Amino Acid Catabolic Pathways of Lactic Acid Bacteria

Fermentation of a wine pomace and microalgae blend to synergistically enhance the functional value of protein- and polyphenol-rich matrices

This study aimed to generate new functional ingredients from microalgae and wine pomace through starter-assisted fermentation. Five lactic acid bacteria (LAB) and five yeasts were variously chosen for their species diversity, origin, and metabolic potential. During fermentation, the combination of Chlorella vulgaris and wine pomace overcame the limited growth observed in pomace substrate, with all LAB and yeasts effectively utilizing sugars and synthesizing microbial metabolites. Additionally, the synergistic interplay between the substrates, alongside the enzyme specificity of the starter cultures, improved the bioavailability of phenolic compounds, particularly flavanols, flavonols, and procyanidins, while simultaneously generating unique peptides in the formulated ingredients. In some cases, these metabolic changes were associated with enhanced antioxidant activity, improved protein digestibility, and overall protein quality. Our findings highlighted the potential of fermented mixed substrates as new functional ingredients, with promising health-promoting benefits and significant potential for applications in the food industry.

Production and transformation of biogenic amines in different food products by the metabolic activity of the lactic acid bacteria

Protein-rich diets often contain high quantities of biogenic amines (BAs), notably histamine and tyramine, which pose substantial health hazards owing to their toxicity. BAs are primarily produced by the microbial decarboxylation of free amino acids. Lactic acid bacteria (LAB) can either produce BAs using substrate-specific decarboxylase enzymes or degrade them into non-toxic compounds using amine-degrading enzymes such as amine oxidase and multicopper oxidase. Furthermore, LAB may inhibit BA-producing microbes by generating bioactive metabolites, including organic acids and bacteriocins. This paper thoroughly explores the processes underlying BA production and degradation in LAB, with a focus on the diversity of enzymes involved. Metabolic mapping of LAB strains at the genus and species levels reveals their involvement in BA metabolism, from production to degradation. The phylogenetic-based evolutionary relatedness of BA-producing and BA-degrading enzymes among LAB strains sheds light on their functional adaptability to various metabolic needs and ecological settings. These findings have significant practical implications for establishing better microbial management strategies in food production, particularly through strategically using starter or bioprotective cultures to reduce BA buildup. By highlighting the evolutionary and metabolic diversity of LAB, this review helps to optimize industrial fermentation processes, improve food safety protocols, and advance future research and innovation in BA management, ultimately protecting consumer health and supporting regulatory compliance.

The development of a whole-cell biosensor enabled the identification of agmatine-producing Hafnia spp. in cheese

Agmatine, the decarboxylation product of arginine, is the precursor of putrescine - a harmful biogenic amine (BA) - that can accumulate in dairy products via bacterial metabolism involving the agmatine deiminase (AGDI) pathway. This first requires agmatine be produced via the decarboxylation of arginine and it remains unknown which microorganisms are responsible for this prior decarboxylation step. In addition, agmatine, as other BA, plays different physiological roles including those of co-transmitter and neuromodulator. Preclinical and clinical studies have shown agmatine to have a neuroprotective effect, rendering it of therapeutic interest being agmatine-producing bacteria proposed as psychobiotics. The identification of BA-producing microorganisms is based on the rise in pH due to the consumption of H+ during such decarboxylation reactions. However, in the detection of agmatine-producing microorganisms in cheese, this would lead to false positives since many bacteria possess arginine deiminase activity; this produces ornithine and ammonium from arginine, which also increases the pH. To overcome this problem, a whole-cell biosensor based on a previously developed agmatine-inducible transcription system was designed, and a protocol optimized for the successful identification of agmatine-producing microorganisms in cheese. The application of this protocol in cheese samples allowed for the isolation of agmatine-producing microorganisms identified as Hafnia spp. and unravels, for first time, the capacity of Hafnia paralvei to produce agmatine. This finding evidence the potential role of Hafnia spp. in putrescine accumulation in dairy products.

Chemotaxis of rhizosphere Pseudomonas sp. induced by foliar spraying of lanthanum reduces cadmium uptake by pakchoi

Foliar application of rare earth micronutrient of lanthanum (La) exhibits great potential in reducing cadmium (Cd) uptake in crops, the underlying mechanisms controlling the interaction between Cd toxicity-relieved crops and soil microbiota are poorly understood. In this study, LaCl3 with the concentrations of 10 and 30 μM was sprayed on pakchoi (Brassica chinensis L.) planting on Cd contaminated solution and soil to determine the changes of root metabolites and rhizosphere bacterial communities. Compared to the control, Cd concentration in pakchoi leaves was significantly decreased by 30.9 % and 22.6 % with the high group under both hydroponic and pot culture by applying 30 μM LaCl3. Herein, the concrete evidence is provided that pakchoi plants in response to foliar-spraying La under soil or solution Cd toxicity can promote the root secretion of amino acids, resulting in a strong enrichment of nitrogen-related microorganisms. To probe this linkage, a Pseudomonas representative specie was isolated that had the ability of consuming alanine, the most oversecreted root exudate due to La application. Further results demonstrated that this strain had the capacities for alleviating Cd toxicity and enhancing crop growth by immobilizing Cd and secreting plant-beneficial metabolites. This study reveals a plant-extrudate-microbiome feedback loop for responding to La-relieved Cd toxicity in crops by the chemotaxis of rhizosphere Pseudomonas toward alanine secreted by pakchoi.

Untargeted metabolomics and physiological phenotypic analyses reveal the defense strategies of nitrite by Lactiplantibacillus plantarum PK25

A comprehensive understanding of the defense strategies against nitrite by Lactiplantibacillus plantarum remains unknown. Herein, the effects of nitrite degradation process on metabolic profiling of L. plantarum PK25 were investigated by metabolomics and phenomenological measurement. A total of 633 metabolites were significantly different at 6, 12, and 24 incubation hours. Specifically, citrulline and lysine reduction facilitated strain survival by limiting cell growth. A significant reduction of unsaturated fatty acids was observed, which could induce reduced cell membrane fluidity to prevent nitrite entry. The accumulation of thymine and cytosine might be resulted from accelerated RNA expression to accelerate the repair of cells. Dopamine and ergothioneine could serve as antioxidants to prevent bacteria from oxidative stress. Furthermore, cell filamentation production, increased hydrophobicity, and altered antioxidant enzyme activity were favorable alterations made by strain. Our study demonstrated the metabolite profile alteration of L. plantarum during nitrite degradation, which provided a theoretical basis for targeting strain function.

The transcriptional regulation effects of histidine, isoleucine and glutamate on free exopolysaccharide biosynthesis of Streptococcus thermophilus 937

Introduction

The free exopolysaccharide (f-EPS) produced by Streptococcus thermophilus is a natural texture modifier and has a variety of prebiotic activities. Our previous studies showed f-EPS production from S. thermophilus 937 was increased 2-fold in the presence of 15 mM of glutamate, isoleucine, and histidine in the chemically defined medium.

Methods

In this study, we used transcriptomics and qPCR to further explore the specific mechanism of the enhanced effect of 3 amino acids on the f-EPS biosynthesis of S. thermophilus 937.

Results

The mRNA-seq analysis and targeted pathway analysis indicated that genes associated with histidine/valine/leucine/ isoleucine/phenylalanine/tyrosine/tryptophan synthesis, galactose metabolism, purine metabolism and quorum sensing in S. thermophilus 937 were significantly upregulated under increasing concentrations of histidine, isoleucine and glutamate in chemically defined medium (CDM). qPCR results showed that the significant upregulation of galactose metabolism- and nucleotide sugar synthesis-related genes was attributed to the increase in glutamate concentration, and glutamate could induce the expression of galR. The upregulation of epsA, epsB, and epsD transcript levels was caused by the increase in histidine concentration. The upregulation of transcript levels of genes related to phenylalanine/tyrosine/tryptophan/histidine/ valine/leucine/isoleucine synthesis was caused by the increase in isoleucine concentrations.

