Molecular techniques reveal more secrets of fermented foods

Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.

Effect of selective fermentation on nutritional parameters and techno-functional characteristics of fermented millet-based probiotic dairy product

The primary goal of this study was to assess the effect of selective fermentation on the nutritional and techno-functional characteristics of fermented millet-skim milk-based product. The product was made with HHB-311 biofortified pearl millet (PM) flour, skim milk powder, and isolated cultures (either alone or in combination) of Limosilactobacillus fermentum MS005 (LF) and Lactobacillus rhamnosus GG 347 (LGG). To optimize fermentation time, time intervals 8, 16, and 24 h were explored, while the temperature was kept 37 °C. Results of protein digestibility showed that LF (16 h) and LGG (24 h) fermented samples had significantly higher (P < 0.05) protein digestibility of 90.75 ± 1.6% and 93.76 ± 3.4%, respectively, than that of control (62.60 ± 2.6%). Further, 16 h fermentation with LF showed enhanced iron (39%) and zinc (14%) bioavailability. The results suggested that LF with 16 h fermentation is most suitable for making millet-based fermented products with superior techno-functional attributes and micronutrient bioavailability.

Characterization and comparison of flavors in fresh and aged fermented peppers: Impact of different varieties

The flavor profiles of fresh and aged fermented peppers obtained from four varieties were thoroughly compared in this study. A total of 385 volatile compounds in fermented pepper samples were detected by flavoromics (two-dimensional gas chromatography-time-of-flight mass spectrometry). As fermentation progressed, both the number and the total concentration of volatile compounds changed, with esters, alcohols, acids, terpenoids, sulfur compounds, and funans increasing, whereas hydrocarbons and benzenes decreased. In contrast to the fresh fermented peppers, the aged fermented samples exhibited lower values of pH, total sugars, and capsaicinoids but higher contents of organic acids and free amino acids. Furthermore, the specific differences and characteristic aroma substances among aged fermented peppers were unveiled by multivariate statistical analysis. Overall, 64 volatiles were screened as differential compounds. In addition, Huanggongjiao samples possessed the most abundant differential volatiles and compounds with odor activity values > 1, which were flavored with fruity, floral, and slightly phenolic odors. Correlation analysis demonstrated that the levels of 23 key aroma compounds (e.g., ethyl 2-methylbutyrate, 1-butanol, and ethyl valerate) showed a significantly positive correlation with Asp, Glu and 5 organic acids. By contrast, there is a negative association between the pH value and total sugar. Overall, aging contributed significantly to the flavor attributes of fermented peppers.

The functionalities and applications of whey/whey protein in fermented foods: a review

Whey, a major by-product of cheese production, is primarily composed of whey protein (WP). To mitigate environmental pollution, it is crucial to identify effective approaches for fully utilizing the functional components of whey or WP to produce high-value-added products. This review aims to illustrate the active substances with immunomodulatory, metabolic syndrome-regulating, antioxidant, antibacterial, and anti-inflammatory activities produced by whey or WP through fermentation processes, and summarizes the application and the effects of whey or WP on nutritional properties and health promotion in fermented foods. All these findings indicate that whey or WP can serve as a preservative, a source of high-protein dietary, and a source of physiologically active substance in the production of fermented foods. Therefore, expanding the use of whey or WP in fermented foods is of great importance for converting whey into value-added products, as well as reducing whey waste and potential contamination.

Culture condition optimization of naturally lacto-fermented cucumbers based on changes in detrimental and functional ingredients

A two-step trial was used to optimize the culture condition of naturally lacto-fermented cucumbers. In the first trial, changes in pH values and total biogenic amines were measured to optimize the pickling juice formula. A 15% crystal sugar solution with low-salt brine at 4 °C was proved to be the best formula. In the second trial, pH values, organic acids, total phenolics, flavonoids, saponins and free amino acids, as well as biogenic amines and nitrites under the optimal pickling formula were measured. The optimal fermentation day was suggested at around 8 days. During the cucumber's fermentation process, the pH value was quickly lowered to <4.6. Meanwhile, the functional ingredients increased significantly. In contrast, total biogenic amines and nitrites did not exceed the risk limit, evidencing the safety and functional characteristics for the naturally lacto-fermented cucumbers. The two-step trial has evidenced the possibility to develop desirable lacto-fermented cucumbers.

