Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Cross-over fermentation dynamics and proteomic properties of acid gels with indigenous Lactobacillus spp. isolated from cheeses

The present study examined the proteomic characteristics and fermentation dynamics of indigenous bacteria isolated from traditional Mihalic cheese in an acid gel matrix. Accordingly, autochthonous strains of Levilactobacillus brevis, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus were adapted to the gel matrix alongside commercial yogurt culture (Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus). The study evaluated bacterial activity, proteolytic behavior, physicochemical characteristics, and textural and sensory properties in acid gel samples. The microorganisms demonstrated high survival rates (>7.35 log₁₀ cfu/g) in the fermented gel system and induced limited acidification throughout the product's shelf life. Regarding proteomic properties, the highest amino acid variation during the shelf life was observed in the FMB sample (28.20%). Furthermore, arginine, leucine, phenylalanine, aspartic acid, lysine, and cysteine reductions were noted in samples containing the isolated microorganisms. Including indigenous microorganisms in the fermented milk increased the levels of essential amino acids. Principal Component Analysis of sensory properties revealed that samples containing indigenous microorganisms differed significantly from the control sample (C), which contained only commercial yogurt culture. The results revealed the proteolytic changes associated with fermentation, including producing free amino acids as nutritional components, forming specific aroma compounds, and modifying textural and sensory properties. These results demonstrate the potential of utilizing local cultures to develop products enriched with novel bioactive components, offering consumers enhanced nutritional and sensory benefits.

Protective Effect of Ganjang, a Traditional Fermented Soy Sauce, on Colitis-Associated Colorectal Cancer in Mice

Colorectal cancer (CRC) is one of the most prevalent causes of cancer-related fatalities globally, and its development is closely associated with dietary and microbial factors. The aim of this study was to investigate the potential of ganjang, a traditional fermented soy sauce, in alleviating colitis-associated colorectal cancer (CAC) in a mouse model induced by azoxymethane/dextran sulfate sodium (AOM/DSS). The bacterial composition of ganjang samples from different regions primarily included Lactobacillus spp. and Bacillus spp. Administration of ganjang to AOM/DSS-induced mice significantly improved CAC-related symptoms, including increased body weight, restored colon length, and reduced spleen size. Additionally, ganjang administration led to a decrease in tumor size and number, the modulation of apoptotic and proliferative markers, decreased inflammatory cytokine levels, and the restoration of the intestinal epithelial barrier. Furthermore, ganjang samples altered the gut microbiota composition by increasing the relative abundance of Lactobacillus spp. These findings suggest that ganjang has potential as a functional food for CRC prevention or mitigation, primarily through the modulation of CAC symptoms, tumor growth, inflammatory responses, intestinal epithelial barrier integrity, and gut microbiota composition.

Study on the Effect of Radish Sprouts on Short-Chain Fatty Acids and Gut Microbial Diversity in Healthy Individuals

This study aimed to assess the impact of radish sprouts on the gut microbiota of healthy individuals. Radish sprout additives, subjected to short-term storage and steam treatment, were used to intervene in an in vitro culture of human gut microbiota. The influence of radish sprouts on the gut microbiota was evaluated by monitoring short-chain fatty acid (SCFA) content and proportion in the fermentation broth, and microbial diversity was assessed using 16S rDNA amplicon sequencing. The results indicated that the gut microbiota produced a substantial amount of SCFA within 48 h of fermentation, with a right-skewed distribution across all groups. The addition of both digestates enhanced Firmicutes diversity, while Bacteroidetes and Proteobacteria diversity remained stable between the control and fresh sprout groups. The 30 s steam treatment group showed an increase in Bacteroidetes and a decrease in Proteobacteria diversity. The abundance of Bacilli, Bacillaceae, and Bacillus was significantly higher in both the fresh and steam-treated groups compared to the control. Both fresh and steam-treated radish sprout digestates enriched gut microbiota diversity, with steam treatment showing superior effects. These findings suggest that radish sprout consumption may positively influence gut microbiota, with steam treatment potentially enhancing these benefits.

