Comparative metabolic expressions of fermented soybeans according to different microbial starters

Addition of Lactobacillus fermentum to Fermented Sea Buckthorn (Hippophae rhamnoides L.) Fruit Vinegar Significantly Improves Its Sour Taste

Fruit vinegar is typically produced through a two-stage deep liquid fermentation involving alcohol fermentation (Saccharomyces cerevisiae) and acetic acid fermentation (Acetobacter pasteurianus). In order to enhance the flavor and texture of sea buckthorn fruit vinegar, Lactobacillus fermentum was introduced into the alcoholic fermentation stage. At the end of fermentation, the total acid and acetic acid of sea buckthorn (Hippophae rhamnoides L.) fruit vinegar were both enhanced compared with sea buckthorn vinegar brewed through the traditional liquid fermentation method, and in terms of the main active ingredients, the total flavonoid content was slightly enhanced. Non-targeted metabolomics (LC-MS) was used to characterize the characteristic metabolite profiles during the fermentation process. A total of 55 differential metabolites, including organic acids, flavonoids, and amino acids, were identified, and the contents of citric acid, malic acid, and manganic acid, which are the sources of the irritating taste of sea buckthorn berry vinegar, were significantly reduced. In addition, the co-fermentation of Lactobacillus fermentum promoted both glycolysis and the TCA cycle and also led to a significant up-regulation of aromatic metabolites, such as ethyl acetate, ethyl lactate, and ethyl caproate. These results will provide new information on the dynamics of the characterized metabolites during the fermentation of sea buckthorn fruit vinegar.

Unraveling key non-volatiles responsible for taste differences of Pixian broad bean paste based on sensory analysis and untargeted metabolomics

Besides aroma, the tastes of Pixian Broad Bean Paste (PBBP) are also important, however, they have not yet been thoroughly elucidated. Therefore, this study employed sensory and untargeted metabolomics approaches to investigate taste characteristics, molecular basis and their metabolic pathways of PBBP from three different manufacturers and two grades. Results showed PBBP was predominantly characterized by strong sour, umami and salty tastes, and significant differences were observed in samples from different manufacturers and grades (p < 0.05), especially higher sourness, saltiness and umami in premium PBBP. Based on non-volatiles, 55 key differential metabolites were identified through orthogonal partial least square discriminant analysis (OPLS-DA, P value<0.05, VIP value>1.0) and Pearson correlation analysis (|ρ| > 0.7). These key differential metabolites responsible for taste differences were metabolized by 36 crucial KEGG pathways (P value<0.05, impact value>0.05). These results could expand our understandings of PBBP taste compounds and their metabolisms, and provide theoretical evidences for further quality improvement.

Analysis of differential metabolites in Liuyang douchi at different fermentation stages based on untargeted metabolomics approach

The quality and flavor of Liuyang Douchi are usually closely related to the metabolites compostion. This work described the metabolic profiles of Liuyang douchi during fermentation. Obvious hydrolysis of carbohydrates, proteins and slight lipids degradation were observed. Notably, the qu-making and pile-fermentation stage of douchi could be easily distinguished according to their metabolites profile, and pile-fermentation stage showed the most abundant metabolites. Specifically, organic acid, such as succinic acid and lactic acid, accumulated during pile-fermentation, as well as amino acids and derivatives. Especially glutamate (Glu), which contributed to the umami taste, increased form 0.82 mg/g to 15.90 mg/g after fermentation. Meanwhile, metabolisms related to amino acids were also the main enrichment metabolic pathways. Among them, some flavor compunds such as phenylacetaldehyde might drived from phenylalanine metabolism. These results could provide a new understanding on the metabolic characteristics during Liuyang douchi fermentation.

