Microbial community analysis of Korean soybean pastes by next-generation sequencing

Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution

The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.

Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation

Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.

Correlation Analysis between Microbial Communities and Flavor Compounds during the Post-Ripening Fermentation of Traditional Chili Bean Paste

Chili bean paste is a traditional flavor sauce, and its flavor compounds are closely related to its microflora. This study focused on investigating the content of bioactive compounds, flavor compounds, and microbial communities during the post-ripening fermentation of chili bean paste, aiming to provide a reference for improving the flavor of chili bean paste by regulating microorganisms. Compared to no post-ripening fermentation, the content of organic acids increased significantly (p < 0.05), especially that of citric acid (1.51 times). Glutamic acid (Glu) was the most abundant of the 17 free amino acids at 4.0 mg/g. The aroma profiles of the samples were significantly influenced by fifteen of the analyzed volatile compounds, especially methyl salicylate, methyl caproate, and 2-octanol (ROAV > 1). Latilactobacillus (27.45%) and Pseudomonas (9.01%) were the dominant bacterial genera, and Starmerella (32.95%) and Pichia (17.01%) were the dominant fungal genera. Weissella, Lacticaseibacillus, Pichia, and Kazachstania had positive effects on volatile flavoring compounds, which enriched the texture and flavor of the chili bean paste. Therefore, the microbial-community activity during the post-ripening fermentation is the key to enhance the flavor quality of the product.

Phenotypic and genomic analyses of bacteriocin-producing probiotic Enterococcus faecium EFEL8600 isolated from Korean soy-meju

Enterococcus faecium is a prevalent species found in fermented soybean products, known for its contributions to flavor development and inhibition of pathogenic microorganisms during fermentation. This study aims to provide comprehensive phenotypic and genomic evidence supporting the probiotic characteristics of E. faecium EFEL8600, a bacteriocin-producing strain isolated from Korean soy-meju. Phenotypic analysis revealed that EFEL8600 produced a peptide with inhibitory activity against Listeria monocytogenes, estimated to be 4.6 kDa, corresponding to the size of enterocins P or Q. Furthermore, EFEL8600 exhibited probiotic traits, such as resilience in gastrointestinal conditions, antioxidant and anti-inflammatory activities, and protection of the intestinal barrier. Safety assessments demonstrated no hemolytic and bile salt deconjugation activities. Genomic analysis revealed the presence of several genes associated with probiotic characteristics and bacteriocin production, while few deleterious genes with a low likelihood of expression or transferring were detected. Overall, this study highlights E. faecium EFEL8600 as a potent anti-listeria probiotic strain suitable for use as a starter culture in soymilk fermentation, providing potential health benefits to consumers.

Diversity of eukaryotic and prokaryotic microbiota revealed by metabarcoding in Neotropical floodplain lakes

The diversity of eukaryotic and prokaryotic communities has been assessed by morphological and genetic approaches, which are used to characterize the microbiota in different environments. Here, planktonic prokaryotic and eukaryotic communities of the Araguaia River, located in the Central region of Brazil, were analyzed based on metabarcoding analysis of rRNA genes to evaluate the diversity of these groups in tropical floodplain lakes. Also, we tested their spatial concordance throughout the Araguaia river. Water samples were collected from 8 floodplain lakes in Araguaia River. The 16S and 18S rRNA genes were amplified and sequenced using Illumina MiSeq. For eukaryotes, 34,242 merged reads were obtained and 225 distinct OTUs were delineated, of which 106 OTUs were taxonomically classified. For prokaryotes, 26,426 sequences were obtained and 351 OTUs were detected. Of them, 231 were classified in at least one taxonomic category. The most representative eukaryotes belonged to Ciliophora, Chlorophyta and Charophyta. The prokaryotic phylum with the most OTUs classified were Proteobacteria, Actinobacteria and Bacteroidetes. The lakes did not show spatial concordance when comparing the similarity between their microbiota. The knowledge of freshwater biodiversity using DNA sequencing for important rivers, such as Araguaia River, can improve microbiota inventories of tropical biodiversity hotspots.

Monitoring the growth dynamics of Tetragenococcus halophilus strains in lupine moromi fermentation using a multiplex-PCR system

OBJECTIVE

The microbiota of a seasoning sauce fermentation process is usually complex and includes multiple species and even various strains of one species. Moreover, composition and cell numbers of individual strains vary over the course of the entire fermentation. This study demonstrates the applicability of a multiplex PCR system to monitor growth dynamics of Tetragenococcus (T.) halophilus strains in order to evaluate their performance and help to select the most competitive starter strain.

RESULTS

In a previous study we isolated T. halophilus strains from multiple lupine moromi fermentation processes and characterized them. In this study we wanted to monitor the growth dynamics of these strains in a competitive lupine moromi model fermentation process using a multiplex PCR system. Therefore, pasteurized lupine koji was inoculated with eight different T. halophilus strains, six from lupine moromi, one from an experimental buckwheat moromi fermentation process and the type strain DSM 20,339^T, to create the inoculated lupine moromi pilot scale fermentation process. With the multiplex PCR system, we could detect that all strains could grow in lupine moromi but, that TMW 2.2254 and TMW 2.2264 outperformed all other strains. Both strains dominated the fermentation after three weeks with cell counts between 4 × 10⁶ to 4 × 10⁷ CFU/mL for TMW 2.2254 and 1 × 10⁷ to 5 × 10⁷ CFU/mL for TMW 2.2264. The pH dropped to value below 5 within the first 7 days, the selection of these strains might be related to their acid tolerance.