Microbial Fermentation in Food and Beverage Industries: Innovations, Challenges, and Opportunities

Microbial fermentation is a primary method by which a variety of foods and beverages are produced. The term refers to the use of microbes such as bacteria, yeasts, and molds to transform carbohydrates into different substances. Fermentation is important for preserving, enhancing flavor, and improving the nutritional quality of various perishable foods. Historical records clearly show that fermented foods and drinks, such as wine, beer, and bread, have been consumed for more than 7000 years. The main microorganisms employed were Saccharomyces cerevisiae, which are predominantly used in alcohol fermentation, and Lactobacillus in dairy and vegetable fermentation. Typical fermented foods and drinks made from yogurt, cheese, beer, wine, cider, and pickles from vegetables are examples. Although there are risks of contamination and spoilage by pathogenic and undesirable microorganisms, advanced technologies and proper control procedures can mitigate these risks. This review addresses microbial fermentation and clarifies its past importance and contribution to food preservation, flavoring, and nutrition. It systematically separates yeasts, molds, and bacteria and explains how they are used in food products such as bread, yogurt, beer, and pickles. Larger producers employ primary production methods such as the artisanal approach, which are explored along with future trends such as solid-state fermentation, the potential of biotechnology in developing new products, and sustainability in new product development. Future research and development strategies can lead to innovations in methods that improve efficiency, product range, and sustainability.

Antilisterial Properties of Selected Strains from the Autochthonous Microbiota of a Swiss Artisan Soft Smear Cheese

High incidences of the foodborne pathogen Listeria monocytogenes have been reported on smear cheeses, and despite increased hygiene efforts, this incidence has remained stable in recent years. Applying antilisterial strains may increase the safety of smear cheeses. To find and test antilisterial strains, we inoculated fresh soft cheeses from nine dairies with the surrogate species Listeria innocua and assessed its growth under standardized ripening conditions. Acetic acid at day 23 (r = -0.66), lactose in fresh cheese (r = -0.63), and glucose at day 10 (r = -0.62), as well as seven amplicon sequence variants (ASVs), were negatively correlated with L. innocua growth. Two of these ASVs were assigned to the genus Leuconostoc of Lactobacillaceae (r = -0.82 and -0.71). Isolates from this family, from Aerococcaceae, and Carnobacteriaceae were characterized according to their inhibitory properties, and those showing antilisterial properties were applied as protective cultures in challenge tests. The combined application of strains of Leuconostoc mesenteroides, Aerococcaceae, and Carnobacteriaceae successfully eliminated low levels of L. innocua in the final products. This is likely explained by antimicrobial compounds, including mesentericin Y105 and acetate, and competition for carbon sources and iron. This study shows a promising way to improve the safety of soft smear cheeses by applying defined protective cultures.

Bioactive Peptides from Fermented Foods: Production Approaches, Sources, and Potential Health Benefits

Microbial fermentation is a well-known strategy for enhancing the nutraceutical attributes of foods. Among the fermentation outcomes, bioactive peptides (BAPs), short chains of amino acids resulting from proteolytic activity, are emerging as promising components thanks to their bioactivities. Indeed, BAPs offer numerous health benefits, including antimicrobial, antioxidant, antihypertensive, and anti-inflammatory properties. This review focuses on the production of bioactive peptides during the fermentation process, emphasizing how different microbial strains and fermentation conditions influence the quantity and quality of these peptides. Furthermore, it examines the health benefits of BAPs from fermented foods, highlighting their potential in disease prevention and overall health promotion. Additionally, this review addresses the challenges and future directions in this field. This comprehensive overview underscores the promise of fermented foods as sustainable and potent sources of bioactive peptides, with significant implications for developing functional foods and nutraceuticals.

Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes

This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.

