Comparison of microbial communities and physiochemical characteristics of two traditionally fermented vegetables

Correlation of physicochemical properties and volatile profiles with microbiome diversity in cucumber during lightly-pickling in seasoning liquid

Lightly-pickled cucumber is a popular pickled product in Asian countries. However, its quality and microbial alteration during pickling and its correlation between microorganisms and quality are still unclear. Changes in physicochemical properties, volatile organic compounds (VOCs), and microbial community during lightly-pickling cucumbers in seasoning liquid and their relationships were investigated. Results showed that the hardness and fracturability decreased with pickling time, modeled by a zero-order kinetic model. The color became brown and dark as pickling extended. Sixty-four VOCs were identified and 13 aroma-active compounds were found using GC-O and odor activity values. (E,Z)-2,6-nonadienal, hexanal, and (E,E)-2,4-heptadienal were the characteristic aroma markers essential for differentiating among the samples with different pickling times. At the genus level, Delftia and Stenotrophomonas dominated in the bacterial community, and Rhodotorula and Naganishia are the dominant fungal genera. The correlation analysis revealed that one bacteria (Acinetobacter) and two fungi (Naganishia and Rhodotorula) were strongly related to quality loss and off-flavors in cucumbers in the late pickling process. This study provides an important reference for facilitating the quality control of lightly-pickled cucumber during processing.

Effect of temperature on the quality and microbial community during Daocai fermentation

Daocai is a traditional salted pickle in the southeastern region of Guizhou with a unique aroma, color, and taste. The quality of Daocai is greatly influenced by the fermentation temperature. In this study, high-throughput sequencing and headspace-gas chromatography-ion mobility spectrometry were used to investigate the changes in microbial community succession and volatile flavor compounds during Daocai fermentation under temperature-controlled (D group) and non-temperature-controlled (C group).We found that the predominant genera in the C group samples were Latilactobacillus(40.57 %), Leuconostoc(21.25 %), Cystofilobasidium(22.12 %), Vishniacozyma(23.89 %), and Leucosporidium(24.95 %), whereas Weissella(29.39 %), Lactiplantibacillus(45.61 %), Mucor(68.26 %), and Saccharomyces(23.94 %) were the predominant genera in the D group. A total of 92 VFCs were detected in Daocai samples, including 5 isothiocyanates, 16 esters, 14 alcohols, 24 aldehydes, 17 ketones, 3 acids, 2 pyrazines, 1 pyridines, 1 thiazoles, 3 furans, 4 alkenes, and 2 nitriles. Further analysis revealed Latilactobacillus, Leuconostoc, Lactococcus, Cystofilobasidium, Leucosporidium, Holtermanniella, and Dioszegia as key bacteria involved in flavor formation. They are closely related to the formation of flavors such as aldehydes, furans, pyridines, and alkenes. This study contributes to our understanding of the relationship between bacterial communities and the flavor formation during Daocai fermentation.

The terroir of Tempeh: Strong region-specific signatures in the bacterial community structures across Indonesia

Tempeh, a soybean product from Indonesia, is created through fermentation by Rhizopus spp. and associated bacteria. Here, we aim to get an overview of the variability of the tempeh microbiota across Indonesia and disentangle influencing factors. We found high variability in bacterial abundance (103 - 109 copies g-1), richness (nASV = 40 - 175 ASVs), and diversity (H' = 0.9 - 3.5) in tempeh. The primary factor affecting this variation was the region, where the tempeh was produced. Interestingly, tempeh samples obtained from geographically close areas tended to share similar bacterial profiles, suggesting a "terroir" of tempeh. Additionally, tempeh wrapped in banana leaves had a higher abundance of enterobacteria in comparison to tempeh wrapped in plastic but also tended to have a higher total bacterial and lactobacilli abundance. Despite all variability, the tempeh core microbiome consists Lactobacillales and Enterobacteriales. This study demonstrates a high variability of bacterial diversity in traditional tempeh from local producers highlighting a strong regional influence across Indonesia.

The quality characteristics and microbial communities of three components in traditional split-fermented red sour soup

Red sour soup is a Guizhou specialty condiment made by the natural fermentation of tomatoes and chili. In this study, three components (tomato acid, chili acid, and tomato and chili mixed acid) of split-fermented red sour soup were explored to compare the quality characteristics and microbial communities in the middle and late fermentation stages. The titratable acidity of mixed acids was lower than that of tomato acid and chili acid in the middle stage, but it was significantly increased in the late stage. The cell viability of lactic acid bacteria was mostly higher than that of yeasts during the whole fermentation. Also significantly increased in the late stage of fermentation were sensory scores and the signal intensity of sour substances. However, the signal intensity of both bitter and salty substances decreased, and the total amount of free amino acids was reduced. In addition, the antioxidant capacity of the samples and the dominant microorganisms were different between the two fermentation stages, Lactobacillus and Kazachstania were the key common genus of the different components of split-fermented red sour soup. It is anticipated that this study would provide us an insight into the quality characteristics and microbial communities of split-fermented red sour soup.