Comparisons of Physicochemical Properties, Bacterial Diversities, Isoflavone Profiles and Antioxidant Activities on Household and Commercial doenjang

In this study, the physicochemical properties (pH, acidity, salinity, and soluble protein), bacterial diversities, isoflavone contents, and antioxidant activities of doenjang (fermented soy paste), household doenjang (HDJ), and commercial doenjang (CDJ), were assessed and compared. The values of pH 5.14-5.94 and acidity 1.36-3.03%, indicated a similar level in all doenjang. The salinity was high in CDJ at 12.8-14.6%, and the protein contents (25.69-37.54 mg/g) were generally high in HDJ. Forty-three species were identified from the HDJ and CDJ. The main species were verified to be Bacillus amyloliquefaciens (B. amyloliquefaciens), B. amyloliquefaciens subsp. plantarum, Bacillus licheniformis, Bacillus sp. and Bacillus subtilis. Comparing the ratios of isoflavone types, the HDJ has an aglycone ratio of >80%, and 3HDJ indicates a ratio of isoflavone to aglycone of 100%. In the CDJ, except 4CDJ, glycosides account for a high proportion of more than 50%. The results of antioxidant activities and DNA protection effects were variedly confirmed regardless of HDJs and CDJs. Through these results, it is judged that HDJs have a variety of bacterial species compared to CDJs, and these are biologically active and converted from glycoside to aglycone. Bacterial distribution and isoflavone contents could be used as basic data.

Safety Assessment Systems for Microbial Starters Derived from Fermented Foods

Microorganisms involved in food fermentation not only improve the aroma and taste of the food, but also enhance its preservation. Thus, they are added as starter cultures to boost the final product quality of commercial fermented foods. Although these microorganisms originate from fermented foods and have a long history of consumption, the European Union recently applied the concept of Qualified presumption of Safety (QPS), which is a safety evaluation system for microorganisms used in food or feed in Europe. The QPS system is a species-level safety system and shares results with the European Novel Food System, a strain-level safety evaluation system. In the United States, microorganisms added to fermented foods are considered as food additives or Generally Recognized as Safe substance. In Korea, food microbe lists are presented at the species level. Moreover, the nation has established a strain-oriented evaluation system that applies temporary safety evaluation methods for food raw materials as well as new raw materials. However, when it comes to microorganisms isolated from traditional fermented foods and other fermented food products, there is no definition of the term "species," and there is a lack of an evaluation system at the species level. Therefore, such an evaluation system for microbial species used in Korean fermented foods is necessary.

Exploring Core Microbiota Based on Characteristic Flavor Compounds in Different Fermentation Phases of Sufu

Sufu, a Chinese traditional fermented soybean product, has a characteristic foul smell but a pleasant taste. We determined the core functional microbiota and their metabolic mechanisms during sufu fermentation by examining relationships among bacteria, characteristic flavor compounds, and physicochemical factors. Flavor compounds in sufu were detected through headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry, and the microbial community structure was determined through high-throughput 16S rRNA sequencing. The results showed that the fermentation process of sufu could be divided into early and late stages. The early stage was critical for flavor development. Seven microbiota were screened based on their abundance, microbial relevance, and flavor production capacity. Five microbes were screened in the early stage: Pseudomonas, Tetragenococcus, Lysinibacillus, Pantoea, and Burkholderia–Caballeronia–Paraburkholderia. Three microbes were screened in the late stage: Exiguobacterium, Bacillus, and Pseudomonas. Their metabolic profiles were predicted. The results provided a reference for the selection of enriched bacterial genera in the fermentation process and controlling applicable process conditions to improve the flavor of sufu.

Plant-Based Alkaline Fermented Foods as Sustainable Sources of Nutrients and Health-Promoting Bioactive Compounds

Traditional food fermentation is a practice that precedes human history. Acidic products such as yogurts and sourdoughs or alcoholic beverages produced through lactic acid or yeast fermentations, respectively, are widely described and documented. However, a relatively less popular group of fermented products known as alkaline fermented foods are common traditional products in Africa and Asia. These products are so called “alkaline” because the pH tends to increase during fermentation due to the formation of ammonia resulting from protein degradation by Bacillus species. Plant-based alkaline fermented foods (AFFs) are generally produced from legumes including soybean, non-soybean leguminous seeds, and other non-legume plant raw materials. Alkaline fermented food products such as natto, douchi, kinema, doenjang, chongkukjang, thua nao, meitauza, yandou, dawadawa/iru, ugba, kawal, okpehe, otiru, oso, ogiri, bikalga, maari/tayohounta, ntoba mbodi, cabuk, and owoh are produced at small industrial scale or household levels and widely consumed in Asia and Africa where they provide essential nutrients and health-promoting bioactive compounds for the population. Alkaline food fermentation is important for sustainable food security as it contributes to traditional dietary diversity, significantly reduces antinutritional components in raw plant materials thereby improving digestibility, improves health via the production of vitamins, and may confer probiotic and post-biotic effects onto consumers. In this review, we present currently available scientific information on plant-based AFFs and their role as sustainable sources of nutrients and bioactive compounds for improved health. Finally, we provide perspectives on research needs required to harness the full potential of AFFs in contributing to nutrition and health.

