31 after 24, 72, and 120 h).The number of lactic acid bacteria (179 × 106 CFU/g) and mesophilic bacteria (213 × 106 CFU/g) was high. Based on metaproteomic analysis, Actinobacteria, Proteobacteria, and Firmicutes phyla dominated the fermentation medium, and the Actinobacteria was associated with the matrix of maize during starch degradation. Fermentation parameters (pH, lactic acid and titratable sugar) were considered to be regulated during the first 24 h of the fermentation process for ensure the microbiological safety of maize dough. Assuming that metaproteomics as culture-free methods can be an excellent tool for find mechanisms for faster optimization of a new product, is indeed a good tool for investigating fermentative microbiota.

Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics

Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.

Metagenomic and metaproteomic analyses of microbial amino acid metabolism during Cantonese soy sauce fermentation

Cantonese soy sauce is an important type of traditional Chinese brewed soy sauce that was developed in southern China, mainly in Guangdong. Due to the long fermentation period and complex microbiota in Cantonese soy sauce, there are few reports on the microbial metaproteomics of Cantonese soy sauce. In this study, integrative metagenomic and metaproteomic analyzes were used to identify the changes in the dominant microbiota and amino acid synthesis-related enzymes and metabolism during Cantonese soy sauce fermentation. Metagenomic analysis revealed that Tetragenococcus halophilus, Weissella confusa, Weissella paramesenteroides, Enterobacter hormaechei, and Aspergillus oryzae were the dominant microbiota. Using the Top 15 dominant microbiota identified by metagenomics as the database, LTQ Orbitrap Velos Pro ETD mass spectrometry was used to obtain metaproteomic information about the microbes in the soy sauce, and the results indicated that the active enzymes involved in the metabolism of amino acids were secreted by microorganisms such as A. oryzae, T. halophilus, and Zygosaccharomyces rouxii. During the Cantonese soy sauce fermentation process. Among them, early fermentation (0-15d) was dominated by A. oryzae and T. halophilus, mid-term fermentation (60-90d) was dominated by Z. rouxii, A. oryzae, and T. halophilus, and late fermentation (90-120d) was dominated by A. oryzae, Z. rouxii, and T. halophilus. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the main enzymes involved in the metabolism of umami amino acids were aspartate aminotransferase, citrate synthase, aconitase, and isocitrate dehydrogenase, which were produced by Z. rouxii and A. oryzae during early fermentation (0-15 d) and the middle fermentation stage (60-90 d). This study constructed a regulatory network of enzymes potentially involved in the metabolism of flavor amino acids, which provided a theoretical basis for studying the amino acid metabolism of Cantonese soy sauce.

Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis

The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.

Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage

AIMS

Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.

METHODS AND RESULTS

whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.

CONCLUSIONS

Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.

A systematic review on the flavor of soy-based fermented foods: Core fermentation microbiome, multisensory flavor substances, key enzymes, and metabolic pathways

The characteristic flavor of fermented foods has an important impact on the purchasing decisions of consumers, and its production mechanisms are a concern for scientists worldwide. The perception of food flavor is a complex process involving olfaction, taste, vision, and oral touch, with various senses contributing to specific properties of the flavor. Soy-based fermented products are popular because of their unique flavors, especially in Asian countries, where they occupy an important place in the dietary structure. Microorganisms, known as the souls of fermented foods, can influence the sensory properties of soy-based fermented foods through various metabolic pathways, and are closely related to the formation of multisensory properties. Therefore, this review systematically summarizes the core microbiome and its interactions that play an active role in representative soy-based fermented foods, such as fermented soymilk, soy sauce, soybean paste, sufu, and douchi. The mechanism of action of the core microbial community on multisensory flavor quality is revealed here. Revealing the fermentation core microbiome and related enzymes provides important guidance for the development of flavor-enhancement strategies and related genetically engineered bacteria.

Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods

Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.