Fermentation of Rice, Oat, and Wheat Flour by Pure Cultures of Common Starter Lactic Acid Bacteria: Growth Dynamics, Sensory Evaluation, and Functional Properties

Recent consumer demand for non-dairy alternatives has forced many manufacturers to turn their attention to cereal-based non-alcoholic fermented products. In contrast to fermented dairy products, there is no defined and standardized starter culture for manufacturing cereal-based products. Since spontaneous fermentation is rarely suitable for large-scale commercial production, it is not surprising that manufacturers have started to adopt centuries-known dairy starters based on lactic acid bacteria (LABs) for the fermentation of cereals. However, little is known about the fermentation processes of cereals with these starters. In this study, we combined various analytical tools in order to understand how the most common starter cultures of LABs affect the most common types of cereals during fermentation. Specifically, 3% suspensions of rice, oat, and wheat flour were fermented by the pure cultures of 16 LAB strains belonging to five LAB species-Lacticaseibacillus paracasei, Lactobacillus delbrueckii, Lactobacillus helveticus, Streptococcus thermophilus, and Lactococcus lactis. The fermentation process was described in terms of culture growth and changes in the pH, reducing sugars, starch, free proteins, and free phenolic compounds. The organoleptic and rheological features of the obtained fermented products were characterized, and their functional properties, such as their antioxidant capacity and angiotensin-converting enzyme inhibitory activity, were determined.

Lactic acid bacteria in Asian fermented foods and their beneficial roles in human health

Fermented foods have been a staple in human diets for thousands of years, garnering attention for their health and medicinal benefits. Rich in lactic acid bacteria (LAB) with probiotic properties, these foods play a crucial role in positively impacting the host's gut microbiome composition and overall health. With a long history of safe consumption, fermented foods effectively deliver LAB to humans. Intake of LAB from fermented foods offers three main benefits: (1) enhancing digestive function and managing chronic gastrointestinal conditions, (2) modulating the immune system and offering anti-inflammatory effects to prevent immune-related diseases, and (3) synthesizing vitamins and various bioactive compounds to improve human health. In this review, we highlighted the diverse LAB present in Asian fermented foods and emphasized LAB-rich fermented foods as a natural and effective solution for health enhancement and disease prevention.

Black Goji Berry (Lycium ruthenicum) Juice Fermented with Lactobacillus rhamnosus GG Enhances Inhibitory Activity against Dipeptidyl Peptidase-IV and Key Steps of Lipid Digestion and Absorption

With the global increase in hyperglycemia and hyperlipidemia, there is an urgent need to explore dietary interventions targeting the inhibition of dipeptidyl peptidase-IV (DPP-IV) and lipid digestion and absorption. This study investigated how Lactobacillus rhamnosus GG (LGG) affects various aspects of black goji berry (BGB) (Lycium ruthenicum Murr.) juice, including changes in physicochemical and functional properties, as well as microbiological and sensory attributes. Throughout the fermentation process with 2.5-10% (w/v) BGB, significantly improved probiotic viability, lactic acid production, and decreased sugar content. While total flavonoids increase, anthocyanins decrease, with no discernible change in antioxidant activities. Metabolite profiling reveals elevated phenolic compounds post-fermentation. Regarding the inhibition of lipid digestion and absorption, fermented BGB exhibits improved bile acid binding, and disrupted cholesterol micellization by approximately threefold compared to non-fermented BGB, while also increasing pancreatic lipase inhibitory activity. Furthermore, a decrease in cholesterol uptake was observed in Caco-2 cells treated with fermented BGB (0.5 mg/mL), with a maximum reduction of 16.94%. Fermented BGB also shows more potent DPP-IV inhibition. Sensory attributes are significantly improved in fermented BGB samples. These findings highlight the potential of BGB as a bioactive resource and a promising non-dairy carrier for LGG, enhancing its anti-hyperglycemic and anti-hyperlipidemic properties.

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling

Cheese taste and flavour properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of Lactococcus lactis, Lactobacillus plantarum and Propionibacterium freudenreichii during a seven-week cheese production process. Using genome-scale metabolic models and omics data integration, we modeled and calibrated individual dynamics using monoculture experiments, and coupled these models to capture the metabolism of the community. This model accurately predicts the dynamics of the community, enlightening the contribution of each microbial species to organoleptic compound production. Further metabolic exploration revealed additional possible interactions between the bacterial species. This work provides a methodological framework for the prediction of community-wide metabolism and highlights the added value of dynamic metabolic modeling for the comprehension of fermented food processes.

CRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3

Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.

Effect of Coriander Seed Addition at Different Stages of Brewing on Selected Parameters of Low-Alcohol Wheat Beers

In recent years, there has been a significant decline in interest in high-alcohol beers, while interest in low- and non-alcohol beers is growing. The aim of this study was to investigate the influence of the addition of coriander seeds at various stages of the production of low-alcohol wheat beer (mashing, boiling, and fermentation). The presented article uses biological methods to produce low-alcohol beer. For this purpose, first, the mashing process was modified (breaking 44 °C for 20 min, followed by 75 °C for 60 min). The chemical composition and aroma components of the obtained beers were determined using various chromatographic methods (HPLC, GC-MS, and GC-O). Differences were found between the aroma components depending on the stage of production at which the coriander seeds were added. Beers with the addition of coriander seeds at the fermentation stage had the highest terpene content (linalool, camphor, trans-linalool oxide, and γ-terpinene) and boiling (myrcene, limonene, citronellol, and geraniol). The least desirable process is the addition of coriander seeds at the mashing stage due to the lowest content of volatile compounds. Additionally, beers with the addition of coriander seeds for fermentation were characterized by a higher content of antioxidant compounds. This proves that the addition of coriander seeds during beer production could improve the fermentation process and modify the quality of the obtaining beer.

Software-based screening for efficient sgRNAs in Lactococcus lactis

BACKGROUND

The two essential editing elements in the clustered regularly interspaced short palindromic repeats (CRISPR) editing system are promoter and single-guide RNA (sgRNA), the latter of which determines whether Cas protein can precisely target a specific location to edit the targeted gene. Therefore, the selection of sgRNA is crucial to the efficiency of the CRISPR editing system. Various online prediction tools for sgRNA are currently available. These tools can predict all possible sgRNAs of the targeted gene and rank sgRNAs according to certain scoring criteria according to the demands of the user.

RESULTS

We designed sgRNAs for Lactococcus lactis NZ9000 LLNZ_RS02020 (ldh) and LLNZ_RS10925 (upp) individually using online prediction software - CRISPOR - and successfully constructed a series of knockout strains to allow comparison of the knockout efficiency of each sgRNA and analyze the differences between software predictions and actual experimental results.

CONCLUSION

Our experimental results showed that the actual editing efficiency of the screened sgRNAs did not match the predicted results - a phenomenon that suggests that established findings from eukaryotic studies are not universally applicable to prokaryotes. Software prediction can still be used as a tool for the initial screening of sgRNAs before further selection of suitable sgRNAs through experimental experience. © 2023 Society of Chemical Industry.

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

The three distinct medicinal parts of Angelica sinensis (Oliv.) Diels (Ang) roots are the head, body, and tail (ARH, ARB, and ART, respectively). How endophytic fungi shape the differences in metabolic components among these parts remains unclear. We quantified the distribution of active components and endophytic fungi along the ARH, ARB, and ART and their relationships. Based on the metabolic components and their abundances detected via non-target metabolism, the different medicinal parts were distinguishable. The largest number of dominant metabolic components was present in ART. The difference between ART and ARH was the greatest, and ARB was in a transitional state. The dominant active molecules in ART highlight their effects in haemodynamics improvement, antibacterial, anti-inflammatory, and hormone regulation, while ARH and ARB indicated more haemostasis, blood enrichment, neuromodulation, neuroprotection and tranquilisation, hepatoprotection, and antitumour activities than that of ART. The ARHs, ARBs, and ARTs can also be distinguished from each other based on the endophytic fungi at the microbiome level. The most dominant endophytic fungi were distributed in ART; the differences between ART and ARH were the largest, and ARB was in a transition state, which is consistent with the metabolite distributions. Structural equation modelling showed that the endophytic fungi were highly indicative of the metabolic components. Correlation analysis further identified the endophytic fungi significantly positively correlated with important active components, including Condenascus tortuosus, Sodiomyces alcalophilus, and Pleotrichocladium opacum. The bidirectional multivariate interactions between endophytic fungi and the metabolic components shape their spatial variations along the longitudinal direction in the Ang root.

