Effect of co-culture with Tetragenococcus halophilus on the physiological characterization and transcription profiling of Zygosaccharomyces rouxii

Functional roles and engineering strategies to improve the industrial functionalities of lactic acid bacteria during food fermentation

In order to improve the flavor profiles, food security, probiotic effects and shorten the fermentation period of traditional fermented foods, lactic acid bacteria (LAB) were often considered as the ideal candidate to participate in the fermentation process. In general, LAB strains possessed the ability to develop flavor compounds via carbohydrate metabolism, protein hydrolysis and amino acid metabolism, lipid hydrolysis and fatty acid metabolism. Based on the functional properties to inhibit spoilage microbes, foodborne pathogens and fungi, those species could improve the safety properties and prolong the shelf life of fermented products. Meanwhile, influence of LAB on texture and functionality of fermented food were also involved in this review. As for the adverse effect carried by environmental challenges during fermentation process, engineering strategies based on exogenous addition, cross protection, and metabolic engineering to improve the robustness and of LAB were also discussed in this review. Besides, this review also summarized the potential strategies including microbial co-culture and metabolic engineering for improvement of fermentation performance in LAB strains. The authors hope this review could contribute to provide an understanding and insight into improving the industrial functionalities of LAB.

Comparative Transcriptomic Analysis of the Flavor Production Mechanism in Yogurt by Traditional Starter Strains

Synergistic fermentation of milk by Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus is one of the key factors that determines the quality of yogurt. In this study, the mechanism whereby yogurt flavor compounds are produced by mixture of S. thermophilus SIT-20.S and L. delbrueckii ssp. bulgaricus SIT-17.B were investigated by examining these strains' flavor production, growth, and gene transcription. The results showed that yogurt produced by a 10:1 mixture of the aforementioned strains had the highest abundance of acetoin, whereas yogurt produced by a 1:1 mixture had the highest abundance of diacetyl and acetaldehyde. In addition, the growth of S. thermophilus SIT-20.S was enhanced in the 10:1 mixture. Transcriptomic analysis revealed differentially expressed genes in the flavor-compound-related pathways of S. thermophilus SIT-20.S and L. delbrueckii ssp. bulgaricus SIT-17.B in yogurts produced by 10:1 and 1:1 mixture compared with those produced by either strain alone. Mixed fermentations regulated the expression of genes related to glycolysis, resulting in an increase of pyruvate, which is an important precursor for diacetyl and acetoin synthesis. The gene encoding the acetoin reductase (SIT-20S_orf01454) was decreased in S. thermophilus SIT-20.S, which ensured the accumulation of acetoin. Besides, gene encoding the acetaldehyde dehydrogenase (SIT-20S_orf00949) was upregulated in S. thermophilus SIT-20.S, and the expression of alcohol dehydrogenase (SIT-20S_orf01479; SIT-17B_orf00943) was downregulated in both strains, maintaining the abundance of acetaldehyde. In addition, the gene encoding the NADH oxidase (SIT-17B_orf00860) in L. delbrueckii ssp. bulgaricus SIT-17.B were upregulated, which promoted the accumulation of diacetyl and acetoin. In conclusion, we characterized the mechanism by which S. thermophilus and L. delbrueckii ssp. bulgaricus synergistically generated yogurt flavor compounds during their production of yogurt and highlighted the importance of appropriate proportions of fermentation starters for improving the flavor of yogurts.

Effect of Yeast Inoculation on the Bacterial Community Structure in Reduced-Salt Harbin Dry Sausages: A Perspective of Fungi-Bacteria Interactions

Yeast strains are promising starters to compensate for the flavor deficiencies of reduced-salt dry sausages, but their influence on the bacterial community's structure has not yet been clarified. In this study, the effect of separately inoculating Pichia kudriavzevii MDJ1 (Pk) and Debaryomyces hansenii HRB3 (Dh) on the bacterial community structure in reduced-salt dry sausage was investigated. The results demonstrated that the inoculation of two yeast strains significantly reduced the pH, and enhanced the total acid content, lactic acid bacteria (LAB) counts, and total bacterial counts of reduced-salt sausages after a 12-day fermentation (p < 0.05). Furthermore, high-throughput sequencing results elucidated that the inoculation of yeast strains significantly affected the bacterial composition of the dry sausages. Especially, the relative abundance of bacteria at the firmicute level in the Pk and Dh treatments exhibited a significant increase of 83.22% and 82.19%, respectively, compared to the noninoculated reduced-salt dry sausage treatment (Cr). The relative abundance of Latilactobacillus, especially L. sakei (0.46%, 2.80%, 65.88%, and 33.41% for the traditional dry sausage (Ct), Cr, Pk, and Dh treatments, respectively), increased significantly in the reduced-salt sausages inoculated with two yeast strains. Our work demonstrates the dynamic changes in the bacterial composition of reduced-salt sausages inoculated with different yeast strains, which could provide the foundation for the in-depth study of fungi-bacteria interactions in fermented foods.