The optimization of sequential fermentation in the dealcoholized apple juice for reducing lipids

Yeast and lactic acid bacteria are widely used in fermented foods and the nutrients and metabolites produced by fermentation have cholesterol degrading effects. This study utilized Xinjiang Aksu apples as the material to optimize the sequential fermentation process of different strains and construct a fermentation kinetic model to develop a functional fermentation product with low-sugar, probiotics-rich and lipid-lowering properties. The sequential fermentation of dealcoholized apple juice with Saccharomyces cerevisiae and Lactobacillus plantarum was optimized by response surface design, based on which a sequential fermentation kinetic model was constructed. The changes of short-chain fatty acids, cholesterol elimination rate and hydrophobic properties during the fermentation process were studied. The results showed that the kinetic model established under the optimal conditions could effectively predict the dynamic changes of the basic indexes during the fermentation process. After fermentation, the viable number of L. plantarum was 4.96 × 108 CFU/mL, short-chain fatty acids increased, the cholesterol elimination rate reached 45.06%, and the hydrophobicity was 51.37%, which had favorable lipid-lowering properties and hydrophobic effect. This research will provide a theoretical basis and technical support for the monitoring of microbial dynamics and functionalization development of sequentially fermented apple juice with different strains.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05741-z.

Characterization of lactic acid bacteria isolated from street pickles of Dhaka, Bangladesh

Traditionally fermented pickles are a popular street food in Bangladesh famous for their unique flavors and health benefits. Pickles are often prepared by fermentation using lactic acid bacteria (LAB) that can act as probiotics. The study was aimed to isolate and characterize lactic acid bacteria from pickle samples collected from streets of Dhaka city, as well as assess the microbial quality of pickles for food safety. A total of 30 pickle samples of different kinds were collected from streets of Dhaka city. Isolation and identification were conducted using conventional cultural and biochemical tests, followed by molecular confirmation of identity. Antibiotic susceptibility of isolates was investigated against 7 antibiotics of different groups. Antimicrobial activity of LAB isolates was analyzed by well-diffusion assay and phenotypic enterocin activity assay. Physiological characterizations of LAB were performed to determine their tolerance to temperature, salt, pH, bile, carbohydrate fermentation pattern, proteolytic activity and biofilm formation. Fifty isolates were obtained from pickle samples, of which 18% was identified as LAB, including Enterococcus faecalis (6) and Enterococcus faecium (3). The rest included S. aureus (18), E. coli (11), Klebsiella spp. (5), Salmonella (3), Shigella (3) and Pseudomonas aeruginosa (1). Antibiotic resistance pattern revealed higher occurrence of resistance against azithromycin among the non-LAB isolates, but none of the LAB isolates were found to resist any of the antibiotics used. Antimicrobial activity of LAB isolates was not observed against the foodborne isolates. All LAB isolates fermented a wide range of carbohydrates and showed adequate tolerance to salt, pH, temperature and bile. Out of 9 isolates, 5 displayed proteolytic activity, and 6 were found as strong biofilm producer. These results suggest that although the LAB isolates from street pickles collected from Dhaka does not have antimicrobial activities, they still have potential to be used as probiotics. It also shows high occurrence of antibiotic resistant foodborne pathogens in pickles, indicating that consumption of such street food can be serious health hazard.

Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations

BACKGROUND

Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we performed a large-scale and comprehensive investigation for the BGCs in global food fermentations by metagenomics analysis.

RESULTS

We recovered 653 bacterial metagenome-assembled genomes (MAGs) from 367 metagenomic sequencing datasets covering 15 general food fermentation types worldwide. In total, 2334 secondary metabolite BGCs, including 1003 novel BGCs, were identified in these MAGs. Bacillaceae, Streptococcaceae, Streptomycetaceae, Brevibacteriaceae and Lactobacillaceae contained high abundances of novel BGCs (≥ 60 novel BGCs). Among 2334 BGCs, 1655 were habitat-specific, originating from habitat-specific species (80.54%) and habitat-specific genotypes within multi-habitat species (19.46%) in different food fermentation types. Biological activity analysis suggested that 183 BGC-producing secondary metabolites exhibited high probabilities of antibacterial activity (> 80%). These 183 BGCs were distributed across all 15 food fermentation types, and cheese fermentation contained the most BGC number.

CONCLUSIONS

This study demonstrates that food fermentation systems are an untapped reservoir of BGCs and bioactive secondary metabolites, and it provides novel insights into the potential human health benefits of fermented foods. Video Abstract.

Exploration of microbial profile of traditional starters and its influence on aroma profile and quality of Chinese steamed bread

BACKGROUND

Chinese steamed bread (CSB) is a popular staple food in China with traditional ethnic characteristics. CSB with traditional starters has good flavor and texture but is unstable and requires a long preparation time. Therefore, it is necessary to analyze the traditional starters (ST) and their influence on the flavor and quality of steamed bread to meet people's requirements as a staple food.

