Metagenomic analysis of kimchi, a traditional Korean fermented food

Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food

Suansun, made from fresh bamboo shoots fermented without salt, is a traditional food in China’s southern region and is popular for its nutritious and unique flavor. To comprehensively understand the microbial species and characteristics of suansun, Illumina HiSeq metagenomic sequencing technology was used to sequence suansun’s fermentation broth obtained from six traditional producing areas in southern China, and the microbial community structure, diversity, and functional genes were analyzed. A total of 8 phyla, 16 classes, 30 orders, 63 families, 92 genera, and 156 species of microorganisms were identified in the suansun samples, with Lactiplantibacillus predominating, accounting for up to 81% of the species, among which 12 species, including Lactiplantibacillus plantarum, were the main species. A total of 12,751 unigenes were annotated to 385 metabolic pathway classes, of which 2927 unigenes were involved in carbohydrate metabolism. Lactiplantibacillus fermentum, Lactiplantibacillus plantarum, and Lactiplantibacillus brucei were involved in the metabolism of most nutrients and flavor substances in suansun. Overall, these results provide insights into the suansun microbiota and shed light on the fermentation processes carried out by complex microbial communities.

Metaproteomic Insights Into the Microbial Community in Pozol

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

Metagenomic Analysis of Bacterial Diversity in Traditional Fermented Foods Reveals Food-Specific Dominance of Specific Bacterial Taxa

Traditional fermented foods have been recognized by various communities to be good for health since ancient times. There is a provincial legacy of traditional fermented foods among the ethnic population of North-East India. Fermented bamboo shoots (local name: Tuaither), soybeans (Bekang), and pork fat (Sa-um) are famous in the Mizoram state and represent a primary portion of the daily diet. These foods are prepared using methods based on cultural traditions inherited from previous generations, and prepared using a relatively uncontrolled fermentation process. Analysis of the bacterial diversity in these foods can provide important information regarding the flavor and texture of the final products of fermentation. Unfortunately, studies on the microbial composition and health benefits of such traditional fermented foods have rarely been documented. Therefore, the present study aims to highlight this bacterial diversity, along with the proximate composition of different traditional fermented foods (Tuaither, Bekang and Sa-um) primarily consumed in Mizoram state, India. Samples were collected on three different days of fermentation (3rd, 5th and 7th day), and bacterial diversity analysis was performed using the V3-V4 variable region of 16S rRNA gene with Illumina sequencing. Results revealed differences in the bacterial composition of dominant group members among all of the three food types. Firmicutes (82.72–94.00%), followed by Proteobacteria (4.67–15.01%), were found to dominate to varying degrees in all three of the fermented foods. However, at genus level high variation was observed in bacterial composition among these three different types of fermented foods. Lactobacillus (91.64–77.16%), Staphylococcus (52.00–17.90%), and Clostridium (72.48–55.40%) exhibited the highest relative abundances in the Tuaither, Bekang and Sa-um foods, respectively, in descending order from the 3rd to 7th day of fermentation. A few of the bacterial genera such as Lactobacilli were positively correlated with fermented bamboo shoot samples, and Staphylococcus was positively correlated with protein, carbohydrate and crude fiber content in soybean samples. In general, Tuaither, Bekang and Sa-um exhibited distinct differences in bacterial composition. This variation may be due to differences in the raw materials and/or methods used in the preparation of the different fermented food products. This is the first study to describe the bacterial composition of these traditional fermented foods using high-throughput sequencing techniques, and could help to drive research attention to comprehensive studies on improving understanding of the role of microbial communities in the preparation of traditional foods and their health benefits.

Application of Response Surface Methodology Based on a Box-Behnken Design to Determine Optimal Parameters to Produce Brined Cabbage Used in Kimchi

The factors of brine time, concentration, and temperature, affect the high-quality production of brined cabbage used in Kimchi. Although changes in Kimchi cabbage quality depending on brine time and concentration have been reported, changes in brine temperature have not been explored. Here, we optimized the brine process considering specific conditions of temperature (15–25 °C), concentration (10–14%), and osmosis duration (14–18 h) affecting the characteristics such as pH, titratable acidity, soluble solid content, glucose, fructose, and lactic acid bacteria and mass transport (salt gain, water loss, and weight reduction). The optimal parameters were determined using multivariate statistical analysis using the Box–Behnken design combined with response surface methodology. For each response as qualitative characteristics, second order polynomial models were developed using multiple regression analysis. Analysis of variance was performed to check the adequacy and accuracy of the fitted models. The brine temperature and concentration affected salt gain and water loss; the optimal brining temperature, concentration, and time were 19.17 °C, 10.53%, and 15.38 h, respectively. Statistical regression analysis indicated that standardized brined cabbage can be produced efficiently using a brining tank at controllable temperature.

Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap)

The phloem sap tapped from unopened inflorescence (spadix) of coconut palm using a novel collecting device, "coco-sap chiller," has been branded Kalparasa® (henceforth as Kalparasa in the text) to distinguish its properties not found in sap harvested by traditional methods. To know its hitherto unidentified microbiome profile, we employed high-throughput sequencing to uncover the bacteriome and mycobiome in fresh and 12-h fermented samples. Fresh Kalparasa had a pH of 7.2, which dropped to 4.5 after 12 h, signifying fermentation of the sap. Diversity analysis indicated fresh Kalparasa having higher bacterial species than the fermented one. Contrary to this, fresh sap had lower fungal/yeast diversity than the fermented sample. Fresh Kalparasa had relatively higher abundance of probiotic-type Leuconostoc genus followed by equal proportions of Gluconobacter, Acetobacter, and Fructobacillus. The 12-h fermented Kalparasa showed a significant increase in Gluconobacter with a sharp decrease in Leuconostoc. Mycobiome data revealed fresh Kalparasa to be preponderant in Saccharomyces and Hanseniaspora genera of yeasts while the fermented sap had higher representation of Hanseniaspora and Cortinarius and lesser Saccharomyces. This suggested that the fermentation of Kalparasa was probably driven by symbiotic culture of bacteria and yeasts (SCOBY), particularly acetic acid bacteria and non-Saccharomyces yeasts. The bacteriome-function predictions highlighted the enrichment of glycerophospholipid, ABC transporters, purine, and pyrimidine metabolisms. Based on our findings, Kalparasa containing large population of Leuconostoc mesenteroides, Fructobacillus fructosus, Saccharomyces cerevisiae, and Hanseniaspora guilliermondii can be promoted as a healthy "unfermented" plant edible food containing live probiotic-type microbiome during its consumption.