Antioxidant capacities and non-volatile metabolites changes after solid-state fermentation of soybean using oyster mushroom (Pleurotus ostreatus) mycelium

Given the abundance of beneficial properties and enzymes secreted by edible oyster mushrooms, their mycelium could serve as a starter for fermented foods to enhance their nutritional and bioactive quality. This study aimed to investigate the effects on the nutritional ingredients, antioxidant activity, and non-volatile metabolites during solid-state fermentation (SSF) of soybeans by Pleurotus ostreatus mycelium. The results indicated that the contents of dietary fiber and starch in fermented soybeans decreased, while the amounts of protein and lipid increased after SSF (P < 0.05). Analysis of the total phenolic content (TPC) and antioxidant activities of the fermented soybeans revealed that the methanolic extracts significantly increased TPC and antioxidant activities against intracellular reactive oxygen species (ROS) in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, as well as against DPPH and ABTS radicals in vitro. A total 154 differential metabolites were identified after SSF, and a Spearman correlation study revealed a direct relationship between antioxidant activities and certain metabolites including phenolic compounds, oligopeptides, and free fatty acids etc. Among these metabolites, phenolic compounds produced by the shikimic acid pathway were diverse in variety and had the greatest multiple differences. The study discovered that a potential mechanism involving SSF with P. ostreatus mycelium increased the antioxidant activity of soybeans.

Analysis of Different Strains Fermented Douchi by GC×GC-TOFMS and UPLC-Q-TOFMS Omics Analysis

Douchi is a kind of soybean-fermented food in China. To explore the common and differential compounds in different Douchi, Douchi was fermented by Aspergillus niger, Rhizopus arrhizus, and Bacillus circulans, respectively, and co-fermented by the three strains in this study. The common and characteristic flavor compounds and common and characteristic non-volatile components of different strains of fermented Douchi were explored through GC×GC-TOFMS and UPLC-Q-TOFMS omics analysis. The result suggested that Pyrazines, ketones, and alkenes such as tetramethyl-pyrazine, 2,5-dimethyl pyrazine, furaneol, 2,3-butanedione, gamma-terpinene might contribute to the basic flavor of the Douchi fermented by A. niger, R. arrhizus, and B. circulans. Peptides, amines, and flavonoids, such as N-acetylhistamine, 7,3',4'-trihydroxyflavone, (3S,8As)-3-isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione might contribute to the basic function of the above three Douchi. The common metabolic pathways involved in the fermentation were isoflavonoid biosynthesis, flavonoid biosynthesis, etc. Ketones and esters such as 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyran-4-one, 3-octanone, 5-methylfurfural and nonanal contributed to the unique flavor, while betaine, oleanolic acid, saikosaponin D and leucine might contribute to the unique function of A. niger fermented Douchi. Alkenes, pyrazine, and ketones such as α-terpinene, ethyl-pyrazine, dihydro-3-methyl-2(3H)-furanone, and linalool might contribute to unique flavor, while cordycepin, 2-Phenylacetamide might contributed to the unique function of R. arrhizus fermented Douchi. The unique flavor of B. circulans fermented Douchi might derived from ketones and esters such as 3-acetyl-2-butanone, 2-tridecanone, propionic acid-2-phenylethyl ester, while vitexin, astragalin, and phenethylamine might contribute to the unique function. Compared with single-strain fermented Douchi, the flavor substances and non-volatile components in multi-strain fermented Douchi were more abundant, such as hexadecanoic acid methyl ester, benzeneacetic acid ethyl ester, 9,12-octadecadienoic acid ethyl ester, nuciferine, and erucamide. It was speculated that there were common and differential substances in Douchi fermented by Aspergillus niger, Rhizopus arrhizus, and Bacillus circulans, which might contribute to the basic and unique flavor and function. Compared with single-strain fermented Douchi, the flavor substances and metabolites in multi-strain fermented Douchi were more abundant. This study provided a reference for the research of flavor and functional substances of Douchi.

Determination of extracellular proteinase in L. helveticus Lh191404 based on whole genome sequencing and proteomics analysis

Lactobacillus helveticus exhibits a remarkable proteolytic system. However, the etiology of these protein hydrolysis characteristics, whether caused by extracellular proteinases (EP) or cell envelope proteinases (CEP), has been puzzling researchers. In this study, third-generation Nanopore whole genome sequencing and proteomics analysis were used to unravel the root cause of the aforementioned confusion. The genome of L. helveticus Lh191404 was 2,117,643 bp in length, with 67 secreted proteins were found. Combined with proteomic analysis, it was found that the protein composition of extraction from CEP and EP were indeed the same substance. Bioinformatics analysis indicated that the CEP belonged to the PrtH1 Variant (PrtH1_V) genotype by phylogenetic analysis. The three-dimensional structures of various domains within the PrtH1_V-191404 had been characterized, providing a comprehensive understanding of its structural features. Results of proteinase activity showed that the optimal reaction temperature was 40 °C, with a pH of 6.50. These findings suggested that the origin of EP in L. helveticus Lh191404 may be due to CEP being released into the substrate after detaching from the cell wall. This research is of guiding significance for further understanding the operational mechanism of the protein hydrolysis system in lactic acid bacteria.

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.

Microbial community succession and its correlation with the dynamics of flavor compound profiles in naturally fermented stinky sufu

Wuhan stinky sufu is a traditional fermented soybean product with a short ripening period and unique flavor. The aim of this study was to explore the characteristic flavor compounds and core functional microbiota of naturally fermented Wuhan stinky sufu. The results indicated that 11 volatile compounds including guaiacol, 2-pentylfuran, dimethyl trisulfide, dimethyl disulfide, acetoin, 1-octen-3-ol, (2E)-2-nonenal, indole, propyl 2-methylbutyrate, ethyl 4-methylvalerate, nonanal were characteristic aroma compounds, and 6 free amino acids (Ser, Lys, Arg, Glu, Met and Pro) were identified as taste-contributing compounds. 4 fungal genera (Kodamaea, unclassified_Dipodascaceae, Geotrichum, Trichosporon), and 9 bacterial genera (Lysinibacillus, Enterococcus, Acidipropionibacterium, Bifidobacterium, Corynebacterium, Lactococcus, Pseudomonas, Enterobacter, and Acinetobacter) were identified as the core functional microbiota with positive effects on the production of flavor compounds. These findings would enhance the understanding of core flavor-producing microorganisms in naturally fermented soybean products and potentially provide guidance for enhancing the quality of sufu.

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.

Comprehensive investigation on volatile and non-volatile metabolites in low-salt doubanjiang with different fermentation methods

Doubanjiang is a well-known fermented condiment in China, but the high-salt concentration in its traditional manufacture process greatly lengthens the fermentation time, and leads to potential health risks. Here, the effects of salt reduction and co-inoculated starters (Tetragenococcus halophilus and Zygosaccharomyces rouxii) on the volatile metabolites (VMs) and non-volatile metabolites (NVMs) of doubanjiang were investigated using metabolomics technology and chemometrics analysis. Results showed that 75 VMs were identified, and 12 of them had significant aroma contribution (ROVAs ≥ 1). In addition, 106 NVMs were defined as significantly different metabolites (p < 0.05; VIP ≥ 1). Salt reduction could significantly increase the concentrations of VMs, but this strategy also promoted some undesirable odors like 2-phetylfuran and hexanoic acid, which could be totally suppressed by inoculation of starter. Moreover, the two starters improved amino acid, ester, and acid metabolites. This study provides a deeper insight into the development of low-salt fermented foods.

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.

Metabolomic analysis of the effects of a mixed culture of Saccharomyces cerevisiae and Lactiplantibacillus plantarum on the physicochemical and quality characteristics of apple cider vinegar

Introduction

This study compared differences in physicochemical characteristics of the vinegar made by a mixed culture (MC) of Saccharomyces cerevisiae and Lactiplantibacillus plantarum and a pure culture (PC) of Saccharomyces cerevisiae.

Methods

The fermentation process was monitored, and metabolomics analysis by Liquid Chromagraphy-Mass Spectrometry (LC-MS) was applied to the compositional differences between PC and MC vinegars, combined with quantification of organic acids, amino acids and B vitamins.