Effects of pickle brine and glycine addition on biogenic amine production in pickle fermentation

This study investigated the effects of different pickle brines and glycine additions on biogenic amine formation in pickle fermentation. The results showed that the brines with higher biogenic amine content led to the production of more biogenic amines in the simulated pickle fermentation system. This was related to the abundance of biogenic amine-producing microorganisms in the microbial communities of the brines. Metagenome analysis of the brines and metatranscriptome analysis of the fermentation systems showed that putrescine was primarily from Lactobacillus, Oenococcus, and Pichia, while histamine and tyramine were primarily from Lactobacillus and Tetragenococcus. Addition of glycine significantly reduced the accumulation of biogenic amines in the simulated pickle fermentation system by as much as 70 %. The addition of glycine had no inhibitory effect on the amine-producing microorganisms, but it down-regulated the transcription levels of the genes for enzymes related to putrescine synthesis in Pichia, Lactobacillus, and Oenococcus, as well as the histidine decarboxylase genes in Lactobacillus and Tetragenococcus. Catalytic reaction assay using crude solutions of amino acid decarboxylase extracted from Lactobacillus brevis showed that the addition of glycine inhibited 45 %-55 % of ornithine decarboxylase and tyrosine decarboxylase activities. This study may provide a reference for the study and control of the mechanism of biogenic amine formation in pickle fermentation.

Revealing core functional microorganisms in the fermentation process of Qicaipaojiao (Capsicum annuum L.) based on microbial metabolic network

Paojiao, a typical Chinese traditional fermented pepper, is favored by consumers for its unique flavor profile. Microorganisms, organic acids, amino acids, and volatile compounds are the primary constituents influencing the development of paojiao's flavor. To elucidate the key flavor compounds and core microorganisms of Qicaipaojiao (QCJ), this study conducted a comprehensive analysis of the changes in taste substances (organic acids and amino acids) and volatile flavor compounds during QCJ fermentation. Key flavor substances in QCJ were identified using threshold aroma value and odor activity value and the core microorganisms of QCJ were determined based on the correlation between dominant microorganisms and the key flavor substances. During QCJ fermentation, 16 key taste substances (12 free amino acids and 4 organic acids) and 12 key aroma substances were identified. The fermentation process involved 10 bacteria and 7 fungal genera, including Lactiplantibacillus, Leuconostoc, Klebsiella, Pichia, Wickerhamomyces, and Candida. Correlation analysis revealed that the core functional microorganisms encompassed representatives from 8 genera, including 5 bacterial genera (Lactiplantibacillus, Weissella, Leuconostoc, Klebsiella, and Kluyvera) and 3 fungal genera (Rhodotorula, Phallus, and Pichia). These core functional microorganisms exhibited significant correlations with approximately 70 % of the key flavor substances (P < 0.05). This study contributes to an enhanced understanding of flavor formation mechanisms and offers valuable insight into flavor quality control in food fermentation processes.

Two-stage fermentation of corn and soybean meal mixture by Bacillus subtilis and Lactobacillus acidophilus to improve feeding value: optimization, physicochemical property, and microbial community

Microbial treatment can reduce the antinutritional factors and allergenic proteins in corn-soybean meal mixture (CSMM), but the role of the microbial community in hypoallergenicity and digestibility during the fermentation process remains unclear. Therefore, the fermentation strains of Bacillus and LAB were determined, and the compatibility and fermentation process of two-stage solid fermentation composite bacteria were optimized, and the dynamic changes in physicochemical property and microbial community during two-stage fermentation were investigated. Results showed that Bacillus subtilis NCUBSL003 and Lactobacillus acidophilus NCUA065016 were the best fermentation combinations. The optimal fermentation conditions were inoculum 7.14%, solid-liquid ratio of 1:0.88 and fermentation time of 74.30 h. The contents of TI, β-conglycinin and glycinin decreased significantly after fermentation. Besides, TCA-SP, small peptides and FAA increased. Bacillus and Lactobacillus were the main genera. Pathogenic bacteria genera were inhibited effectively. This study suggests the feasibility of two-stage fermentation in improving the nutrient values and safety of the CSMM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01426-7.