Microbial food: microorganisms repurposed for our food

Sustainable food production is a key to solve complicated and intertwined issues of overpopulation, climate change, environment and sustainability. Microorganisms, which have been routinely consumed as a part of fermented foods and more recently as probiotic dietary supplements, can be repurposed for our food to present a sustainable solution to current food production system. This paper begins with three snapshots of our future life with microbial foods. Next, the importance, possible forms, and raw materials (i.e. microorganisms and their carbon and energy sources) of microbial foods are discussed. In addition, the production strategies, further applications and current limitations of microbial foods are discussed.

Fungal Community Analyses of Endophytic Fungi from Two Oak Species, Quercus mongolica and Quercus serrata, in Korea

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics

The taste and quality of soy sauce, a fermented liquid condiment popular worldwide, is greatly influenced by microbial metabolism during fermentation. To investigate the fermentative features of ganjang (a Korean traditional soy sauce), ganjang batches using meju (fermented soybean) bricks and solar salts were prepared, and organic compounds, microbial communities, metagenomes, and metatranscriptomes of ganjang were quantitively analyzed during fermentation. Polymeric compound analysis in the ganjang treated with/without microbial inhibitors revealed that indigenous enzymes of meju bricks might be primarily responsible for degrading polymeric compounds. Through metagenome binning and microbe sequencing, 17 high-quality genome sequences representing all major ganjang microbiota were obtained, and their transcriptional expressions were quantitatively analyzed by mapping metatranscriptome reads normalized by spike-in RNA sequencing to the 17 genomes, which revealed that microbial metabolism might primarily occur while meju bricks are in the ganjang solution and decrease significantly after the removal of meju bricks. Metabolic pathways for carbohydrates, proteins, and lipids of the major ganjang microbiota were reconstructed, and their metabolic genes were transcriptionally analyzed, revealing that facultative lactic acid fermentation by Tetragenococcus was the major fermentation process active in the ganjang fermentation and that aerobic respiration by facultatively aerobic bacteria such as Chromohalobacter, Halomonas, and Marinobacter was also an important metabolic process during fermentation. Although the abundances of Fungi and the corresponding transcriptional expression levels were generally much lower than those of Bacteria, our analysis suggests that yeasts such as Debaryomyces and Wickerhamomyces might be in large part responsible for producing biogenic amines and flavors.

IMPORTANCE The taste and quality of soy sauce, a popular fermented liquid condiment worldwide, is greatly influenced by microbial metabolism during fermentation. Spontaneous fermentation of ganjang (a Korean traditional soy sauce) in a nonsterile environment leads to the growth of diverse bacteria and fungi during fermentation, making it difficult to understand the mechanism of ganjang fermentation. Genome-centered metatranscriptomic analysis, combined with organic compound analysis, quantitative metagenome and metatranscriptome analyses, and metabolic pathway reconstruction and expressional analysis of the major ganjang microbiota during fermentation, would provide comprehensive insights into the metabolic features of ganjang fermentation.

Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

Lactic Acid Bacteria Exopolysaccharides Producers: A Sustainable Tool for Functional Foods

Lactic acid bacteria (LAB) used in the food industry, mainly for the production of dairy products, are able to synthetize exopolysaccharides (EPS). EPS play a central role in the assessment of rheological and sensory characteristics of dairy products since they positively influence texture and organoleptic properties. Besides these, EPS have gained relevant interest for pharmacological and nutraceutical applications due to their biocompatibility, non-toxicity and biodegradability. These bioactive compounds may act as antioxidant, cholesterol-lowering, antimicrobial and prebiotic agents. This review provides an overview of exopolysaccharide-producing LAB, with an insight on the factors affecting EPS production, their dairy industrial applications and health benefits.

Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples

Purpose

Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.

Methods

The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.

Results

Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).

Conclusion

The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

Virome studies of food production systems: time for 'farm to fork' analyses

The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.

Kimchi bacteriophages of lactic acid bacteria: population, characteristics, and their role in watery kimchi

The bacteriophages (phages) in the watery kimchis (Baek-kimchi and Dongchimi) were characterized to determine the phage ecology of lactic acid bacteria (LAB). Kimchi obtained from the Seoul markets had an average of 2.1 log phage particles/mL, corresponding to 28% of the bacterial counts on a log scale. High counts of 5.5-6.5 log particles/mL of phages were noted in the early phase of fermentation (reaching pH 4), and 2.1-3.0 log phage particles/mL were found in the later phase, with some fluctuation in numbers. The LAB hosts changed from Weissella and Leuconostoc to Lactobacillus during Dongchimi fermentation. Fifteen phages, except for those of Lactobacillus, were isolated from diverse strains in the early phase. Five Weissella phages were Podoviridae, and all 10 Leuconostoc phages were Myoviridae. Phages had narrow and different host infection spectra to strains of the same species and high acidic stability. Therefore, the mortality and diversity of LAB during natural kimchi fermentation may be related to the specific phages of the hosts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10068-021-00930-y.