Safety and Technological Characterization of Staphylococcus xylosus and Staphylococcus pseudoxylosus Isolates from Fermented Soybean Foods of Korea

We evaluated the antibiotic susceptibilities, hemolytic activities, and technological properties of 36 Staphylococcus xylosus strains and 49 S. pseudoxylosus strains predominantly isolated from fermented soybean foods from Korea. Most of the strains were sensitive to chloramphenicol, erythromycin, gentamycin, kanamycin, lincomycin, oxacillin, tetracycline, and trimethoprim. However, 23 strains exhibited potential phenotypic acquired resistance to erythromycin, lincomycin, and tetracycline. Based on breakpoint values for staphylococci from the Clinical and Laboratory Standards Institute, >30% of the isolates were resistant to ampicillin and penicillin G, but the population distributions in minimum inhibitory concentration tests were clearly different from those expected for acquired resistance. None of the strains exhibited clear α- or β-hemolytic activity. S. xylosus and S. pseudoxylosus exhibited salt tolerance on agar medium containing 20% and 22% (w/v) NaCl, respectively. S. xylosus and S. pseudoxylosus strains possessed protease and lipase activities, which were affected by the NaCl concentration. Protease activity of S. pseudoxylosus was strain-specific, but lipase activity might be a characteristic of both species. This study confirms the potential of both species for use in high-salt soybean fermentation, but the safety and technological properties of strains must be determined to select suitable starter candidates.

Detection of the microbial diversity and flavour components of northeastern Chinese soybean paste during storage

A combination of 16S rDNA and GC-IMS was used to study the changes in the composition of microorganisms and volatile organic compounds (VOCs) during the storage of northeastern Chinese soybean paste. Firmicutes and Actinobacteriota dominated the microbial communities of the soybean paste at the phylum level, bacterial profiles of different samples were different at genus level. Fifty-one VOCs were identified from soybean paste, most of which existed in the early storage stage. Most esters and alcohols decreased with the extension of the storage time, while acids and pyrazines accumulated in the later period of storage. Esters, alcohols, acids and aldehyde compounds are the key substances in the volatile components of soybean paste, which give the soybean paste the sour, sweet, rose, mushroom and smoky flavor characteristics. The biomarker Bacillus-velezensis in soybean paste is directly related to ester features; Kroppenstedtia, Sporolactobacillus-nakayamae, and Corynebacterium-stationis are positively associated with the biosynthesis of aldehydes.

Community structure of yeast in fermented soy sauce and screening of functional yeast with potential to enhance the soy sauce flavor

Yeast plays an important role in the formation of desirable aroma during soy sauce fermentation. In this study, the structure and diversity of yeast communities in seven different soy sauce residues were investigated by ITS sequencing analysis, and then the aroma characteristics of selected yeast species were examined by a combination of gas chromatography-mass spectrometry (GC-MS), headspace solid-phase microextraction (SPME) and liquid-liquid extraction (LLE). A total of 18 yeast genera were identified in seven soy sauce residues. Among them, Candid and Zygosaccharomyces were detected in all samples, followed by Millerozyma, Wickerhamiella, Meyerozyma, Trichosporon and Wickerhamomyces, which were found in more than two-thirds of the samples. Subsequently, eight representative species, isolated from soy sauce residues, were subjected to environmental stress tolerance tests and aroma production tests. Among them, three isolated species were regarded as potential aroma-enhancing microbes in soy sauce. Wickerhamiella versatilis could increase the contents of ethyl ester compounds and alcohols, thereby improving the fruity and alcoholic aroma of soy sauce. Candida sorbosivorans enhanced sweet and caramel-like aroma of soy sauce by producing 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) and 3-hydroxy-2-methyl-4h-pyran-4-one (maltol). Starmerella etchellsii could enhance the contents of 2,6-dimethylpyrazine, methyl pyrazine and benzeneacetaldehyde. This study is of great significance for the development and application of flavor functional yeasts in soy sauce fermentation.

Fermentation of Cereals and Legumes: Impact on Nutritional Constituents and Nutrient Bioavailability

Fermented food products, especially those derived from cereals and legumes are important contributors to diet diversity globally. These food items are vital to food security and significantly contribute to nutrition. Fermentation is a process that desirably modifies food constituents by increasing the palatability, organoleptic properties, bioavailability and alters nutritional constituents. This review focuses on deciphering possible mechanisms involved in the modification of nutritional constituents as well as nutrient bioavailability during the fermentation of cereals and legumes, especially those commonly consumed in developing countries. Although modifications in these constituents are dependent on inherent and available nutrients in the starting raw material, it was generally observed that fermentation increased these nutritive qualities (protein, amino acids, vitamins, fats, fatty acids, etc.) in cereals and legumes, while in a few instances, a reduction in these constituents was noted. A general reduction trend in antinutritional factors was also observed with a corresponding increase in the nutrient bioavailability and bioaccessibility. Notable mechanisms of modification include transamination or the synthesis of new compounds during the fermentation process, use of nutrients as energy sources, as well as the metabolic activity of microorganisms leading to a degradation or increase in the level of some constituents. A number of fermented products are yet to be studied and fully understood. Further research into these food products using both conventional and modern techniques are still required to provide insights into these important food groups, as well as for an overall improved food quality, enhanced nutrition and health, as well as other associated socioeconomic benefits.