Effects of Fermentation with Tetragenococcus halophilus and Zygosaccharomyces rouxii on the Volatile Profiles of Soybean Protein Hydrolysates

The effects of fermentation with lactic acid bacteria (LAB) and yeast on the aroma of samples were analyzed in this work. The volatile features of different soybean hydrolysates were investigated using both GC-MS and GC-IMS. Only 47 volatile flavor compounds (VFCs) were detected when using GC-IMS, while a combination of GC-MS and GC-IMS resulted in the identification of 150 compounds. LAB-yeast fermentation could significantly increase the diversity and concentrations of VFCs (p < 0.05), including alcohols, acids, esters, and sulfurs, while reduce the contents of aldehydes and ketones. Hierarchical clustering and orthogonal partial least squares analyses confirmed the impact of fermentation on the VFCs of the hydrolysates. Seven compounds were identified as significant compounds distinguishing the aromas of different groups. The partial least squares regression analysis of the 25 key VFCs (ROAV > 1) and sensory results revealed that the treatment groups positively correlated with aromatic, caramel, sour, overall aroma, and most of the key VFCs. In summary, fermentation effectively reduced the fatty and bean-like flavors of soybean hydrolysates, enhancing the overall flavor quality, with sequential inoculation proving to be more effective than simultaneous inoculation. These findings provided a theoretical basis for improving and assessing the flavor of soybean protein hydrolysates.

Arginine deiminase pathway of Tetragenococcus halophilus contributes to improve the acid tolerance of lactic acid bacteria

Arginine deiminase pathway, controlled by arginine deiminase, ornithine carbamoyltransferase and carbamate kinase, could affect and modulate the intracellular pH homeostasis of lactic acid bacteria under acid stress. Herein, strategy based on exogenous addition of arginine had been proposed to improve the robustness of Tetragenococcus halophilus during acid stressed condition. Results indicated cells cultured in the presence of arginine acquired high tolerance to acid stress mainly through maintaining the homeostasis of intracellular microenvironment. Additionally, metabolomic analysis and q-PCR showed the content of intracellular metabolites and expression levels of genes involved in ADI pathway significantly increased when cells encountered acid stress with the presence of exogenous arginine. Furthermore, Lactococcus lactis NZ9000 with heterologous overexpression of arcA and arcC from T. halophilus exhibited high stress tolerance to acidic condition. This study may provide an insight into the systematical understanding about the mechanism underlying acid tolerance and improve the fermentation performance of LAB during harsh condition.

A systematic review on the flavor of soy-based fermented foods: Core fermentation microbiome, multisensory flavor substances, key enzymes, and metabolic pathways

The characteristic flavor of fermented foods has an important impact on the purchasing decisions of consumers, and its production mechanisms are a concern for scientists worldwide. The perception of food flavor is a complex process involving olfaction, taste, vision, and oral touch, with various senses contributing to specific properties of the flavor. Soy-based fermented products are popular because of their unique flavors, especially in Asian countries, where they occupy an important place in the dietary structure. Microorganisms, known as the souls of fermented foods, can influence the sensory properties of soy-based fermented foods through various metabolic pathways, and are closely related to the formation of multisensory properties. Therefore, this review systematically summarizes the core microbiome and its interactions that play an active role in representative soy-based fermented foods, such as fermented soymilk, soy sauce, soybean paste, sufu, and douchi. The mechanism of action of the core microbial community on multisensory flavor quality is revealed here. Revealing the fermentation core microbiome and related enzymes provides important guidance for the development of flavor-enhancement strategies and related genetically engineered bacteria.