Discussion

This indicates that 3 amino acids have different mechanisms for enhancing the biosynthesis of f-EPS in S. thermophilus 937.

Post-acidification of fermented milk and its molecular regulatory mechanism

The fermented milk products with lactic acid bacteria (LAB) are widely accepted by consumers. During the chilled-chain transportation and storage, LAB in the product keep producing lactic acid, and this will lead to post-acidification, which can affect the flavor, consumer acceptance and even shelf-life of the product. LAB is the determining factor affecting post-acidification. The acid production pathway in LAB and methods inhibiting post-acidification received widespread attention. This review will focus on the post-acidification from the perspective of fermentation starters, including acid production pathway in LAB, main factors and key enzymes affecting post-acidification. Lactobacillus delbrueckii subsp. bulgaricus is a key bacterial species responsible for post acidification in the fermented milk products. The different species and strains presented various differences in process like acid production, acid resistance and post-acidification. Furthermore, multiple factors, such as milk composition, fermentation temperature, and homogenization, also can influence post-acidification. Lactose transport and utilization pathways, as well as its subsequent products metabolic pathway directly influence the post-acidification. F0F1-ATPase, β-galactosidase, and lactate dehydrogenase are recognized as important enzymes related to post-acidification. The degree of post-acidification is mainly related to the acid production and acid resistance abilities of the fermentation starters, so the key enzymes related to post-acidification are mostly taking part in these two capacities. Recently, some new post-acidification related biomarker genes were found, providing a reference adjusting post-acidification without affecting fermentation rate and bacteria viability. To clarify the post-acidification mechanism at the molecular level will help control post- acidification.

Enhancing fermented vegetable flavor with Lactobacillus plantarum and Rhodotorula mucilaginosa

The formation of flavor in fermented vegetables is directly associated with the interactions among the resident microbial strains. This study explored the cooperative dynamics between Lactobacillus plantarum and Rhodotorula mucilaginosa in a simulated cabbage juice system. The obtained results indicated that the co-cultivation of these strains accelerated fermentation kinetics and enhanced lactic acid production. The strains achieved a balanced consumption of substrates within the co-fermentation system through the exchange of metabolites. Additionally, co-fermentation facilitated the synthesis of characteristic flavor compounds while reducing the levels of undesirable flavors. Growth monitoring and transcriptomic analysis revealed that L. plantarum, as the dominant strain, perceived the surrounding environment through quorum sensing signals and upregulated genes related to the synthesizing of key compounds, enhancing product yields and forming biofilms to adapt to the symbiotic environment. Conversely, R. mucilaginosa responded to the stress induced by L. plantarum via upregulating transporters of metabolites, genes related to antioxidant stress, and longevity regulating, ultimately achieving coexistence with L. plantarum. This research provides a comprehensive understanding of the interplay between microbial strains in modulating fermentation processes and flavor profiles in vegetable fermentation.

Transcriptional Analysis and Identification of a Peptidoglycan Hydrolase (PGH) and a Ribosomal Protein with Antimicrobial Activity Produced by Lactiplantibacillus paraplantarum

The growing challenge of antibiotic resistance has intensified the search for new antimicrobial agents. Promising alternatives include peptidoglycan hydrolases (PGHs) and certain ribosomal proteins, both of which exhibit antimicrobial activity. This study focuses on a Lactiplantibacillus paraplantarum strain, isolated from fermented meat, capable of inhibiting pathogens such as Listeria innocua, Salmonella Typhimurium, Escherichia coli, Staphylococcus aureus, and Weissella viridescens. The highest growth and antimicrobial activity were observed at a high nitrogen concentration (5.7 g/L). Two antimicrobial proteins were identified: the 50S ribosomal protein L14 (RP uL14) and 6-phospho-N-acetylmuramidase (MupG), a PGH. Partial purification and characterization of these proteins were achieved using SDS-PAGE, zymography, and LC-MS/MS. Transcriptional data (RT-qPCR) showed that higher nitrogen concentrations enhanced MupG expression, while increased carbon concentrations boosted RP uL14 expression. These findings highlight the importance of nutritional sources in maximizing the production of novel antimicrobial proteins, offering a potential path to develop effective alternatives against antibiotic-resistant bacteria.

Efficient metabolic pathway modification in various strains of lactic acid bacteria using CRISPR/Cas9 system for elevated synthesis of antimicrobial compounds

Lactic acid bacteria (LAB) are known to exhibit various beneficial roles in fermentation, serving as probiotics, and producing a plethora of valuable compounds including antimicrobial activity such as bacteriocin-like inhibitory substance (BLIS) that can be used as biopreservative to improve food safety and quality. However, the yield of BLIS is often limited, which poses a challenge to be commercially competitive with the current preservation practice. Therefore, the present work aimed to establish an optimised two-plasmid CRISPR/Cas9 system to redirect the carbon flux away from lactate towards compounds with antimicrobial activity by disrupting lactate dehydrogenase gene (ldh) on various strains of LAB. The lactic acid-deficient (ldhΔ) strains caused a metabolic shift resulting in increased inhibitory activity against selected foodborne pathogens up to 78 % than the wild-type (WT) strain. The most significant effect was depicted by Enterococcus faecalis-ldh∆ which displayed prominent bactericidal effects against all foodborne pathogens as compared to the WT that showed no antimicrobial activity. The present work provided a framework model for economically important LAB and other beneficial bacteria to synthesise and increase the yield of valuable food and industrial compounds. The present work reported for the first time that the metabolism of selected LAB can be manipulated by modifying ldh to attain metabolites with higher antimicrobial activity.

Characterization of the microbial communities and their correlations with volatile flavor compounds and physicochemical factors in Bashang suancai, a traditional Chinese pickle

Bashang suancai is one of the most wellknown traditional fermented vegetables in North China. The study examined the variations in bacterial diversity, physicochemical properties, and volatile flavor compounds (VFCs) of Bashang suancai over a 7-day fermentation period, utilizing Illumina NovaSeq sequencing and headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). The leading bacterial phyla were Firmicutes, Proteobacteria, and Cyanobacteria, while the predominant bacterial species included Vibrio, Lactiplantibacillus, Cyanobacteriales, Weissella, and Latilactobacillus. The bacterial community diversity decreased significantly following 7 days of fermentation. The microbial profiles were markedly affected by pH, reducing sugar content (RSC), and salt content (SC). A total of 187 VFCs were identified from the specimens. Following 5 days of fermentation, the taste compounds achieved equilibrium, with isothiocyanates, alcohols, and esters predominating among the volatile molecules. Spearman correlation analysis revealed that a strong link between Latilactobacillus, Levilactobacillus, Lactiplantibacillus, Weissella, and Vibrio with the flavor of pickles. This study established a significant foundation for identifying strains that enhance taste development and improve the nutritional and sensory quality of Bashang suancai.

Successful combination of lactic acid bacteria and yeast fermentation and enzymatic treatment to re-cycle industrial bread by-products for bread making

Bread industry generates significant amounts of by-products which are discarded every day with relevant economic and environmental repercussions, despite they still contain high concentrations of potentially exploitable nutrients. Aiming to develop new sustainable solutions, this study explored the synergistic application of enzymatic treatment and sourdough fermentation to re-cycle industrial bread by-products for new sourdough bread making. Lactiplantibacillus plantarum SD69.B2 and Saccharomyces cerevisiae SD69.E3 were used as starters, while α-amylase, amyloglucosidase and protease were assessed for their ability to hydrolyze starch and proteins, providing more available carbon and nitrogen sources for the microorganisms. The bread waste-based sourdoughs made by combining protease and L. plantarum SD69.B2 alone or in combination with S. cerevisiae SD69.E3 were selected based on acidification and growth kinetics, and their biochemical, amino acid, and peptide profiles were also characterized demonstrating promising properties. Therefore, they were used, at different percentages, for bread making. Although a slightly acidic pH and a low leavening power, due to the denatured proteins and gelatinized starch in the bread by-products, the texture and sensory analyses of new breads revealed better textural attributes, smell, acidic taste, and overall acceptability compared to the control. The possible reasons behind such features were discussed. The overall results demonstrated that the approach proposed in this study was effective to valorize bread by-products, and it represents a starting point to develop strategies responding to the current perspective of circular economy in food industry.

Mathematical modeling and comparative metabolomics analyses of interactions between Lactiplantibacillus plantarum and Morganella morganii

Morganella morganii is a spoilage microorganism in fish products that produces harmful biogenic amines (BAs). It has been discovered that Lactiplantibacillus plantarum His6 can inhibit the growth of this bacterium. The aim of this study was to quantitatively assess the inhibitory impact of the bioprotective culture Lpb. plantarum His6 on M. morganii YC16 in the matrix (fish and rice) using predictive microbiology models, and elucidate the interaction mechanism through untargeted metabolomics. The mathematical model results showed the inhibition effect of Lpb. plantarum His6 on M. morganii YC16 was dependent on temperature and inoculation concentration. In addition, the simultaneous growth of Lpb. plantarum His6 and M. morganii YC16 could be well simulated with the Lotka-Volterra model. Furthermore, significant decreased in histamine levels was observed in co-(1:3) at 25 °C. Finally, based on the metabolomics data, it was speculated that Lpb. plantarum His6 may enhance bacteriocin production while reducing the yield of glycerophospholipids and fatty acids associated with outer membrane formation, thereby inhibiting the growth of M. morganii YC16. These findings provide valuable insights into the interaction behavior and mechanism of Lpb. plantarum His6 and M. morganii YC16 in co-culture, facilitating the design of the biopreservation strategies for fish products.

Selection and characterization of spontaneous phage-resistant mutant of Limosilactobacillus fermentum

Phage infection remains a major cause of fermentation failures in the dairy industry. The development of phage-resistant mutants of important fermentation strains is an effective measure used to address phage-related issues. This study employed the secondary culture method to screen for spontaneous phage-resistant mutants from the phage sensitive strain Limosilactobacillus fermentum IMAU32646 (L. fermentum IMAU32646). The phenotypic characteristics, technological attributes, probiotic characterization, adsorption characteristics and mutant genes were investigated. The results showed that the mutant strain displayed a high degree of phage-resistance and stability. The mutant strain produced more lactic acid during fermentation than the sensitive strain, while maintaining identical cell structure and morphologies. The mutant strain exhibited superior tolerance to acid and bile salts compared to the sensitive strain. Furthermore, the adsorption rate of phage LFP01 on the mutant strain was significantly lower than that of the sensitive strain. Following genome re-sequencing analysis showed that adsorption interference and blocked DNA injection were responsible for its phage-resistance. These results may provide a new strategy for avoiding phage contamination and industrial application of phage-resistant strains with good characteristics.

Pathway and Production Differences in Branched-Chain Hydroxy Acids as Bioactive Metabolites in Limosilactobacillus fermentum, Ligilactobacillus salivarius, and Latilactobacillus sakei

Branched-chain hydroxy acids (BCHAs) as bioactive metabolites of Lactobacillaceae include 2-hydroxy isovaleric acid (HIVA), 2-hydroxy isocaproic acid (HICA), and 2-hydroxy-3-methyl isovaleric acid (HMVA). Combining targeted and untargeted metabolomics, this study elucidates differences in extracellular BCHA production in Limosilactobacillus fermentum, Ligilactobacillus salivarius, and Latilactobacillus sakei alongside comparing comprehensive metabolic changes. Through targeted metabolomics, BCHA production among 38 strains exhibited strain specificity, except for L. sakei, which showed significantly lower BCHA production. Explaining the lower production in L. sakei, which lacks the branched-chain amino acid (BCAA)-utilizing pathway, comparison of BCHA production by precursor reaction revealed that the pathway utilizing BCAAs is more dominant than the pathway utilizing pyruvate. Expanding upon the targeted approach, untargeted metabolomics revealed the effects of the reaction compound on other metabolic pathways besides BCHAs. Metabolism alterations induced by BCAA reactions varied among species. Significant differences were observed in glycine, serine, and threonine metabolism, pyruvate metabolism, butanoate metabolism, and galactose metabolism (p < 0.05). These results emphasize the importance of the synergy between fermentation strains and substrates in influencing nutritional components of fermented foods. By uncovering novel aspects of BCAA metabolism pathways, this study could inform the selection of fermentation strains and support the targeted production of BCHAs.

A Comprehensive Review on the Biogenic Amines in Cheeses: Their Origin, Chemical Characteristics, Hazard and Reduction Strategies

Most of the biogenic amines are naturally found in fermented foods as a consequence of amino acid decarboxylation. Their formation is ascribable to microorganisms (starters, contaminants and autochthonous) present in the food matrix. The concentration of these molecules is important for food security reasons, as they are involved in food poisoning illnesses. The most frequent amines found in foods are histamine, putrescine, cadaverine, tyramine, tryptamine, phenylethylamine, spermine and spermidine. One of the most risk-prone foods are cheeses, mostly ripened ones, which could easily accumulate amines due to their peculiar manufacturing process and ripening. Cheeses represent a pivotal food in our diet, providing for nutrients such as amino acids, calcium, vitamins and others; thus, since they are widely consumed, it is important to evaluate the presence of toxic molecules to avoid consumers' poisoning. This review aimed to gather general information on the role of biogenic amines, their formation, the health issues and the microorganisms and processes that produce/reduce them, with a focus on their content in different types of cheese (from soft to hard cheeses) and the biotic and abiotic factors that influence their formation or reduction and concentration. Finally, a multivariate analysis was performed on the biogenic amine content, derived from data available in the literature, to obtain more information about the factors influencing their presence in cheeses.

Apple Blossom Agricultural Residues as a Sustainable Source of Bioactive Peptides through Microbial Fermentation Bioprocessing

This study explored the impact of starter-assisted fermentation on apple blossoms to enhance their potential as a source of antioxidant and antifungal molecules. Fructobacillus fructosus PL22 and Wickerhamomyces anomalus GY1 were chosen as starters owing to their origin and promising ability to modify plant secondary metabolites. An initial assessment through microbiological and physicochemical analyses showed superior outcomes for starter-assisted fermentation compared to the spontaneous process. Enzymatic hydrolysis of proteins, primarily controlled by starters, orchestrated the generation of new low-molecular-weight peptides. W. anomalus GY1 also induced modifications in the phenolic profile, generating a diverse array of bioactive metabolites. These metabolic changes, particularly the release of potentially bioactive peptides, were associated with significant antioxidant activity and marked antifungal efficacy against three common mold species. Our results shed light on the potential of microbial starters to valorize agricultural wastes and convert them into a valuable resource for industry.

Impact of Different Carbon Sources on Volatile Organic Compounds (VOCs) Produced during Fermentation by Levilactobacillus brevis WLP672 Measured Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS)

Bacterial fermentation is considered to be a cost-effective means of generating desired flavour compounds from plant-based substrates. However, the wide range of substrates present in plants makes it challenging to understand how individual components impact on flavour volatile organic compound (VOC) production. To simplify this, a defined medium can be used to better understand VOCs production with regard to individual compounds. In the current study, the VOCs produced by the lactic acid bacterium, Levilactobacillus brevis WLP672, growing in a defined medium containing different carbon sources (either glucose (DM), fructose (DMFr) or citrate (DMCi)) under a range of fermentation conditions (time: 0, 7, and 14 days; and temperature: 25 and 35 °C) were assessed using proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS). Among the detected mass peaks (m/z), after 7 days of fermentation, the concentrations of m/z 45.033 (t.i. acetaldehyde), m/z 49.011 (t.i. methanethiol), and m/z 89.060 (t.i. ethyl acetate) were significantly (p < 0.05) higher in DM at 35 °C than all other treatments at either temperature. The knowledge obtained will help to produce desirable LAB fermentation flavour VOCs or VOC mixtures that could be used in developing plant-based analogues with acceptable sensory properties.

Bacterial Growth Modulatory Effects of Two Branched-Chain Hydroxy Acids and Their Production Level by Gut Microbiota

Branched-chain hydroxy acids (BCHAs), produced by lactic acid bacteria, have recently been suggested as bioactive compounds contributing to the systemic metabolism and modulation of the gut microbiome. However, the relationship between BCHAs and gut microbiome remains unclear. In this study, we investigated the effects of BCHAs on the growth of seven different families in the gut microbiota. Based on in vitro screening, both 2-hydroxyisovaleric acid (HIVA) and 2-hydroxyisocaproic acid (HICA) stimulated the growth of Lactobacillaceae and Bifidobacteriaceae, with HIVA showing a significant growth promotion. Additionally, we observed not only the growth promotion of probiotic Lactobacillaceae strains but also growth inhibition of pathogenic B. fragilis in a dosedependent manner. The production of HIVA and HICA varied depending on the family of the gut microbiota and was relatively high in case of Lactobacillaceae and Lachnosporaceae. Furthermore, HIVA and HICA production by each strain positively correlated with their growth variation. These results demonstrated gut microbiota-derived BCHAs as active metabolites that have bacterial growth modulatory effects. We suggest that BCHAs can be utilized as active metabolites, potentially contributing to the treatment of diseases associated with gut dysbiosis.

Characterization of a Ligilactobacillus salivarius Strain Isolated from a Cheese Seal Which Was Last Used in 1936

Cheesemaking played a pivotal role in the life of the Pyrenean villages where cheese was a most prized commodity and the subject of much local competition. In one of them (Sasa de Sobrepuerto), Mrs. Sebastiana Palacio decided in 1877 to label all the cheeses made in her household with a seal to differentiate them from those made by other local producers. The cheese seal was last used in 1936 and, since then, it has been kept under excellent storage conditions. Since well-preserved cheese seals are rare, and bacterial cells may survive desiccation for long periods, the objective of this work was to isolate and characterize any lactic acid bacteria that survived in the seal. Analysis of the milky crust material revealed the presence of sheep caseins. Culture-based analysis led to the isolation of a strain of Bacillus licheniformis and a strain of Ligilactobacillus salivarius (L. salivarius SP36). The latter was characterized in vitro for safety and dairy-related functional properties. Its genome encodes several genes involved in protein, peptide, and amino acid catabolism, and flavor. Overall, the phenotypic and genetic features of this strain support a high potential for being used as adjunct culture in cheesemaking.

Scrutinizing a Lactococcus lactis mutant with enhanced capacity for extracellular electron transfer reveals a unique role for a novel type-II NADH dehydrogenase

Lactococcus lactis, a lactic acid bacterium used in food fermentations and commonly found in the human gut, is known to possess a fermentative metabolism. L. lactis, however, has been demonstrated to transfer metabolically generated electrons to external electron acceptors, a process termed extracellular electron transfer (EET). Here, we investigated an L. lactis mutant with an unusually high capacity for EET that was obtained in an adaptive laboratory evolution (ALE) experiment. First, we investigated how global gene expression had changed, and found that amino acid metabolism and nucleotide metabolism had been affected significantly. One of the most significantly upregulated genes encoded the NADH dehydrogenase NoxB. We found that this upregulation was due to a mutation in the promoter region of NoxB, which abolished carbon catabolite repression. A unique role of NoxB in EET could be attributed and it was directly verified, for the first time, that NoxB could support respiration in L. lactis. NoxB, was shown to be a novel type-II NADH dehydrogenase that is widely distributed among gut microorganisms. This work expands our understanding of EET in Gram-positive electroactive microorganisms and the special significance of a novel type-II NADH dehydrogenase in EET.IMPORTANCEElectroactive microorganisms with extracellular electron transfer (EET) ability play important roles in biotechnology and ecosystems. To date, there have been many investigations aiming at elucidating the mechanisms behind EET, and determining the relevance of EET for microorganisms in different niches. However, how EET can be enhanced and harnessed for biotechnological applications has been less explored. Here, we compare the transcriptomes of an EET-enhanced L. lactis mutant with its parent and elucidate the underlying reason for its superior performance. We find that one of the most significantly upregulated genes is the gene encoding the NADH dehydrogenase NoxB, and that upregulation is due to a mutation in the catabolite-responsive element that abolishes carbon catabolite repression. We demonstrate that NoxB has a special role in EET, and furthermore show that it supports respiration to oxygen, which has never been done previously. In addition, a search reveals that this novel NoxB-type NADH dehydrogenase is widely distributed among gut microorganisms.

Resistance role of Lactobacillus sp. and Lactococcus sp. to copper ions in healthy children's intestinal microorganisms

Heavy metal exposure is closely associated with gut microbe function and tolerance. However, intestinal microbe responses in children to different copper ion (Cu2+) concentrations have not yet been clarified. Here, in vitro cultivation systems were established for fecal microbe control and Cu2+-treated groups in healthy children. 16S rDNA high-throughput sequencing, meta-transcriptomics and metabolomics were used here to identify toxicity resistance mechanisms at microbiome levels. The results showed that Lactobacillus sp. and Lactococcus sp. exerted protective effects against Cu2+ toxicity, but these effects were limited by Cu2+ concentration. When the Cu2+ concentration was ≥ 4 mg/L, the abundance of Lactobacillus sp. and Lactococcus sp. significantly decreased, and the pathways of antioxidant activity and detoxification processes were enriched at 2 mg/L Cu2+, and beneficial metabolites accumulated. However, at high concentrations of Cu2+ (≥4 mg/L), the abundance of potential pathogen increased, and was accompanied by a downregulation of genes in metabolism and detoxification pathways, which meant that the balance of gut microbiota was disrupted and toxicity resistance decreased. From these observations, we identified some probiotics that are tolerant to heavy metal Cu2+, and warn that only when the concentration limit of Cu2+ in food is 2 mg/L, then a balanced gut microbiota can be guaranteed in children, thereby providing protection for their health.

Changes in Chemical Composition of Lentils, Including Gamma-Aminobutyric Acid and Volatile Compound Formation during Submerged and Solid-State Fermentation with Pediococcus acidilactici

The aim of this study was to evaluate and compare the characteristics of non-treated and fermented [via submerged (SMF) and solid-state (SSF) fermentation using Pediococcus acidilactici] lentils (Lens culinaris) grown either in pure stands (L) or relay intercropped with winter rye (LR). It was observed that the lentils were suitable substrate for lacto-fermentation. Most of the free amino acid concentrations increased in lentils after both fermentations. The highest concentration of γ-aminobutyric acid was found in SSF LR samples. However, fermentation led to higher biogenic amines (BA) content in lentils. The most abundant fatty acid in lentils was C18:2. SSF lentils showed more complex volatile compound (VC) profiles (with between nine and seventeen new VCs formed), whereas, in SMF samples, between two and five newly VCs were formed. When comparing lentil grown types, L contained significantly higher concentrations of Na, K, Ca, P, Mn, and Se, while LR contained significantly higher concentrations of Fe and Ni. To sum up, fermentation with lactic acid bacteria (LAB) contributed to the improved biological value of lentils; still, the quantity of BA needs to be considered. Further investigations into the P. acidilactici metabolism of certain compounds (such as phenolic and antinutritional compounds) in lentils during fermentation ought to be carried out.

Synergistic effect of the coculture of Leuconostoc pseudomesenteroides and Lactococcus lactis, isolated from honeybees, on the generation of plant-based dairy alternatives based on soy, pea, oat, and potato drinks

The production of plant-based dairy alternatives has been majorly focused on the improvement of sensorial, technological and nutritional properties, to be able to mimic and replace milk-based fermented products. The presence of off-flavours and antinutrients, the lack of production of dairy-like flavours or the metabolic inaccessibility of plant proteins are some of the challenges to overcome to generate plant-based dairy alternatives. However, in the present study, it is demonstrated how the synergistic effect of two LAB strains, when cocultured, can simultaneously solve those challenges when fermenting in four different plant-based raw materials: soy, pea, oat, and potato drinks (SPOP). The fermentation was performed through the mono- and co-culture of the two LAB strains isolated from Apis mellifera (honeybee): Leuconostoc pseudomesenteroides NFICC 2004 and Lactococcus lactis NFICC 2005. Firstly, the coculture of both strains demonstrated to increase the acidification rate of the four plant matrices. Moreover, L. pseudomesenteroides (LP) demonstrated to in situ produce high concentrations of mannitol when fructose was present as C-source. Furthermore, L. pseudomesenteroides, which encoded for PII-proteinase, demonstrated to break down SPOP proteins, releasing free amino acids that were used by L.lactis (LL) for growth and metabolism. Lastly, the analysis of their co-metabolic volatile performance showed the principal ability of removal of the main off-flavours found in SPOP, such as hexanal, 1-octen-3-ol, 2-pentylfuran, pentanal, octanal, heptanal, and nonanal, mainly led by L. pseudomesenteroides, as well as the production of dairy-like flavours, such as diacetyl and 3-methyl-1-butanol, triggered by L. lactis metabolism. Overall, these findings endorsed the use of honeybee isolated strains as starter cultures, demonstrated the potential of coupling genotypes and phenotypes of multiple strains to improve the organoleptic properties suggesting a potential of combining plant-based matrices for the generation of future high-quality plant-based dairy alternatives.

Metabolomics analysis of okara probiotic beverages fermented with Lactobacillus gasseri and Limosilactobacillus fermentum by LC-QTOF-MS/MS

In this study, okara was fermented with probiotic strains Lactobacillus gasseri LAC 343 and Limosilactobacillus fermentum PCC, respectively. Significant increases in cell count (by 2.22 log CFU/mL for LAC and 0.82 log CFU/mL for PCC) and significant decreases in pH (by 1.31 for LAC and 1.03 for PCC) were found in fermented okara slurry. In addition, strain LAC tended to produce amino acids, while strain PCC depleted most amino acids. An untargeted metabolomic-based approach using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was used to further understand the compositional changes and potential health benefits by identifying bioactive metabolites in fermented okara slurry. We successfully identified various beneficial bioactive compounds including γ-aminobutyric acid, indolelactic acid, d-phenyllactic acid, and p-hydroxyphenyllactic acid which had differences in fold-changes in okara slurry fermented with different strains. Our study indicated the feasibility of using probiotics to ferment okara for novel functional food development.

Volatile Organic Compounds (VOCs) Produced by Levilactobacillus brevis WLP672 Fermentation in Defined Media Supplemented with Different Amino Acids

Fermentation by lactic acid bacteria (LAB) is a promising approach to meet the increasing demand for meat or dairy plant-based analogues with realistic flavours. However, a detailed understanding of the impact of the substrate, fermentation conditions, and bacterial strains on the volatile organic compounds (VOCs) produced during fermentation is lacking. As a first step, the current study used a defined medium (DM) supplemented with the amino acids L-leucine (Leu), L-isoleucine (Ile), L-phenylalanine (Phe), L-threonine (Thr), L-methionine (Met), or L-glutamic acid (Glu) separately or combined to determine their impact on the VOCs produced by Levilactobacillus brevis WLP672 (LB672). VOCs were measured using headspace solid-phase microextraction (HS-SPME) gas chromatography-mass spectrometry (GC-MS). VOCs associated with the specific amino acids added included: benzaldehyde, phenylethyl alcohol, and benzyl alcohol with added Phe; methanethiol, methional, and dimethyl disulphide with added Met; 3-methyl butanol with added Leu; and 2-methyl butanol with added Ile. This research demonstrated that fermentation by LB672 of a DM supplemented with different amino acids separately or combined resulted in the formation of a range of dairy- and meat-related VOCs and provides information on how plant-based fermentations could be manipulated to generate desirable flavours.

Ecological diversity and associated volatilome of typical mountain Caciotta cheese from Italy

Traditional products are particularly appreciated by consumers and among these products, cheese is a major contributor to the Italian mountainous area economics. In this study, shotgun metagenomics and volatilomics were used to understand the biotic and abiotic factors contributing to mountain Caciotta cheese typicity and diversity. Results showed that the origin of cheese played a significant role; however, curd cooking temperature, pH, salt concentration and water activity also had an impact. Viral communities exhibited higher biodiversity and discriminated cheese origins in terms of production farms. Among the most dominant bacteria, Streptococcus thermophilus showed higher intraspecific diversity and closer relationship to production farm when compared to Lactobacillus delbrueckii. However, despite a few cases in which the starter culture was phylogenetically separated from the most dominant strains sequenced in the cheese, starter cultures and dominant cheese strains clustered together suggesting substantial starter colonization in mountain Caciotta cheese. The Caciotta cheese volatilome contained prominent levels of alcohols and ketones, accompanied by lower proportions of terpenes. Volatile profile not only demonstrated a noticeable association with production farm but also significant differences in the relative abundances of enzymes connected to flavor development. Moreover, correlations of different non-homologous isofunctional enzymes highlighted specific contributions to the typical flavor of mountain Caciotta cheese. Overall, this study provides a deeper understanding of the factors shaping typical mountain Caciotta cheese, and the potential of metagenomics for characterizing and potentially authenticating food products.

Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat

The genus Dellaglioa (D.) actually comprises two species, i.e., D. algida and the recently described species D. carnosa. Both species are adapted to cold and have been typically recovered from meat products. However, their importance has thus far been underestimated, since routine culture-based analysis failed to support their growth. Furthermore, their occurrence on meat packed under high-oxygen MA conditions (HiOx-MAP) is controversial because they have been described as being oxygen-sensitive. In this study, we focused on the targeted isolation of Dellaglioa spp. from HiOx-MAP meat samples and the characterization of our isolates regarding their adaption to HiOx-MAP conditions, their spoilage potential, as well as food safety aspects. We used a medium recently developed specifically for strains of this genus and investigated ten meat batches from seven different suppliers. Our study confirms that the occurrence of Dellaglioa spp. on HiOx-MAP meat is non-sporadic, reaching cell counts ranging from log10 5.8-7.1 CFU/cm2 at a late stage of chilled storage. Autochthonous Dellaglioa spp. and Leuconostoc (L.) gasicomitatum dominated the microbiota of the beef steaks with similar growth behavior. Our results suggest that Dellaglioa spp. benefits from the heme-dependent respiration of oxygen by L. gasicomitatum. Furthermore, whole genome analysis revealed the presence of genes predictively involved in oxidative stress defense, survival, and adaptation in meat environments. Moreover, we predict a weak aminogenic potential of D. algida strains. Tyramine production from tyrosine seems to be a species-specific characteristic of D. carnosa. The extent to which D. algida and D. carnosa occurrence is influenced by or even dependent on the composition of the entire microbiota remains to be investigated.

Effect of the initial pH of the culture medium on the nutrient consumption pattern of Bifidobacterium animalis subsp. lactis Bb12 and the improvement of acid resistance by purine and pyrimidine compounds

AIMS

During fermentation, the accumulation of acidic products can induce media acidification, which restrains the growth of Bifidobacterium animalis subsp. lactis Bb12 (Bb12). This study investigated the nutrient consumption patterns of Bb12 under acid stress and effects of specific nutrients on the acid resistance of Bb12.

METHODS AND RESULTS

Bb12 was cultured in chemically defined medium (CDM) at different initial pH values. Nutrient consumption patterns were analyzed in CDM at pH 5.3, 5.7, and 6.7. The patterns varied with pH: Asp + Asn had the highest consumption rate at pH 5.3 and 5.7, while Ala was predominant at pH 6.7. Regardless of the pH levels (5.3, 5.7, or 6.7), ascorbic acid, adenine, and Fe2+ were vitamins, nucleobases, and metal ions with the highest consumption rates, respectively. Nutrients whose consumption rates exceeded 50% were added individually in CDM at pH 5.3, 5.7, and 6.7. It was demonstrated that only some of them could promote the growth of Bb12. Mixed nutrients that could promote the growth of Bb12 were added to three different CDM. In CDM at pH 5.3, 5.7, and 6.7, it was found that the viable cell count of Bb12 was the highest after adding mixed nutrients, which were 8.87, 9.02, and 9.10 log CFU ml-1, respectively.

CONCLUSIONS

The findings suggest that the initial pH of the culture medium affects the nutrient consumption patterns of Bb12. Specific nutrients can enhance the growth of Bb12 under acidic conditions and increase its acid resistance.

Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism

Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment.

Inoculation with Lentilactobacillus buchneri alone or in combination with Lentilactobacillus hilgardii modifies gene expression, fermentation profile, and starch digestibility in high-moisture corn

Inoculants combining Lentilactobacillus buchneri and Lentilactobacillus hilgardii have been shown to improve the aerobic stability of high-moisture corn (HMC) and whole-plant corn silage, but the mode of action of this co-inoculation remains to be elucidated. This study used metatranscriptomics to evaluate the effects of inoculation with L. buchneri alone or combined with L. hilgardii on the bacterial community, gene expression, fermentation profile, and starch digestibility in HMC. High-moisture corn not inoculated (Control) or inoculated with L. buchneri NCIMB 40788 (LB) or L. buchneri NCIMB 40788 combined with L. hilgardii CNCM-I-4785 (Combo) was ensiled in mini silo bags for 30, 60, 120, and 180 days. The fermentation profile was evaluated at all time points. Metatranscriptomics was performed on samples collected on day 120. Combo had a greater alpha diversity richness index of contigs than LB and Control, and inoculation with Combo and LB modified the beta-diversity of contigs compared to Control. Out of 69 genes of interest, 20 were differentially expressed in LB compared to Control and 25 in Combo compared to Control. Of those differently expressed genes, 16 (10 of which were associated with carbohydrate metabolism and six with amino acid metabolism) were differently expressed in both LB and Combo compared to Control, and all those genes were upregulated in the inoculated silages. When we compared Combo and LB, we found seven genes expressed differently, four associated with carbohydrate metabolism and downregulated in Combo, and three associated with amino acid metabolism and upregulated in Combo. At day 120, the inoculated silages had more culturable lactic acid bacteria, higher Lactobacillus relative abundance, and lower Leuconostoc relative abundance than Control. The concentration of acetic acid remained low throughout ensiling in Control, but in LB and Combo, it increased up to day 60 and remained stable from day 60 to 180. The 1,2-propanediol was only detected in LB and Combo. Inoculation did not affect the concentration of starch, but starch digestibility was greater in Combo than in Control. Inoculation of HMC with Combo modified the gene expression and fermentation profile compared to Control and LB, improving starch digestibility compared to uninoculated HMC.

Effective mitigation in the amount of acrylamide through enzymatic approaches

Acrylamide (AA), as a food-borne toxicant, is created at some stages of thermal processing in the starchy food through Maillard reaction, fatty food via acrolein route, and proteinous food using free amino acids pathway. Maillard reaction obviously takes place in thermal-based products, being responsible for specific sensory attributes; AA formation, thereby, is unavoidable during the thermal processing. Additionally, AA can naturally occur in soil and water supply. In order to reduce the levels of acrylamide in cooked foods, mitigation techniques can be separated into three different types. Firstly, starting materials low in acrylamide precursors can be used to reduce the acrylamide in the final product. Secondly, process conditions may be modified in order to decrease the amount of acrylamide formation. Thirdly, post-process intervention could be used to reduce acrylamide. Conventional or emerging mitigation techniques might negatively influence the pleasant features of heated foods. The current study summarizes the effect of enzymatic reaction induced by asparaginase, glucose oxidase, acrylamidase, phytase, amylase, and protease to possibly inhibit AA formation or progressively hydrolyze formed AA. Not only enzyme-assisted AA reduction could dramatically maintain bio-active compounds, but also no damaging impact has been reported on the sensorial and rheological properties of the final heated products. The enzyme engineering can be applied to ameliorate enzyme functionality through altering the amino acid sequence like site-specific mutagenesis and directed evolution, chemical modifications by covalent conjugation of L-asparaginase onto soluble/insoluble biocompatible polymers and immobilization. Moreover, it would be possible to improve the enzyme's physical, chemical, and thermal stability, recyclability and prevent enzyme overuse by applying engineered ones. In spite of enzymes' cost-effective and eco-friendly, promoting their large-scale usages for AA reduction in food application and AA bioremediation in wastewater and soil resources.

A Study on the Formation of Flavor Substances by Bacterial Diversity in the Fermentation Process of Canned Bamboo Shoots in Clear Water

Canned bamboo shoots in clear water could produce a unique flavor through bacterial diversity via the fermentation process. Weissella, Streptococcus, Leuconostoc, Acinetobacter, Lactococcus and Lactobacillus were the main microorganisms. Tyrosine was the most abundant free amino acid (FAA), which had a negative correlation with Lactococcus. Ten kinds of flavor substances, such as 3-methyl-1-butanol, acetic acid, 2-phenylethyl ester, benzene acetaldehyde, benzoic acid and ethyl ester, were important influential factors in the flavor of fermented bamboo shoots. Through the verification test of tyrosine and phenylalanine decarboxylase, it was found that Lactococcus lactis TJJ2 could decompose tyrosine and phenylalanine to produce benzaldehyde and benzene acetaldehyde, which provided the fermented bamboo shoots with a grassy aroma.

The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model

The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is hallmarked by the breakdown of lactose to organic acids such as lactate. This leads to a substantial decrease in pH - both in the medium, as well as cytosolic. The latter impairs metabolic activities due to the pH-dependence of enzymes, which compromises microbial growth. To quantitatively elucidate the impact of the acidification on metabolism of L. bulgaricus in an integrated way, we have developed a proton-dependent computational model of lactose metabolism and casein degradation based on experimental data. The model accounts for the influence of pH on enzyme activities as well as cellular growth and proliferation of the bacterial population. We used a machine learning approach to quantify the cell volume throughout fermentation. Simulation results show a decrease in metabolic flux with acidification of the cytosol. Additionally, the validated model predicts a similar metabolic behaviour within a wide range of non-limiting substrate concentrations. This computational model provides a deeper understanding of the intricate relationships between metabolic activity and acidification and paves the way for further optimization of yoghurt production under industrial settings.

Insight into the acid tolerance mechanism of Acetilactobacillus jinshanensis subsp. aerogenes Z-1

Several lactic acid bacteria (LAB) are double-edged swords in the production of Sichuan bran vinegar; on the one hand, they are important for the flavour of the vinegar, but on the other hand, they result in vinegar deterioration because of their gas-producing features and their acid resistance. These characteristics intensify the difficulty in managing the safe production of vinegar using strains such as Acetilactobacillus jinshanensis subsp. aerogenes Z-1. Therefore, it is necessary to characterize the mechanisms underlying their acid tolerance. The results of this study showed a survival rate of 77.2% for Z-1 when exposed to pH 3.0 stress for 1 h. This strain could survive for approximately 15 days in a vinegar solution with 4% or 6% total acid content, and its growth was effectively enhanced by the addition of 10 mM of arginine (Arg). Under acidic stress, the relative content of the unsaturated fatty acid C18:1 (n-11) increased, and eight amino acids accumulated in the cells. Meanwhile, based on a transcriptome analysis, the genes glnA, carA/B, arcA, murE/F/G, fabD/H/G, DnaK, uvrA, opuA/C, fliy, ecfA2, dnaA and LuxS, mainly enriched in amino acid transport and metabolism, protein folding, DNA repair, and cell wall/membrane metabolism processes, were hypothesized to be acid resistance-related genes in Z-1. This work paves the way for further clarifying the acid tolerance mechanism of Z-1 and shares applicable perspectives for vinegar brewing.

Metabolomics and transcriptomics analyses provide new insights into the nutritional quality during the endosperm development of different ploidy rice

Autotetraploid rice is developed from diploid rice by doubling the chromosomes, leading to higher nutritional quality. Nevertheless, there is little information about the abundances of different metabolites and their changes during endosperm development in autotetraploid rice. In this research, two different kinds of rice, autotetraploid rice (AJNT-4x) and diploid rice (AJNT-2x), were subjected to experiments at various time points during endosperm development. A total of 422 differential metabolites, were identified by applying a widely used metabolomics technique based on LC-MS/MS. KEGG classification and enrichment analysis showed the differences in metabolites were primarily related to biosynthesis of secondary metabolites, microbial metabolism in diverse environments, biosynthesis of cofactors, and so on. Twenty common differential metabolites were found at three developmental stages of 10, 15 and 20 DAFs, which were considered the key metabolites. To identify the regulatory genes of metabolites, the experimental material was subjected to transcriptome sequencing. The DEGs were mainly enriched in starch and sucrose metabolism at 10 DAF, and in ribosome and biosynthesis of amino acids at 15 DAF, and in biosynthesis of secondary metabolites at 20 DAF. The numbers of enriched pathways and the DEGs gradually increased with endosperm development of rice. The related metabolic pathways of rice nutritional quality are cysteine and methionine metabolism, tryptophan metabolism, lysine biosynthesis and histidine metabolism, and so on. The expression level of the genes regulating lysine content was higher in AJNT-4x than in AJNT-2x. By applying CRISPR/Cas9 gene-editing technology, we identified two novel genes, OsLC4 and OsLC3, negatively regulated lysine content. These findings offer novel insight into dynamic metabolites and genes expression variations during endosperm development of different ploidy rice, which will aid in the creation of rice varieties with better grain nutritional quality.

Untargeted LC-QTOF-MS/MS-based metabolomics of spent coffee grounds alcoholic beverages fermented with Lachancea thermotolerans and Lactiplantibacillus plantarum

Spent coffee grounds (SCG) is a solid waste generated from coffee brewing. We recently developed a novel SCG hydrolysate-derived alcoholic beverage fermented with Lachancea thermotolerans Concerto and Lactiplantibacillus plantarum ML Prime. To further understand the potential health benefits of the fermented SCG hydrolysate alcoholic beverage, an untargeted metabolomics-based approach (UPLC-QTOF-MS/MS) was applied to detect and identify bioactive metabolites especially low molecular weight compounds. Our results showed that, compared to yeast monoculture-fermented SCG alcoholic beverages, yeast-lactic acid bacterial coculture enriched the beverage with a range of bioactive compounds especially aromatic and branched-chain amino acid derivatives (e.g., 4-hydroxyphenyl lactic acid, phenyl lactic acid, indole lactic acid, (S)-(-)-2-hydroxyisocaproic acid, and 4-hydroxyphenyl ethanol). Although some endogenous phenolic compounds were metabolized during fermentation, many phenolic metabolites (e.g., vinyl phenols, dihydrocaffeic acid, 3,4-dihydroxybenzoic acid, 4-hydroxycoumarin) were produced. Our study provided a theoretical basis for further valorization of SCG hydrolysates from the health benefits point of view and the findings may be extended to other fermented products.

Effects of Fermented Artemisia annua L. and Salicornia herbacea L. on Inhibition of Obesity In Vitro and In Mice

Plant extracts including secondary metabolites have anti-inflammatory and anti-obesity activities. This study was conducted to investigate the anti-obesity properties of fermented Artemisia annua (AW) and Salicornia herbacea (GW) in vitro and in mice. The metabolite profiling of AW and GW extracts was performed using UHPLC-LTQ-Orbitrap-MS/MS, and gene expression was analyzed using real-time PCR for adipocyte difference factors. The anti-obesity effects in mice were measured using serum AST, ALT, glucose, TG, and cholesterol levels. Metabolites of the plant extracts after fermentation showed distinct differences with increasing anti-obesity active substances. The efficacy of inhibitory differentiation adipogenesis of 3T3-L1 adipocytes was better for GW than AW in a concentration-dependent manner. RT-PCR showed that the GW extract significantly reduced the expression of genes involved in adipocyte differentiation and fat accumulation (C/EBPα, PPARγ, and Fas). In C57BL/6 mice fed the HFD, the group supplemented with AW and GW showed reduced liver weight, NAS value, and fatty liver by suppressing liver fat accumulation. The GW group significantly reduced ALT, blood glucose, TG, total cholesterol, and LDL-cholesterol. This study displayed significant metabolite changes through biotransformation in vitro and the increasing anti-obesity effects of GW and AW in mice. GW may be applicable as functional additives for the prevention and treatment of obesity.

Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile

Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpA^Ac for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.

Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications

The human gut harbors native microbial communities, forming a highly complex ecosystem. Synthetic microbial communities (SynComs) of the human gut are an assembly of microorganisms isolated from human mucosa or fecal samples. In recent decades, the ever-expanding culturing capacity and affordable sequencing, together with advanced computational modeling, started a ''golden age'' for harnessing the beneficial potential of SynComs to fight gastrointestinal disorders, such as infections and chronic inflammatory bowel diseases. As simplified and completely defined microbiota, SynComs offer a promising reductionist approach to understanding the multispecies and multikingdom interactions in the microbe-host-immune axis. However, there are still many challenges to overcome before we can precisely construct SynComs of designed function and efficacy that allow the translation of scientific findings to patients' treatments. Here, we discussed the strategies used to design, assemble, and test a SynCom, and address the significant challenges, which are of microbiological, engineering, and translational nature, that stand in the way of using SynComs as live bacterial therapeutics.

Effects of Bacillus coagulans and Lactobacillus plantarum on the Fermentation Characteristics, Microbial Community, and Functional Shifts during Alfalfa Silage Fermentation

This study aimed to investigate the potential of Bacillus coagulans (BC) as an inoculant in alfalfa silage fermentation. Fresh alfalfa was harvested at a dry matter (DM) content of 329.60 g/kg fresh weight (FW), and inoculated without (CON) or with BC (1 × 106 CFU/g FW), Lactobacillus plantarum (LP, 1 × 106 CFU/g FW), and their combinations (LP+BC, 1 × 106 CFU/g FW, respectively). Samples were taken at 3, 7, 14, 30, and 60 d, with three replicates for each. The prolonged ensiling period resulted in a decrease in pH values and an increase in lactic acid (LA) concentrations in alfalfa silages. After 60 d of fermentation, the application of BC and LP decreased the pH values and increased LA concentrations in treated silages, especially when their combination was applied. Application of BC preserved more water-soluble carbohydrates (WSC), and further application of BC increased WSC in LP+BC-treated silage compared to LP-treated silage. There was no significant difference in the crude protein (CP) content between the CON and treated silages, however, the BC and LP treatments reduced the ammonia nitrogen (NH3-N) concentration, especially when their combination was applied. Additionally, the BC and LP-treated silages had lower neutral detergent fiber (NDF) and acid detergent fiber (ADF) when compared to the CON silage (p < 0.001). Inoculants also increased Lactobacillus abundance and decreased Enterococcus abundance after 60 d of fermentation. Spearman's rank correlation analysis revealed a positive correlation between LA concentration and Lactobacillus abundance. It was noteworthy that LP, BC, and their combination increased the relative abundances of carbohydrate metabolism, energy metabolism, cofactors, and vitamin metabolism, decreasing the relative abundances of amino acid metabolism and drug resistance: antimicrobial. Therefore, the inclusion of BC increased the fermentation quality of alfalfa silage, with the optimal combination being LP+BC. According to the findings, BC could be considered a viable bioresource for improving fermentation quality.

Inoculation of Latilactobacillus sakei with Pichia kluyveri or Saccharomyces boulardii improves flavor compound profiles of salt-free fermented wheat-gluten: Effects from single strain inoculation

Wheat-gluten, the protein-rich portion of wheat, can be processed to produce a highly savory sauce product after solid and liquid-state fermentation (SSF and LSF) with the inoculation of selected lactic acid bacteria (LAB) and yeast under salt-free condition. However, limited research has been done on the impact of different types of microbes in this process. This work studied the flavour impact on fermented wheat-gluten by the single inoculation of Latilactobacillus sakei or one yeast (Saccharomyces boulardii or Pichia kluyveri). Glucose was depleted during LSF in all treatments. Lactic acid production increased over time in L. sakei-fermented samples but not in yeast-fermented samples. Cysteine, serine and arginine remained low over LSF in L. sakei-fermented samples but increased in yeast-fermented samples. More fruity esters such as isoamyl acetate and isobutyl acetate were detected in samples fermented by P. kluyveri, while S. boulardii boosted the production of alcohols such as 3-methyl butanol and 2-phenylethyl alcohol. Principal component analysis revealed a clear difference in volatile profiles of the samples fermented with different strains. Therefore, the fermented sauce can potentially be processed into different flavor directions, and based on the flavor profile, be used in different food applications.

Growth promotion effect of red ginseng dietary fiber to probiotics and transcriptome analysis of Lactiplantibacillus plantarum

Background

Red ginseng marc, the residue of red ginseng left after water extraction, is rich in dietary fiber. Dietary fiber derived from fruits or vegetables can promote the proliferation of probiotics, and it is a key technology in the food industry to increase the productivity of probiotics by adding growth-enhancing substances such as dietary fiber. In this study, the effect of red ginseng dietary fiber (RGDF) on the growth of probiotic bacterial strains was investigated at the phenotypic and genetic levels.

Methods

We performed transcriptome profiling of Lactiplantibacillus plantarum IDCC3501 in two phases of culture (logarithmic (L)-phase and stationary (S)-phase) in two culture conditions (with or without RGDF) using RNA-seq. Differentially expressed genes (DEGs) were identified and classified according to Gene Ontology terms.

Results

The growth of L.plantarum IDCC3501 was enhanced in medium supplemented with RGDF up to 2%. As a result of DEG analysis, 29 genes were upregulated and 30 were downregulated in the RGDF-treated group in the L-phase. In the S-phase, 57 genes were upregulated and 126 were downregulated in the RGDF-treated group. Among the upregulated genes, 5 were upregulated only in the L-phase, 10 were upregulated only in the S-phase, and 3 were upregulated in both the L- and S-phases.

Conclusions

Transcriptome analysis could be a valuable tool for elucidating the molecular mechanisms by which RGDF promotes the proliferation of L.plantarum IDCC3501. This growth-promoting effect of RGDF is important, since RGDF could be used as a prebiotic source without additional chemical or enzymatic processing.

Transcriptome-phenotype matching analysis of how nitrogen sources influence Lacticaseibacillus rhamnosus tolerance to heat stress and oxidative stress

BACKGROUND

Spray drying is the most cost-effective production method for lactic acid bacteria starters, but heat and oxidative stresses result in low survival rates. The heat stress and oxidative stress tolerance of Lacticaseibacillus rhamnosus cultured in tryptone-free MRS (NP-MRS) broth was much stronger than that in MRS or tryptone-free MRS broth supplemented with phenylalanine (Phe-MRS). Here, multiple transcriptome-phenotype matching was performed on cells cultured in NP-MRS, MRS and Phe-MRS broths to reveal the mechanism by which nitrogen sources influence L. rhamnosus tolerance to heat stress and oxidative stress.

RESULTS

Compared with cells cultured in NP-MRS broth, 83 overlapping differentially expressed genes (DEGs) were downregulated by either tryptone or phenylalanine. The overlapping DEGs were mainly classified into carbohydrate metabolism and membrane transport pathways, which are often repressed by glucose during carbon catabolite repression (CCR). In the presence of glucose, the heat stress or oxidative stress tolerance of L. rhamnosus hsryfm 1301 was not strengthened by supplementation with secondary carbohydrates. Replacing glucose with mannose, fructose or ribose improved the heat stress and oxidative stress tolerance of L. rhamnosus hsryfm 1301 (5 to 46-fold).

CONCLUSIONS

Alleviation of CCR might be a reason for the resistance of L. rhamnosus hsryfm 1301 to heat stress and oxidative stress in a low-nitrogen environment. The survival rate of L. rhamnosus during spray drying will hopefully be improved by relieving CCR. It is a new discovery that nitrogen sources influence CCR in L. rhamnosus.

Current approaches on the roles of lactic acid bacteria in crop silage

Lactic acid bacteria (LAB) play pivotal roles in the preservation and fermentation of forage crops in spontaneous or inoculated silages. Highlights of silage LAB over the past decades include the discovery of the roles of LAB in silage bacterial communities and metabolism and the exploration of functional properties. The present article reviews published literature on the effects of LAB on the succession, structure, and functions of silage microbial communities involved in fermentation. Furthermore, the utility of functional LAB in silage preparation including feruloyl esterase-producing LAB, antimicrobial LAB, lactic acid bacteria with high antioxidant potential, pesticide-degrading LAB, lactic acid bacteria producing 1,2-propanediol, and low-temperature-tolerant LAB have been described. Compared with conventional LAB, functional LAB produce different effects; specifically, they positively affect animal performance, health, and product quality, among others. In addition, the metabolic profiles of ensiled forages show that plentiful probiotic metabolites with but not limited to antimicrobial, antioxidant, aromatic, and anti-inflammatory properties are observed in silage. Collectively, the current knowledge on the roles of LAB in crop silage indicates there are great opportunities to develop silage not only as a fermented feed but also as a vehicle of delivery of probiotic substances for animal health and welfare in the future.

Biosynthesis of gamma-aminobutyric acid by Lactiplantibacillus plantarum K16 as an alternative to revalue agri-food by-products

Probiotic metabolites, known as postbiotics, have received attention due to their wide variety of promoting health effects. One of the most exciting postbiotic is gamma-aminobutyric acid (GABA), widely produced by lactic acid bacteria, due to its benefits in health. In addition, the performance of the biosynthesis of GABA by Lactiplantibacillus plantarum could be modulated through the modification of fermentation parameters. Due to their high nutritional value, agri-food by-products could be considered a useful fermentation source for microorganisms. Therefore, these by-products were proposed as fermentation substrates to produce GABA in this study. Previously, several experiments in Man Rogosa Sharpe (MRS) broth were performed to identify the most critical parameters to produce GABA using the strain Lactiplantibacillus plantarum K16. The percentage of inoculum, the initial pH, and the concentration of nutrients, such as monosodium glutamate or glucose, significantly affected the biosynthetic pathway of GABA. The highest GABA yield was obtained with 500 mM of monosodium glutamate and 25 g/L of glucose, and an initial pH of 5.5 and 1.2% inoculum. Furthermore, these investigated parameters were used to evaluate the possibility of using tomato, green pepper, apple, or orange by-products to get GABA-enriched fermented media, which is an excellent way to revalorise them.