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

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

•

The effect of salt concentration on soybean paste was studied.

•

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

•

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

•

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

The microbial community, biogenic amines content of soybean paste, and the degradation of biogenic amines by Lactobacillus plantarum HM24

Soybean paste was a traditional fermented product in Northeast China, mainly fermented by molds, yeast, Bacillus, and lactic acid bacteria. This study investigated the dynamic changes of the microbial community and biogenic amine content during the fermentation of the traditional soybean paste. The microbial diversity of soybean paste in different regions was analyzed by MiSeq sequencing technology. The results showed that Penicillium and Tetragenococcus were the dominant microorganisms responsible for the fermentation of soybean paste. Biogenic amine was found in the traditional soybean paste at different fermentation stages, putrescine, and tyramine were the mainly biogenic amines and their content increased with the extension of fermentation time. Serratia in the soybean paste was positively correlated with the formation of spermine, cadaverine (p < .01), and β-phenethylamine (p < .05), Leuconostoc was negatively correlated with tyramine formation (p < .05), and Enterococcus was positively correlated with the formation of histamine, tryptamine and cadaverine (p < .01). Lactobacillus fermentum HM22, Lactobacillus plantarum HM24, and Enterococcus faecalis YF10042 with strong biogenic amine degrading capacity were inoculated into the koji. After 20 days of fermentation, the degradation rates of tryptamine, β-phenylethylamine, putrescine, cadaverine, histamine, and tyramine in soybean paste inoculated with L. plantarum HM24 were 35.31%, 43.14%, 30.18%, 33.44%, 32.74%, and 39.91%, respectively, indicating that the use of L. plantarum HM24 as a starter culture in soybean paste fermentation might be a good strategy for biogenic amines reduction.

Effect of Enterotoxigenic Escherichia coli on Microbial Communities during Kimchi Fermentation

The diverse microbial communities in kimchi are dependent on fermentation period and temperature. Here, we investigated the effect of enterotoxigenic Escherichia coli (ETEC) during the fermentation of kimchi at two temperatures using high-throughput sequencing. There were no differences in pH between the control group, samples not inoculated with ETEC, and the ETEC group, samples inoculated with ETEC MFDS 1009477. The pH of the two groups, which were fermented at 10 and 25°C, decreased rapidly at the beginning of fermentation and then reached pH 3.96 and pH 3.62. In both groups, the genera Lactobacillus, Leuconostoc, and Weissella were predominant. Our result suggests that microbial communities during kimchi fermentation may be affected by the fermentation parameters, such as temperature and period, and not enterotoxigenic E. coli (ETEC).

Characterization and correlation of microbial communities and metabolite and volatile compounds in doenjang fermentation

To investigate the general fermentation features of doenjang, a traditional Korean fermented soybean paste, eleven batches of doenjang were prepared. The bacterial and fungal communities and the metabolites such as free sugars, organic acids, amino acids, and volatile compounds were analyzed during fermentation. Tetragenococcus, Aspergillus, and Debaryomyces were the most common microbes; galactose, fructose, and glucose were the major sugars; and lactate and acetate were the major organic acids. Spearman correlation analyses showed that the quantity of meju was correlated with only Pediococcus and Halomonas abundance, while solar salt concentration was correlated with the relative abundance of many microbial taxa and the amount of glycerol and total volatile compounds. The abundance of heterolactic acid bacteria, such as Tetragenococcus, Pediococcus, Weissella, and Enterococcus, was positively correlated with the levels of lactate, acetate, and ethanol, suggesting that heterolactic acid fermentation may be a major metabolism pathway during the fermentation of doenjang. The abundance of Weissella, Hyphopichia, and Wickerhamomyces was positively correlated with ethyl acetate levels, whereas the abundance of Staphylococcus and Bacillus was positively correlated with the concentration of major volatile compounds, 3-methylbutanoic acid and tetramethylpyrazine, respectively, suggesting that they may play important roles in the production of flavor compounds during fermentation.