Characterization of key flavor substances and their microbial sources in traditional sour bamboo shoots

Identifying key flavor compounds and their producing bacteria in sour bamboo shoots is crucial for flavor stabilization and industrial production. This study analyzed 15 traditional sour bamboo shoot samples from northern Guangdong to determine key flavor substances and microbial community. Results showed key flavor substances were acetic acid (RTC ≥ 50% in 10 samples), lactic acid (RTC ≥ 50% in 5 samples), and p-cresol (ROC ≥ 93%). Lactobacillus (ARA: 54.62%) was the dominant genus, significantly correlated with p-cresol (r = 0.80, p ≤ 0.01). Levilactobacillus (ARA: 3.33%) was positively correlated with lactic acid and p-cresol (r = 0.78, p ≤ 0.01; r = 0.66, p ≤ 0.01). Lentilactobacillus (ARA: 4.29%) was positively correlated with acetic acid (r = 0.85, p ≤ 0.01). Levilactobacillus was isolated, screened, identified, and its ability to produce key flavor substances was tested. Four strains of Levilactobacillus spicheri and their mixed strains produced lactic acid (10.12-16.62 g/kg), acetic acid (10.21-21.60 g/kg), and p-cresol (25.67-143.87 mg/kg). This is the first report of Levilactobacillus spicheri producing p-cresol.

Yeast diversity in open agave fermentations across Mexico

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX-1.0 culture collection by isolating 4524 strains from 68 sites with diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and validated a subset of the strains by ITS and D1/D2 sequencing, which also revealed two potential novel species of Saccharomycetales. Overall, the composition of yeast communities was weakly associated with local variables and types of climate, yet a core set of six species was consistently isolated from most producing regions. To explore the intraspecific variation of the yeasts from agave fermentations, we sequenced the genomes of four isolates of the nonconventional yeast Kazachstania humilis. The genomes of these four strains were substantially distinct from a European isolate of the same species, suggesting that they may belong to different populations. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.

Spatial heterogeneity of microbiota and flavor across different rounds of sauce-flavor baijiu in Northern China

Sauce-flavor baijiu (SFB) is a traditional Chinese distilled liquor crafted through a distinctive brewing process, involving seven rounds of stack fermentation (SF) and pit fermentation (PF). To date, there remains a knowledge gap regarding the microbial succession and flavor throughout all rounds of SFB with distinctive northern characteristics. Through LEfSe analysis, Saccharopolyspora, Virgibacillus, Thermoascus and Thermomyces, and Lactobacillus and Issatchenkia were found to be the most differentially representative genera in SF and PF, respectively. A total of 93 volatile flavor compounds were found in base baijius through the gas-chromatography mass spectrometry. Moreover, 29 volatile flavor substances with significant difference in base baijius of different rounds were revealed using the OPLS-DA model and VIP values and Spearman correlation analysis shows that bacteria have a greater impact on differential flavor compounds than fungi. This study provides a new perspective and insight into the brewing of northern SFB.

Effects of inoculation with a binary mixture of Lactobacillus plantarum and Leuconostoc citreum on cell wall components of Chinese Dongbei suancai

This study aimed to investigate the effects of inoculation with a starter culture consisting of Lactobacillus plantarum LNJ002 and Leuconostoc citreum BNCC 194779 on microbial community, cell wall polysaccharide characteristics, cell wall degrading enzymes, and microstructure during Chinese Dongbei suancai fermentation. The results showed that Lactobacillus (98.75%) was the dominant genus during fermentation of Dongbei suancai. The principal coordinates analysis (PCoA) suggested that inoculation with Lactobacillus promoted the stability of microbial community structure during Chinese Dongbei suancai fermentation. Besides, the lower content in cellulose (80.28 ± 2.61 ug/mg) and pectin (53.56 ± 2.67 ug/mg) observed in the inoculated fermented suancai. Simultaneously, the inoculated fermented suancai had the most decreases in SR 1 (70.35%) and SR 3 (72.06%) and the most increase in SR 2 (950%), which suggested that inoculation intensified the decrease of the linearity and the RG-1 branching degree of pectin. The contents of polygalacturonase (PG) and pectin methylesterase (PME) in inoculated fermented suancai were 21.06% and 21.86% higher than those in naturally fermented suancai. In addition, the surface of suancai leaves gradually changed from smooth to rough during fermentation, which was accelerated by inoculation. Moreover, Lactobacillus, Aspergillus, Wallemia and Mucor were all negatively correlated with cellulose and GalA. These results revealed that inoculation promoted the formation of dominant genus structure during suancai fermentation, changed the effects of enzymes on the degradation of cell wall components, thereby accelerated the formation of Chinese Dongbei suancai texture.

Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables

An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenome-assembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.

Dynamic Changes in Flavor and Microbiota in Traditionally Fermented Bamboo Shoots (Chimonobambusa szechuanensis (Rendle) Keng f.)