RESULTS

The count of yeast, lactic acid bacteria and total microbial population significantly varied in different traditional starters; Saccharomyces and Lactobacillus were the predominant genera. Among the tested samples, fungi were found in ST from Shijiazhuang (SJ), Handan (HD) and Langfang (LF), while bacteria were found in ST from Tangshan (TS) and SJ at sub-predominant levels. In terms of the bread quality, the highest specific volume and porosity were in XT-CSB (Xingtai); the highest height/diameter ratio was in SJ-CSB; and the highest sensory score was in TS-CSB. A total of 26 aroma compounds (VIP > 1; variable importance for predictive components) were identified to discriminate CSB fermented with different starters, which were separated by stepwise canonical discriminant analysis using two functions. The correlation analysis among microbiota, aroma compounds and bread quality showed a higher contribution of bacteria than of fungi.

CONCLUSION

Differences in microbial profiles caused different aroma profiles and quality of CSB; and the CSB fermented with traditional starters were sufficiently separated by stepwise canonical discriminant analysis based on aroma compounds. © 2023 Society of Chemical Industry.

Metagenomic and physicochemical analysis of Kombucha beverage produced from tea waste

Kombucha beverage produced through fermentation of sugared tea using bacteria and yeast has gained attention for its beneficial health benefits. However, the cost linked to the raw materials often increases the upstream process expenses, thereby the overall operating expenditures. Thus, there is a need to explore alternative waste and cost-effective raw materials for Kombucha fermentation. The present study, compared the physico-chemical and microbial growth pattern of Kombucha beverage production using tea waste from the tea processing industries with that of the green/black tea, reporting similar trends irrespective of its type. Further, the amplicon sequencing of 16S rRNA showed dominant presence of Komagataeibacter rhaeticus and high throughput sequencing of ITS1 confirmed the presence of yeast species similar to Brettanomyces bruxellensis in the tea waste based Kombucha beverage. Appreciable amount of carbohydrates (8.5/100 g) and energy (34 kcal/100 g) with appropriate organoleptic properties favourable for human consumption were also observed during the nutritional content and qualitative property assessment. The overall study showed a broad taxonomic and functional diversity existing during Kombucha fermentation process with tea waste to maintain a sustained eco-system to facilitate cost-effective beverage production with desired properties for safe consumption.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05476-3.

Probiotics in the Sourdough Bread Fermentation: Current Status

Sourdough fermentation is an ancient technique to ferment cereal flour that improves bread quality, bringing nutritional and health benefits. The fermented dough has a complex microbiome composed mainly of lactic acid bacteria and yeasts. During fermentation, the production of metabolites and chemical reactions occur, giving the product unique characteristics and a high sensory quality. Mastery of fermentation allows adjustment of gluten levels, delaying starch digestibility, and increasing the bio-accessibility of vitamins and minerals. This review focuses on the main steps of sourdough fermentation, the microorganisms involved, and advances in bread production with functional properties. The impact of probiotics on human health, the metabolites produced, and the main microbial enzymes used in the bakery industry are also discussed.

Application progress of intelligent flavor sensing system in the production process of fermented foods based on the flavor properties

Fermented foods are sensitive to the production conditions because of microbial and enzymatic activities, which requires intelligent flavor sensing system (IFSS) to monitor and optimize the production process based on the flavor properties. As the simulation system of human olfaction and gustation, IFSS has been widely used in the field of food with the characteristics of nondestructive, pollution-free, and real-time detection. This paper reviews the application of IFSS in the control of fermentation, ripening, and shelf life, and the potential in the identification of quality differences and flavor-producing microbes in fermented foods. The survey found that electronic nose (tongue) is suitable to monitor fermentation process and identify food authenticity in real time based on the changes of flavor profile. Gas chromatography-ion mobility spectrometry and nuclear magnetic resonance technology can be used to analyze the flavor metabolism of fermented foods at various production stages and explore the correlation between flavor substances and microorganisms.