Safety Evaluation and In vivo Strain-Specific Functionality of Bacillus Strains Isolated from Korean Traditional Fermented Foods

Unveiling and understanding differences in physiological features below the species level may serve as an essential fast-screening tool for selecting strains that can promote a specific probiotic effect. To study the intra-species diversity of Bacillus, a genus with a wide range of enzyme activities and specificity, 190 Bacillus strains were isolated from traditional Korean fermented food products. Altogether, in the preliminary safety screening, 8 of these strains were found negative for lecithinase and hemolysis activity and were selected for further investigations. On the basis of different levels of enzyme functionalities (high or low proteolytic, amylolytic, and lipolytic (PAL) activities), two Bacillus subtilis strains were selected for an in vivo study. Each of the two strains was separately administered at a level of 1 × 10⁸ CFU per day to C57BL/6 mice that were fed 60% high-fat diet ad libitum for 8 weeks, while Xenical, an anti-obesity drug, was used as a positive control in the experimental setup. B. subtilis M34 and B. subtilis GS40a with low and high amylolytic activities, respectively, induced significantly different and contrasting physiological effects. The production of short-chain fatty acids appeared to be closely associated with a shift in the gut microbiota.

Fermentation for future food systems: Precision fermentation can complement the scope and applications of traditional fermentation

Modern biotechnology holds great potential for expanding the scope of fermentation to create novel foods and improve the sustainability of food production.

Genetic Background Behind the Amino Acid Profiles of Fermented Soybeans Produced by Four Bacillus spp

Strains of four Bacillus spp. were respectively inoculated into sterilized soybeans and the free amino acid profiles of the resulting cultures were analyzed to discern their metabolic traits. After 30 days of culture, B. licheniformis showed the highest production of serine, threonine, and glutamic acid; B. subtilis exhibited the highest production of alanine, asparagine, glycine, leucine, proline, tryptophan, and lysine. B. velezensis increased the γ-aminobutyric acid (GABA) concentration to >200% of that in the control samples. B. sonorensis produced a somewhat similar amino acid profile with B. licheniformis. Comparative genomic analysis of the four Bacillus strains and the genetic profiles of the produced free amino acids revealed that genes involved in glutamate and arginine metabolism were not common to the four strains. The genes gadA/B (encoding a glutamate decarboxylase), rocE (amino acid permease), and puuD (γ-glutamyl-γ-aminobutyrate hydrolase) determined GABA production, and their presence was species-specific. Taken together, B. licheniformis and B. velezensis were respectively shown to have high potential to increase concentrations of glutamic acid and GABA, while B. subtilis has the ability to increase essential amino acid concentrations in fermented soybean foods.

Taxonomic Composition and Diversity of the Gut Microbiota in Relation to Habitual Dietary Intake in Korean Adults

We investigated associations of habitual dietary intake with the taxonomic composition and diversity of the human gut microbiota in 222 Koreans aged 18-58 years in a cross-sectional study. Gut microbiota data were obtained by 16S rRNA gene sequencing on DNA extracted from fecal samples. The habitual diet for the previous year was assessed by a food frequency questionnaire. After multivariable adjustment, intake of several food groups including vegetables, fermented legumes, legumes, dairy products, processed meat, and non-alcoholic beverages were associated with major phyla of the gut microbiota. A dietary pattern related to higher α-diversity (HiαDP) derived by reduced rank regression was characterized by higher intakes of fermented legumes, vegetables, seaweeds, and nuts/seeds and lower intakes of non-alcoholic beverages. The HiαDP was positively associated with several genera of Firmicutes such as Lactobacillus, Ruminococcus, and Eubacterium (all p < 0.05). Among enterotypes identified by principal coordinate analysis based on the β-diversity, the Ruminococcus enterotype had higher HiαDP scores and was strongly positively associated with intakes of vegetables, seaweeds, and nuts/seeds, compared to the two other enterotypes. We conclude that a plant- and fermented food-based diet was positively associated with some genera of Firmicutes (e.g., Lactobacillus, Ruminococcus, and Eubacterium) reflecting better gut microbial health.

Traditional fermented soybean products: processing, flavor formation, nutritional and biological activities

Traditional fermented soybean food has emerged as an important part of people's dietary structure because of the unique flavors and improved health benefit. During fermentation, the nutrients in soybean undergo a series of biochemical reactions catalyzed naturally by microorganism secreted enzymes. Thereafter, many functional and bioactive substances such as bioactive peptides, unsaturated fatty acids, free soy isoflavones, vitamins and minerals are produced, making fermented soy products more advantageous in nutrition and health. This review comprehensively discusses the historical evolution, distribution, traditional fermentation processing, main sources and characteristics of fermented strains, flavor components, nutritional properties, and biological activities of four traditional fermented soybean foods including douchi, sufu, dajiang, and soy sauce. In the end, we introduce four major challenges encountered by traditional fermented soybean foods including high salt content, formation of biogenic amine, the presence of pathogenic microorganisms and mycotoxins, and quality inconsistency. We conclude that the establishment of scientific quality standard and innovated fermentation processing is the potential solutions to combat the issues and improve the safety of traditional fermented soybean products.

Culture-dependent and -independent investigations of bacterial migration into doenjang from its components meju and solar salt

We determined bacterial migration into doenjang from its components, meju and solar salt using culture-based and 16S rRNA gene-based culture-independent techniques (pyrosequencing of total DNA). Pyrosequencing results suggested that the bacterial communities of meju, but not solar salt, significantly affected those of doenjang communities. Culture-based pyrosequencing analysis yielded similar results. These results indicate that most predominant bacterial species in doenjang migrated from meju, not solar salt. We therefore believe that the present study is one of the most comprehensive comparisons of bacterial communities of fermented soybeans using culture-dependent and -independent methods. Furthermore, pyrosequencing of the V3 and V4 regions of bacterial 16S rRNA did not distinguish among Bacillus amyloliquefaciens, B. siamensis, and B. velezensis as well as between Enterococcus faecium and E. hirae.

