Monitoring the microbial community succession and diversity of Liangzhou fumigated vinegar during solid-state fermentation with next-generation sequencing

Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics

Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.

Dynamics and biodiversity of microbial community among seasons in Shanxi mature vinegar fermentation by semisolid-solid process

The dynamic succession and seasonal characteristics of microbiota throughout the Shanxi mature vinegar (SMV) fermentation by the semisolid-solid process were explored using high-throughput sequencing techniques. The results showed that the richness and diversity of fungi were higher than those of bacteria in a complete seasonal SMV fermentation cycle, and the microbial community was dominated by 11 taxa of bacteria and 16 taxa of fungi. In all four seasons, lactic acid bacteria and acetic acid bacteria were the dominant bacteria, while the dominant fungi varied. Saccharomyces and Pichia played an important role in spring. Aspergillus and Issatchenkia were enriched in the summer. Kazachstania was the dominant microorganism in autumn. While Mesenteroides and Meyerozyma were enriched in winter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis demonstrated that seasonality had a more decisive impact on microbiota composition than the fermentation stage within a season, and the microbiota structure in summer was significantly different from that in the other three seasons. Combined with the highest operational taxonomic units (OTUs) percentage (37%) of summer fungi in the Venn diagrams, it is speculated that the specific fungi may be the root cause for the relatively low SMV quality in summer. This work provided critical insights into the dynamic succession of the microbial community in SMV fermentation from a seasonality view, and the results could enrich our understanding of the microbiota involved in SMV fermentation and guide process control.

IMPORTANCE

Understanding the changes in microbial communities across different seasons is crucial for ensuring the quality of Shanxi mature vinegar (SMV) by the semisolid-solid process. In a complete seasonal cycle, the richness and diversity of fungi were higher than those of bacteria. The microbial community in summer fermentation was significantly different compared to the other three seasons. For example, the dominant microorganisms such as Acetobacter and Lactobacillus decreased in summer. Screening or modifying this group of bacteria to enhance their tolerance to high fermentation temperature is an approach to improve industrial SMV fermentation. Through co-occurrence network analysis, eight highly connected genera were identified, which may play important roles in ecosystem stability. These results also lay a theoretical foundation for the further development of multi-microbial co-fermentation. This work provides an understanding of SMV fermentation from a seasonal perspective and offers new guidance for the process control of grain vinegar brewing.

Synergistic Fermentation with Functional Microorganisms Improves Safety and Quality of Traditional Chinese Fermented Foods

Traditional fermented foods are favored by people around the world for their positive health and taste advantages. Many of the fermented foods, including Chinese traditional fermented foods, are produced through mixed-culture fermentation. Apart from reducing the formation of harmful compounds such as ethyl carbamate (EC) and biogenic amines (BAs) during food fermentation, it is also difficult to precisely control and regulate the fermentation process based on the control of environmental conditions alone, due to the complex microbiota and an unclarified fermentation mechanism. In this review, key microorganisms involved in Chinese fermented foods such as baijiu, soy sauce, and vinegar production are elaborated, and relations between microbial composition and the aroma or quality of food are discussed. This review focuses on the interpretation of functions and roles of beneficial (functional) microorganisms that participate in food fermentation and the discussion of the possibilities of the synergistic use of functional microorganisms to improve the safety and quality of Chinese fermented foods. Conducting work toward the isolation of beneficial microorganisms is a challenge for modern food fermentation technology. Thus, methods for the isolation and mutagenesis of functional microbial strains for synergistic food fermentation are summarized. Finally, the limitations and future prospects of the use of functional microorganisms in traditional Chinese fermented foods are reviewed. This review provides an overview of the applications of synergistic fermentation with functional microorganisms in the improvement of the safety or sensory qualities of fermented foods.

Integrated Microbiota and Metabolome Analysis to Assess the Effects of the Solid-State Fermentation of Corn-Soybean Meal Feed Using Compound Strains

Solid-state fermentation is known to improve plant-based feed nutritional quality; however, the association between microbes and metabolite production in fermented feed remains unclear. We inoculated corn-soybean-wheat bran (CSW) meal feed with Bacillus licheniformis Y5-39, Bacillus subtilis B-1, and lactic acid bacteria RSG-1. Then, 16S rDNA sequencing and untargeted metabolomic profiling were applied to investigate changes in the microflora and metabolites, respectively, and their integrated correlations during fermentation were assessed. The results indicated that trichloroacetic acid soluble protein levels showed a sharp increase, while glycinin and β-conglycinin levels showed a sharp decrease in the fermented feed, as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Pediococcus, Enterococcus, and Lactobacillus were predominant in the fermented feed. Overall, 699 significantly different metabolites were identified before and after fermentation. Arginine and proline, cysteine and methionine, and phenylalanine and tryptophan metabolism were the key pathways, with arginine and proline metabolism being the most important pathway in the fermentation process. By analyzing the correlation between the microbiota and metabolite production, lysyl-valine and lysyl-proline levels were found to be positively correlated with Enterococcus and Lactobacillus abundance. However, Pediococcus was positively correlated with some metabolites contributing to nutritional status and immune function. According to our data, Pediococcus, Enterococcus, and Lactobacillus mainly participate in protein degradation, amino acid metabolism, and lactic acid production in fermented feed. Our results provide new insights into the dynamic changes in metabolism that occurred during the solid-state fermentation of corn-soybean meal feed using compound strains and should facilitate the optimization of fermentation production efficiency and feed quality.