Results

A total of 71 differential metabolites including amino acids, organic acids and carbohydrates, and six possible key metabolic pathways were identified. MC enhanced the malic acid utilization and pyruvate acid metabolism during fermentation, increasing substrate-level phosphorylation, and supplying more energy for cellular metabolism. Higher acidity at the beginning of acetic acid fermentation, resulting from lactic acid production by Lactiplantibacillus plantarum in MC, suppressed the cellular metabolism and growth of Acetobacter pasteurianus, but enhanced its alcohol metabolism and acetic acid production in MC. MC vinegar contained more vitamin B, total flavonoids, total organic acids, amino acids and had a higher antioxidant capacity. MC enhanced the volatile substances, particularly ethyl lactate, ethyl caprate and ethyl caproate, which contributed to a stronger fruity aroma.

Discussion

These results indicated the mixed culture in alcoholic fermentation can effectively enhance the flavor and quality of apple cider vinegar.

Improvement of physicochemical characteristics, flavor profiles and functional properties in Chinese radishes via spontaneous fermentation after drying

Spontaneously dried-fermented radishes have been consumed in China for hundreds of years and are usually fermented for a long time to acquire high quality. In this study, the spontaneously dried-fermented radishes with short-term manufacturing periods were made from five different varieties of radishes that grew in the same environment. In addition, the physicochemical characteristics (i.e., moisture content, soluble solid, and pH value), flavor profiles (i.e., free amino acids, organic acids, and volatile compounds), and functional properties (i.e., total phenolics content, total flavonoids content, sulforaphane content, and γ-aminobutyric acid [GABA] content) of these five raw radishes and spontaneously dried-fermented radishes were analyzed and compared. In detail, the content of volatile and nonvolatile compounds increased, especially in oxalic acid, succinic acid, and umami free amino acids. Furthermore, functional components, such as sulforaphane and GABA, were also enriched via spontaneous fermentation after drying. In addition, the results of principal component analysis, hierarchical clustering analysis, and redundancy analysis showed that there were significant discrepancies appeared when raw radishes were processed via spontaneous fermentation or not. These results suggested that the process of spontaneous fermentation after drying may contribute to improving the quality of fresh radishes. Notably, radishes with red skin and flesh were regarded as exceptional varieties for processing, because of the preferable flavor profiles and affluent functional substances via spontaneous fermentation after drying. Therefore, these findings could deliver a systematical insight into developing processed radishes with high quality. PRACTICAL APPLICATION: The spontaneously dried-fermented radishes were manufactured through the process of spontaneous fermentation after drying, which acquired tasty and healthy characteristics by accumulating the volatile and nonvolatile compounds as well as the functional components, like total phenolics, total flavonoids, sulforaphane, and γ-aminobutyric acid. Importantly, because of the excellent processing properties, the radishes with red skin and flesh could be more appropriate to produce spontaneously dried-fermented radishes. Our findings may provide a practical strategy for developing vegetable relishes with superb flavor profiles and good functional properties in pickled vegetables.

Monitoring the Aroma Compound Profiles in the Microbial Fermentation of Seaweeds and Their Effects on Sensory Perception

Seaweeds have a variety of biological activities, and their aromatic characteristics could play an important role in consumer acceptance. Here, changes in aroma compounds were monitored during microbial fermentation, and those most likely to affect sensory perception were identified. Ulva sp. and Laminaria sp. were fermented and generally recognized as safe microorganisms, and the profile of volatile compounds in the fermented seaweeds was investigated using headspace solid-phase microextraction with gas chromatography–mass spectrometry. Volatile compounds, including ketones, aldehydes, alcohols, and acids, were identified during seaweed fermentation. Compared with lactic acid bacteria fermentation, Bacillus subtilis fermentation could enhance the total ketone amount in seaweeds. Saccharomyces cerevisiae fermentation could also enhance the alcohol content in seaweeds. Principal component analysis of volatile compounds revealed that fermenting seaweeds with B. subtilis or S. cerevisiae could reduce aldehyde contents and boost ketone and alcohol contents, respectively, as expected. The odor of the fermented seaweeds was described by using GC–olfactometry, and B. subtilis and S. cerevisiae fermentations could enhance pleasant odors and reduce unpleasant odors. These results can support the capability of fermentation to improve the aromatic profile of seaweeds.