Distinct Roles for Bacterial and Fungal Communities During the Curing of Vanilla

Vanilla produces aroma after curing. There were a few reports about the possible involvement of microorganisms during the curing process. Bacterial and fungal community was analyzed to explore the distinct roles. Alpha diversity analysis indicated that the abundance and diversity of microorganisms did not increase regularly as the curing progressed. Weighted and unweighted principal coordinates analysis (PCoA) showed that the fungal community of blanching beans was significantly different from those of the vanilla beans of other stages, respectively. Bacillus and Aspergillus were the dominant genus during the curing process. Correlation analysis indicated that the bacterial and fungal structure was positively related to the vanillin formation, respectively. The study was conducive to reveal the formation of flavor components and the biosynthesis of vanillin. Furthermore, it proposed the possible curing methods of regulating the bacterial and fungal community to increase vanillin formation.

Physicochemical Factors Affecting Microbiota Dynamics During Traditional Solid-State Fermentation of Chinese Strong-Flavor Baijiu

Spontaneous solid-state fermentation (SSF) of Chinese Baijiu involves diverse microbes from Daqu and pit mud (PM). Given that the transfer of interphase microflora during the fermentation is a continuous and dynamic process, longitudinal studies are essential to provide ecological insights into community stability and response to consecutive disturbances in the process. In this context, this study aimed to generate a comprehensive longitudinal characterization of the microbiota during the fermentation processes of Chinese strong-flavor Baijiu (CSFB) differing in cellar ages with consideration for potential relation to physicochemical variables. The microecology variations observed during the 6-years cellar SSF (SCSSF) and 30-years cellar SSF (TCSSF) processes reveal that fungal composition contributes to a larger extent than bacterial composition to such variations. Orders of Lactobacillales, Anaerolineales, Enterobacteriales, Bacillales, Eurotiales, and Saccharomycetales dominated (average relative abundances >10%) the microbiota in both SCSSF and TCSSF processes but with a different percentage in the operational taxonomic unit (out) abundances. Compared with the SCSSF process, TCSSF possessed slower microbial succession rates, which were in accordance with the profile of physicochemical properties. From a network perspective, the microbial community structure observed in the TCSSF processes was more stable than that in the SCSSF. This may benefit from the milder physicochemical conditions of the TCSSF processes, especially the temperature, which is also more beneficial to the growth of some groups that have negative effects on fermentation, such as Staphylococcus, Pseudomonas, and Acinetobacter.

Isolation, identification and characterization of Staphylococcus sp. from Indian ethnic fermented fish product

Staphylococci from Sheedal of Northeast India was isolated, identified and characterized. All the isolated staphylococci were found to be coagulase negative. Based on the rpoB gene sequences followed by analysis using NCBI-BLAST software, seven species of Staphylococcus namely, S. piscifermentans, S. condimenti, S. arlettae, S. sciuri, S. warneri, S. nepalensis and S. hominis were recognized. Phylogenetic analyses revealed three major cluster groups. All the seven Staphylococcus showed their NaCl tolerance from 2 to 8%. No species was able to grow at 55°C. Except S. arlettae and S. sciuri, all the isolated staphylococcal species exhibited growth at pH 4-8. No isolated species was able to ferment mannitol, sucrose and arabinose. All the species exhibited moderate to maximum proteolytic and lipolytic activities. All the seven species were found to be sensitive to the antibiotics, namely, erythromycin, norfloxacin, ampicillin, streptomycin and vancomycin, whereas all were resistant to co-trimoxazole. Only S. piscifermentans was found antagonist to Salmonella enterica, Escherichia coli and Bacillus subtilis, although the clear zone was minimal. All the staphylococcal species except S. arlettae and S. sciuri exhibited hydrophobicity ranging from 25 to 66%. The observed characteristics of isolated Staphylococci from Sheedal revealed their role in fish fermentation.

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste

Pixian broad bean paste (PBP) is a traditional Chinese condiment, famous for its distinctive flavor. Microbial communities play a vital role in producing the unique flavor of PBP, and a significant accumulation of these volatile flavors occurs during the post-fermentation stage of its production. However, little is known about the relationship between the microbes and flavor compounds in PBP. In this study, high-throughput sequencing (HTS) analysis revealed that Leuconostoc (8.30%), Lactobacillus (7.05%), Weissella (5.80%) and Staphylococcus (4.03%) were the dominant bacterial genera, while the most prevalent yeast genera were Zygosaccharomyces (41.45%) and Pichia (5.83%). Gradual accumulations of free amino acids (glutamic acid and asparagine), organic acids (malic acid and tartaric acid), and unique volatiles (aldehydes, phenols and pyrazines) were evident throughout the post-fermentation process. Analysis of the Pearson's correlation coefficients between 66 key microbes and the key flavors was investigated. Nine core microbes were identified based on the linear discriminant analysis (LDA) scores ≥ 4 (or an average abundance >0.1%) and a high correlation with at least two flavor categories (P < 0.05, |ρ| > 0.8), namely Kosakonia, Kazachstania, Debaryomyces, Lactobacillus, Myroides, Stenotrophomonas, Ochrobactrum, Wohlfahrtiimonas, and Lactococcus genera. These results provide a clearer insight into microbial succession during PBP post-fermentation, thereby contributing to further quality improvement of PBP.

A Bottom-Up Approach To Develop a Synthetic Microbial Community Model: Application for Efficient Reduced-Salt Broad Bean Paste Fermentation

Humans have used high salinity for the production of bean-based fermented foods over thousands of years. Although high salinity can inhibit the growth of harmful microbes and select functional microbiota in an open environment, it also affects fermentation efficiency of bean-based fermented foods and has a negative impact on people's health. Therefore, it is imperative to develop novel defined starter cultures for reduced-salt fermentation in a sterile environment. Here, we explored the microbial assembly and function in the fermentation of traditional Chinese broad bean paste with 12% salinity. The results revealed that the salinity and microbial interactions together drove the dynamic of community and pointed out that five dominant genera (Staphylococcus, Bacillus, Weissella, Aspergillus, and Zygosaccharomyces) may play different key roles in different fermentation stages. Then, core species were isolated from broad bean paste, and their salinity tolerance, interactions, and metabolic characteristics were evaluated. The results provided an opportunity to validate in situ predictions through in vitro dissection of microbial assembly and function. Last, we reconstructed the synthetic microbial community with five strains (Aspergillus oryzae, Bacillus subtilis, Staphylococcus gallinarum, Weissella confusa, and Zygosaccharomyces rouxii) under different salinities and realized efficient fermentation of broad bean paste for 6 weeks in a sterile environment with 6% salinity. In general, this work provided a bottom-up approach for the development of a simplified microbial community model with desired functions to improve the fermentation efficiency of bean-based fermented foods by deconstructing and reconstructing the microbial structure and function.IMPORTANCE Humans have mastered high-salinity fermentation techniques for bean-based fermented product preparation over thousands of years. High salinity was used to select the functional microbiota and conducted food fermentation production with unique flavor. Although a high-salinity environment is beneficial for suppressing harmful microbes in the open fermentation environment, the fermentation efficiency of functional microbes is partially inhibited. Therefore, application of defined starter cultures for reduced-salt fermentation in a sterile environment is an alternative approach to improve the fermentation efficiency of bean-based fermented foods and guide the transformation of traditional industry. However, the assembly and function of self-organized microbiota in an open fermentation environment are still unclear. This study provides a comprehensive understanding of microbial function and the mechanism of community succession in a high-salinity environment during the fermentation of broad bean paste so as to reconstruct the microbial community and realize efficient fermentation of broad bean paste in a sterile environment.

Exploring the diversity and role of microbiota during material pretreatment of light-flavor Baijiu

Baijiu (Chinese liquor) is a type of traditional distilled alcoholic beverage produced through spontaneous solid-state fermentation with sorghum as the primary material. Material processing, including sorghum soaking, steaming and cooling which is carried out in an open environment, is an integral part of Baijiu manufacturing. However, the microbiota involved in material pretreatment and its associate with the alcoholic fermentation is unclear. This research is aimed to exploring the diversity and role of microbiota during material pretreatment of light-flavor Baijiu. Results showed that Cyanobacteria, Epicoccum, and Cladosporium predominated in the sorghum at the beginning of soaking. Lactobacillus and Pichia became the predominant bacterial and fungal genera by the end of soaking. With the dynamics of microbiota, the pH declined sharply and the categories and concentration of volatile flavors such as alcohols, esters, acids, phenols, ketones, and aldehydes increased. Correlation analysis indicated that Lactobacillus and Pichia showed positive correlation with various flavors during soaking. Furthermore, SourceTracker analysis revealed that the microbiota involved during cooling processing was an important source of the Lactobacillus during fermentation of light-flavor Baijiu. This study illustrates the role of microbiota during material pretreatment and the association with alcoholic fermentation, which contributes to reveal the mechanism of Baijiu manufacturing.

The effect of salt concentrations on the fermentation of doenjang, a traditional Korean fermented soybean paste

Four sets of doenjang (traditional Korean fermented soybean paste) with 9%, 12%, 15%, and 18% solar salt concentrations were prepared and their pH, microbial abundances and communities, metabolites, and volatile compounds were analyzed periodically during the entire fermentation. The speeds of decrease in pH and increase in microbial abundances, representing microbial activity, were higher during early fermentation in lower (9% and 12%) salt doenjang. Microbial abundances in 15% and 18% salt doenjang were significantly lower than in the 9% and 12% salt doenjang, indicating low microbial activity. Community analysis revealed that Bacillus, Staphylococcus, and Clostridium and Aspergillus, Scopulariopsis, Fusarium, Mucor, and Penicillium, which might be derived from doenjang-meju used for preparing doenjang, were identified as major bacterial and fungal genera, respectively, in all doenjang samples. Weissella, Tetragenococcus, Oceanobacillus, and Debaryomyces, not dominant in doenjang-meju, were also identified as major groups in low salt doenjang. Metabolite analysis showed that amino acid profiles were relatively similar independent of salt concentrations and microbial growth, indicating important roles of indigenous proteases present in doenjang-meju, not microbial activity during doenjang fermentation, in amino acid production. The metabolism of free sugars to organic acids and biogenic amine production were greater in lower salt doenjang, which might be associated with the growth of microbes, particularly lactic acid bacteria. A higher level of and more diverse volatile compounds were identified in lower salt doenjang, indicating close association with microbial growth. This study provides a deeper understanding of doenjang fermentation and insight into the development of low salt doenjang.