Comprehensive review of clean-label antimicrobials used in dairy products

Consumers expect safe, healthy, natural, and sustainable food. Within the food industry, ingredient use is changing due to these consumer demands. While no single agreed-upon definition of clean label exists, a "clean label" in the context of food refers to a product that has a simplified and transparent ingredient list, with easily recognizable and commonly understood components to the general public. Clean-label products necessitate and foster a heightened level of transparency between companies and consumers. Dairy products are vulnerable to being contaminated by both pathogens and spoilage microorganisms. These microorganisms can be effectively controlled by replacing conventional antimicrobials with clean-label ingredients such as protective cultures or bacterial/fungal fermentates. This review summarizes the perspectives of consumers and the food industry regarding the definition of "clean label," and the current and potential future use of clean-label antimicrobials in dairy products. A key goal of this review is to make the concept of clean-label antimicrobial agents better understood by both manufacturers and researchers.

Exploring Microbial Contributions to Nutraceutical Production: From Natural to Designed Foods

For ages, societies throughout the world have used fermentation as a traditional method for food processing and preservation, helping to create a wide range of staple foods and delicacies. Due to its possible health advantages, mostly attributable to the inclusion of bioactive substances known as nutraceuticals, fermented foods have attracted a lot of interest recently. This in-depth analysis examines the wide range of nutraceuticals present in fermented foods, as well as how they are made, what health benefits they may have, and how they may be used in the nutraceutical and functional food businesses. By stressing how important fermented foods are as a source of beneficial bioactive components that support human health and well-being. Numerous bioactive substances found in fermented foods have been the subject of recent scientific studies. These molecules may find use in the pharmaceutical and nutraceutical sectors. Streptococcus thermophilus, Lactobacillus gasseri, Lactobacillus delbrueckii, Lactobacillus bulgaricus, and Lactobacillus johnsonii are just a few examples of the probiotic bacteria that live in fermented foods and formulas. This review elucidates the importance of microorganisms sourced from fermented foods as potent agents for diverse nutraceuticals and their potential role in preventing various diseases whilst serving as functional food supplements.

The Rising Role of Omics and Meta-Omics in Table Olive Research

Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.

The Impacts of Acidophilic Lactic Acid Bacteria on Food and Human Health: A Review of the Current Knowledge

The need to improve the safety/quality of food and the health of the hosts has resulted in increasing worldwide interest in acidophilic lactic acid bacteria (LAB) for the food, livestock as well as health industries. In addition to the use of acidophilic LAB with probiotic potential for food fermentation and preservation, their application in the natural disposal of acidic wastes polluting the environment is also being investigated. Considering this new benefit that has been assigned to probiotic microorganisms in recent years, the acceleration in efforts to identify new, efficient, promising probiotic acidophilic LAB is not surprising. One of these effots is to determine both the beneficial and harmful compounds synthesized by acidophilic LAB. Moreover, microorganisms are of concern due to their possible hemolytic, DNase, gelatinase and mucinolytic activities, and the presence of virulence/antibiotic genes. Hence, it is argued that acidophilic LAB should be evaluated for these parameters before their use in the health/food/livestock industry. However, this issue has not yet been fully discussed in the literature. Thus, this review pays attention to the less-known aspects of acidophilic LAB and the compounds they release, clarifying critical unanswered questions, and discussing their health benefits and safety.