Mechanism of Inhibiting the Growth and Aflatoxin B1 Biosynthesis of Aspergillus flavus by Phenyllactic Acid

Phenyllactic acid (PLA), a promising food preservative, is safe and effective against a broad spectrum of food-borne pathogens. However, its mechanisms against toxigenic fungi are still poorly understood. In this study, we applied physicochemical, morphological, metabolomics, and transcriptomics analyses to investigate the activity and mechanism of PLA inhibition of a typical food-contaminating mold, Aspergillus flavus. The results showed that PLA effectively inhibited the growth of A. flavus spores and reduced aflatoxin B₁ (AFB₁) production by downregulating key genes associated with AFB₁ biosynthesis. Propidium iodide staining and transmission electron microscopy analysis demonstrated a dose-dependent disruption of the integrity and morphology of the A. flavus spore cell membrane by PLA. Multi-omics analyses showed that subinhibitory concentrations of PLA induced significant changes in A. flavus spores at the transcriptional and metabolic levels, as 980 genes and 30 metabolites were differentially expressed. Moreover, KEGG pathway enrichment analysis indicated PLA-induced cell membrane damage, energy-metabolism disruption, and central-dogma abnormality in A. flavus spores. The results provided new insights into the anti-A. flavus and -AFB₁ mechanisms of PLA.

Transcriptomics Reveals the Effect of Strain Interactions on the Growth of A. Oryzae and Z. Rouxii

The microbial community structure in traditional fermented foods is quite complex, making the relationship between strains unclear. In this regard, the co-culture system can simulate microbial interactions during food fermentation and reveal the morphological changes, metabolic processes, and gene expression of microbial communities. The present study sought to investigate the effects of microbial interactions on the growth of Aspergillus oryzae and Zygosaccharomyces rouxii through omics. After co-cultivation, the pH value and dry weight were consistent with the pure culture of Z. rouxii. Additionally, the consumption of reducing sugar decreased, and the enzymatic activity increased compared with the pure culture of fungus. The analysis of volatile organic compounds (VOCs) and transcriptomics showed that co-culture significantly promoted the effect on Z. rouxii. A total of 6 different VOCs and 2202 differentially expressed genes were identified in the pure and co-culture of Z. rouxii. The differentially expressed genes were mainly related to the endonucleolytic cleavage of rRNA, ribosome biogenesis in eukaryotes, and RNA polymerase metabolic pathways. The study results will provide insights into the effect of microbial interactions on the growth of A. oryzae and Z. rouxii.

Identification and validation of core microbes associated with key aroma formation in fermented pepper paste (Capsicum annuumL.)

Fermented peppers are usually obtained by the spontaneous fermentation of microorganisms attached to fresh peppers, and the variable microbial composition would lead to inconsistencies in flavor between batches. To demonstrate the roles of microorganisms in flavor formation, the core microbes closely associated with the key aroma compounds of fermented pepper paste were screened and validated in this study. Lactobacillus was the dominant bacterial genus in fermented pepper paste, whereas the main fungal genera were Alternaria and Kazachstania. Nine strains of the genera Lactobacillus, Weissella, Bacillus, Zygosaccharomyces, Kazachstania, Debaryomyces, and Pichia were isolated from fermented pepper paste. Eleven key aroma compounds were identified using gas chromatography combined with olfactometry and relative odor activity values. Correlation analysis showed that Zygosaccharomyces and Kazachstania were positively correlated with the majority of the key aroma compounds, whereas Lactobacillus was negatively correlated with them. Thus, Zygosaccharomyces and Kazachstania were identified as core genera associated with the key odorants. Finally, Zygosaccharomyces bisporus, Kazachstania humilis, and Lactiplantibacillus plantarum were used as starter cultures for fermented peppers, confirming that Z. bisporus and K. humilis were more beneficial for the key aroma compounds (e.g., acetate, linalool, and phenyl ethanol) rather than L. plantarum. This study contributed to understanding the flavor formation mechanism and provided references for the quality control of food fermentation.