The Technological Perspectives of Kombucha and Its Implications for Production

Fermentation is one of the oldest biotechnological tools employed by mankind. Fermenting food gives them better sensory and nutritional qualities, the latter including vitamins, phenolic compounds, antioxidants, and antimicrobials. Kombucha is the result of the fermentation of a sweetened Camellia sinensis infusion by the action of a symbiotic community of yeasts and bacteria organized in a cellulosic biofilm called SCOBY and has gained great prominence among fermented foods and beverages, with a considerable increase in its popularity in the last decade, both among consumers and within the scientific community. This is explained by the particular functional and microbial characteristics of this beverage, such as its antioxidant and antimicrobial potential, long-term stable microbial communities, its suitability for fermentation under different conditions of time and temperature, and amenability to other carbon sources besides sucrose. Thus, this review aims to present and discuss the functional, microbial, and physicochemical aspects of kombucha fermentation, covering the many challenges that arise in its production, in domestic, commercial, and legislation contexts, and the next steps that need to be taken in order to understand this drink and its complex fermentation process.

Deciphering the Microbiota and Volatile Profiles of Algerian Smen, a Traditional Fermented Butter

In Algeria, Smen is a fermented butter produced in households using empirical methods. Smen fermentation is driven by autochthonous microorganisms; it improves butter shelf-life and yields highly fragrant products used as ingredients in traditional dishes as well as in traditional medicine. The present study is aimed at investigating microbial diversity and dynamics during Algerian Smen fermentation using both culture-dependent and culture-independent approaches, as well as by monitoring volatile organic compound production. To reach this goal, fifteen Smen samples (final products) produced in households from different regions in Algeria were collected and analyzed. In addition, microbial and volatile compound dynamics at the different stages of Smen manufacturing were investigated for one Smen preparation. The results showed that Smen is a microbiologically safe product, as all hygiene and safety criteria were respected. The dominant microorganisms identified by both techniques were LAB and yeasts. Lactococcus spp. and Streptococcus thermophilus were the main bacterial species involved in spontaneous raw milk fermentation preceding butter-making, while lactobacilli and enterococci were the only bacteria found to be viable during Smen maturation. Regarding fungal diversity, yeast species were only recovered from two mature Smen samples by culturing, while different species (e.g., Geotrichum candidum, Moniliella sp.) were identified in all samples by the culture-independent approach. Using microbial analysis of a single batch, many of these were found viable during manufacturing. Concerning the volatile profiles, they were highly diverse and characterized by a high prevalence of short chain fatty acids, methylketones, and esters. Correlation analysis between microbial diversity and volatile profiles showed that several yeast (Moniliella sp., K. marxianus) and LAB (e.g., Lactococcus spp., S. thermophilus) species were strongly correlated with one or more volatile organic compound families, including several ethyl esters and methyl ketones that can be linked to pleasant, sweetly floral, fruity, buttery, and creamy odors. This study clearly identified key microorganisms involved in Smen fermentation and maturation that could be used in the future for better fermentation control and improvement of quality attributes.

Nutritional Content Dynamics and Correlation of Bacterial Communities and Metabolites in Fermented Pickled Radishes Supplemented With Wheat Bran

Wheat bran supplementation in cereal food processing improves the nutritional value and quality of the final products. However, whether wheat bran has the potential as a biofortifier to enhance nutritional and flavor of fermented vegetables remains unknown. The study aimed to evaluate the potential of wheat bran supplementation for nutrition and flavor fortification during radish fermentation, and to explore the role of microorganisms in nutritional and flavor development. Using high-throughput sequencing coupled with high-performance liquid chromatography and headspace solid-phase microextraction-gas chromatography-mass spectrometry, the microbial community profiles and nutritional and flavor changes of wheat bran-treated samples were analyzed and compared with control samples. Correlation analysis between bacteria taxa with metabolites were also performed. The results showed that wheat bran treatment increased the content of most free amino acids (FAAs), α-linolenate, thiamine, and riboflavin in the samples (p < 0.05). In addition, the increased consumption of reducing sugar and glutamate in the wheat bran-treated samples was due to the production of secondary metabolites such as lactic acid, ethanol, acetic acid, and GABA (p < 0.05). Moreover, compared with control samples, the flavor of the wheat bran-treated pickled radish was preferable. Wheat bran increased the amount of alcohol, ester, acid, and ketones compounds but reduced the number of sulfides, which increased the aroma but decreased the pungent flavor. Additionally, the correlation analysis suggested that Lactobacillus, the most dominant genus, was boosted by wheat bran and was positively associated with most of FAAs, GABA, and lactate, while negatively associated with most sulfides. Therefore, compared with the control, wheat bran treatment could improve the nutritional values and sensorial properties of radish pickles. New areas of research should explore the co-fermentation of other vegetables with wheat bran, and the potential of this processing technique to provide consumers with products of high nutritional quality.

