Role of combinated lactic acid bacteria in bacterial, viral, and metabolite dynamics during fermentation of vegetable food, kimchi

Impact of essential and optional ingredients on microbial and metabolic profiles of kimchi

This study aimed to examine the impacts of essential and optional ingredients on the microbial and metabolic profiles of kimchi during 100 days of fermentation, using a mix-omics approach. Kimchi manufactured without essential ingredients (e.g., red pepper, garlic, ginger, green onion, and radish) had lower lactic acid content. The absence of garlic was associated with a higher proportion of Latilactobacillus and Lactococcus, while the absence of red pepper was associated with a greater proportion of Leuconostoc than the control group. In addition, red pepper and garlic served as primary determinants of the levels of organic acids and biogenic amines. Sugar was positively correlated with the levels of melibiose, and anchovy sauce was positively correlated with the levels of amino acids such as methionine, leucine, and glycine. These findings contribute to a fundamental understanding of how ingredients influence kimchi fermentation, offering valuable insights for optimizing kimchi production to meet various preferences.

Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE

Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.

Identification of safe putative probiotics from various food products

The objective of this study was to isolate, identify, and assess the safety and functionality in vitro of putative probiotic bacterial strains. Isolation procedures were based on standard methods using elective and selective media. The isolates were identified by comparative 16S rRNA sequencing analysis while their safety was determined according to the safety tests recommended by the FAO/WHO such as antibiotic resistance, hemolysin, and biogenic amine production. Most of the isolates did not pass the in vitro safety tests; therefore, only Lactiplantibacillus plantarum (from ant intestine and cheese), Lacticaseibacillus paracasei (from goat milk and kimchi), Enterococcus faecium (from chili doenjang and vegetables with kimchi ingredients), Limosilactobacillus fermentum (from saliva), and Companilactobacillus alimentarius (from kimchi) were identified and selected for further studies. The isolates were further differentiated by rep-PCR and identified to the strain level by genotypic (16S rRNA) and phenotypic (Gen III) approaches. Subsequently, the strain tolerance to acid and bile was evaluated resulting in good viability after simulated gastrointestinal tract passage. Adhesion to mucin in vitro and the presence of mub, mapA, and ef-tu genes confirmed the adhesive potential of the strains and the results of features associated with adhesion such as hydrophobicity and zeta potential extended the insights. This study reflects the importance of fermented and non-fermented food products as a promising source of lactic acid bacteria with potential probiotic properties. Additionally, it aims to highlight the challenges associated with the selection of safe strains, which often fail in the in vitro tests, thus hindering the possibilities of "uncovering" novel and safe probiotic strains.

Integrated metatranscriptomics and metabolomics reveal microbial succession and flavor formation mechanisms during the spontaneous fermentation of Laotan Suancai

Laotan Suancai, a Chinese traditional fermented vegetable, possesses a unique flavor that depends on the fermentative microbiota. However, the drivers of microbial succession and the correlation between flavor and active microbiota remain unclear. A total of 21 characteristic flavor metabolites were identified in Laotan Suancai by metabolomics, including 8 sulfides, 6 terpenes, 3 organic acids, 2 isothiocyanates, 1 ester, and 1 pyrazine. Metatranscriptome analysis revealed variations in the active microbiota at different stages of fermentation, and further analysis indicated that organic acids were the primary drivers of microbial succession. Additionally, we reconstructed the metabolic network responsible for the formation of characteristic flavor compounds and identified Companilactobacillus alimentarius, Weissella cibaria, Lactiplantibacillus plantarum, and Loigolactobacillus coryniformis as the core functional microbes involved in flavor development. This study contributed to profoundly understanding the relationship between the active microbiota and flavor quality formation, as well as the targeted selection of starters with flavor regulation abilities.