Different Reactions in Each Enterotype Depending on the Intake of Probiotic Yogurt Powder

Probiotics can be used as a nutritional strategy to improve gut homeostasis. We aimed to evaluate the intestinal microbiota profile of 18 subjects after ingestion of probiotic yogurt powder (PYP) based on enterotype. The subjects were classified into three enterotypes according to their microbial community: Bacteroides (n = 9, type B), Prevotella (n = 3, type P), and Ruminococcus (n = 6, type R). We performed controlled termination in a transient series that included a control period of three weeks before probiotic intake, PYP intake for three weeks, and a three-week washout period. Fecal microbiota composition was analyzed by sequencing the V3-V4 super variable region of 16S rRNA. Based on the Bristol stool shape scale, abnormal stool shape improved with PYP intake, and bowel movements were activated. The abundance of Faecalibacterium, Eggerthella, and Leuconostoc, which ferment and metabolize glucose, showed a strong correlation with type B Bacteroides, and glucose metabolism improvement was observed in all type B subjects. Alkaline phosphatase was significantly improved only in type B. In addition, the abundance of type B Bacteroides showed a negative correlation with that of Lactobacillus. The abundance of Streptococcus, Agathobacter, and Christensenella, which are involved in lipid metabolism, showed a strong correlation with that of type P Prevotella, and triglyceride metabolism improvement was observed in all type P subjects. The gut microbiota showed only short-term changes after PYP intake and showed resilience by returning to its original state when PYP intake was interrupted. In summary, the different responses to PYP intake may result from the different enterotypes and associated strains; therefore, the probiotic composition should be adjusted based on the individual enterotype.

Molecular identification and relative abundance of microorganisms in douchi koji and salted egg white sufu during processing

A novel animal protein-based douchi koji-inoculated steamed salted egg white sufu (SEWS) has been developed. This study determined the relative abundance of microorganisms in the douchi koji and semi-finished (5-day fermentation) and finished (5-day fermentation and 14-day ripening) SEWS by using 16S and 18S ribosomal DNA and gene-cloning methods. The results revealed that Bacillus spp. and Aspergillus oryzae were dominant in the douchi koji. In the semi-finished SEWS, the percentages of Bacillus amyloliquefaciens and Bacillus subtilis were considerably lower, whereas those of Enterococcus and Staphylococcus were substantially higher. In the finished SEWS, Bacillus spp. became dominant again and A. oryzae was the only fungus detected. In conclusion, by using molecular techniques, microbial population dynamics in SEWS can be evaluated. During processing, the relative abundance of microorganisms in SEWS changed and Bacillus spp. and A. oryzae remained dominant. This study provides crucial information for designing starter cultures for producing SEWS.

Characteristics on host specificity, infection, and temperature stability of Weissella phages from watery kimchi

Three bacteriophages (phage), ΦWC53, ΦWC54, and ΦWC56, of Weissella were isolated from watery kimchi and characterized. ΦWC53 belonged to Siphoviridae and ΦWC54 and ΦWC56 belonged to Myoviridae family. By one-step growth, the burst sizes were 5-260 particles/infected cells and the latent periods were 20-45 min. The phages infected Weissella spp., Leuconostoc mesenteroides, and Lactobacillus spp., differently by showing clear or turbid plaques. The phage adsorption rates on lactic acid bacteria were high on Weissella and low on Leuconostoc and Lactobacillus. However, the adsorption of ΦWC53 occurred variously among Weissella spp. and Weissella host grew well in the liquid culture without lysis after challenging by ΦWC53. Tolerances of these phages to temperature showed more various than those to pH. ΦWC53 was stable at 7 °C and 30 °C, but ΦWC54 and ΦWC56 were stable only at 7 °C. Therefore, three Weissella phages belonged to the different families and indicated diverse infection patterns on Weissella, Leuconostoc, and Lactobacillus with various stabilities for pH and temperature.

Genotoxicity and subchronic general toxicity assessments of Lactobacillus curvatus WiKim 38 using Sprague-Dawley rats

Lactobacillus curvatus WiKim 38 (LCW), isolated from kimchi, has shown novel immunomodulatory and anti-inflammatory properties. In the present study, to obtain data on the safety of LCW, we performed three genotoxicity (bacterial reverse mutation, chromosome aberration, and micronucleus) and two general toxicity (single-dosing and 13-week repeated-dosing) studies. In the genotoxicity assessment, LCW showed no increased reverse mutation for 4 strains of Salmonella typhimurium and a strain of Escherichia coli. In addition, LCW did not induce chromosome aberrations at concentrations up to 5000 μg/mL in cultured Chinese hamster lung (CHL) cells and did not induce an increased frequency of micronuclei in the bone marrow cells of rats at concentrations up to 2000 mg/kg. In the acute toxicity study using Sprague-Dawley (SD) rats, the approximate lethal dose of LCW was determined to be over 5000 mg/kg body weight (b.w.) in both sexes. Finally, in the subchronic toxicity study, no LCW-related adverse effects were observed at concentrations up to 5000 mg/kg b.w./day. Consequently, LCW is considered not to have mutagenic effects, and its no-observed-adverse-effect-level (NOAEL) is 5000 mg/kg b.w., equivalent to approximately 4.71 × 109 CFU/kg b.w., suggesting the LCW could be a potential probiotic for humans based on its safety profile.

Regional Diets Targeting Gut Microbial Dynamics to Support Prolonged Healthspan

In the last 150 years, we have seen a significant increase in average life expectancy, associated with a shift from infectious to non-communicable diseases. The rising incidence of these diseases, for which age is often the largest risk factor, highlights the need for contemporary societies to improve healthy ageing for their growing silver generations. As ageing is an inevitable, non-reversing and highly individualised process, we need to better understand how non-genetic factors like diet choices and commensal gut microbes can modulate the biology of ageing. In this review, we discuss how geographical and ethnic variations influence habitual dietary patterns, nutrient structure, and gut microbial profiles with potential impact on the human healthspan. Several gut microbial genera have been associated with healthy elderly populations but are highly variable across populations. It seems unlikely that a universal pro-longevity gut microbiome exists. Rather, the optimal microbiome appears to be conditional on the microbial functionality acting on regional- and ethnicity-specific trends driven by cultural food context. We also highlight dietary and microbial factors that have been observed to elicit individual and clustered biological responses. Finally, we identify next generation avenues to modify otherwise fixed host functions and the individual ageing trajectory by manipulating the malleable gut microbiome with regionally adapted, personalised food intervention regimens targeted at prolonging human healthspan.