Constructing Micro-Landscapes: Management and Selection Practices on Microbial Communities in a Traditional Fermented Beverage

Colonche is a traditional beverage produced in Mexico by the fermentation of fruits of several cacti species. In the Meridional Central Plateau region of Mexico, where this study was conducted, it is mainly produced with fruits of Opuntia streptacantha; there, the producers perform spontaneous fermentation and/or fermentations through inoculums. Several factors can change the microbial community structure and dynamics through the fermentation process, but little attention has been directed to evaluate what type and extent of change the human practices have over the microbial communities. This study aims to assess the microbiota under spontaneous and inoculated fermentation techniques, the microorganisms present in the inoculums and containers, and the changes of microbiota during the process of producing colonche with different techniques. We used next-generation sequencing of the V3-V4 regions of the 16S rRNA gene and the ITS2, to characterize bacterial and fungal diversity associated with the different fermentation techniques. We identified 701 bacterial and 203 fungal amplicon sequence variants (ASVs) belonging to 173 bacterial and 187 fungal genera. The alpha and beta diversity analysis confirmed that both types of fermentation practices displayed differences in richness, diversity, and community structure. Richness of bacteria in spontaneous fermentation (0D = 136 ± 0.433) was higher than in the inoculated samples (0D = 128 ± 0.929), while fungal richness in the inoculated samples (0D = 32 ± 0.539) was higher than in spontaneous samples (0D = 19 ± 0.917). We identified bacterial groups like Lactobacillus, Leuconostoc, Pediococcus and the Saccharomyces yeast shared in ferments managed with different practices; these organisms are commonly related to the quality of the fermentation process. We identified that clay pots, where spontaneous fermentation is carried out, have an outstanding diversity of fungal and bacterial richness involved in fermentation, being valuable reservoirs of microorganisms for future fermentations. The inoculums displayed the lowest richness and diversity of bacterial and fungal communities suggesting unconscious selection on specific microbial consortia. The beta diversity analysis identified an overlap in microbial communities for both types of fermentation practices, which might reflect a shared composition of microorganisms occurring in the Opuntia streptacantha substrate. The variation in the spontaneous bacterial community is consistent with alpha diversity data, while fungal communities showed less differences among treatments, probably due to the high abundance and dominance of Saccharomyces. This information illustrates how traditional management guides selection and may drive changes in the microbial consortia to produce unique fermented beverages through specific fermentation practices. Although further studies are needed to analyze more specifically the advantages of each fermentation type over the quality of the product, our current analysis supports the role of traditional knowledge driving it and the relevance of plans for its conservation.

Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China

Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.

Effect of Brine fermented Pickling to Physicochemical, Anti-nutritional, and Microbiological Attributes of Pickled gboma Eggplant (Solanum macrocarpon)

Gboma eggplant (Solanum macrocarpon) has low calorie, high phenolic and antioxidant, excellent dietary fibre and mineral content. Besides healthy effects, gboma eggplant also contained numerous anti-nutrients unbeneficial for human health. Due to high moisture content, gboma eggplant was highly perishable during post-harvest. This research observed the changes of nutritional proximate, mineral contents, acidification indexes, anti-nutrients, phytochemical and antioxidant properties, texture profiles, microbiological characteristics of both raw and pickled gboma eggplant. Gboma eggplant fruits were soaked in clean water for 2 minutes before cutting their calyx lobes. The pre-treated fruits were submerged in sterilized brine (5% salt) for 8 days. Periodically, pickled samples were taken to examine physicochemical, anti-nutritional, and microbiological attributes of pickled gboma eggplant. Results showed that nutritional proximate of moisture, ash, protein, fat, fibre, carbohydrate was varied slightly during fermentation. There was a decreasing trend of moisture and carbohydrate; meanwhile, there was an increasing trend of ash, protein, fibre during 8 days of fermentation. There was no significant difference of fat during pickling. There was a minor increment of mineral contents in all samples. There was accumulation of phenyllactic acid, ascorbic acid content and titratable acidity with exception of pH. Anti-nutrient contents like tannin, phytate, oxalate, steroidal glycoalkaloid greatly decreased in raw and pickled eggplant. Remarkable increments of total phenolic, flavonoid, DPPH free radical scavenging and FRAP ferric reducing antioxidant of raw and pickled eggplant was presented. Texture profiles of hardness, crispness, fracturability, crunchiness revealed a minor reduction of sensory scores during 8 days of fermentation. Lactic acid bacteria, Bacillus significantly proliferated; meanwhile, Micrococcus and S. aureus were absolutely retarded in pickled eggplant. Yeast and fungi increased in the first 4 days and decreased afterwards. There was no significant difference of proximate compositions; mineral contents; phenyllactic acid, ascorbic acid content, pH and titratable acidity; anti-nutritional contents; phytochemical and antioxidant properties; texture profile (sensory score); microbiological load (with exception of S. aureus) between pickled gloma eggplants at day 6th and day 8th of fermentation. At a quick glance, the length of fermentation could be shorted to 6 days instead of 8 days. However, at the 6th day, S. aureus load was still presented at 0.33±0.01 log CFU/g. The fermentation should be lasted to 8th day so that S. aureus load could be dropped down to zero to ensure microbial food safety. Raw gboma eggplant should be fermented in 8% brine solution for 8 days to obtain the best physicochemical, anti-nutritional, and microbiological properties of pickle. Findings of this research suggested that fermentation pickling would be an appropriate approach to improve nutritional, physicochemical and functional criteria while controlling toxic chemical residues, retarding the growth and proliferation of spoilage and pathogen microorganisms.