Dissecting flavor formation and microbial succession during traditional fermentation help to promote standardized and large-scale production in the sour shoot industry. The principal objective of the present research is to elucidate the interplay between the physicochemical attributes, flavor, and microbial compositions of sour bamboo shoots in the process of fermentation. The findings obtained from the principal component analysis (PCA) indicated notable fluctuations in both the physicochemical parameters and flavor components throughout the 28 day fermentation process. At least 13 volatile compounds (OAV > 1) have been detected as characteristic aroma compounds in sour bamboo shoots. Among these, 2,4-dimethyl Benzaldehyde exhibits the highest OAV (129.73~668.84) and is likely the primary contributor to the sour odor of the bamboo shoots. The analysis of the microbial community in sour bamboo shoots revealed that the most abundant phyla were Firmicutes and Proteobacteria, while the most prevalent genera were Enterococcus, Lactococcus, and Serratia. The results of the correlation analysis revealed that Firmicutes exhibited a positive correlation with various chemical compounds, including 3,6-nonylidene-1-ol, 2,4-dimethyl benzaldehyde, silanediol, dimethyl-, nonanal, and 2,2,4-trimethyl-1,3-pentylenediol diisobutyrate. Similarly, Lactococcus was found to be positively correlated with several chemical compounds, such as dimethyl-silanediol, 1-heptanol, 3,6-nonylidene-1-ol, nonanal, 2,2,4-trimethyl-1,3-pentanediol diisobutyrate, dibutyl phthalate, and TA. This study provides a theoretical basis for the standardization of traditional natural fermented sour bamboo production technology, which will help to further improve the flavor and quality of sour bamboo.

Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods

Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.

Evaluation and comparison of physicochemical properties, volatile substances, and microbial communities of leaf mustard (Brassica juncea var. multiceps) under natural and inoculated fermentation

Due to the uncontrolled fermentation process and unstable quality of naturally fermented leaf mustard, inoculated fermentation is receiving more attention. Here, the physicochemical properties, volatile compounds, and microbial community in leaf mustard under natural fermentation (NF) and inoculated fermentation (IF) were analyzed and compared. The contents of total acid, crude fiber, and nitrite of leaf mustard were measured. Headspace-solid phase microextraction-gas chromatography-mass spectrometry and orthogonal projection on latent structure-discriminant analysis were used to analyze the differences of volatile compounds in NF and IF leaf mustard. Moreover, Illumina MiSeq high-throughput sequencing technology was employed to reveal the composition of microbiota. The results showed that the nitrite content in leaf mustard after IF (3.69 mg/kg) was significantly lower than that after NF (4.43 mg/kg). A total of 31 and 25 kinds of volatile components were identified in IF and NF, respectively. Among the detected compounds, 11 compounds caused the differences between IF and NF leaf mustard. The results of inter-group difference analysis showed that there were significant differences in fungal flora between IF and NF samples. Saccharomycetes, Kazachstania, and Ascomycota were the landmark microorganisms in IF leaf mustard and the landmark microorganisms in NF were Mortierellomycota, Sordariomycetes, and Eurotiomycetes. The abundance of probiotics (such as Lactobacillus) in IF leaf mustard (51.22%) was higher than that in NF (35.20%) and the abundance of harmful molds (such as Mortierella and Aspergillus) was opposite. Therefore, IF leaf mustard showed the potential to reduce the content of nitrite and harmful molds and increase the beneficial volatile compounds and probiotics. PRACTICAL APPLICATION: Leaf mustard of inoculated fermentation (IF) showed better fermented characteristics than natural fermentation in terms of lower nitrite content, greater beneficial volatile substances, and better potential for increasing probiotics and reducing harmful molds. These results provided a theoretical basis for IF leaf mustard and contributed to the industrial production of fermented leaf mustard.

Characteristic volatiles fingerprints in olive vegetable stored at different conditions by HS-GC-IMS

The olive vegetable is popular food owing to its unique flavor. This study innovatively used headspace-gas chromatography-ion mobility spectrometry to evaluate olive vegetables' volatiles under different conditions. A total of 57 volatile compounds were determined from olive vegetables, including 30 aldehydes, 8 ketones, 5 alcohols, 2 esters, 8 hydrocarbons, 1 furans, 3 sulfur compounds. The PCA distinguished the olive vegetable stored at different conditions by volatiles. The gallery plot showed that olive vegetables stored at 4 °C for 21 d produced more limonene, which had a desirable fruity odor. The (E)-2-octenal, (E)-2-pentenal, (E,E)-2,4-heptadienal, 5-methylfurfural, and heptanal in fresh olive vegetables were lowest and increased with storage time. Furthermore, the change of volatiles was the least when the olive vegetable was stored at 0 °C. This study can provide theoretical bases for improving the flavor quality of olive vegetables and developing traditional food for standardized industrial production.