ODFM, an omics data resource from microorganisms associated with fermented foods

ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites

Background

Salting is a traditional procedure for producing pickled vegetables. Salting can be used as a pretreatment, for safe lactic acid fermentation and for salt stock preparation. This study aimed to provide valuable knowledge to improve pickle production by investigating the dynamics of microbiota and metabolites during the pretreatment and salt stock preparation processes, which have previously been overlooked. The differences in these process conditions would be expected to change the microbiota and consequently influence the content of metabolites in pickles.

Methods

Samples, collected from eight commercial pickle manufacturers in Japan, consisted of the initial raw materials, pickled vegetables and used brine. The microbiota were analyzed by 16S rRNA sequencing and the metabolites quantified by liquid chromatograph-mass spectrometry. Statistical analyses helped to identify any significant differences between samples from the initial raw materials, pretreatment process and salt stock preparation process groups.

Results

Under pretreatment conditions, aerobic and facultative anaerobic bacteria were predominant, including Vibrio, a potentially undesirable genus for pickle production. Under salt stock preparation conditions, the presence of halophilic bacteria, Halanaerobium, suggested their involvement in the increase in pyruvate derivatives such as branched-chain amino acids (BCAA). PICRUSt analysis indicated that the enhanced production of BCAA in salt stock was caused not by quantitative but by qualitative differences in the biosynthetic pathway of BCAA in the microbiota.

Conclusion

The differences in the microbiota between pretreatment and previously studied lactic acid fermentation processes emphasized the importance of anaerobic conditions and low pH under moderate salinity conditions for assuring safe pickle production. The results from the salt stock preparation process suggested that the Halanaerobium present may provide a key enzyme in the BCAA biosynthetic pathway which prefers NADH as a coenzyme. This feature can enhance BCAA production under anaerobic conditions where NADH is in excess. The effects shown in this study will be important for adjusting pickling conditions by changing the abundance of bacteria to improve the quality of pickled vegetables.

Bacteriocinogenic Bacillus spp. Isolated from Korean Fermented Cabbage (Kimchi)—Beneficial or Hazardous?

Bacillus velezensis ST03 and ST32, Bacillus amyloliquefaciens ST06 and ST109, and Bacillus subtilis ST08 were isolated from artisanal-produced kimchi and were identified based on 16S rRNA partial sequencing. DNA obtained from the investigated bacilli generated positive results for lichenicidin, iturin, subtilosin, and surfactin on a strain-specific basis. The strains were found to produce antimicrobial metabolites with activity levels ranging between 800 and 1600 AU/mL on a strain-specific basis, as determined against Listeria monocytogenes ATCC15313. Moreover, all tested strains in this study were still active after treatment with proteolytic enzymes, even with reduced inhibition zones compared to the controls, pointing to additional antimicrobial activity possibly related to a non-proteinaceous molecular structure. Most probably these strains may express surfactin as an additional factor in their complex antimicrobial activity. B. amyloliquefaciens ST09 and B. velezensis ST03 and ST32 were characterized as positive for β-hemolysis. B. subtilis ST08 was shown to be positive for hblC and nheC and B. amyloliquefaciens ST109 for nheB. B. amyloliquefaciens ST109 generated positive results for gelatinase activity. The ability of the studied Bacillus strains to metabolize different carbohydrate sources was done based on the API50CHB test, while the enzyme production profile was recorded by the APIZym kit. All studied strains were positive producers for biogenic amines production. Studied Bacillus spp. strains were resistant to some of the evaluated antibiotics, tested according to recommendations of CLSI and EFSA.

Viruses in fermented foods: are they good or bad? Two sides of the same coin

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Integrative Metagenomics-Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu

Xiaoqu, one of three traditional jiuqu in China, is a saccharifying and fermenting agent used in Xiaoqu jiu brewing, with different ingredient compositions and preparation techniques used in various regions. The yield and quality of Xiaoqu jiu are significantly affected by the metabolites and microbiota of Xiaoqu; however, the associated relationship remains poorly understood. This study aimed to analyze this relationship in three typical traditional Xiaoqu from the Guizhou province in China. The non-volatile metabolites of Xiaoqu were detected using gas chromatography time-of-flight mass spectrometry, whereas the classification and metabolic potential of the microbiota were investigated using metagenomic sequencing. Results show that Firmicutes, Proteobacteria, and Actinobacteria represent the dominant bacterial phyla, with Lactobacillus, Bacillus, Acinetobacter, Leuconostoc, and Weissella found to be the dominant bacterial genera. Meanwhile, Ascomycota, Mucoromycota, and Basidiomycota are the dominant fungal phyla with Aspergillus, Saccharomyces, Pichia, Rhizopus, and Phycomyces being the predominant fungal genera. Functional annotation of the microbiota revealed a major association with metabolism of carbohydrates, cofactors, and vitamins, as well as amino acids. A total of 39 significantly different metabolites (SDMs) were identified that are involved in 47 metabolic pathways, primarily that of starch and sucrose; glycine, serine, and threonine; glyoxylate and dicarboxylate; pyruvate; as well as biosynthesis of pantothenate and CoA. Further, based on Spearman's correlation analysis, Aspergillus, Saccharomyces, Lactobacillus, Acetobacter, Weissella, Pantoea, Desmospora, and Bacillus are closely correlated with production of physicochemical indexes and SDMs. Moreover, the metabolic network generated for the breakdown of substrates and formation of SDMs in Xiaoqu was found to primarily center on the metabolism of carbohydrates and the tricarboxylic acid cycle. These results provide insights into the functional microorganisms and metabolic patterns present in traditional Guizhou Xiaoqu and might guide researchers in the production of stable and efficient Xiaoqu in the future.