The Clash of Microbiomes: From the Food Matrix to the Host Gut

Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific community. Therefore, several studies have been conducted in animal and human hosts to decipher which of these products may have a beneficial outcome against specific ailments. However, despite the accumulating literature, a relatively small number of products have been authorized as ‘functional foods’ by regulatory bodies. Data inconsistency and lack of in-depth preclinical characterization of functional products could heavily contribute to this issue. Today, the increased availability of omics platforms and bioinformatic algorithms for comprehensive data analysis can aid in the systematic characterization of microbe–microbe, microbe–matrix, and microbe–host interactions, providing useful insights about the maximization of their beneficial effects. The incorporation of these platforms in food science remains a challenge; however, coordinated efforts and interdisciplinary collaboration could push the field toward the dawn of a new era.

Why the importance of geo-origin tracing of edible bird nests is arising?

Edible bird's nest (EBN) swiftlet existed naturally 48,000 years ago in caves as their natural dwellings. Nowadays, edible bird's nest has become a very important industry due to its high nutritional, medicinal and economic value. Additionally, edible bird's nest has a long quality guarantee period. Obviously, the nutritional components and medicinal functions vary depending on geographical origins. Recently, the global demand for edible bird's nest has markedly increased, accompanied by the increasing attention of all key players of the global food trade system, i.e., producers, consumers, traders and the authorities to obtain safe and high-quality edible bird's nest. Hence, this target can be accomplished via the enforcement of an efficient and universal geo-tracing technique. Current methods of the geo-tracking of edible bird's nest, i.e., automation, physical and analytical techniques have several limitations and all of them fail to discriminate different quality grades of edible bird's nest. Meanwhile, in many studies and applications, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) has proven to be a "cutting edge" technique for greatly enhance food traceability from field to fork through its ability in distinguishing the food products in terms of their quality and safety. This article provides an overview of (1) edible bird's nest as a multiuse strategic food product, (2) quality issues associated with edible bird's nest including implications that the site of acquisition of the edible bird's nest has food safety implications, (3) current regulations and geo-tracking approaches to ensure the safety and quality of edible bird's nest with the special focus on polymerase chain reaction-denaturing gradient gel electrophoresis technique as a vigorous and universal geo-tracing tool to be suggested for edible bird's nest geo-traceability.

The Fungal Communities and Flavor Profiles in Different Types of High-Temperature Daqu as Revealed by High-Throughput Sequencing and Electronic Senses

Polymicrobial co-fermentation is among the distinct character of high-temperature Daqu. However, fungal communities in the three types of high-temperature Daqu, namely, white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, are yet to be characterized. In this study, the fungal diversity, taste, and aroma profiles in the three types of high-temperature Daqu were investigated by Illumina MiSeq high-throughput sequencing, electronic tongue, and electronic nose, respectively. Ascomycota and Basidiomycota were detected as the absolute dominant fungal phylum in all types of high-temperature Daqu samples, whereas Thermomyces, Thermoascus, Aspergillus, Rasamsonia, Byssochlamys, and Trichomonascus were identified as the dominant fungal genera. The fungal communities of the three types of high-temperature Daqu differed significantly (p < 0.05), and Thermomyces, Thermoascus, and Monascus could serve as the biomarkers in white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, respectively. The three types of high-temperature Daqu had an extremely significant difference (p < 0.01) in flavor: white high-temperature Daqu was characterized by sourness, bitterness, astringency, richness, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds; black high-temperature Daqu was characterized by aftertaste-A, aftertaste-B, methane-aliph, hydrogen, and aromatic compounds; and yellow high-temperature Daqu was characterized by saltiness, umami, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds. The fungal communities in the three types of high-temperature Daqu were significantly correlated with taste but not with aroma, and the aroma of high-temperature Daqu was mainly influenced by the dominant fungal genera including Trichomonascus, Aspergillus, Thermoascus, and Thermomyces. The result of the present study enriched and refined our knowledge of high-temperature Daqu, which had positive implications for the development of traditional brewing technique.