Proteomics as a New-Generation Tool for Studying Moulds Related to Food Safety and Quality

Mould development in foodstuffs is linked to both spoilage and the production of mycotoxins, provoking food quality and food safety concerns, respectively. The high-throughput technology proteomics applied to foodborne moulds is of great interest to address such issues. This review presents proteomics approaches useful for boosting strategies to minimise the mould spoilage and the hazard related to mycotoxins in food. Metaproteomics seems to be the most effective method for mould identification despite the current problems related to the bioinformatics tool. More interestingly, different high resolution mass spectrometry tools are suitable for evaluating the proteome of foodborne moulds able to unveil the mould's response under certain environmental conditions and the presence of biocontrol agents or antifungals, being sometimes combined with a method with limited ability to separate proteins, the two-dimensional gel electrophoresis. However, the matrix complexity, the high ranges of protein concentrations needed and the performing of multiple steps are some of the proteomics limitations for the application to foodborne moulds. To overcome some of these limitations, model systems have been developed and proteomics applied to other scientific fields, such as library-free data independent acquisition analyses, the implementation of ion mobility, and the evaluation of post-translational modifications, are expected to be gradually implemented in this field for avoiding undesirable moulds in foodstuffs.

Structural characterization and hepatoprotective activity of exopolysaccharide from Bacillus velezensis SN-1

BACKGROUND

Exopolysaccharide biopolymers produced by microorganisms are crucial to the environment. They contribute to areas such as the health and bionanotechnology sectors, food and cosmetic industries as gelling agents, and environmental sector as flocculants owing to their biodegradability and non-toxic nature. The current study aimed to isolate the fraction of released exopolysaccharide (rEPS) by Bacillus velezensis SN-1 from Chinese Da-Jiang.

RESULTS

The weighted average molecular weight of the major isolated component, rEPS-2, was 202 kDa, and its monosaccharide composition included mannose, glucose, and galactose at a molar ratio of 0.38:0.30:0.32. Further, the rEPS-2 was characterized using methylation analysis and one-dimensional/two-dimensional nuclear magnetic resonance (1D/2D NMR) spectroscopy. In vivo hepatoprotective effects indicated that rEPS-2 could alleviate carbon tetrachloride (CCl₄ )-induced liver injury in mice by lowering the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and the malondialdehyde (MDA) levels. Furthermore, rEPS-2 can increase the expression of antioxidant genes HO-1, GCLC and NQO1 in the Nrf2/ARE signaling pathway, thereby increasing the activity of antioxidant enzymes superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and reduced catalase (CAT) in liver cells. Furthermore, the rEPS-2 can be used and modulate the gut microbiota of mice with liver injury caused by CCl₄ .

CONCLUSIONS

These results suggest that rEPS-2 has promising potential to serve as hepatoprotective agents. © 2022 Society of Chemical Industry.

The differences in carbohydrate utilization ability between six rounds of Sauce-flavor Daqu

Sauce-flavor Daqu is an important source of fermentation power in baijiu brewing. Revealing carbohydrate metabolism will help to explore the underlying reasons for the difference in fermentation performance of Daqu. In this study, metagenomic and metaproteomic technologies were performed to explore the carbohydrate metabolism network and its active functional microorganisms of Sauce-flavor Daqu. The sugar profile was analyzed using LC-MS to confirm the metabolic network. The results showed that 23 fungi and 5 bacteria were involved in carbohydrate metabolism. Starch metabolism, cellulose metabolism, and glucan metabolism were the main metabolic pathways, in which fungi especially Aspergillus were more involved than bacteria. Among these active microorganisms, Saccharomycopsis fibuligera, Aspergillus oryzae, Monascus purpureus, Byssochlamys spectabilis, Lichtheimia ramosa, Thermomyces lanuginosus, and Thermoascus aurantiacus were significant functional microorganisms with the ability to produce multiple enzymes. Lichtheimia ramosa, Lichtheimia corymbifera and Kroppenstedtia eburnea were biomarkers of Daqu in the first round, granting it a better liquefaction ability. β-amylase derived from wheat also played an important role in starch degradation, and the synergistic effect with α-amylase endowed Daqu with higher liquefaction power in the first two rounds. The results of this study are of great significance for the analysis of the mechanism of Daqu fermentation and provide a reliable theoretical basis for strengthening the fermentation performance of Daqu.

Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms

Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers' expectations of healthy products.