Non-beany flavor soymilk fermented by lactic acid bacteria: Characterization, stability, antioxidant capacity and in vitro digestion

LAB fermentation could reduce the beany flavor, the sensitization of soymilk and improve the digestibility of soymilk, easy to be accepted by consumers. This study evaluated the characterization, stability, in vitro digestion and antioxidant capacity of soymilk fermented by different Lactic acid bacteria (LAB). The results showed that fat content of L.plantarum-S (0.77 g/100 mL) was the lowest, which proved that L.plantarum had a significant effect on lipid degradation, the protein content of L.delbrueckii-S (23.01 mg/mL) was higher. L.delbrueckii-S and L.paracasei-S were more acceptable to people, as well as high overall ratings. L.paracasei fermented soymilk has better suspension stability and smaller particle size. The fermented soymilk showed higher free amino acids (FAA) content, peptide content and stronger antioxidant activity than soymilk after digestion. The soymilk fermented by L. plantarum contained higher FAA content and L.delbrueckii contained the highest peptide content compared with other strains. L.acidophilus-S and L.rhamnosus-S showed stronger DPPH scavenging rate and FARP, which were 57.03 % and 52.78 % stronger than unfermented soymilk, respectively. These results may be provided a theoretical basis for the strain screening of fermented soymilk.

Comparative Metabolomic Analysis of Moromi Fermented Using Different Aspergillus oryzae Strains

Aspergillus oryzae (A. oryzae) is an important starter in the fermentation of koji and moromi. However, the effect of different A. oryzae strains on the quality of moromi has rarely been studied. For this reason, this study analyzed the physicochemical properties, enzyme activity, sensory quality, and metabolite profiles of moromi samples fermented using two strains (A. oryzae KCCM12012P (moromi-1) and KCCM12804P (moromi-2)), which were newly isolated from fermented soy foods, and compared them to those of a commercialized A. oryzae strain (control). Amino-type nitrogen contents of moromi-1 and moromi-2 samples were higher than that of control moromi, and their amylase and protease activities were also higher. Moreover, metabolite profiles of moromi were significantly altered according to strains. In particular, the levels of many amino acids, peptides, nucleotides, and acidic compounds were altered, which resulted in changes in the sensory quality of moromi. Although volatile compounds were not investigated, the results suggested that the quality of moromi was significantly different for newly isolated strains, especially A. oryzae KCCM12804P, and they were superior to the commercial strain in terms of taste-related substances. Therefore, these strains could be used as good starters to produce moromi and soy sauce with good sensory quality.

The application of enzymatic fermented soybean effectively regulates associated microbial communities in tea soil and positively affects lipid metabolites in tea new shoots

Compared with traditional organic fertilizer, fermented soybean is a better fertilizer resource in tea plantations. The application of organic fertilizer is a feasible practice to mitigate the soil degradation caused by the overuse of chemical fertilizers, which can effectively regulate soil microbial communities in tea plantations. However, the effects of fermented soybean on soil microbial communities, soil metabolites and metabolites in tea new shoots have not been systematically demonstrated, and their interactions have never been studied. Here, we investigated the responses of the soil microbial community, soil metabolites and metabolites of tea new shoots to urea fertilization (UF), naturally fermented soybean fertilization (NFS) and enzymatic fermented soybean fertilization (EFS), and analyzed the relationships between soil microbes, soil metabolites and metabolites in tea new shoots. The results showed that soil bacterial communities were dominated by Pseudomonas, Romboutsia, Candidatus_Nitrosotalea and Helicobacter, and soil fungal communities were dominated by Peziza, Fusarium, Candida and Cheilymenia at the genus level. In EFS, bacterial genera (Glutamicibacter and Streptomyces) and fungal genera (Candida and Actinomucor) presented high abundances, which were correlated with soil carbohydrate and lipid including D-Mannitol, D-Sorbitol, 9,12-Octadecadienoic acid and (Z)-13-Docosenoic acid. Enzymatic fermented soybean fertilization also affected the lipid metabolites in tea new shoots. Glycerolipids and glycerophospholipids significantly increased in EFS, which positively correlated with some soil microbial communities. Besides, the application of fermented soybean fertilizer could increase the contents of TP, AP and AK, which were also important environmental factors affecting the structure of soil microbial community in tea plantation. It was concluded that fermented soybean fertilization could improve soil nutrition, regulate associated microbial communities, and positively affect lipid metabolites in tea new shoots. This study not only explores the relationships between soil microbes and metabolites in tea plants, but also provides feasible technical guidance to cultivate high-quality tea using soybean as high-grade fertilizer.

Genomic and Metabolic Features of an Unexpectedly Predominant, Thermophilic, Assistant Starter Microorganism, Thermus thermophilus, in Chinese Inner Mongolian Cheese

Inner Mongolian cheese is a traditional dairy product in China. It is produced without rennet, using naturally acidified milk that is simmered to achieve whey separation. In order to analyse the impact of simmering on the microbial community structure, high-throughput sequencing was performed to obtain bacterial 16S rRNA sequences from cheeses from the Ordos (ES), Ulanqab (WS), Horqin (KS) and Xilingol (XS) grasslands of Inner Mongolia. The relative abundance of an unexpected microorganism, Thermus thermophilus, ranged from 2% to 9%, which meant that its dominance was second only to that of lactic acid bacteria (LABs). Genome sequencing and fermentation validation were performed in T. thermophilus N-1 isolated from the Ordos, and it was determined that T. thermophilus N-1 could ingest and metabolise lactose in milk to produce lactate during the simmering process. T. thermophilus N-1 could also produce acetate, propionate, citrate and other organic acids through a unique acetate production pathway and a complete propionate production pathway and TCA cycle, which may affect texture and flavour development in Inner Mongolian cheese. Simultaneously, the large amount of citrate produced by T. thermophilus N-1 provides a necessary carbon source for continuous fermentation by LABs after the simmering step. Therefore, T. thermophilus N-1 contributes to cheese fermentation as a predominant, thermophilic, assistant starter microorganism unique to Chinese Inner Mongolian cheese.

Metabolomics Approaches for the Comprehensive Evaluation of Fermented Foods: A Review

Fermentation is an important process that can provide new flavors and nutritional and functional foods, to deal with changing consumer preferences. Fermented foods have complex chemical components that can modulate unique qualitative properties. Consequently, monitoring the small molecular metabolites in fermented food is critical to clarify its qualitative properties and help deliver personalized nutrition. In recent years, the application of metabolomics to nutrition research of fermented foods has expanded. In this review, we examine the application of metabolomics technologies in food, with a primary focus on the different analytical approaches suitable for food metabolomics and discuss the advantages and disadvantages of these approaches. In addition, we summarize emerging studies applying metabolomics in the comprehensive analysis of the flavor, nutrition, function, and safety of fermented foods, as well as emphasize the applicability of metabolomics in characterizing the qualitative properties of fermented foods.

Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation

Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.

Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps)

Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.

Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review

Metabolomics can be applied for comparative and quantitative analyses of the metabolic changes induced by microorganisms during fermentation. In particular, mass spectrometry (MS) is a powerful tool for metabolomics that is widely used for elucidating biomarkers and patterns of metabolic changes. Fermentation involves the production of volatile metabolites via diverse and complex metabolic pathways by the activities of microbial enzymes. These metabolites can greatly affect the organoleptic properties of fermented foods. This review provides an overview of the MS-based metabolomics techniques applied in studies of fermented foods, and the major metabolic pathways and metabolites (e.g., sugars, amino acids, and fatty acids) derived from their metabolism. In addition, we suggest an efficient tool for understanding the metabolic patterns and for identifying novel markers in fermented foods.

Microbial Community Dynamics and Metabolome Changes During Spontaneous Fermentation of Northeast Sauerkraut From Different Households

Sauerkraut, one of the most popular traditional fermented vegetable foods in northern China, has been widely consumed for thousands of years. In this study, the physicochemical characteristics, microbial composition and succession, and metabolome profile were elucidated during the fermentation of traditional northeast sauerkraut sampled from different households. The microbial community structure as determined by high-throughput sequencing (HTS) technology demonstrated that Firmicutes and Proteobacteria were the predominant phyla and Weissella was the most abundant genus in all samples. Except for Weissella, higher relative abundance of Clostridium was observed in #1 sauerkraut, Clostridium and Enterobacter in #2 sauerkraut, and Lactobacillus in #3 sauerkraut, respectively. Meanwhile, Principal component analysis (PCA) revealed significant variances in the volatilome profile among different homemade sauerkraut. Acids and lactones were dominant in the #1 sauerkraut. The #2 sauerkraut had significantly higher contents of alcohols, aldehydes, esters, sulfides, and free amino acids (FAAs). In comparison, higher contents of terpenes and nitriles were found in the #3 sauerkraut. Furthermore, the potential correlations between the microbiota and volatilome profile were explored based on Spearman’s correlation analysis. Positive correlations were found between Clostridium, Enterobacter, Lactobacillus, Leuconostoc, Weissella and most volatile compounds. Pseudomonas, Chloroplast, Rhizobium, Aureimonas, and Sphingomonas were negatively correlated with volatile compounds in sauerkraut. This study provided a comprehensive picture of the dynamics of microbiota and metabolites profile during the fermentation of different homemade northeast sauerkraut. The elucidation of correlation between microbiota and volatile compounds is helpful for guiding future improvement of the fermentation process and manufacturing high-quality sauerkraut.

Functional Microbiota for Polypeptide Degradation during Hypertonic Moromi-Fermentation of Pixian Broad Bean Paste

Traditional fermented bean pastes are indispensable seasonings in many East Asian countries. They are produced via hypertonic solutions by spontaneous fermentation. Functional, unknown microbiota carry great risks for food safety and stable quality. Thus, analysis and subsequent utilization of functional microbiota will be a good strategy to resolve these problems. During bean fermentation, the microbial functions were divided into two stages, including first stage-raw material (polypeptide) degradation and second stage-amino acid catabolism. In this study, we aimed to analyze the functional microbiota of first stage. Omics-studies, including high-throughput sequencing, correlation analysis and extracellular proteome, were used to generate candidate functional microbes for polypeptide degradation in this study. Then, we cultured the candidate functional microbes. After the batch fermentation and enzymatic analysis, we found three strains secreted peptidase and resulted amino acid accumulation, involving Aspergillus niger, Candida zeylanoides and Bacillus licheniformis. Thus, A. niger, C. zeylanoides and B. licheniformis conducted the functional microbiota for polypeptide degrading during hypertonic moromi fermentation. This study supplies a strategy for functional microbiota analysis. In addition, this is the first report that C. zeylanoides can secrete proteome and produce amino acids from polypeptide.

Structural and metabolic performance of p-cresol producing microbiota in different carbon sources

p-Cresol (PC) is a potential off-flavor and carcinogenic compound that affects food flavor and safety. However, controlling the production of PC when making fermented food is hindered by a lack of knowledge of the microbial diversity and the growth requirements of the microbiota that produce PC. To address this, the present study used three media with selected carbon sources (glucose, ethanol and lactic acid) to explore the microbial origin of PC and to determine the preferred carbon source for the PC-producing microbiota in the pit mud of the strong-aroma type Baijiu. The results showed that the different carbon sources affected the microbial structure, especially of the PC-producing microbiota. Glucose led to the highest production of PC and lactic acid to the lowest. The production of PC was significantly correlated (p < 0.05, |ρ| > 0.6) with Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella Soehngenia, Clostridium and Sedimentibacter in the glucose medium; with Proteiniborus, Ruminococcus and Sporanaerobacter in the ethanol medium; and with Lutispora and Tepidimicrobium in the lactic acid medium. Multiphasic metabolite target analysis further indicated that the PC-producing microbiota could also metabolize flavor compounds. Lactic acid could inhibit the production of PC and ensure that the microbiota produced the appropriate flavor compounds during culture. Collectively, Dorea, Sporanaerobacter, Tepidimicrobium, Tissierella_Soehngenia, Clostridium, Sedimentibacter, Proteiniborus, Ruminococcus and Lutispora were identified as potential PC producers in three media with glucose preferred as the carbon source. These findings provide a perspective on the microbiota and carbon source preference for ultimately improving the quality of distilled alcoholic beverage.