A Review on the General Cheese Processing Technology, Flavor Biochemical Pathways and the Influence of Yeasts in Cheese

Cheese has a long history and this naturally fermented dairy product contains a range of distinctive flavors. Microorganisms in variety cheeses are an essential component and play important roles during both cheese production and ripening. However, cheeses from different countries are still handmade, the processing technology is diverse, the microbial community structure is complex and the cheese flavor fluctuates greatly. Therefore, studying the general processing technology and relationship between microbial structure and flavor formation in cheese is the key to solving the unstable quality and standardized production of cheese flavor on basis of maintaining the flavor of cheese. This paper reviews the research progress on the general processing technology and key control points of natural cheese, the biochemical pathways for production of flavor compounds in cheeses, the diversity and the role of yeasts in cheese. Combined with the development of modern detection technology, the evolution of microbial structure, population evolution and flavor correlation in cheese from different countries was analyzed, which is of great significance for the search for core functional yeast microorganisms and the industrialization prospect of traditional fermented cheese.

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.

Polysaccharides from fermented Asparagus officinalis with Lactobacillus plantarum NCU116 alleviated liver injury via modulation of glutathione homeostasis, bile acid metabolism, and SCFA production

Lactic acid bacteria strain (LAB) NCU116 fermented Asparagus officinalis polysaccharides (FAOP) have been proven to cause substantial changes in physicochemical properties such as monosaccharide composition and molecular weight, accounting for their enhanced immune activity than unprocessed Asparagus officinalis polysaccharides (AOP). In the current study, the hepatoprotective effects of FAOP in mice with cyclophosphamide (CTX)-induced hepatotoxicity were investigated. FAOP were more effective than AOP in alleviating CTX-induced hepatic damage, including inhibition of hepatic biochemical markers (ALT, AST, AKP and LDH) and pro-inflammatory cytokines (TNF-α and IL-1β) as well as reinforcement of antioxidant systems (T-AOC, SOD, CAT, and MDA). In particular, compared with AOP, FAOP showed superior performance by promoting GSH biosynthesis, and normalizing the expression level of bile acid receptors (FXR and SHP) and key enzymes in bile acid synthesis (CYP7A1, CYP8B1 and CYP27A1). Modulation of disordered homeostasis of bile acids by FAOP can be attributed to the upregulation of hepatic short chain fatty acid (SCFA) receptors GPR41 and GPR109A as well as intestinal SCFA production. Furthermore, serum metabolomics study validated the hepatoprotective superiority of FAOP than AOP with evidence from variations in bile acid compositions and the construction of related metabolic pathways. Therefore, LAB NCU116 fermentation of Asparagus officinalis was practical and effective to obtain promising hepatoprotective polysaccharides, which might arise from enhanced SCFA production than unprocessed AOP.

Enhancing Micronutrients Bioavailability through Fermentation of Plant-Based Foods: A Concise Review

Plant-based foods are rich sources of vitamins and essential micronutrients. For the proper functioning of the human body and their crucial role, trace minerals (iron, zinc, magnesium, manganese, etc.) are required in appropriate amounts. Cereals and pulses are the chief sources of these trace minerals. Despite these minerals, adequate consumption of plant foods cannot fulfill the human body’s total nutrient requirement. Plant foods also contain ample amounts of anti-nutritional factors such as phytate, tannins, phenols, oxalates, etc. These factors can compromise the bioavailability of several essential micronutrients in plant foods. However, literature reports show that fermentation and related processing methods can improve nutrient and mineral bioavailability of plant foods. In this review, studies related to fermentation methods that can be used to improve micronutrient bioavailability in plant foods are discussed.