Core microbes closely related with the nutrients and flavor of sweet fermented oats (whole grain food) from China

Increased attention has been given to whole grain and plant-based foods due to health concerns. Sweet fermented oats (SFOs) are such traditional fermented food from China. However, reports on their microbiota and relations with the nutrients and flavor were scarcely few, hindering their wider application. The comprehensive microbial composition, metabolic compounds and their correlations of representative SFOs from northwestern China were firstly investigated. Firmicutes predominated the microbial communities, followed by Proteobacteria. Weissella, Bacillus and Lactobacillus were dominant bacterial genera, biomarkers and core bacteria as well. GC-MS (Gas Chromatography-Mass Spectrometer) identified the metabolic compounds, among which the categories fatty acids and carboxylic acids most abundant. Eighteen chemicals showed significant differences among the five SFOs, including ethyl octanoate, neryl acetate, L-sorbose, diglycerol, cellotetraose etc. Fatty acids, carboxylic acids, amino acids, peptides, oligosaccharides, and monosaccharides were the key substances responsible for the unique flavor and rich nutrients in SFOs. The core bacteria were closely related to chemical acids, esters, flavone and alcohol. Pediococcus showed a negative correlation with 2,3-butanediol. SFOs were made in the laboratory with the core bacterial strains, obtaining a high abundance of nutrient chemicals and sensory evaluation value. The research provided a foundation for the improvement, further application and industrialization of SFOs.

Innovative beverage creation through symbiotic microbial communities inspired by traditional fermented beverages: current status, challenges and future directions

Fermented beverages (FBs) are facing challenges in functional performance and flavor complexity, necessitating the development of new multi-functional options. Traditional fermented beverages (TFBs), both alcoholic and nonalcoholic, have gained increased attention for their health-promoting effects during the COVID-19 pandemic. This review summarized the primary commercially available probiotics of FBs, along with the limitations of single and mixed probiotic FBs. It also examined the recent research progress on TFBs, emphasizing the typical microbial communities (MC) of TFBs, and TFBs made from crops (grains, vegetables, fruits, etc.) worldwide and their associated functions and health benefits. Furthermore, the construction, technical bottlenecks of the synthetic MC involved in developing innovative FBs were presented, and the promising perspective of FBs was described. Drawing inspiration from the MC of TFBs, developing of stable and multifunctional FBs using synthetic MC holds great promise for beverage industry. However, synthetic MC suffers from structural instability and poorly acknowledged interaction mechanisms, resulting in disappointing results in FBs. Future researches should prioritize creating synthetic MC fermentation that closely resemble natural fermentation, tailored to meet the needs of different consumers. Creating personalized FBs with high-tech intelligence is vital in attracting potential consumers and developing novel beverages for the future.

Characterization of microbiota of naturally fermented sauerkraut by high-throughput sequencing

Sauerkraut is a traditionally fermented cabbage, with a unique taste and beneficial properties, in northeast China. The taste and flavor of sauerkraut vary from region to region, owing to the differences in microorganisms. Illumina MiSeq sequencing was used to identify and quantify the microbial community composition of the broth and leaves of the naturally fermented Suan-cai collected from northeast China. The alpha and beta diversity of the samples from three areas in Heilongjiang province shown that the complexity of bacterial diversity of the three samples was C, A and B in turn. The Lactobacillus widely existed in fermented sauerkraut, of these, Latilactobacillus sakei, Loigolactobacillus coryniformis subsp. torquens, Lactiplantibacillus plantarum subsp. plantarum, and Secundilactobacillus malefermentans were more abundant in the sauerkraut leaves than in fermentation broth. Other genera of lactic acid bacteria Pediococcus and Leuconostoc, which have potential probiotic properties, were also present. However, some harmful bacteria such as Arcobacter and Acinetobacter were also detected.

Fermented Vegetables and Legumes vs. Lifestyle Diseases: Microbiota and More

Silages may be preventive against lifestyle diseases, including obesity, diabetes mellitus, or metabolic syndrome. Fermented vegetables and legumes are characterized by pleiotropic health effects, such as probiotic or antioxidant potential. That is mainly due to the fermentation process. Despite the low viability of microorganisms in the gastrointestinal tract, their probiotic potential was confirmed. The modification of microbiota diversity caused by these food products has numerous implications. Most of them are connected to changes in the production of metabolites by bacteria, such as butyrate. Moreover, intake of fermented vegetables and legumes influences epigenetic changes, which lead to inhibition of lipogenesis and decreased appetite. Lifestyle diseases' feature is increased inflammation; thus, foods with high antioxidant potential are recommended. Silages are characterized by having a higher bioavailable antioxidants content than fresh samples. That is due to fermentative microorganisms that produce the enzyme β-glucosidase, which releases these compounds from conjugated bonds with antinutrients. However, fermented vegetables and legumes are rich in salt or salt substitutes, such as potassium chloride. However, until today, silages intake has not been connected to the prevalence of hypertension or kidney failure.