Application and Effect of Pediococcus pentosaceus and Lactiplantibacillus plantarum as Starter Cultures on Bacterial Communities and Volatile Flavor Compounds of Zhayu, a Chinese Traditional Fermented Fish Product

Zhayu is a type of traditional fermented fish product in China that is made through the fermentation of salted fish with a mixture of cereals and spices. Inoculation fermentation was performed using Pediococcus pentosaceus P1, Lactiplantibacillus plantarum L1, and a mixture of two strains, which were isolated from cured fish in Hunan Province. Compared with the natural fermentation, inoculation with lactic acid bacteria (LAB) accelerated the degradation of myosin and actin in Zhayu, increased the trichloroacetic acid (TCA)-soluble peptide content by about 1.3-fold, reduced the colony counts of Enterobacteriaceae and Staphylococcus aureus by about 40%, and inhibited their lipid oxidation. In the texture profile analysis performed, higher levels of hardness and chewiness were observed in the inoculation groups. In this study, the bacterial community and volatile flavor compounds were detected through 16S high-throughput sequencing and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). Inoculation with L. plantarum L1 reduced around 75% abundance of Klebsiella compared with the natural fermentation group, which was positively correlated with 2,3-Butanediol, resulting in a less pungent alcohol odor in Zhayu products. The abundances of 2-pentylfuran and 2-butyl-3-methylpyrazine were increased over threefold in the L1 group, which may give Zhayu its unique flavor and aroma.

Investigating the mechanism of the flavor formation in Sichuan sun vinegar based on flavor-orientation and metagenomics

Fermentation and aging are the key stages of flavor formation in Sichuan sun vinegar (SSV), but the generation mechanisms of the flavor produced by these processes are unknown. However, complex microbial metabolism is critical to the flavor development of SSV. In this study, we analyzed the key flavor compounds present in SSV. Combined with odor activity value (OAV), the main aroma components of SSV were screened, and the relationship between microorganisms and key flavor formation was predicted using metagenomic sequencing technology. The results revealed 38 key flavor compounds in SSV. Lactobacillus, Weissella, Acetobacter, Lichtheimia, Pediococcus, Oenococcus, Brettanomyces, Kazachstania, Pichia, Xanthomonas, Lenconostoc are widely involved in the production of key flavor compounds such as 2,3-butanediol, 2-Furanmethanol, phenylethanol, 3-(Methylthio)-1-propanol, acetic acid, lactic acid, butyric acid, isovaleric acid and other organic acids. Among them, Lichtheimia and Lactobacillus are important genera for the degradation of starch, arabinoxylan and cellulose. The acetaldehyde,4-ethyl-2-methoxy-phenol and 2-methoxy-4-methyl-phenol production pathway may be related to Lactobacillus, Acetobacter and Brettanomyces. This study provides a new understanding of the key flavor-formation stage and flavor compound generation mechanism of SSV and provides a reference for the screening and isolation of functional strains and the reconstruction of microbial communities.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Electrochemical Determination of Antioxidant Capacity of Traditional Homemade Fruit Vinegars Produced with Double Spontaneous Fermentation

In the current study, the antioxidant activity of traditional homemade fruit vinegars (HMV) was estimated by measuring the rate of homogeneous redox reaction with 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical cation (ABTS•+) using cyclic voltammetry. The antioxidant capacity of six HMV produced using traditional methods and the physicochemical characterization were measured in different vinegar production steps throughout a double spontaneous fermentation process, i.e., without any addition of yeasts or acetic acid bacteria. Their antioxidant capacity was compared with seven fruit commercial vinegars (ComV). Furthermore, the antioxidant capacity was independently measured with the TEAC (Trolox equivalent antioxidant capacity) assay, aiming at correlating with the electrochemical experimental data. Obtained results from both methods, the electrochemical and TEAC assays, interestingly indicated that all HMV have at least 10 times higher antioxidant activity than ComV. Furthermore, the large range of values for antioxidant capacity in samples of commercial vinegars from apples attested the importance of the raw material quality and technological procedures. The positive correlation between total phenolic content and antioxidant capacity measured by the two type of assays indicated that rose hip homemade vinegar (HMV5) has the highest antioxidant capacity. In contrast, the lowest levels of phenolic compounds and antioxidant capacity were found in apple and persimmon homemade vinegars (HMV1 and HMV6, respectively) which indicated that the type of fruit is crucial towards the production of high-quality vinegars. In this way, the use of traditional processes for the production of fruit vinegars proved to be very promising in terms of producing differentiated vinegars and, concomitantly, reaching high levels of health-promoting antioxidant capacities.

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.

Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature

In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model’s fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh.