Culture fermentation of Lactobacillus in traditional pickled gherkins: Microbial development, chemical, biogenic amine and metabolite analysis

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses.IMPORTANCELactobacillaceae, a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality of Lactobacillaceae; and (iv) fermentation capabilities across the family, shedding light on the metabolic basis of Lactobacillaceae-based commercial products. This quantitative understanding of Lactobacillaceae metabolic properties and their genomic basis will have profound implications for the food industry and biosustainability, offering new insights and tools for strain selection and manipulation.

Lactiplantibacillus sp. G6 isolated from goose intestine as starter culture for degrading nitrite and improving quality in Chinese pickle fermentation

Animal intestines is considered as a source of lactic acid bacteria (LAB) that have potential to decrease the nitrite level during fermentation of food such as pickles. It was hypothesized that optimized level of LAB has a high capacity to degrade nitrite during Chinese pickle fermentation and benefit a higher acceptability of the Chinese pickle product. This study aims to investigate the performance of a goose intestine-isolated LAB strain G6 under the species Lactiplantibacillus plantarum as a starter culture of Chinese pickles. The results showed that Lactiplantibacillus sp. G6 had a nitrite degradation rate close to 100% under the MRS broth condition of 25 °C, 2% inoculum volume and pH at 5. As a starter culture for Chinese pickle, this strain was able to achieve a higher LABs amount, lower nitrite residue after fermentation, compared with the group without the starter, which implicates its feasibility of applying on fermented food for reducing nitrite level.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01433-8.

Potential neuroprotective benefits of plant-based fermented foods in Alzheimer's disease: an update on preclinical evidence

Alzheimer's disease (AD) currently lacks effective treatments, making its prevention a critical focus. While accumulating evidence supports that plant-based fermented foods may contribute to AD prevention, the neuroprotective effect of plant-based fermented foods on AD has not been comprehensively reviewed. In this study, we conducted a systematic review of preclinical studies on the efficacy of plant-based fermented foods in AD. The literature search was based on databases including PubMed, Embase, Web of Science, and Scopus. The PICO approach was employed for report inclusion, and each report was assessed for risk of bias using the SYRCLE's RoB tool. From the analysis of 25 retrieved reports, we extracted essential details, including bibliographic information, animal models and characteristics, sources of plant-based fermented foods, dosages, administration routes, durations, and outcome measures. Our findings indicate that plant-based fermented foods may positively impact acute and long-term cognitive function, as well as beta-amyloid-mediated neurodegeneration. This review sheds light on the potential neuroprotective benefits of plant-based fermented foods for various AD-related aspects, including oxidative stress, synaptotoxicity, neuroinflammation, tau hyperphosphorylation, dysfunctional amyloidogenic pathways, and cognitive deficits, as observed in rodent models of AD. However, the small number of studies obtained from our literature search and the finding that many of them were of moderate methodological quality suggest the need for further investigation to substantiate the beneficial potential of this class of functional food for the management of AD.

The consequences of fermentation metabolism on the qualitative qualities and biological activity of fermented fruit and vegetable juices

Fermentation of fruit and vegetable juices with probiotics is a novel nutritional approach with potential health benefits. Lactic acid fermentation-based biotransformation results in changes in the profile and nature of bioactive compounds and improves the organoleptic properties, shelf life and bioavailability of vitamins and minerals in the fermented juices. This process has been shown to enrich the phenolic profile and bioactivity components of the juices, resulting in a new type of functional food with improved health benefits. Fruits and vegetables are the ideal substrate for microbial growth, and fruit and vegetable juice will produce rich nutrients and a variety of functional activities after fermentation, so that the high-quality utilization of fruits and vegetables is realized, and the future fermented fruit and vegetable juice products have a wide application market. This paper explores the typical fermentation methods for fruit and vegetable juices, investigates the bioactive components, functional activities, and the influence of fermentation on enhancing the quality of fruit and vegetable juices. The insights derived from this study carry significant implications for guiding the development of fermented fruit and vegetable juice industry.

Chemical changes of potential probiotic Lactiplantibacillus plantarum and Lactobacillus pentosus starter cultures in natural Gemlik type black olive fermentation

The aim of this study was to determine the ability of probiotic Lactiplantibacillus plantarum and Lactobacillus pentosus starter cultures to maintain Olea europaea L. cv. Gemlik fermentation and some chemical changes occurred by HPLC. It was observed that starter cultures decreased the pH by increasing the acidity of the fermentation medium. In addition, it was determined that the number of yeast-mold (Y-M) and aerobic mesophilic bacteria (AMB) were lower than the number of lactic acid bacteria (LAB) in the samples with starter cultures. As the fermentation period progressed, it was observed that the amount and variety of phenolic substances increased, albeit slightly, in the brined olive samples to which the starter culture was added. Alcohols, biogenic amines, sugars and organic acids increased or decreased in all samples. During the fermentation gallic acid, apigenin, kaempferol, curcumin, vanillin, caffeic acid, salicylic acid, putrescine, triamine, spermidine and maleic acid could not be detected.

Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar

Traditional bran vinegar brewing unfolds through natural fermentation, a process driven by spontaneous microbial activity. The unique metabolic activities of various microorganisms lead to distinct flavors and qualities in each batch of vinegar, making it challenging to consistently achieve the desired characteristic flavor compounds. Therefore, identifying the critical microbial species responsible for flavor production and designing starter cultures with improved fermentation efficiency and characteristic flavors are effective methods to address this discrepancy. In this study, 11 core functional microbial species affecting the fermentation flavor of Sichuan shai vinegar (Cupei were placed outside solarization and night-dew for more than one year, and vinegar was the liquid leached from Cupei) (SSV), were revealed by combining PacBio full-length diversity sequencing based on previous metagenomics. The effects of environmental factors and microbial interactions on the growth of 11 microorganisms during fermentation were verified using fermentation experiments. Ultimately, the microbial community was strategically synthesized using a 'top-down' approach, successfully replicating the distinctive flavor profile of Sichuan shai vinegar (SSV). The results showed that the interaction between microorganisms and environmental factors affected microorganism growth. Compared with traditional fermentation, the synthetic microbial community's vinegar-fermented grains (Cupei) can reproduce the key flavor of SSV and is conducive to the production of amino acids. In this study, the key flavor of SSV was reproduced through rational design of the synthetic microbial community. This achievement holds profound significance for the broader application of microbiome assembly strategies in the realm of fermented foods.

Characterizing the impact of species/strain-specific Lactiplantibacillus plantarum with community assembly and metabolic regulation in pickled Suancai

To investigate the colonization and impact of the specific Lactiplantibacillus plantarum strains, four isolated strains were applied in pickled Suancai which is a traditional pickled mustard (Brassica juncea). Results showed that strain-8 with the highest lactic acid bacteria (LAB) counts and acetic acid (p < 0.05). There were 11.42 % ∼ 32.35 % differential volatile compounds detected, although nitriles, esters, and acids were predominant. L. plantarum disturbed the microbial community, in which the microbial composition of strain-11 was most similar to the naturally fermented sample. Amino acids, carbohydrate metabolism, and metabolism of cofactors and vitamins were the main functional classes because of the similar dominant microbes (Lactiplantibacillus and Levilactobacillus). The functional units were separated based on NMDS analysis, in which bacterial chemotaxis, amino acid-related units, biotin metabolism, fatty acid biosynthesis, and citrate cycle were significantly different calculated by metagenomeSeq and Benjamin-Hochberg methods (p < 0.05). The contents of most flavor compounds were consistent with their corresponding enzymes. In particular, glucosinolates metabolites were different and significantly related to the myrosinase and metabolic preference of LAB. Therefore, this study revealed the impact mechanism of the specific L. plantarum strains and provided a perspective for developing microbial resources to improve the flavor diversity of fermented vegetables.

Exploring potential correlations between bacterial communities, organic acids, and volatile metabolites of traditional fermented sauerkraut collected from different regions of Heilongjiang Province in Northeast China

In this study, the bacterial communities and flavor metabolites of 27 traditional naturally fermented sauerkraut samples collected from nine regions of Heilongjiang Province in Northeast China were investigated. The dominant genera were Lactobacillus, Pseudomonas, Alcaligenes, Arcobacter, Pseudarcobacter, Lactococcus, Comamonas, Pediococcus, Prevotella, and Insolitispirillum. A total of 148 volatile compounds were detected in seven categories; esters and acids were the most abundant volatiles. Additionally, the highest content (15.96 mg/g) of lactic acid was detected in YC1. Acetic acid, oleic acid, palmitic acid, elaidic acid, and dehydroacetic acid were the key differential volatile compounds, which may be related to the bacterial communities. Spearman's correlation analysis revealed that Lactococcus and Lactobacillus were significantly positively correlated with flavor metabolites, suggesting that they may play a more significant role in flavor formation. The results of this study can help in the development of better quality of fermented vegetables.

Response Surface Methodology for Optimization of Operational Parameters To Remove Ciprofloxacin from Contaminated Water in the Presence of a Bacterial Consortium

Ciprofloxacin (CFX) is a broad-spectrum fluoroquinolone antibiotic that is widely used to treat bacterial infections in humans and other animals. However, its unwanted occurrence in any (eco)system can affect nontarget bacterial communities, which may also impair the performance of the natural or artificially established bioremediation system. The problem could be minimized by optimization of operational parameters via modeling of multifactorial tests. To this end, we used a Box-Behnken design in response surface methodology (RSM) to generate the experimental layout for testing the effect of the CFX biodegradation for four important parameters, that is, temperature (°C), pH, inoculum size (v/v %), and CFX concentration (mg L^-1). For inoculation, a consortium of three bacterial strains, namely, Acenitobacter lwofii ACRH76, Bacillus pumilus C2A1, and Mesorihizobium sp. HN3 was used to degrade 26 mg L^-1 of CFX. We found maximum degradation of CFX (98.97%; initial concentration of 25 mg L^-1) at 2% inoculum size, 7 pH, and 35 °C of temperature in 16 days. However, minimum degradation of CFX (48%; initial concentration of 50 mg L^-1) was found at pH 6, temperature 30 °C, and inoculum size 1%. Among different tested parameters, pH appears to be the main limiting factor for CFX degradation. Independent factors attributed 89.37% of variation toward CFX degradation as revealed by the value of the determination coefficient, that is, R ² = 0.8937. These results were used to formulate a mathematical model in which the computational data strongly correlated with the experimental results. This study showcases the importance of parameter optimization via RSM for any bioremediation studies particularly for antibiotics in an economical, harmless, and eco-friendly manner.

Fate of Bioactive Compounds during Lactic Acid Fermentation of Fruits and Vegetables

Consumption of lactic acid fermented fruits and vegetables has been correlated with a series of health benefits. Some of them have been attributed to the probiotic potential of lactic acid microbiota, while others to its metabolic potential and the production of bioactive compounds. The factors that affect the latter have been in the epicenter of intensive research over the last decade. The production of bioactive peptides, vitamins (especially of the B-complex), gamma-aminobutyric acid, as well as phenolic and organosulfur compounds during lactic acid fermentation of fruits and vegetables has attracted specific attention. On the other hand, the production of biogenic amines has also been intensively studied due to the adverse health effects caused by their consumption. The data that are currently available indicate that the production of these compounds is a strain-dependent characteristic that may also be affected by the raw materials used as well as the fermentation conditions. The aim of the present review paper is to collect all data referring to the production of the aforementioned compounds and to present and discuss them in a concise and comprehensive way.

Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength

In this study, whole-genome resequencing of two native probiotic Lactiplantibacillus plantarum strains—UTNGt21A and UTNGt2—was assessed in order to identify variants and perform annotation of genes involved in bacterial adaptability to different stressors, as well as their antimicrobial strength. A total of 21,906 single-nucleotide polymorphisms (SNPs) were detected in UTNGt21A, while 17,610 were disclosed in the UTNGt2 genome. The comparative genomic analysis revealed a greater number of deletions, transversions, and transitions within the UTNGt21A genome, while a small difference in the number of insertions was detected between the strains. A divergent number of types of variant annotations were detected in both strains, and categorized in terms of low, moderate, and high modifier impact on the protein effectiveness. Although both native strains shared common specific genes involved in the stress response to the gastrointestinal environment, which may qualify as a putative probiotic (bile salt, acid, temperature, osmotic stress), they were different in their antimicrobial gene cluster organization, with UTNGt21A displaying a complex bacteriocin gene arrangement and dissimilar gene variants that might alter their defense mechanisms and overall inhibitory capacity. The genome comparison revealed 34 and 9 genomic islands (GIs) in the UTNGt21A and UTNGt2 genomes, respectively, with the overrepresentation of genes involved in defense mechanisms and carbohydrate utilization. In addition, pan-genome analysis disclosed the presence of various strain-specific genes (shell genes), suggesting a high genome variation between strains. This genome analysis illustrates that the bacteriocin signature and gene variants reflect a niche-inherent pattern. These extensive genomic datasets will guide us to understand the potential benefits of the native strains and their utility in the food or pharmaceutical sectors.

Modelling and predicting population of core fungi through processing parameters in spontaneous starter (Daqu) fermentation

Traditional fermented foods are usually produced by spontaneous fermentation with multiple microorganisms. Environmental factors play important roles in microbial succession. However, it is still unclear how the processing parameters regulate the microbiota during fermentation. Here, we reveal the effects of processing parameters on the core microbiota in spontaneous fermentation of Chinese liquor starter. Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis, Aspergillus and Saccharomyces were identified as core microbiota using amplicon sequencing and metaproteomics analysis. Fermentation moisture gradually decreased from 34.8% to 14.2%, and fermentation temperature varied between 17.0 °C and 35.3 °C during the fermentation. Mantel test showed that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.05) significantly affected the core microbiota. Moreover, structural equation modelling analysis indicated that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.001) were respectively influenced by the processing parameters, room humidity and room temperature. The succession of Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis and Aspergillus were significantly affected by room humidity (P < 0.05), and the succession of Saccharomyces was significantly affected by room temperature (P < 0.001). Further, models were constructed to predict the population of core microbiota by room humidity and room temperature, using Gaussian process regression and linear regression (P < 0.05). This work would be beneficial for regulating microorganisms via controlling processing parameters in spontaneous food fermentations.