Seasonal dynamics of microbiota and physicochemical indices in the industrial-scale fermentation of Sichuan Baoning vinegar

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Differences between the microbiomes in every-two seasons were observed.

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The increase in total acidity of vinegar Pei was lowest in the summer (3.40 g/100 g).

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Lactic acid and acetic acid contents in raw vinegar from each season were different.

We investigated the impact of seasons of the year on microbiota and physicochemical indices in industrial-scale fermentation of Sichuan Baoning vinegar. Illumina HiSeq sequencing results showed significant differences (P < 0.05) between the microbiomes of vinegar Pei in every-two seasons, except for bacterial communities between summer and autumn. Total acid, reducing sugar, starch, and alcohol contents of vinegar Pei from the same sampling day of each season were measurably different. Although total acid content in vinegar Pei was similar at the end of fermentation (P > 0.05), the increase in total acidity was highest in the autumn. Acetic acid content in raw vinegar was highest in the autumn (3472.42 mg/100 mL), and lowest in the summer (2304.01 mg/100 mL). This study provides a theoretical basis for the production of Sichuan bran vinegar with consistent quality and provides insights into the quality control of traditional fermented foods.

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.

How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities

This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile. IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.

Natural Environmental Variation Determines Microbial Diversity Patterns in Serofluid Dish, a Traditional Chinese Fermented Vegetable Food

Serofluid dish is a traditional fermented food that contains rich microbial populations. To gain insight into the environmental variables shaping the microbial diversity patterns, serofluid dish samples were collected from different areas, and 16S rRNA sequencing was performed. Analyses revealed both species and community diversity, including phylotype richness, Shannon index and phylogenetic diversity, were mostly influenced by pH. Additionally, such effects were corroborated by the Mantel test of pairwise UniFrac distances and variable selection of multiple linear regression models. Eventually, correlations between dominant lineages and the pH of serofluid dish other than geographical distance explained a large portion of the changes in microbial composition and diversity. Lactobacillus and related genera, Pediococcus and Acetobacter were largely driven by the variability of pH, and higher richness was observed under moderate pH ranges. Collectively, the results demonstrated that a microbial diversity pattern in serofluid dish is predictable by natural environmental variation and can be better understood through pH conditions.

Exploring the Fungal Community and Its Correlation with the Physicochemical Properties of Chinese Traditional Fermented Fish (Suanyu)

Suanyu is a traditional natural fermented fish product from Southwest China that contains very complex microflora. The main purpose of this study was to explore the fungal community and its relationship with the physicochemical properties of Suanyu. The fungal community structure of Suanyu from the main provinces (Guizhou and Hunan) was studied via high-throughput sequencing. The correlation between dominant fungi and physicochemical characteristics was analyzed via Spearman's correlation coefficient. The results showed that the pH value, total volatile base nitrogen content, and thiobarbituric acid reactive substance content ranges of Suanyu samples were 4.30-5.50, 17.11-94.70 mg/100 g, and 0.61 to 3.62 mg/kg, respectively. The average contents of total volatile base nitrogen, thiobarbituric acid reactive substance, and total BAs in Suanyu from Guizhou were lower than those from Hunan. The main BAs were phenethylamine, putrescine, cadaverine, histamine, and tyramine. Ascomycota was the dominant fungal phylum, and Kodamaea, Debaryomyces, Wallemia, Zygosaccharomyces, and unclassified Dipodascaceae were the dominant fungal genera in different samples. Moreover, high abundance levels of Kodamaea and Zygosaccharomyces were found in Suanyu from Guizhou. According to the correlation analysis, Kodamaea and Zygosaccharomyces were negatively correlated with TBARS (R² = -0.43, -0.51) and TVBN (R² = -0.37, -0.29), and unclassified Dipodascaceae was significant negatively correlated with tyramine (R² = -0.56). This study expands the understanding of the fungal community and the fermentation characteristics of the dominant fungi in Suanyu.