Supercooling as a potentially improved storage option for commercial kimchi

The supercooling degree (SD), which refers to the difference between the ice nucleation temperature and freezing point of kimchi, varies depending on the type of kimchi, manufacturer, recipe, and manufacturing season. The aim of this study is to investigate the major influencing factors for the supercooled storage of kimchi and to analyze the possibility of supercooled storage for commercial kimchi. Pearson correlation analysis determined that, in commercial kimchi manufactured between March and July 2018, the SD of kimchi correlated to the number of aerobic bacteria (P < 0.01), however, was not associated with lactic acid bacteria. Moreover, the ice nucleation temperature of saline solution inoculated with aerobic bacteria was reduced from -3.03 ± 0.04 to -6.18 ± 0.11 °C by 10 kGy gamma ray sterilization. Meanwhile, the ice nucleation temperatures of 1.8 kg of commercial red cabbage kimchi and 500 g of white cabbage kimchi manufactured in February 2020 were -3.93 ± 0.06 °C and -3.57 ± 0.06 °C, respectively, and they could be stored at -2.5 °C for 12 weeks without freezing. Additionally, supercooled storage of kimchi at -2.5 °C caused a fermentation delay effect compared to control storage at 1 °C, considering the acidity and amount of lactic acid bacteria. Therefore, if the number of aerobic bacteria is controlled during the manufacturing process of kimchi, supercooled storage at temperatures below -2.5 °C may extend the shelf life of kimchi. PRACTICAL APPLICATION: We have shown that aerobic bacteria are the key influencing factor for ice nucleation of kimchi during supercooled storage. Aside from the initial sterilization process, fermentation of kimchi can also be delayed by lowering the storage temperature below -2.5 °C. Moreover, the method of direct cool refrigeration may have an industrial-level application.

Proteomic evaluation of kimchi, a traditional Korean fermented vegetable, and comparison of kimchi manufactured in China and Korea

Kimchi is a traditional Korean fermented vegetable, which is also widely consumed in Japan and China. However, little is known about the kimchi proteome. In this study, Korean and Chinese kimchi proteomes were evaluated by shotgun proteomics. A total of 250 proteins were annotated, and 29 of these were expressed at > 1% of the average relative abundance. Discrimination of the geographical origins of Korean and Chinese kimchi samples was possible using multivariate analysis of the proteomic data, and 23 proteins were expressed differently between the two types (p < 0.001), and represent possible markers to discriminate between Chinese and Korean kimchi. This study provides important insights into the kimchi proteome and illustrates the proteomic differences caused by geographical origin.

Deciphering the succession patterns of bacterial community and their correlations with environmental factors and flavor compounds during the fermentation of Zhejiang rosy vinegar

Zhejiang Rosy Vinegar (ZRV) is a traditional condiment in Southeast China, produced using semi-solid-state fermentation techniques under an open environment, yet little is known about the functional microbiota involved in the flavor formation of ZRV. In this study, 43 kinds of volatile flavor substances were identified by HS-SPME/GC-MS, mainly including ethyl acetate (relative content at the end of fermentation: 1104.1 mg/L), phenylethyl alcohol (417.6 mg/L) and acetoin (605.2 mg/L). The most abundant organic acid was acetic acid (59.6 g/L), which kept rising during the fermentation, followed by lactic acid (7.0 g/L), which showed a continuously downward trend. Amplicon sequencing analysis revealed that the richness and diversity of bacterial community were the highest at the beginning and then maintained decreasing during the fermentation. The predominant bacteria were scattered in Acetobacter (average relative abundance: 63.7%) and Lactobacillus (19.8%). Both sequencing and culture-dependent analysis showed Lactobacillus dominated the early stage (day 10 to 30), and Acetobacter kept highly abundant from day 40 to the end. Spearman correlation analysis displayed that the potential major groups involved in the formation of flavor compounds were Acetobacter and Lactobacillus, which were also showed strong relationships with other bacteria through co-occurrence network analysis (edges attached to Acetobacter: 61.7%; Lactobacillus: 14.0%). Moreover, structural equation model showed that the contents of ethanol, titratable acid and reducing sugar were the major environmental factors playing essential roles in influencing the succession of bacterial community and their metabolism during the fermentation. Overall, these findings illuminated the dynamic profiles of bacterial community and flavor compounds and the potential functional microbes, which were expected to help us understand the formation of flavor substances in ZRV.

The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds

The microbial community during fermented vegetable production has a large impact on the quality of the final products. Lactic acid bacteria have been well-studied in such processes, but knowledge about the roles of non-lactic acid bacteria is limited. This study aimed to provide useful knowledge about the relationships between the microbiota, including non-lactic acid bacteria, and metabolites in commercial pickle production by investigating Japanese pickles fermented in rice-bran. The samples were provided by six manufacturers, divided into two groups depending on the production conditions. The microbiological content of these samples was investigated by high-throughput sequencing, and metabolites were assessed by liquid chromatography-mass spectrometry and enzymatic assay. The data suggest that Halomonas, halophilic Gram-negative bacteria, can increase glutamic acid content during the pickling process under selective conditions for bacterial growth. In contrast, in less selective conditions, the microbiota consumed glutamic acid. Our results indicate that the glutamic acid content in fermented pickle is influenced by the microbiota, rather than by externally added glutamic acid. Our data suggest that both lactic acid bacteria and non-lactic acid bacteria are positive key factors in the mechanism of commercial vegetable fermentation and affect the quality of pickles.

Effect of Dietary Acetic Acid Supplementation on Plasma Glucose, Lipid Profiles, and Body Mass Index in Human Adults: A Systematic Review and Meta-analysis

BACKGROUND

Acetic acid is a short-chain fatty acid that has demonstrated biomedical potential as a dietary therapeutic agent for the management of chronic and metabolic illness comorbidities. In human beings, its consumption may improve glucose regulation and insulin sensitivity in individuals with cardiometabolic conditions and type 2 diabetes mellitus. Published clinical trial evidence evaluating its sustained supplementation effects on metabolic outcomes is inconsistent.

OBJECTIVE

This systematic review and meta-analysis summarized available evidence on potential therapeutic effects of dietary acetic acid supplementation via consumption of acetic acid-rich beverages and food sources on metabolic and anthropometric outcomes.

METHODS

A systematic search was conducted in Medline, Scopus, EMBASE, CINAHL Plus, and Web of Science from database inception until October 2020. Randomized controlled trials conducted in adults evaluating the effect of dietary acetic acid supplementation for a minimum of 1 week were included. Meta-analyses were performed using a random-effects model on fasting blood glucose (FBG), triacylglycerol (TAG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), glycated hemoglobin (HbA1c), body mass index (BMI), and body fat percentage. Statistical heterogeneity was assessed by calculation of Q and I² statistics, and publication bias was assessed by calculation of Egger's regression asymmetry and Begg's test.

RESULTS

Sixteen studies were included, involving 910 participants who consumed between 750 and 3600 mg acetic acid daily in interventions lasting an average of 8 weeks. Dietary acetic acid supplementation resulted in significant reductions in TAG concentrations in overweight and obese but otherwise healthy individuals (mean difference [MD] = -20.51 mg/dL [95% confidence intervals = -32.98, -8.04], P = .001) and people with type 2 diabetes (MD = -7.37 mg/dL [-10.15, -4.59], P < .001). Additionally, acetic acid supplementation significantly reduced FBG levels (MD = -35.73 mg/dL [-63.79, -7.67], P = .01) in subjects with type 2 diabetes compared with placebo and low-dose comparators. No other changes were seen for other metabolic or anthropometric outcomes assessed. Five of the 16 studies did not specify the dose of acetic acid delivered, and no studies measured blood acetate concentrations. Only one study controlled for background acetic acid-rich food consumption during intervention periods. Most studies had an unclear or high risk of bias.

CONCLUSION

Supplementation with dietary acetic acid is well tolerated, has no adverse side effects, and has clinical potential to reduce plasma TAG and FBG concentrations in individuals with type 2 diabetes, and to reduce TAG levels in people who are overweight or obese. No significant effects of dietary acetic acid consumption were seen on HbA1c, HDL, or anthropometric markers. High-quality, longer-term studies in larger cohorts are required to confirm whether dietary acetic acid can act as an adjuvant therapeutic agent in metabolic comorbidities management.

Development of a High-Throughput Microfluidic qPCR System for the Quantitative Determination of Quality-Relevant Bacteria in Cheese

The composition of the cheese microbiome has an important impact on the sensorial quality and safety of cheese. Therefore, much effort has been made to investigate the microbial community composition of cheese. Quantitative real-time polymerase chain reaction (qPCR) is a well-established method for detecting and quantifying bacteria. High-throughput qPCR (HT-qPCR) using microfluidics brings further advantages by providing fast results and by decreasing the cost per sample. We have developed a HT-qPCR approach for the rapid and cost-efficient quantification of microbial species in cheese by designing qPCR assays targeting 24 species/subspecies commonly found in cheese. Primer pairs were evaluated on the Biomark (Fluidigm) microfluidic HT-qPCR system using DNA from single strains and from artificial mock communities. The qPCR assays worked efficiently under identical PCR conditions, and the validation showed satisfying inclusivity, exclusivity, and amplification efficiencies. Preliminary results obtained from the HT-qPCR analysis of DNA samples of model cheeses made with the addition of adjunct cultures confirmed the potential of the microfluidic HT-qPCR system to screen for selected bacterial species in the cheese microbiome. HT-qPCR data of DNA samples of two downgraded commercial cheeses showed that this approach provides valuable information that can help to identify the microbial origin of quality defects. This newly developed HT-qPCR system is a promising approach that will allow simultaneous monitoring of quality-relevant species in fermented foods with high bacterial diversity, thereby opening up new perspectives for the control and assurance of high product quality.

Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

Pantoea agglomerans is a Gram-negative facultative anaerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts

Correlating Capsaicinoid Levels and Physicochemical Proper-ties of Kimchi and Its Perceived Spiciness

Capsaicinoid content, among other factors, affects the perception of spiciness of commercial kimchi. Here, we investigated whether the physicochemical properties of kimchi affect the spicy taste of capsaicinoids perceived by the tasting. High-performance liquid chromatography (HPLC) was used to evaluate the capsaicinoid content (mg/kg) of thirteen types of commercial kimchi. The physicochemical properties such as pH, titratable acidity, salinity, free sugar content, and free amino acid content were evaluated, and the spicy strength grade was determined by selected panel to analyze the correlation between these properties. Panels were trained for 48 h prior to actual evaluation by panel leaders trained for over 1000 h according to the Spectrum^TM method. Partial correlation analysis was performed to examine other candidate parameters that interfere with the sensory evaluation of spiciness and capsaicinoid content. To express the specific variance after eliminating the effects of other variables, partial correlations were used to estimate the relationships between two variables. We observed a strong correlation between spiciness intensity ratings and capsaicinoid content, with a Pearson’s correlation coefficient of 0.78 at p ≤ 0.001. However, other specific variables may have influenced the relationship between spiciness intensity and total capsaicinoid content. Partial correlation analysis indicated that the free sugar content most strongly affected the relationship between spiciness intensity and capsaicinoid content, showing the largest first-order partial correlation coefficient (r_xy/z: 0.091, p ≤ 0.01).

Microbial communities and gene contributions in smokeless tobacco products

Smokeless tobacco products (STP) contain bacteria, mold, and fungi due to exposure from surrounding environments and tobacco processing. This has been a cause for concern since the presence of microorganisms has been linked to the formation of highly carcinogenic tobacco-specific nitrosamines. These communities have also been reported to produce toxins and other pro-inflammatory molecules that can cause mouth lesions and elicit inflammatory responses in STP users. Moreover, microbial species in these products could transfer to the mouth and gastrointestinal tract, potentially altering the established respective microbiotas of the consumer. Here, we present the first metagenomic analysis of select smokeless tobacco products, specifically US domestic moist and dry snuff. Bacterial, eukaryotic, and viral species were found in all tobacco products where 68% of the total species was comprised of Bacteria with 3 dominant phyla but also included 32% Eukarya and 1% share abundance for Archaea and Viruses. Furthermore, 693,318 genes were found to be present and included nitrate and nitrite reduction and transport enzymes, antibiotic resistance genes associated with resistance to vancomycin, β-lactamases, their derivatives, and other antibiotics, as well as genes encoding multi-drug transporters and efflux pumps. Additional analyses showed the presence of endo- and exotoxin genes in addition to other molecules associated with inflammatory responses. Our results present a novel aspect of the smokeless tobacco microbiome and provide a better understanding of these products' microbiology. KEY POINTS: • The findings presented will help understand microbial contributions to overall STP chemistries. • Gene function categorization reveals harmful constituents outside canonical forms. • Pathway genes for TSNA precursor activity may occur at early stages of production. • Bacteria in STPs carry antibiotic resistance genes and gene transfer mechanisms.

Diversity and dynamics of bacterial and fungal communities in cider for distillation

Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p < 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p < 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.

Differences in the bacterial profiles and physicochemical between natural and inoculated fermentation of vegetables from Shanxi Province

Purpose

Fermented vegetables can be divided into two types, natural fermented and artificially inoculated fermented. By detecting and identifying the changes of bacterial diversity using physical and chemical indicators during natural and inoculation fermentation, we analyzed and determined the dominant bacteria in the fermentation process and revealed the relationship between bacteria and volatile substances.

Methods

We used the Illumina Miseq to sequence the bacteria in fermented vegetable samples at different fermentation periods, and calculated the total number of mesophilic microorganisms and lactic acid bacteria. We used the pH and nitrite to monitor the acidification process. GC-MS was used to determine volatile flavor compounds. Finally, we analyzed the correlation between volatile flavor compounds and bacteria.

Results

Total mesophilic microorganisms and the number of lactic acid bacteria in the inoculated fermentation were higher than the natural fermentation. The bacterial diversity Shannon and Simpson indexes of the natural fermentation, higher than those of inoculated fermentation in 0~7 days, were between 55~71% and 36~45%, respectively. On the 7th day, the proportion ofLactobacillusin the natural fermentation and inoculated fermentation were 53.4% and 90.2%, respectively, which were significantly different.Lactobacilluswas the dominant genus in the fermented vegetables and an important genus to promote the formation of volatile flavors.Lactobacilluswas negatively correlated with two volatile substances (4-[2,2,6-trimethyl-7-oxabicyclo [4.1.0] hept-1-yl]-3-Buten-2-one (K4) and a-Phellandrene (X1)) and played a leading role in the fermentation process.

Conclusions

Results demonstrated that the total number of mesophilic microorganisms and lactic acid bacteria in inoculated fermentation were more than those in natural fermentation. Inoculated fermentation can shorten the fermentation cycle and reduce the content of nitrite. Lactic acid bacteria were the dominant bacteria in fermented vegetables.

Bacterial compositions of indigenous Lanna (Northern Thai) fermented foods and their potential functional properties

Many indigenous fermented foods of Northern Thailand and neighbouring regions have traditionally been known for their health benefits. In this study, we explored the communities of bacteria in selected fermented foods which are commonly consumed among ethnic groups around Northern Thailand, for which information on their microbial compositions or their functional properties is still limited. The selected food groups included Thua Nao (alkaline fermented soybean product), Nham (fermented pork sausage/loaf), Nam phak (fermented Chinese cabbage) and Miang (fermented leaves from Miang Tea trees). Bacteria in these fermented foods were isolated and enumerated. Bacterial communities were determined using a culture-independent (pyrosequencing) approach. Lactic acid bacteria were recovered from all of these fermented food samples, with levels ranging from 3.1 to 7.5 log CFU/g throughout the fermentation processes. Analysis of the 16S rRNA gene from the fermented food samples using 454-pyrosequencing resulted in 113,844 sequences after quality evaluation. Lactic acid bacteria were found in high proportions in Nham, Nam phak and Miang. Bacillus was predominant in Thua nao, in which significant proportions of Lactic acid bacteria of the family Leuconostocaceae were also found. Groups of lactic acid bacteria found varied among different food samples, but three genera were predominant: Lactococcus, Lactobacillus and Leuconostoc, of which many members are recognised as probiotics. The results showed that these traditional Thai fermented food products are rich sources of beneficial bacteria and can potentially be functional/probiotic foods.

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

Kimchi markedly induces apoptosis in HT-29 human colon carcinoma cells

This study investigated kimchi-induced apoptosis in HT-29 human colon carcinoma cells. Three types of kimchi samples were prepared: standardized kimchi brined with general commercial Baechu cabbage by a standardized recipe (SK), Amtak Baechu kimchi brined with Amtak Baechu cabbage by a standardized recipe (AmK), and anticancer kimchi brined with organically cultivated Baechu cabbage by a functional recipe (AK). MTT assay, qRT-PCR, and Western blotting analysis were performed. The results indicate that AmK and AK, especially AK significantly upregulated mRNA expression of apoptosis-related genes Bim, Bax, Bak, caspase-8, -9, -3, and p53 but suppressed Bcl-xL and Bcl-2 expression. In addition, AK treatment significantly upregulated protein expression levels of caspase-3 but strikingly reduced the protein expression level of Bcl-2 (p < .05), followed by AmK treatment. Our data suggest that AK and AmK can markedly suppress the proliferation of HT-29 cells via activation of apoptosis. PRACTICAL APPLICATIONS: Colon cancer is the fourth cancer with the highest incidence in the world. Cell apoptosis is a type of programmed cell death and plays an important role in the cancer cells study. Kimchi is a traditional fermented food in Korea, with a relatively high daily consumption. Our present study used three kinds of kimchi which prepared with different main ingredients and recipes. The results suggest that organically cultivated Baechu cabbage and functional recipe in kimchi preparation play an important role in the anticancer efficacy of kimchi, which has been shown to promote induction of apoptosis in HT-29 cells.