Two sides of the same coin: Meta-analysis uncovered the potential benefits and risks of traditional fermented foods at a large geographical scale

Traditional fermented foods, which are well-known microbial resources, are also bright national cultural inheritances. Recently, traditional fermented foods have received great attention due to their potential probiotic properties. Based on shotgun metagenomic sequencing data, we analyzed the microbial diversity, taxonomic composition, metabolic pathways, and the potential benefits and risks of fermented foods through a meta-analysis including 179 selected samples, as well as our own sequencing data collected from Hainan Province, China. As expected, raw materials, regions (differentiated by climatic zones), and substrates were the main driving forces for the microbial diversity and taxonomic composition of traditional fermented foods. Interestingly, a higher content of beneficial bacteria but a low biomass of opportunistic pathogens and antibiotic resistance genes were observed in the fermented dairy products, indicating that fermented dairy products are the most beneficial and reliable fermented foods. In contrast, despite the high microbial diversity found in the fermented soy products, their consumption risk was still high due to the enrichment of opportunistic pathogens and transferable antibiotic resistance genes. Overall, we provided the most comprehensive assessment of the microbiome of fermented food to date and generated a new view of its potential benefits and risks related to human health.

Effects of trace PFOA on microbial community and metabolisms: Microbial selectivity, regulations and risks

Perfluorooctanoic acid (PFOA), a "forever chemical", is continuously discharged and mitigated in the environment despite its production and use being severely restricted globally. Due to the transformation, attachment, and adsorption of PFOA in aquatic environments, PFOA accumulates in the porous media of sediments, soils, and vadose regions. However, the impact of trace PFOA in the porous media on interstitial water and water safety is not clear. In this work, we simulated a porous media layer using a sand column and explored the effects of µg-level PFOA migration on microbial community alternation, microbial function regulation, and the generation and spread of microbial risks. After 60 days of PFOA stimulation, Proteobacteria became the dominant phylum with an abundance of 91.8%, since it carried 71% of the antibiotic resistance genes (ARGs). Meanwhile, the halogen-related Dechloromonas abundance increased from 0.4% to 10.6%. In addition, PFOA significantly stimulated protein (more than 1288%) and polysaccharides (more than 4417%) production by up-regulating amino acid metabolism (p< 0.001) and membrane transport (p < 0.001) to accelerate the microbial aggregation. More importantly, the rapidly forming biofilm immobilized and blocked PFOA. The more active antioxidant system repaired the damaged cell membrane by significantly up-regulating glycerophospholipid metabolism and peptidoglycan biosynthesis. It is worth noting that PFOA increased the abundance of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in porous media by 30% and 106%. PFOA increased the proportion of vertical transmission ARGs (vARGs), and co-occurrence network analysis (r ≥ 0.8, p ≤ 0.01) verified that vARGs were mainly mediated by HBPs. A comprehensive understanding of PFOA interactions with its microecological environment is provided.

Effects of amino acid composition of yeast extract on the microbiota and aroma quality of fermented soy sauce

Yeast extracts, of which amino acids are the main component, can be directly applied to improve the flavor of final soy sauce. In this study, the potential of commercial yeast extracts was explored from amino acid approach to enhance the flavor quality of soy sauce by shaping the core fermentation microbiota. Alkaline and neutral amino acids favored the competitive benefits of flavor-producing bacteria, while acidic amino acids promoted the stress resistance of the fermentation microbiota, especially the abundance of Lactobacillus, which increased to 18.03-23.78% and became the predominant microbiota. The mass ratio of neutral-nonpolar: neutral-polar: acidic: alkaline amino acids was 40: 18: 27: 15, which provided the optimal improvement of soy sauce aroma. The formulation and activated the metabolic pathways of 3-methyl-1-butyraldehyde, 3-methyl-1-butanol and 2-methyl-1-propanol through Leu and Ile, resulting in a 52.6% increase in malt-like aroma. This study provides a new idea for the regulation of soy sauce fermentation.

Bacterial communities in home-made Doushen with and without chili pepper

Doushen is a traditional Chinese fermented soybean product prepared with sterilizated soybeans under open conditions. However, little is known on the bacterial community and their influence on the flavor of Doushen. In the present study, Doushen samples with and without chili pepper were collected to reveal the bacterial community and assess a correlation between bacterial community and VFCs in the two kinds of Doushen samples. We identified four phyla and 97 bacterial genera in the two kinds of Doushen samples. In addition, a total of 17 significantly different OTUs were detected by LEfSe (Line Discriminant Analysis (LDA) Effect Size). Results of Principal coordinates analysis (PCoA), unweighted pair-group method (UPGMA) and functional and phenotypes prediction showed that bacterial communities in the two kinds of Doushen were significantly different. Spearman correlation analysis showed that all the dominant genera, except Clostridium Sensu stricto 1, were significantly correlated with the characteristic VFCs. This study provides a theoretical basis for improving the flavour quality of traditional homemade Doushen.