Dynamics of microbial communities, flavor, and physicochemical properties of pickled chayote during an industrial-scale natural fermentation: Correlation between microorganisms and metabolites

Pickled chayote is a Chinese fermented vegetable with unique flavors and is favored by local consumers. However, little is known about its quality changes and microbial community succession during fermentation and the relationship between microbes and quality. In the work, the physicochemical quality attributes (pH, acidity, nitrite, texture, and color) and flavor properties (sugars, organic acids, free amino acid [FAA], and volatiles) were investigated. The results revealed that organic acids, FAAs, and key volatiles (esters, terpenes, alcohols, and phenols) significantly increased during fermentation. Lactobacillus was the dominant bacterial genus with Lactobacillus alimentarius being the prevalent species; Kazachstania and Pichia were dominant fungal genera with Kazachstania humilis and Pichia membranifaciens being the prevalent species. The microbial metabolic network found that bacteria (L. alimentarius, L. futsaii, and L. paralimentarius) and fungi (K. humilis and P. membranifaciens) played significant roles in the physicochemical changes and flavor production of pickled chayote.

Bioinformatics analysis of amino acid decarboxylases related to four major biogenic amines in pickles

Microbial amino acid decarboxylases (AADs) produce biogenic amines (BAs) in fermented food. However, a systematic comparison of the AADs' properties from different microorganisms in pickle fermentation remains unexplored. Here, we bioinformatically analyzed the amino acid sequences of AADs corresponding to four major BAs for common microorganisms in pickle fermentation. We showed that their sequences, besides tyrosine decarboxylase, differed among microorganisms. Overall, the AAD sequences varied lesser among bacterial species than between bacteria and fungi, with those in Lactobacillus sharing occasionally high similarity with other bacteria. Most AADs were predicted as stable cytosolic endoenzymes. Molecular docking showed that most commonly used spice components in pickle production, especially pepper, chili, and ginger, strongly bind to the AAD active sites, thus may inhibit the enzymes and reduce the BA accumulation. This study provides insights for deeply understanding the different microbial AAD properties in pickle fermentation and reducing BAs by appropriately using spices.

Microbial Diversity and Quality-Related Physicochemical Properties of Spicy Cabbage in Northeastern China and Their Correlation Analysis

Chinese spicy cabbage (CSC) is a popular special fermented food in Northeast China. The bacterial community and quality of CSC from different regions of northeastern China (Group_J: Jilin province, Group_L: Liaoning province, Group_H: Heilongjiang province) at retail (Group_P) and home-made (Group_C) were investigated in this study. The determination of the microbial community was achieved using high-throughput sequencing and the quality-related physicochemical characteristics included pH, salinity, total acid (TA), amino acid nitrogen (AAN), reducing sugar (RS), nitrite, and biogenic amines (BAs). Based on OPLS-DA analysis, there was a difference between the quality of Group_C and Group_P. No significant difference was observed in province grouping. Proteobacteria and Firmicutes were the dominant phyla, and the dominant genera were Lactobacillus, Pantoea, Weissella, and Pseudomonas. All groups had significant differences in community structure (p < 0.05). Compared with Group_C, the relative abundance of opportunistic pathogens (Pseudomonas and Serratia) in Group_P was lower. Pseudomonas and Serratia were the biomarkers in Group_H. At the genus level, Lactobacilluss and Weissella had a positive correlation with pH, Cadaverrine, and salinity (p < 0.05), however, they were negatively related to tryptamine. Pseudomonas was negatively correlated with salinity (p < 0.05). Bacterial community and physicochemical parameters of CSC, as well as the correlation between them, were discussed in this study, providing a reference for future studies on CSC inoculation and fermentation.

Draft Genome Sequence of a Kazachstania humilis Strain Isolated from Agave Fermentation

The ascomycetous yeast Kazachstania humilis is an active species in backslopped sourdough and in the spontaneous fermentation of several traditional foods and beverages. Here, we report the draft genome sequence of a K. humilis strain isolated from agave must from a traditional distillery in Mexico.

Microbial Communities and Physiochemical Properties of Four Distinctive Traditionally Fermented Vegetables from North China and Their Influence on Quality and Safety

The bacterial communities and physicochemical characteristics of four types of extremely distinctive traditionally fermented vegetables (pickled pepper (PP), pickled Brassica napobrassica (PBN), salted flowers of wild chives (SFWC), and pickled cucumber (PC)) were identified and compared from north China. Lactobacillus was the main bacterial genus in PP and PBN samples, with Oceanobacillus only being observed in PBN. The predominant genus in SFWC was Weissella, while in PC they were were Carnimonas and Salinivibrio. At the species level, Companilactobacillus ginsenosidimutans, Fructilactobacillus fructivorans, and Arcobacter marinus were abundant in PP and PBN. Levilactobacillus brevis and Companilactobacillus alimentarius were enriched in PP, and L. acetotolerans, Ligilactobacillus acidipiscis and Pediococcus parvulus were observed in PBN. Weissella cibaria and Kosakonia cowanii were abundant in SFWC. Moreover, tartaric acid was the most physicochemical factor influencing microbial composition, followed by malic acid, titratable acidity (TA), and lactic acid. Furthermore, functional analysis demonstrated that the most genes of the bacterial profiles correlated with carbohydrate metabolism. However, some foodborne pathogens were existed, such as Staphylococcus and Arcobacter marinus. The results of this study provide detailed insight into the relationship between the bacterial communities and physicochemical indices of fermented vegetables, and may improve the quality and safety of traditional Chinese fermented vegetables.

Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California

BACKGROUND

Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures.

RESULTS

Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO₂ levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival.

CONCLUSIONS

The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO₂ promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California.

The interaction between Lactobacillus plantarum SC-5 and its biogenic amine formation with different salt concentrations in Chinese Dongbei Suancai

Dongbei Suancai (DBSC) - a Chinese cabbage-based sauerkraut is a traditional fermented food which is popular in Asian countries. The biogenic amines that are usually generated during spontaneous fermentation have raised public health concern, while inoculation technology may solve this problem. In the current research, the biogenic amines, as well as their interactions with the microbial community in DBSC inoculated with Lactobacillus plantarum SC-5 or spontaneously fermented without inoculation were systematically investigated throughout 60 d fermentation. High-performance liquid chromatography analysis showed that the predominant biogenic amines in DBSC including putrescine, tyramine, spermidine, cadaverine and histamine increased during fermentation. Inoculated DBSC had a significantly lower content of total biogenic amines than the spontaneously fermented DBSC (216.72-237.33 mg/kg vs. 234.62-266.81 mg/kg) during 60 days' fermentation (P < 0.05). High throughput sequencing based on 16S rDNA identified 70 species in the bacterial community belonging to 7 genera of lactic acid bacteria, of which Lactobacillus, Leuconostoc and Lactococcus were dominant. Furthermore, six common genera of bacteria were positively correlated with biogenic amines based on Spearman's rank correlation test. Notably, the abundance of Lactobacillus plantarum SC-5 was negatively correlated with the content of biogenic amines in DBSC. In conclusion, inoculation of the proper starter like Lactobacillus plantarum SC-5 can reduce total biogenic amines in DBSC possibly by modifying the microbial communities in the fermented sauerkraut, which provides practical guidance for industrial production of high quality DBSC.

Characterization of aroma and bacteria profiles of Sichuan industrial paocai by HS-SPME-GC-O-MS and 16S rRNA amplicon sequencing

Sichuan industrial paocai and traditional home-made paocai have different aroma profiles due to different manufacturing techniques, but detailed information about the aroma profiles and aroma-producing microorganism of Sichuan industrial paocai remain largely elusive. For this reason, we established and validated an external standard method of headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) combined with gas chromatography-olfactometry (GC-O) for identification and accurate quantitation of aroma-active compounds in Sichuan industrial paocai. This method was combined with 16S rRNA amplicon sequencing to comprehensively analyze the aroma and bacteria profiles of Sichuan industrial paocai. A total of 121 volatile compounds were identified, among which 36 odorants were identified as aroma-active compounds with aroma intensities (AIs) ranging from 0.67 to 5.00 by GC-O. The types of aroma-active compounds in Sichuan industrial paocai were variety-specific to some extent, but the aroma-active compounds shared by different varieties of Sichuan industrial paocai (i.e., skeleton aroma-active compounds) were phenylethyl alcohol, acetic acid, butanoic acid, 2-methylbutanoic acid, ethyl hexanoate, 4-ethylphenol and 4-ethylguaiacol. Moreover, 17 key aroma-active compounds of AI > 1 in radish paocai were quantitated by external standard method, and their odor activity values (OAVs) were calculated based on the odor thresholds. Further, 12 aroma-active compounds with OAV ≥ 1 in one of the radish paocai were selected to construct the recombination model, which revealed good agreement with the original sample. Furthermore, Lactobacillus, Pediococcus, Pseudomonas and Sphingomonas were the dominant bacteria in Sichuan industrial paocai. Correlation analysis between 16 dominant bacteria and 36 aroma-active compounds showed that Pediococcus, Arcobacter and Lactobacillus could be the core aroma-producing bacteria of Sichuan industrial paocai.

Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps)

Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.

Culture-independent analysis of the bacterial community in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial community using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from 6 samples. Firmicutes and Proteobacteria were the main phyla in all of the samples. Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated clear differences were there between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole-genome analysis of Levilactobacillus suantsaii, Latilactobacillus sakei subsp. sakei, and Weissella cibaria showed that they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.