Effect of Fungi on Metabolite Changes in Kimchi During Fermentation

The purpose of this study is to investigate the effect of fungi on kimchi metabolites during fermentation. A gas chromatography-mass spectrometry (GC-MS) based metabolite profiling approach in combination with principal component analysis (PCA) is performed to differentiate metabolites produced by fungi or bacteria. To avoid bacterial growth, kimchi is treated with 100 μg/mL of ampicillin every three days from 30 to 50 days of fermentation. The relative content of the major fungi at 50 days of fermentation, between the control group and the ampicillin treatment group, was not significantly different. The administration of ampicillin changed the metabolites in kimchi by affecting the growth of kimchi bacteria. Based on the pattern of change of each metabolite, the changed metabolites are grouped into four categories: (1) metabolites produced or consumed by fungi, (2) metabolites involving both fungi and bacteria, (3) metabolites produced or consumed by bacteria, and (4) metabolites of undetermined origin. Alanine, thymine, galacturonic acid, and malonic acid can be regarded as the metabolites produced by fungi between 30 and 50 days of fermentation. In contrast, malic acid, oxaloacetic acid, galactitol, glucose, and mannitol are presumed to be the metabolites mainly consumed by fungi. This study is meaningful as the first study conducted by inhibiting growth of bacteria to identify the metabolites contributed by fungi or bacteria in the kimchi fermentation process. These results could be used to make customized kimchi that controls the production of desired metabolites by selectively controlling the formation of microbial communities in the kimchi industry.

The Microbial Diversity of Non-Korean Kimchi as Revealed by Viable Counting and Metataxonomic Sequencing

Kimchi is recognized worldwide as the flagship food of Korea. To date, most of the currently available microbiological studies on kimchi deal with Korean manufactures. Moreover, there is a lack of knowledge on the occurrence of eumycetes in kimchi. Given these premises, the present study was aimed at investigating the bacterial and fungal dynamics occurring during the natural fermentation of an artisan non-Korean kimchi manufacture. Lactic acid bacteria were dominant, while Enterobacteriaceae, Pseudomonadaceae, and yeasts progressively decreased during fermentation. Erwinia spp., Pseudomonasveronii, Pseudomonasviridiflava, Rahnellaaquatilis, and Sphingomonas spp. were detected during the first 15 days of fermentation, whereas the last fermentation phase was dominated by Leuconostoc kimchi, together with Weissellasoli. For the mycobiota at the beginning of the fermentation process, Rhizoplaca and Pichia orientalis were the dominant Operational Taxonomic Units (OTUs) in batch 1, whereas in batch 2 Protomyces inundatus prevailed. In the last stage of fermentation, Saccharomyces cerevisiae, Candida sake,Penicillium, and Malassezia were the most abundant taxa in both analyzed batches. The knowledge gained in the present study represents a step forward in the description of the microbial dynamics of kimchi produced outside the region of origin using local ingredients. It will also serve as a starting point for further isolation of kimchi-adapted microorganisms to be assayed as potential starters for the manufacturing of novel vegetable preserves with high quality and functional traits.

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10⁻⁵ and 7.7 × 10⁻¹ copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.

Technologically relevant Bacillus species and microbial safety of West African traditional alkaline fermented seed condiments

Fermented food condiments serve as a major source of nutrients to many homes in West Africa, especially among the rural poor who use these condiments as a cheap source of protein substitute for milk and other animal protein sources. Traditional fermented West African condiments are produced by spontaneous fermentation of legumes and protein-rich seeds of both cultivated and wild plant species. These fermented condiments are culturally accepted and widely produced in the West African sub-region, and rely on indigenous microbiota responsible for taste, texture, aroma development and the overall unique product characteristics. Detailed understanding of fermentation microbiota and their unique technological and functional properties are fundamental in developing products with enhanced quality and safety, as well as development of specific locally adapted starter cultures. Technologically relevant Bacillus spp., mainly Bacillus subtilis, are the predominant fermentative bacteria responsible for the natural fermentation of condiments across West Africa. Other species of Bacillus including B. amyloliquefaciens, B. licheniformis, B. pumilus, B. megaterium, B. sphaericus, B. cereus, B. badius and B. fusiformis are also frequently involved in the fermentation process. These bacterial species are responsible for flavor development, bio-conversion of complex food molecules, and production of antimicrobial compounds that impact shelf-life and safety, and in some instances, may confer host-beneficial health effects beyond basic nutrition. First, this review provides currently available information on the technologically relevant Bacillus species isolated from fermented food condiments in nine (9) West African countries. In addition, perspectives on harnessing the potentials of the technologically beneficial bacterial strains in fermented condiments in West Africa for enhanced food safety, quality and overall food security is presented.

Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces

Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.

Latilactobacillus curvatus: A Candidate Probiotic with Excellent Fermentation Properties and Health Benefits

Latilactobacillus curvatus is a candidate probiotic that has been included in the list of recommended biological agents for certification by the European Food Safety Authority. According to the published genomic information, L. curvatus has several genes that encode metabolic pathways of carbohydrate utilization. In addition, there are some differences in cell surface complex related genes of L. curvatus from different sources. L. curvatus also has several genes that encode bacteriocin production, which can produce Curvacin A and Sakacin P. Due to its ability to produce bacteriocin, it is often used as a bioprotective agent in fermented meat products, to inhibit the growth of a variety of pathogenic and spoilage bacteria. L. curvatus exerts some probiotic effects, such as mediating the production of IL-10 by dendritic cells through NF-κB and extracellular regulated protein kinases (ERK) signals to relieve colitis in mice. This review is the first summary of the genomic and biological characteristics of L. curvatus. Our knowledge on its role in the food industry and human health is also discussed, with the aim of providing a theoretical basis for the development of applications of L. curvatus.

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing

Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.

Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures

Microorganisms grow in concert, both in natural communities and in artificial or synthetic co-cultures. Positive interactions between associated microbes are paramount to achieve improved substrate conversion and process performance in biotransformation and fermented food production. The mechanisms underlying such positive interactions have been the focus of numerous studies in recent decades and are now starting to be well characterized. Lactic acid bacteria (LAB) contribute to the final organoleptic, nutritional, and health properties of fermented food products. However, interactions in LAB co-cultures have been little studied, apart from the well-characterized LAB co-culture used for yogurt manufacture. LAB are, however, multifunctional microorganisms that display considerable potential to create positive interactions between them. This review describes why LAB co-cultures are of such interest, particularly in foods, and how their extensive nutritional requirements can be used to favor positive interactions. In that respect, our review highlights the benefits of co-cultures in different areas of application, details the mechanisms underlying positive interactions and aims to show how mechanisms based on nutritional interactions can be exploited to create efficient LAB co-cultures.