Peptides in Brewed Wines: Formation, Structure, and Function

The traditional low-alcoholic beverages, such as grape wine, sake, and rice wine, have been consumed all over the world for thousands of years, each with their unique methods of production that have been practiced for centuries. Moderate consumption of wine is generally touted as beneficial for health, although there is ongoing debate for the responsible components in wine. In this review, the structural and functional characteristics, the formation mechanisms, and their health-promoting activities of peptides in three brewed wines, grape wine, Chinese rice wine (also called Chinese Huangjiu or Chinese yellow wine), and Japanese sake, are discussed. The formation of peptides in wine imparts sensorial, technological, and biological attributes. Prospects on future research, with an emphasis on the peptide characterization, formation mechanism, physiological activity, and molecular mechanisms of action, are presented.

Chemical Characteristics of Three Kinds of Japanese Soy Sauce Based on Electronic Senses and GC-MS Analyses

Japanese soy sauce has become more acceptable by Chinese consumers due to its umami taste. However, the volatile flavor compounds and taste characters have not been fully clarified. This study aimed to explore the flavor characteristics of three kinds of Japanese soy sauce, including Koikuchi Shoyu, Usukuchi Shoyu, and Amakuchi Shoyu. The secret of volatile flavor substances was investigated by Gas Chromatography-Mass Spectrometry (GC-MS) and electronic nose, while taste compounds were investigated by silylation GC-MS and electronic tongue (E-tongue). A total of 173 volatile flavor substances and 160 taste compounds were identified. In addition, 28 aroma compounds with odor activity values (OAV) ≥ 1 were considered as the typical flavors. We found that alcohols and aldehydes were in high abundance in Japanese soy sauce, but only a small portion of pyrazines and esters were. Based on electronic nose and GC-MS analysis, Koikuchi Shoyu gives more contribution to aroma compounds, while Usukuchi Shoyu and Amakuchi Shoyu give the sourness and sweetness features based on E-tongue and silylation GC-MS analysis. In this study, 50 kinds of sugars were detected that contributed to the sweetness of soy sauce. This study will provide new insight into the flavor characteristics of Japanese soy sauce that potentially contribute to the innovation and development of soy sauce.

Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues

Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

Probiotics for cancer alternative prevention and treatment

Cancer is a fatal malignancy with high clinical significance and remains one of the major causes of illness and death. It has no suitable cure existing till now. The safety and stability of the standard chemotherapeutics drugs and synthetic agents used to manage cancer are doubtful. These agents are affecting the quality of life or contributing for development of drug resistance and are not affordable to the majority of the patients. Therefore, scientists are looking into clinical management of the cancer with high efficiency. This review focuses on the role of probiotics as alternative prevention and treatment of cancer. In this regard, we discuss the alternative cancer biotherapeutic drugs including live or dead probiotics and their metabolites, such as short chain fatty acids, inhibitory compounds of protein, polysaccharide, nucleic acid and ferrichrome in in vitro, in vivo and clinical studies. We also discuss the effectiveness of these biotherapeutics in prevention and treatment of various types of cancer linked with probiotic bacterial or fungal strains, probiotic dose, and time of exposure. More in vivo mainly clinical trials are necessary to further reveal and approve the significant role of live and dead probiotics as well as their metabolic products in cancer prevention and treatment. Finally, the majority of the positive results provided by probiotic treatments are limited to experimental settings. To minimize side effects associated with probiotics, short and long term effect studies in the direction of methodology standardization are required.

Effect of olive leaf extract combined with Saccharomyces cerevisiae in the fermentation process of table olives

Yeasts have a great importance in the table olives quality and have been proved more and more as starter cultures. Moreover, the addition of olive leaf extract (OLE) could enhance the nutritional value of table olives, but there are no studies in which added OLE has been combined with yeasts during fermentation. The aim of this work was to determine if the quality and functional value of table olives increases when OLE and a yeast starter are used during a Spanish-style olive fermentation process. Several combinations were used: (1) fermentations trials with OLE combined with a strain of Saccharomyces cerevisiae; (2) fermentations with OLE; (3) control fermentations, with no extract or starter culture. During fermentation performed with the addition of OLE and yeasts, the yeast number remained stable for most of the time, resulting in a slight decrease of yeasts by the end of the process. The phenolic profile of olive flesh and brines of the trials was analysed during the fermentation. The addition of OLE increased the concentration of phenols in olive flesh and brines at the end of the fermentation; in these fermentations, hydroxytyrosol was the most abundant, at around 1700 mg/kg in olive flesh and 3500 mg/L in brines olive flesh, whereas in the control fermentation the concentrations were around 900 mg/kg and 2500 mg/L, respectively. In spite of adding OLE, the fermentation resulted in olives without bitterness. We can conclude that yeast inoculation combined with OLE improves safety, nutritional value and other properties of the final product, without affecting its sensorial qualities.