Structure characterization, antioxidant and emulsifying capacities of exopolysaccharide derived from Tetragenococcus halophilus SNTH-8

Tetragenococcus halophilus exopolysaccharides (THPS) are metabolites released by T. halophilus SNTH-8 to resist a high-salt environment. Although many studies have investigated the mechanisms underlying salt tolerance shown by T. halophilus, structural characteristics as well as antioxidant and emulsifying capacities of THPS remain unclear. In this study, we isolated and purified two components, THPS-1 and THPS-2, from T. halophilus SNTH-8. Purified THPS-1 and THPS-2 were composed of arabinose, xylose, fucose, galactose, glucose, and glucuronic acid at a molar ratio of 1.66:38.95:2.11:26.12:29.73:1.43 and 0.46:40.3:0.54:30.8:1.36:25.54, respectively. The average molecular weights of THPS-1 and THPS-2 were 14.98 kDa and 21.03 kDa, respectively. Moreover, the structures of THPS-1 and THPS-2 were investigated via fourier-transform infrared spectroscopy(FT-IR), nuclear magnetic resonance spectroscopy(NMR), scanning electron microscopy(SEM), and methylation analysis. THPS-1 was a highly branched polysaccharide with a backbone of α-D-(1,4)-Xyl, α-D-(1,6)-Glc and α-D-Xyl as the terminal, while THPS-2 was a highly branched polysaccharide with a backbone of α-D-(1,4)-Xyl and β-D-GlcA as the terminal. The branches were identified as β-D-(1,4,6)-Gal and β-D-(1,6)-Gal. Both THPS-1 and THPS-2 exhibited high antioxidant and emulsifying capacities. Overall, our structural analysis of THPS may further enhance research on natural emulsifiers and antioxidants.

Potential of Probiotics as an Adjunct for Patients with Major Depressive Disorder

Major depressive disorder (MDD) is an enfeebling disease with a lifetime incidence of 20%. While accumulating studies implicate a correlation between the disease and gut microbiota, data show that not every patient responded to probiotic treatments. To comprehensively assess the potential role of probiotics in MDD, this study first summarizes the current pathological hypothesis of the disease from a life-stage perspective, focuses on the potential role of "depression gut microbiota." Currently available managements are then briefly summarized and novel bio-materials having potential therapeutic effects on MDD are also evaluated. To harness the positive effect of probiotics, prebiotics, and postbiotics, clinical evidence and their applications on MDD patients are listed. Factors that may counteract the pre/probiotic applications, such as diet, physiology, gender difference, and use of antibiotics and antidepressants are also discussed. The endocannabinoid (eCBs) system may be promising targets for probiotic therapy. More evidence is needed to demonstrate the hierarchical factors in the complex network driving the disease, and probiotic can be one promising adjunct for patients with MDD.

Characterization of selected Chinese soybean paste based on flavor profiles using HS-SPME-GC/MS, E-nose and E-tongue combined with chemometrics

Headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC/MS) with electronic nose (E-nose) and electronic tongue (E-tongue) was applied for flavor characterization of traditional Chinese fermented soybean paste. Considering geographical distribution and market representation, twelve kinds of samples were selected to investigate the feasibility. A total of 57 volatile organic compounds (VOCs) were identified, of which 8 volatiles were found in all samples. Linear discrimination analysis (LDA) of fusion data exhibited a high discriminant accuracy of 97.22%. Compared with partial least squares regression (PLSR), support vector machine regression (SVR) analysis exhibited a more satisfying performance on predicting the content of esters, total acids, reducing sugar, salinity and amino acid nitrogen, of which correlation coefficients for prediction (Rp) were about 0.803, 0.949, 0.960, 0.896, 0.923 respectively. This study suggests that intelligent sensing technologies combined with chemometrics can be a promising tool for flavor characterization of fermented soybean paste or other food matrixes.

Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation

Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.