Comparative Genomic Analysis of Food-Originated Coagulase-Negative Staphylococcus: Analysis of Conserved Core Genes and Diversity of the Pan-Genome

To shed light on the genetic differences among food-originated coagulase-negative Staphylococcus (CNS), we performed pan-genome analysis of five species: Staphylococcus carnosus (two strains), Staphylococcus equorum (two strains), Staphylococcus succinus (three strains), Staphylococcus xylosus (two strains), and Staphylococcus saprophyticus (one strain). The pan-genome size increases with each new strain and currently holds about 4,500 genes from 10 genomes. Specific genes were shown to be strain dependent but not species dependent. Most specific genes were of unknown function or encoded restriction-modification enzymes, transposases, or prophages. Our results indicate that unique genes have been acquired or lost by convergent evolution within individual strains.

Variations in Fungal Community and Diversity in Doushen With Different Flavors

Doushen, a traditional Chinese fermented soybean product, may be spiced or spicy depending on whether pepper powder is added. While numerous studies have investigated the microbial communities of other fermented foods, little is known on the fungal diversity of Doushen. Therefore, in this study, we investigated the fungal community and diversity in both spiced and spicy Doushen. Our results revealed that fungal species richness significantly differed between the samples with different flavors. A total of nine phyla and 188 fungal genera were identified, and Ascomycota and Aspergillus were predominant in all samples. Based on linear discriminant analysis, a total of 57 OTUs were significantly different between the two samples. Results of non-metric multidimensional scaling and unweighted pair-group analysis suggested that the presence of pepper powder affects the microbial community in Doushen. Network analysis showed that microbial interactions between fungal communities in Doushen with different flavors were significantly different. The results on the enumeration and identification of fungi were consistent with the composition of the dominant genera in the samples with different flavors. This study provides a theoretical basis for future research on food ecology in Doushen.

Fermented foods in a global age: East meets West

Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.

Meta-omics reveal microbial assortments and key enzymes in bean sauce mash, a traditional fermented soybean product

BACKGROUND

Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study first investigated the metaproteome of bean sauce mash. This was followed by an analysis of its biological functions and its microbial community to reveal information about strains and about the expressed proteins to better understand the roles of the microbiota in bean sauce mash.

RESULTS

The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of the Penicillium and Rhizopus genera and were classified into 100 cellular components, 238 biological processes, and 220 molecular function categories by gene ontology (GO) annotation. Enzymes associated with glycolysis metabolic pathways were also identified. These can provide the energy required for microbial fermentation. Illumina MiSeq sequencing technology results showed that the microorganism communities of bean sauce mash exhibited a high level of diversity. Microbiological analysis demonstrated that the Penicillium, Mucor, Fusarium, Aspergillus, and Rhizopus fungi, and Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium genera were predominant 22 samples.

CONCLUSION

The profiles and insights in the current study are important for research on bean sauce mash and related products in terms of their food microbial ecology. The information obtained from this study will help the development of stable sufu starter cultures with unique sensory qualities. © 2019 Society of Chemical Industry.

Dynamic Changes in the Bacterial Community During the Fermentation of Traditional Chinese Fish Sauce (TCFS) and Their Correlation with TCFS Quality

This study revealed for the first time the dynamic changes of the bacterial community during the fermentation of traditional Chinese fish sauce (TCFS) using high-throughput sequencing. In the early phase of TCFS fermentation, Shewanella (approximately 90%) within Proteobacteria was the dominant bacteria. Then, Halanaerobium (3%-86%) within Firmicutes rapidly replaced Shewanella as the dominant genus until the 12th month. Lactococcus (3.31%) and Bacillus (45.56%) belonging to Firmicutes were detected abundantly in the 3rd and 9th months after fermentation, respectively. In the late phase (12-15 months), Tetragenococcus within Firmicutes replaced Halanaerobium as the most dominant bacteria (29.54%). Many other genera including Pseudomonas, Psychrobacter, Tissierella, Carnobacterium and Gallicola were abundantly present in the 15th month after fermentation. Furthermore, the relationships between the bacterial community and major functional substances of TCFS, including amino nitrogen (AAN), free amino acids (FAAs), total soluble nitrogen (TSN), and trimethylamine (TMA), were investigated by partial least squares regression (PLSR). Tetragenococcus was positively correlated with the formation of TMA, while Halanaerobium showed the opposite result, suggesting that Tetragenococcus might be a good starter for TCFS fermentation. These results contribute to our knowledge about bacterial participation in the process of TCFS fermentation and will help improve the quality of fermented seafood.