Anti-Obesity Effect of Kimchi with Starter Cultures in 3T3-L1 Cells

Lactic acid bacteria (LAB) isolated from kimchi have various functions, including antioxidant, anti-inflammation, and anti-obesity activities, and are therefore widely used in the food, pharmaceutical, and medical fields. To date, the health functionalities of LAB have been widely reported; however, those of kimchi fermented with LAB as a starter have rarely been reported. Therefore, research on the selection of LAB with anti-obesity activity and the health functionality of kimchi fermented with LAB is needed. In the present study, LAB with anti-obesity activity were initially selected by measuring the Oil-Red O intensity. Among the four LAB strains, anti-obesity activity was confirmed by measuring cell viability, lipid levels, and lipid accumulation. Then, starter kimchi (SK) was prepared by inoculating selected LABs, and its pH, total acidity, and salinity were compared with those of naturally fermented kimchi (NK). Lastly, anti-obesity activity was also investigated in 3T3-L1 cells. Selected LAB showed no cytotoxicity up to 107 CFU/ml, with Lactobacillus brevis JC7 and Leuconostoc mesenteroides KCKM0828 having higher inhibitory effects on TG, TC content and lipid accumulation. Most SKs showed fermentation properties similar to those of the NK. SKs showed no cytotoxicity at concentrations of up to 1,000 μg/ml. SKs showed strong inhibitory effects on TG content, lipid accumulation, and obesity-related gene and protein expressions. Taken together, the utilization of LAB as a starter could improve the health benefits of kimchi.

The insights into the phage communities of fermented foods in the age of viral metagenomics

Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.

Advancing Insights into Probiotics during Vegetable Fermentation

Fermented vegetables have a long history and are enjoyed worldwide for their unique flavors and health benefits. The process of fermentation improves the nutritional value, taste, and shelf life of foods. Microorganisms play a crucial role in this process through the production of metabolites. The flavors of fermented vegetables are closely related to the evaluation and succession of microbiota. Lactic acid bacteria (LABs) are typically the dominant bacteria in fermented vegetables, and they help inhibit the growth of spoilage bacteria and maintain a healthy gut microbiota in humans. However, homemade and small-scale artisanal products rely on spontaneous fermentation using bacteria naturally present on fresh vegetables or from aged brine, which may introduce external microorganisms and lead to spoilage and substandard products. Hence, understanding the role of LABs and other probiotics in maintaining the quality and safety of fermented vegetables is essential. Additionally, selecting probiotic fermentation microbiota and isolating beneficial probiotics from fermented vegetables can facilitate the use of safe and healthy starter cultures for large-scale industrial production. This review provides insights into the traditional fermentation process of making fermented vegetables, explains the mechanisms involved, and discusses the use of modern microbiome technologies to regulate fermentation microorganisms and create probiotic fermentation microbiota for the production of highly effective, wholesome, safe, and healthy fermented vegetable foods.

Leuconostoc performance in soy-based fermentations - Survival, acidification, sugar metabolism, and flavor comparisons

Leuconostoc spp. is often regarded as the flavor producer, responsible for the production of acetoin and diacetyl in dairy cheese. In this study, we investigate seven plant-derived Leuconostoc strains, covering four species, in their potential as a lyophilized starter culture for flavor production in fermented soy-based cheese alternatives. We show that the process of lyophilization of Leuconostoc can be feasible using a soy-based lyoprotectant, with survivability up to 63% during long term storage. Furthermore, the storage in this media improves the subsequent growth in a soy-based substrate in a strain specific manner. The utilization of individual raffinose family oligosaccharides was strain dependent, with Leuconostoc pseudomesenteroides NFICC99 being the best consumer. Furthermore, we show that all investigated strains were able to produce a range of volatile flavor compounds found in dairy cheese products, as well as remove certain dairy off-flavors from the soy-based substrate like hexanal and 2-pentylfuran. Also here, NFICC99 was strain producing most cheese-related volatile flavor compounds, followed by Leuconostoc mesenteroides NFICC319. These findings provide initial insights into the development of Leuconostoc as a potential starter culture for plant-based dairy alternatives, as well as a promising approach for generation of stable, lyophilized cultures.

Effect of the addition of maltodextrin on metabolites and microbial population during kimchi fermentation

Gelatinized starch sauce, one of the sub-ingredients have been widely used in kimchi for their roles in increasing viscosity of kimchi seasoning, and fermentation. Gelatinized glutinous rice (GGR), which is one of the most used starch sources in kimchi preparation. However, GGR is accelerated to the fermentation process but lead to a reduction in the shelf life of the kimchi. Therefore, in this study, we demonstrate the effectiveness of using maltodextrin (MD) as a novel starch source instead of GGR to slow down the rate of kimchi fermentation. The properties of the kimchi with MD and GGR fermentation (free sugar content, organic acid content, pH, and acidity) as well as their microbial growth rates after 12 days of fermentation were compared. After fermentation of 12 days, the free sugar of GGR-kimchi (GGRK) increased more rapidly than those of MD-kimchi (MDK), while higher sugar alcohol (mannitol) and organic acid contents were observed for GGRK than for MDK. Furthermore, initial aerobic and lactic acid bacteria counts were higher for GGRK than for MDK. These results indicate that fermentation proceeds at a slower rate in MDK than in GGRK, and they will provide a basis for further research into storage of kimchi.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05742-y.

Effect of fermentation by Pediococcus pentosaceus and Staphylococcus carnosus on the metabolite profile of sausages

A multi-omics approach was applied to investigate the differences and correlations between characteristic volatile flavor substances and non-volatile metabolites in sausages fermented by Pediococcus pentosaceus (P. pentosaceus) and Staphylococcus carnosus (S. carnosus) alone and in a mixture. Twenty-seven volatile metabolites were identified by headspace solid-phase microextraction/gas chromatography-mass. According to orthogonal projections to latent structures-differential analysis, 17 characteristic volatile metabolites were detected in the sausages of different treatments. Utilizing ultra-high-performance liquid chromatography coupled with a mass spectrometer to analyze metabolite profiles, 42.03% of the non-volatile metabolites were classified as lipids and lipid-like molecules, 25.00% of organic acids and derivatives, and others. Seventeen characteristic flavor substances were significantly correlated with twenty differential non-volatile metabolites, and the non-volatile metabolites changed significantly. Differences in the characteristics and combinations of microorganisms themselves have a decisive role in the development of flavor substances and non-volatile metabolites in sausages.

Effects of post-fermentation on the flavor compounds formation in red sour soup

Red Sour Soup (RSS) is a traditional fermented food in China. After two rounds of fermentation, sour soup has a mellow flavor. However, the microbial composition and flavor formation processes in post-fermentation in RSS are unclear. This study investigates the bacteria composition of RSS during the post-fermentation stage (0–180 days) using high-throughput sequencing. The results show that lactic acid bacteria (LAB) are dominant during the post-fermentation process, and their abundance gradually increases with fermentation time. Additionally, gas chromatography-mass spectrometry was used to detect volatile flavor compounds in the post-fermentation process. Seventy-seven volatile flavor compounds were identified, including 24 esters, 14 terpenes, 9 aromatic hydrocarbons, 9 alkanes, 6 heterocyclic compounds, 3 alcohols, 3 acids, 3 ketones, 2 phenols, 2 aldehydes, 1 amine, and 1 other. Esters and aromatic hydrocarbons are the main volatile compounds in RSS during the post-fermentation process. Orthogonal partial least squares screening and correlation analysis derived several significant correlations, including 48 pairs of positive correlations and 19 pairs of negative correlations. Among them, Acetobacter spp., Clostridium spp. and Sporolactobacillus spp. have 15, 14, 20 significant correlation pairs, respectively, and are considered the most important bacterial genera post-fermentation. Volatile substances become abundant with increasing fermentation time. LAB are excessive after more than 120 days but cause a drastic reduction in volatile ester levels. Thus, the post-fermentation time should be restricted to 120 days, which retains the highest concentrations of volatile esters in RSS. Overall, these findings provide a theoretical basis to determine an optimal post-fermentation time duration, and identify essential bacteria for manufacturing high-quality starter material to shorten the RSS post-fermentation processing time.

Real-Time Monitoring the Effects of Storage Conditions on Volatile Compounds and Quality Indexes of Halal-Certified Kimchi during Distribution Using Electronic Nose

The food logistics system is an essential sector for maintaining and monitoring the safety and quality of food products and becoming more crucial, especially during and after the pandemic of COVID-19. Kimchi is a popular traditional fermented food originally from Korea and easily changes because of the storage conditions. This study aims to evaluate the effects and the contributions of temperature to volatile compounds, quality indexes, and the shelf life of Halal-certified Kimchi, and to identify alcohol and find the correlation between the identified variables using an electronic nose and conventional method with the integration of multivariate analysis. Thirty-two volatile compounds (VOCs) were detected and correlated with pH, titratable acidity (TA), and lactic acid bacteria (LAB) counts during storage time. Ethanol was also found in the ripened Kimchi and possibly became the critical point of halal Kimchi products besides total acidity, pH, and LAB. Furthermore, the correlation between pH and benzaldehyde, titratable acidity and 3-methylbutanoic acid, and among lactic acid bacteria with ethanol, acetic acid, ethyl acetate, and 3-methylbutanoic acid properly can be used as a given set of variables in the prediction of food quality during storage and distribution.