Heat Adaptation Induced Cross Protection Against Ethanol Stress in Tetragenococcus halophilus: Physiological Characteristics and Proteomic Analysis

Ethanol is a toxic factor that damages membranes, disturbs metabolism, and may kill the cell. Tetragenococcus halophilus, considered as the cell factory during the manufacture of traditional fermented foods, encounters ethanol stress, which may affect the viability and fermentative performance of cells. In order to improve the ethanol tolerance of T. halophilus, a strategy based on cross protection was proposed in the current study. The results indicated that cross protection induced by heat preadaptation (45°C for 1.5 h) could significantly improve the stress tolerance (7.24-fold increase in survival) of T. halophilus upon exposure to ethanol (10% for 2.5 h). Based on this result, a combined analysis of physiological approaches and TMT-labeled proteomic technology was employed to investigate the protective mechanism of cross protection in T. halophilus. Physiological analysis showed that the heat preadapted cells exhibited a better surface phenotype, higher membrane integrity, and higher amounts of unsaturated fatty acids compared to unadapted cells. Proteomic analysis showed that a total of 163 proteins were differentially expressed in response to heat preadaptation. KEGG enrichment analysis showed that energy metabolism, membrane transport, peptidoglycan biosynthesis, and genetic information processing were the most abundant metabolic pathways after heat preadaptation. Three proteins (GpmA, AtpB, and TpiA) involved in energy metabolism and four proteins (ManM, OpuC, YidC, and HPr) related to membrane transport were up-regulated after heat preadaptation. In all, the results of this study may help understand the protective mechanisms of preadaptation and contribute to the improvement of the stress resistance of T. halophilus during industrial processes.

Cell surface properties and transcriptomic analysis of cross protection provided between heat adaptation and acid stress in Tetragenococcus halophilus

Cross protection is a widely existed phenomenon in microorganisms which subjected to a mild stress develop tolerance to other stresses, yet the underlying mechanisms for this protection have not been fully elucidated. Here, we report that heat preadaptation induced cross protection against acid stress in Tetragenococcus halophilus, and the cross protective mechanisms were revealed based on cell surface characterizations and transcriptomic analysis. The results showed that heat preadaptation of T. halophilus at 45 °C for 1.5 h improved the acid tolerance of cells at pH 2.5, and the preadapted cells exhibited higher pH_i compared with the un-preadapted cells during acid stress. Analysis of the cell surface properties suggested that the heat-treated cells displayed smoother surface, lower roughness and higher integrity than those of untreated cells. Meanwhile, the distributions of membrane fatty acids also changed in response to acid stress, and the treated cells reveled lower ratio of unsaturated to saturated fatty acids. RNA-Sequencing was employed to further elucidate the cross protective mechanism induced by heat preadaptation, and the results showed that the differentially expressed genes (DGEs) were mainly involved in cellular metabolism and membrane transport during heat preadaptation. A detailed analysis of gene expression profile of cells between heat treated and untreated revealed that genes associated with energy metabolism, amino acid metabolism and genetic information processing were induced upon heat stress. Results presented in this study may broaden our understanding on cross protection and provide a potential strategy to enhance the performance of cells during industrial processes.

Loss of FGFR3 Delays Acute Myeloid Leukemogenesis by Programming Weakly Pathogenic CD117-Positive Leukemia Stem-Like Cells

Chemotherapeutic patients with leukemia often relapse and produce drug resistance due to the existence of leukemia stem cells (LSCs). Fibroblast growth factor receptor 3 (FGFR3) signaling mediates the drug resistance of LSCs in chronic myeloid leukemia (CML). However, the function of FGFR3 in acute myeloid leukemia (AML) is less understood. Here, we identified that the loss of FGFR3 reprograms MLL-AF9 (MA)-driven murine AML cells into weakly pathogenic CD117-positive leukemia stem-like cells by activating the FGFR1-ERG signaling pathway. FGFR3 deletion significantly inhibits AML cells engraftment in vivo and extends the survival time of leukemic mice. FGFR3 deletion sharply decreased the expression of chemokines and the prolonged survival time in mice receiving FGFR3-deficient MA cells could be neutralized by overexpression of CCL3. Here we firstly found that FGFR3 had a novel regulatory mechanism for the stemness of LSCs in AML, and provided a promising anti-leukemia approach by interrupting FGFR3.