Impact of salt concentration on bacterial diversity and changes in biogenic amines during fermentation of farmhouse soybean paste in Northeast China

Farmhouse soybean paste in Northeast China is a traditional fermented product made from soybean, and more than 11% (w/w) salt is usually added during production to control the fermentation process. In this study, the variations in bacterial diversity, biogenic amines(BAs) and physicochemical properties during the natural fermentation of soybean paste with different salt concentrations (8%, 9%, 10%, 11%, and 12%) were studied. The results show that at 0 days (0 d) of fermentation in soybean paste, the dominant genera included Staphylococcus, unidentified Clostridiales, and Sporolactobacillus. During fermentation from 30 d to 90 d, the dominant genera were Tetragenococcus and Staphylococcus. However, the proportions of the dominant genera were different depending on the salt concentration. Putrescine(Put), tryptamine(Try), β-phenethylamine(Phe), cadaverine(Cad), histamine(His), and tyramine(Tyr) showed negative correlations with salt concentration. The amino type nitrogen(ANN), titratable acidity(TTA) and total number of colonies were also negatively correlated with salt concentration. Analysis of the correlation between genera and BAs showed that 12 genera were positively correlated with BAs, and 4 genera were negatively correlated with BAs. The results of this study indicated that salt has a significant impact on bacterial diversity during the fermentation of soybean paste, which in turn affects the changes in bacterial metabolites. From the perspective of food safety, the amount of salt added in the soybean paste can be reduced to 10% under the existing fermentation conditions.

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The effect of salt concentration on soybean paste was studied.

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Salt concentration affected the bacterial diversity and BAs in soybean paste.

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There was a species succession process in the initial 30 days of fermentation.

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There was correlation between the BAs and some bacteria in soybean paste.

Dynamic changes of phenolic acids and antioxidant activity of Citri Reticulatae Pericarpium during aging processes

Citri reticulatae pericarpium (CRP) shows multiple bioactivities, including antioxidant, anti-tumor, and anti-inflammation. The folk proverb "CRP, the older, the better" means storing for longer time would improve its quality, which attributed to the influence of bioactive compounds. The aim of this work was to study which compounds are the factors that long storage would influence the quality of CRP. 161 compounds, including 65 flavonoids, 51 phenolic acids, 27 fatty acids, and 18 amino acids were identified through derivatization and non-derivatization liquid chromatography mass spectrometry approaches. Their dynamic changes indicated phenolic acids, which were reported to have various activities, were the main increased components. Furthermore, the representative phenolic acids were quantified and correlation analysis between their contents and antioxidant activity implicated they were the possible indicators that long storage would improve CRP quality. The results would provide basis for quality control of CRP during storage.

Metaproteomic Insights Into the Microbial Community in Pozol

Pozol is an acidic, refreshing, and non-alcoholic traditional Mayan beverage made with nixtamalized corn dough that is fermented spontaneously. The extensive analysis of the microbiology, biochemistry and metaproteomics of pozol allowed the construction of a comprehensive image of the fermentation system. The main changes in both the substrate and the microbiota occurred in the first 9 h of fermentation. The increase in microorganisms correlated with the drop in pH and with the decrease in the contents of carbohydrates, lipids, and nitrogen, which shows that this stage has the highest metabolic activity. Bacterial proteins were mainly represented by those of lactic acid bacteria, and among them, the proteins from genus Streptococcus was overwhelmingly the most abundant. Yeast proteins were present in all the analyzed samples, while proteins from filamentous fungi increased up to 48 h. The metaproteomic approach allowed us to identify several previously unknown enzyme complexes in the system. Additionally, enzymes for hydrolysis of starch, hemicellulose and cellulose were found, indicating that all these substrates can be used as a carbon source by the microbiota. Finally, enzymes related to the production of essential intermediates involved in the synthesis of organic acids, acetoin, butanediol, fatty acids and amino acids important for the generation of compounds that contribute to the sensorial quality of pozol, were found.