Differential behavior of Lactobacillus helveticus B1929 and ATCC 15009 on the hydrolysis and angiotensin-I-converting enzyme inhibition activity of fermented ultra-high temperature milk and nonfat dried milk powder

Consumers' growing interest in fermented dairy foods necessitates research on a wide array of lactic acid bacterial strains to be explored and used. This study aimed to investigate the differences in the proteolytic capacity of Lactobacillus helveticus strains B1929 and ATCC 15009 on the fermentation of commercial ultra-pasteurized (UHT) skim milk and reconstituted nonfat dried milk powder (at a comparable protein concentration, 4%). The antihypertensive properties of the fermented milk, measured by angiotensin-I-converting enzyme inhibitory (ACE-I) activity, were compared. The B1929 strain lowered the pH of the milk to 4.13 ± 0.09 at 37°C after 24 h, whereas ATCC 15009 needed 48 h to drop the pH to 4.70 ± 0.18 at 37°C. Two soluble protein fractions, one (CFS1) obtained after fermentation (acidic conditions) and the other (CFS2) after the neutralization (pH 6.70) of the pellet from CFS1 separation, were analyzed for d-/l-lactic acid production, protein concentration, the degree of protein hydrolysis, and ACE-I activity. The CFS1 fractions, dominated by whey proteins, demonstrated a greater degree of protein hydrolysis (7.9%) than CFS2. On the other hand, CFS2, mainly casein proteins, showed a higher level of ACE-I activity (33.8%) than CFS1. Significant differences were also found in the d- and l-lactic acid produced by the UHT milk between the 2 strains. These results attest that milk casein proteins possessed more detectable ACE-I activity than whey fractions, even without a measurable degree of hydrolysis. Findings from this study suggest that careful consideration must be given when selecting the bacterial strain and milk substrate for fermentation.

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.

Impact of Aging Microbiome on Metabolic Profile of Natural Aging Huangjiu through Machine Learning

Aging is a time-consuming step in the manufacturing of fermented alcoholic beverages. Natural-aging huangjiu sealed in pottery jars was taken as an example to investigate the changes of physiochemical indexes during aging and to quantify intercorrelations between aging-related factors and metabolites through machine learning methods. Machine learning models provided significant predictions for 86% of metabolites. Physiochemical indexes well reflected the metabolic profile, and total acid was the most important index that needed to be controlled. For aging-related factors, several aging biomarkers of huangjiu were also well predicted. Feature attribution analysis showed aging year was the most powerful predictive factor, and several microbial species were significantly associated with aging biomarkers. Some of the correlations, mostly connected to environmental microorganisms, were newly found, showing considerable microbial influence on aging. Overall, our results reveal the potential determinants that affect the metabolic profile of aged huangjiu, paving the way for a systematical understanding of changes in metabolites of fermented alcoholic beverages.

Rapid Quantitative Analysis of Metabolites in Kimchi Using LC-Q-Orbitrap MS

Kimchi is a traditional Korean salted spontaneous lactic acid bacteria (LAB)-fermented food made using various vegetables. Organic acids, free sugars, and amino acids are key metabolites produced during LAB fermentation that determine the taste and quality of kimchi. However, each metabolite is typically analyzed using an independent analytical method, which is time-consuming and expensive. Therefore, in this study, we developed a method based on LC-Q-Orbitrap MS using which 20 types of representative fermented kimchi metabolites were selected and simultaneously analyzed within 10 min. The established method was validated, and its detection and quantification limits, linearity, precision, and accuracy were found to satisfy the Association of Official Agricultural Chemists (AOAC) validation guidelines. The 20 metabolites were simultaneously extracted from kimchi with different degrees of fermentation and quantitatively analyzed using LC-Q-Orbitrap MS. These results were analyzed using linear discriminant analysis and heat mapping, and the metabolites were grouped into early, middle, and late stages of fermentation. Malic acid (6.518-7.701 mMol) was only present in the initial stage of fermentation, and l-phenylalanine rapidly increased from the middle stage (2.180 mMol) to late stage (4.770 mMol). Lactic acid, which is representative of the sour taste of kimchi, was detected in the middle stage and increased rapidly up to 74.452 mMol in the late stage. In summary, in this study, 20 major kimchi metabolites were accurately analyzed within 10 min and grouped based on the degree of fermentation. Therefore, the method established in this study accurately and rapidly provides information on kimchi consumption and fermentation that could be highly valuable to the kimchi industry and kimchi consumers.

Mycotoxins in soybean-based foods fermented with filamentous fungi: Occurrence and preventive strategies

Fermented soybean products are widely consumed worldwide, and their popularity is increasing. Filamentous fungi, such as Actinomucor, Aspergillus, Monascus, Mucor, Penicillium, Rhizopus, and Zymomonas, play critical roles in the fermentation processes of many soybean foods. However, besides producing essential enzymes for food fermentation, filamentous fungi can release undesirable or even toxic metabolites into the food. Mycotoxins are toxic secondary metabolites produced by certain filamentous fungi and may be detected during the food production process. Without effective prevention strategies, mycotoxin contamination in fermented soybean products poses a risk to human health. This review focused on the changes in mycotoxigenic fungal abundance and mycotoxin contamination at different stages during the production of soybean-based fermented foods, as well as effective strategies for preventing mycotoxin contamination in such products. Data from relevant studies demonstrated a tendency of change in the genera of mycotoxigenic fungi and types of mycotoxins (aflatoxins, alternariol, alternariol monomethyl ether, deoxynivalenol, fumonisins, ochratoxin A, rhizoxins, T-2 toxin, and zearalenone) present in the raw materials and the middle and final products. The applicability of traditional chemical and physical mitigation strategies and novel eco-friendly biocontrol approaches to prevent mycotoxin contamination in soybean-based fermented foods were discussed. The present review highlights the risks of mycotoxin contamination during the production of fermented soybean products and recommends promising strategies for eliminating mycotoxin contamination risk in soybean-based fermented foods.

Artificial intelligence-based approaches for traditional fermented alcoholic beverages' development: review and prospect

Traditional fermented alcoholic beverages (TFABs) have gained widespread acceptance and enjoyed great popularity for centuries. COVID-19 pandemics lead to the surge in health demand for diet, thus TFABs once again attract increased focus for the health benefits. Though the production technology is quite mature, food companies and research institutions are looking for transformative innovation in TFABs to make healthy, nutritious offerings that give a competitive advantage in current beverage market. The implementation of intelligent platforms enables companies and researchers to gather, store and analyze data in a more convenient way. The development of data collection methods contributed to the big data environment of TFABs, providing a fresh perspective that helps brewers to observe and improve the production steps. Among data analytical tools, Artificial Intelligence (AI) is considered to be one of the most promising methodological approaches for big data analytics and decision-making of automated production, and machine learning (ML) is an important method to fulfill the goal. This review describes the development trends and challenges of TFABs in big data era and summarize the application of AI-based methods in TFABs. Finally, we provide perspectives on the potential research directions of new frontiers in application of AI approaches in the supply chain of TFABs.

Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process

As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of “Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation”. Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of “Komagataeibacter (90.2%) fermentation” were found. “Lactobacillus (92.2%) fermentation” characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.

Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication

Food fermentation is driven by microorganisms, which usually coexist as multispecies biofilms. The activities and interactions of functional microorganisms and pathogenic bacteria in biofilms have important implications for the quality and safety of fermented foods. It was verified that the biofilm lifestyle benefited the fitness of microorganisms in harsh environments and intensified the cooperation and competition between biofilm members. This review focuses on multispecies biofilm formation, microbial interactions and communication in biofilms, and the application of multispecies biofilms in food fermentation. Microbial aggregation and adhesion are important steps in the early stage of multispecies biofilm formation. Different biofilm-forming abilities and strategies among microorganisms lead to several types of multispecies biofilm formation. The spatial distribution of multispecies biofilms reflects microbial interactions and biofilm function. Then, we discuss the intrinsic factors and external manifestations of multispecies biofilm system succession. Several typical interspecies cooperation and competition modes and mechanisms of microbial communication were reviewed in this review. The main limitations of the studies included in this review are the relatively small number of studies of biofilms formed by functional microorganisms during fermentation and the lack of direct evidence for the formation process of multispecies biofilms and microbial interactions and communication within biofilms. This review aims to provide the food industry with a sufficient understanding of multispecies biofilms in food fermentation. Practical Application: Meanwhile, it offers a reference value for better controlling and utilizing biofilms during food fermentation process, and the improvement of the yield, quality, and safety of fermented products including Chinese Baijiu, cheeese,kefir, soy sauce, kombucha, and fermented olive.

Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods

Horizontal gene transfer (HGT) has contributed significantly to the adaptability of bacteria, yeast and mold in fermented foods, whose evidence has been found in several fermented foods. Although not every HGT has biological significance, it plays an important role in improving the quality of fermented foods. In this review, how HGT facilitated microbial domestication and adaptive evolution in fermented foods was discussed. HGT can assist in the industrial innovation of fermented foods, and this adaptive evolution strategy can improve the quality of fermented foods. Additionally, the mechanism underlying HGT in fermented foods were analyzed. Furthermore, the critical bottlenecks involved in optimizing HGT during the production of fermented foods and strategies for optimizing HGT were proposed. Finally, the prospect of HGT for promoting the industrial innovation of fermented foods was highlighted. The comprehensive report on HGT in fermented foods provides a new trend for domesticating preferable starters for food fermentation, thus optimizing the quality and improving the industrial production of fermented foods.

Fermented Food in Asthma and Respiratory Allergies—Chance or Failure?

In the last few decades, a dramatic increase in the global prevalence of allergic diseases and asthma was observed. It was hypothesized that diet may be an important immunomodulatory factor influencing susceptibility to allergic diseases. Fermented food, a natural source of living microorganisms and bioactive compounds, has been demonstrated to possess health-promoting potentials and seems to be a promising strategy to reduce the risk of various immune-related diseases, such as allergic diseases and asthma. The exact mechanisms by which allergic diseases and asthma can be alleviated or prevented by fermented food are not well understood; however, its potential to exert an effect through modulating the immune response and influencing the gut microbiota has been recently studied. In this review, we provide the current knowledge on the role of diet, including fermented foods, in preventing or treating allergic diseases and asthma.

Two Faces of Fermented Foods-The Benefits and Threats of Its Consumption

In underdeveloped and developing countries, due to poverty, fermentation is one of the most widely used preservation methods. It not only allows extending the shelf life of food, but also brings other benefits, including inhibiting the growth of pathogenic microorganisms, improving the organoleptic properties and product digestibility, and can be a valuable source of functional microorganisms. Today, there is a great interest in functional strains, which, in addition to typical probiotic strains, can participate in the treatment of numerous diseases, disorders of the digestive system, but also mental diseases, or stimulate our immune system. Hence, fermented foods and beverages are not only a part of the traditional diet, e.g., in Africa but also play a role in the nutrition of people around the world. The fermentation process for some products occurs spontaneously, without the use of well-defined starter cultures, under poorly controlled or uncontrolled conditions. Therefore, while this affordable technology has many advantages, it can also pose a potential health risk. The use of poor-quality ingredients, inadequate hygiene conditions in the manufacturing processes, the lack of standards for safety and hygiene controls lead to the failure food safety systems implementation, especially in low- and middle-income countries or for small-scale products (at household level, in villages and scale cottage industries). This can result in the presence of pathogenic microorganisms or their toxins in the food contributing to cases of illness or even outbreaks. Also, improper processing and storage, as by well as the conditions of sale affect the food safety. Foodborne diseases through the consumption of traditional fermented foods are not reported frequently, but this may be related, among other things, to a low percentage of people entering healthcare care or weaknesses in foodborne disease surveillance systems. In many parts of the world, especially in Africa and Asia, pathogens such as enterotoxigenic and enterohemorrhagic Escherichia coli, Shigella spp., Salmonella spp., enterotoxigenic Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus have been detected in fermented foods. Therefore, this review, in addition to the positive aspects, presents the potential risk associated with the consumption of this type of products.