Co-culture with Tetragenococcus halophilus improved the ethanol tolerance of Zygosaccharomyces rouxii by maintaining cell surface properties

The accumulation of ethanol has a negative effect on the viability and fermentation performance of microorganisms during the production of fermented foods because of its toxicity. In this study, we investigated the effect of co-culture with Tetragenococcus halophilus on ethanol stress resistance of Zygosaccharomyces rouxii. The result showed that co-culture with T. halophilus promoted cell survival of Z. rouxii under ethanol stress, and the tolerance improved with increasing co-culture time when ethanol content was 8%. Physiological analysis showed that the co-cultured Z. rouxii cells maintained higher intracellular content of trehalose and amino acids including tyrosine, tryptophan, arginine and proline after 8% ethanol stress for 90 min. The membrane integrity analysis and biophysical analysis of the cell surface indicated that the presence of ethanol resulted in cell membrane damage and changes of Young's modulus value and roughness of cell surface. While the co-cultured Z. rouxii cells exhibited better membrane integrity, stiffer and smoother cell surface than single-cultured cells under ethanol stress. As for transcriptomic analyses, the genes involved in unsaturated fatty acid biosynthesis, trehalose biosynthesis, various types of N-glycan biosynthesis, inositol phosphate metabolism, MAPK signaling pathway and tight junction had higher expression in co-cultured Z. rouxii cells with down-regulation of majority of gene expression after stress. And these genes may function in the improvement of ethanol tolerance of Z. rouxii in co-culture.

Heat preadaptation improved the ability of Zygosaccharomyces rouxii to salt stress: a combined physiological and transcriptomic analysis

Zygosaccharomyces rouxii plays important roles in the brewing process of fermented foods such as soy sauce, where salt stress is a frequently encountered condition. In this study, effect of heat preadaptation on salt tolerance of Z. rouxii and the protective mechanisms underlying heat preadaptation were investigated based on physiological and transcriptomic analyses. Results showed that cells subjected to heat preadaptation (37 °C, 90 min) prior to salt stress aroused many physiological responses, including maintaining cell surface smooth and intracellular pH level, increasing Na⁺/K⁺-ATPase activity. Cells subjected to heat preadaptation increased the amounts of unsaturated fatty acids (palmitoleic C16:1, oleic C18:1, linoleic C18:2) and decreased the amounts of saturated fatty acids (palmitic C16:0, stearic C18:0) which caused the unsaturation degree (unsaturated/saturated = U/S ratio) increased by 2.4 times when compared with cells without preadaptation under salt stress. Besides, salt stress led to increase in contents of 5 amino acids (valine, proline, threonine, glycine, and tyrosine) and decrease of 2 amino acids (serine and lysine). When comparing the cells pre-exposed to heat preadaptation followed by challenged with salt stress and the cells without preadaptation under salt stress, the serine, threonine, and lysine contents increased significantly. RNA sequencing revealed that the metabolic level of glycolysis by Z. rouxii was weakened, while the metabolic levels of the pentose phosphate pathway and the riboflavin were enhanced in cells during heat preadaptation. Results presented in this study may contribute to understand the bases of adaptive responses in Z. rouxii and rationalize its exploitation in industrial processes.Key points• Heat preadaptation can improve high salinity tolerance of Z. rouxii.• Combined physiological and transcriptomic analyses of heat preadaptation mechanisms.• Provide theoretical support for the application of Z. rouxii.

Tartary buckwheat protein hydrolysates enhance the salt tolerance of the soy sauce fermentation yeast Zygosaccharomyces rouxii

Supplementation of protein hydrolysate is an important strategy to improve the salt tolerance of soy sauce aroma-producing yeast. In the present study, Tartary buckwheat protein hydrolysates (BPHs) were prepared and separated by ultrafiltration into LM-1 (<1 kDa) and HM-2 (1-300 kDa) fractions. The supplementation of HM-2 fraction could significantly improve cell growth and fermentation of soy sauce aroma-producing yeast Zygosaccharomyces rouxii As2.180 under high salt (12%, w/w) conditions. However, the LM-1 fraction inhibited strain growth and fermentation. The addition of HM-2 promoted yeast cell accumulation of K⁺, removal of cytosolic Na⁺ and accumulation of glycerol. Furthermore, the HM-2 fraction improved the cell membrane integrity and mitochondrial membrane and decreased intracellular ROS accumulation of the strain. The above results indicated that the supplementation of BPHs with a molecular weight of 1-300 kDa is a potentially effective and feasible strategy for improving the salt tolerance of soy sauce aroma-producing yeast Z. rouxii.