Microbial Communities and Physicochemical Characteristics of Traditional Dajiang and Sufu in North China Revealed by High-Throughput Sequencing of 16S rRNA

The process of soybean fermentation has been practiced for more than 3,000 years. Although Dajiang and Sufu are two popular fermented soybean products consumed in North China, limited information is available regarding their microbial composition. Hence, the current study sought to investigate, and compare, the physicochemical indicators and microbial communities of traditional Dajiang and Sufu. Results showed that the titratable acidity (TA), and salinity, as well as the lactic acid, and malic acid contents were significantly higher in Sufu samples compared to Dajiang. Furthermore, Sufu samples contain abundant sucrose and fructose, while the acetic acid content was lower in Sufu compared to Dajiang samples. Moreover, the predominant bacterial phyla in Dajiang and Sufu samples were Firmicutes and Proteobacteria, while the major genera comprise Bacillus, Lactobacillus, Tetragenococcus, and Weissella. Moreover, Dajiang samples also contained abundant Pseudomonas, and Brevundimonas spp., while Halomonas, Staphylococcus, Lysinibacillus, Enterobacter, Streptococcus, Acinetobacter, and Halanaerobium spp. were abundant in Sufu samples. At the species level, Bacillus velezensis, Tetragenococcus halophilus, Lactobacillus rennini, Weissella cibaria, Weissella viridescens, Pseudomonas brenneri, and Lactobacillus acidipiscis represented the major species in Dajiang, while Halomonas sp., Staphylococcus equorum, and Halanaerobium praevalens were the predominant species in Sufu. Acetic acid and sucrose were found to be the primary major physicochemical factor influencing the bacterial communities in Dajiang and Sufu, respectively. Furthermore, Bacillus subtilis is strongly correlated with lactic acid levels, L. acidipiscis is positively correlated with acetic acid levels, while Staphylococcus sciuri and S. equorum are strongly, and positively, correlated with malic acid. Following analysis of carbohydrate and amino acid metabolism in all samples, cysteine and methionine metabolism, as well as fatty acid biosynthesis-related genes are upregulated in Dajiang compared to Sufu samples. However, such as the Staphylococcus, W. viridescens, and P. brenneri, as potentially foodborne pathogens, existed in Dajang and Sufu samples. Cumulatively, these results suggested that Dajiang and Sufu have unique bacterial communities that influence their specific characteristics. Hence, the current study provides insights into the microbial community composition in Dajiang and Sufu samples, which may facilitate the isolation of functional bacterial species suitable for Dajiang and Sufu production, thus improving their production efficiency.

Dynamics and correlation of microbial community and flavor in Pixian Douban fermented with closed process of constant temperature

BACKGROUND

As a Chinese traditional flavor condiment, Pixian Douban (PXDB) is produced using a traditional open fermentation process. In this study, an experimental fermentation of PXDB was conducted at 40 °C for 90 days in a closed system, which has not been applied to PXDB production. The flavor, microbial community and correlations of the samples in the closed system were compared with those in the traditional fermentation.

RESULTS

The content of organic acids and free amino acids in the closed fermentation of constant temperature (CFCT) achieved the standards of product quality, although they were lower than those in the traditional fermentation. Of the 140 detected aroma components, 98 were shared in the two fermentation processes. Enterobacter, Bacteroides and Megamonas were the core microbial genera related to 26 flavor components in the traditional fermentation, while Pantoea was the core microbial genus related to 18 flavor components in CFCT. The CFCT has its own unique advantages over traditional fermentation in forming aromas. It produced a greater impact on the succession of fungi than those of bacteria after changing traditional fermentation to CFCT. The influence of microorganisms on the formation of flavor components was relatively more balanced in CFCT, while the changed fermentation process impacted greatly on the functions of Zygosaccharomomyces and Pichia but little on those of Sphingomonas, Megamonas and Parabacteroides.

CONCLUSION

The study indicated that it was feasible to ferment PXDB in the closed system, and provides a basis to realize controllable PXDB production. © 2020 Society of Chemical Industry.

Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.

Purification, Structural Characteristics, and Biological Activities of Exopolysaccharide Isolated From Leuconostoc mesenteroides SN-8

In this study, a novel exopolysaccharide (EPS) was extracted from Leuconostoc mesenteroides Shen Nong's (SN)-8 which can be obtained from Dajiang. After the purification step, EPS-8-2 was obtained with molecular weights of 1.46 × 105 Da. The structural characterization of EPS indicated that the EPS belonged to the class polysaccharide, mainly composed of glucan and also contained certain mannose residues that were found to be connected by α-1,6 glycosidic bonds. Moreover, the results demonstrated that EPS displayed a significant capacity to scavenge free radical to some extent, and this anti-oxidant potential was found to be concentration dependent. The results further revealed that EPS displayed a significant inhibitory potential on the growth of HepG2 cells by promoting apoptosis and induced cell cycle arrest in G1 and G2 phases. Overall, these results suggested that EPS can be explored as a possible anti-cancer agent.

Physicochemical, flavor and microbial dynamic changes during low-salt doubanjiang (broad bean paste) fermentation

This study aimed to elaborate the roles of salt concentration on doubanjiang (broad bean paste) fermentation. Three sets of doubanjiang samples which had lower salt concentration than commercial doubanjiang were prepared and the physicochemical parameters, biogenic amines, flavor, microbial dynamics were analyzed during fermentation. The salt reduction showed significant effect on the dynamics of bacteria and fungi, thus leading to doubanjiang samples with different properties. Salt reduction during fermentation relieved the osmotic pressure towards microbes, which favored the accumulation of amino acid nitrogen, amino acids, and volatile flavor compounds. However, higher concentrations of total acids and biogenic amines and the existence of conditional pathogens, such as Klebsiella, Cronobacter and Acinetobacter genera, were observed in salt reduced doubanjiang samples, which was undesirable for doubanjiang quality. This study would deep our understanding of the roles of salt on doubanjiang fermentation.

Role of lactic acid bacteria in flavor development in traditional Chinese fermented foods: A review

Traditional Chinese fermented foods are favored by consumers due to their unique flavor, texture and nutritional values. A large number of microorganisms participate in the process of fermentation, especially lactic acid bacteria (LAB), which are present in almost all fermented foods and contribute to flavor development. The formation process of flavor is complex and involves the biochemical conversion of various food components. It is very important to fully understand the conversion process to direct the flavor formation in foods. A comprehensive link between the LAB community and the flavor formation in traditional Chinese fermented foods is reviewed. The main mechanisms involved in the flavor formation dominated by LAB are carbohydrate metabolism, proteolysis and amino acid catabolism, and lipolysis and fatty acid metabolism. This review highlights some useful novel approaches for flavor enhancement, including the application of functional starter cultures and metabolic engineering, which may provide significant advances toward improving the flavor of fermented foods for a promising market.

Metatranscriptome-based investigation of flavor-producing core microbiota in different fermentation stages of dajiang, a traditional fermented soybean paste of Northeast China

Dajiang, or naturally fermented soybean paste, has a unique flavor that is influenced by the resident microflora. However, the association between flavor and the core microbiota is unclear. Recent advances in RNA sequencing have identified genes that are actively expressed in complex microbial communities. To this end, we analyzed the time-dependent changes in the microbiota and the metabolite profiles of Dajiang using metatranscriptome sequencing, HS-SPME-GC-MS and amino acid analysis identified 10 volatile compounds that contribute to the development of soybean paste flavor. Further analysis of the correlation between the active microorganisms and the physicochemical characteristics and flavor substances in soybean paste indicated that Lactobacillus and Tetragenococcus were the core genera affecting chromaticity and flavor. These microorganisms produce enzymes that catalyze a series of metabolic pathways that generate flavor substances. Our findings provide new insights into the role of the microbiota in the development of flavor in fermented foods.

Metaproteomics insights into traditional fermented foods and beverages

Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

Extraction and biological activity of exopolysaccharide produced by Leuconostoc mesenteroides SN-8

An exopolysaccharide (EPS)-producing strain SN-8 isolated from Dajiang was identified as Leuconostoc mesenteroides. When sucrose was used as the carbon source for fermentation, the output of EPS was 2.42 g/L. High performance liquid chromatography analysis confirmed the presence of monomers such as glucan and mannose. The molecular weight detection value is 2.0 × 10⁵ Da. Fourier transform infrared spectroscopy displayed the EPS had the basic skeleton and functional groups of a typical polysaccharide structure. Scanning electron microscopy showed smooth surfaces and compact structure. Thermal performance analysis showed that the highest heat resistance temperature of the EPS was 80 °C. Compared with vitamin C, its hydroxyl radical scavenging rate was as high as 32% and 1,1-diphenyl-2-picrylhydrazyl scavenging rate was as high as 40% under the same concentration. The peanut oil was the most emulsifiable at a concentration of 1.5 mg/mL, and the emulsification index was 0.55. These results might show that the EPS had high application value.

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.