Gene expression profile of probiotic Lactobacillus casei Zhang during the late stage of milk fermentation

Proteomics and Metabolomics Analysis Reveal the Regulation Mechanism of Linoleate Isomerase Activity and Function in Propionibacterium acnes

Conjugated linoleic acid (CLA) holds significant application prospects due to its anticancer, anti-atherosclerosis, lipid-lowering, weight-loss, and growth-promoting functions. The key to its efficient production lies in optimizing the biocatalytic performance of linoleic acid isomerase (LAI). Here, we constructed a Propionibacterium acnes mutant library and screened positive mutants with high linoleate isomerase activity. The proteomics and metabolomics were used to explore the mechanism in the regulation of linoleic acid isomerase activity. High-throughput proteomics revealed 104 differentially expressed proteins unique to positive mutant strains of linoleic acid isomerase of which 57 were upregulated and 47 were downregulated. These differentially expressed proteins were primarily involved in galactose metabolism, the phosphotransferase system, starch metabolism, and sucrose metabolism. Differential metabolic pathways were mainly enriched in amino acid biosynthesis, including glutamate metabolism, the Aminoacyl-tRNA biosynthesis pathway, and the ABC transporter pathway. The upregulated metabolites include dl-valine and Acetyl coA, while the downregulated metabolites include Glutamic acid and Phosphoenolpyruvate. Overall, the activity of linoleic acid isomerase in the mutant strain was increased by the regulation of key proteins involved in galactose metabolism, sucrose metabolism, and the phosphotransferase system. This study provides a theoretical basis for the development of high-yield CLA food.

The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture

To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the host, it is important to study them using transcriptomics. In this study, we applied the RNA-Seq technique to study global gene expression of B. longum at different growth phases in order to better understand the response of bifidobacterial cells to the specific conditions of the human gut. We have shown that in the lag phase, ABC transporters, whose function may be linked to active substrate utilization, are increasingly expressed due to preparation for cell division. In the exponential phase, the functions of activated genes include synthesis of amino acids (alanine and arginine), energy metabolism (glycolysis/gluconeogenesis and nitrogen metabolism), and translation, all of which promote active cell division, leading to exponential growth of the culture. In the stationary phase, we observed a decrease in the expression of genes involved in the control of the rate of cell division and an increase in the expression of genes involved in defense-related metabolic pathways. We surmise that the latter ensures cell survival in the nutrient-deprived conditions of the stationary growth phase.

In situ exopolysaccharides from Lactobacillus helveticus MB2-1 in Sayram ketteki yoghurt: Set yoghurts properties and interactions with sodium caseinate

The effects of high exopolysaccharides (EPS) - producing Lactobacillus helveticus MB2-1 on the structure and storage stability of set yoghurts, and the interactions between its EPS (molecular weight 9.34 × 10⁴ Da) from Sayram ketteki yoghurt (SKY) and sodium caseinate (CAS) were studied. The rheology, microstructure, texture and storage stability of the three set yoghurts including control yoghurt (Control), adding-probiotic yoghurt (APY) and SKY were investigated, which showed that the SKY exhibited less shear thinning than the Control and APY, and the textural indexes and storage stability of the SKY were significantly better than that of other two yoghurts (p < 0.05). Moreover, the increased turbidity, decreased ζ potential and surface hydrophobicity of EPS/CAS complex coacervation were determined at EPS/CAS mass ratio of 3 (corresponding to 0.33 g/L of CAS and 1 g/L of EPS), mainly owing to the electrostatic attraction of the two biopolymers to form aggregates. Besides, the higher sizes and more aggregation of EPS/CAS complexes were formed at pH 3.5. Taken together, the results indicated that the high EPS-producing characteristic of L. helveticus MB2-1 could positively influence the qualities of set yoghurts, and the EPS/CAS complex coacervation in dairy products was closely related to the EPS/CAS mass ratio and pH condition.

Transcriptome analysis revealed growth phase-associated changes of a centenarian-originated probiotic Bifidobacterium animalis subsp. lactis A6

Background

The physiology and application characteristics of probiotics are closely associated with the growth phase. Bifidobacterium animalis subsp. lactis A6 is a promising probiotic strain isolated from the feces of a healthy centenarian in China. In this study, RNA-seq was carried out to investigate the metabolic mechanism between the exponential and the stationary phase in B. lactis A6.

Results

Differential expression analysis showed that a total of 815 genes were significantly changed in the stationary phase compared to the exponential phase, which consisted of 399 up-regulated and 416 down-regulated genes. The results showed that the transport and metabolism of cellobiose, xylooligosaccharides and raffinose were enhanced at the stationary phase, which expanded carbon source utilizing profile to confront with glucose consumption. Meanwhile, genes involved in cysteine-cystathionine-cycle (CCC) pathway, glutamate dehydrogenase, branched-chain amino acids (BCAAs) biosynthesis, and Clp protease were all up-regulated in the stationary phase, which may enhance the acid tolerance of B. lactis A6 during stationary phase. Acid tolerance assay indicated that the survival rate of stationary phase cells was 51.07% after treatment by pH 3.0 for 2h, which was 730-fold higher than that of 0.07% with log phase cells. In addition, peptidoglycan biosynthesis was significantly repressed, which is comparable with the decreased growth rate during the stationary phase. Remarkably, a putative gene cluster encoding Tad pili was up-regulated by 6.5 to 12.1-fold, which is consistent with the significantly increased adhesion rate to mucin from 2.38% to 4.90% during the transition from the exponential phase to the stationary phase.

Conclusions

This study reported growth phase-associated changes of B. lactis A6 during fermentation, including expanded carbon source utilizing profile, enhanced acid tolerance, and up-regulated Tad pili gene cluster responsible for bacterial adhesion in the stationary phase. These findings provide a novel insight into the growth phase associated characteristics in B. lactis A6 and provide valuable information for further application in the food industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02474-5.

Comparative effects of the single and binary probiotics of Lacticaseibacillus casei Zhang and Bifidobacterium lactis V9 on the growth and metabolomic profiles in yogurts

In the present study, comparative effects of the single and binary probiotics of Lacticaseibacillus casei Zhang (L. casei Zhang) and Bifidobacterium lactis V9 (B. lactis V9) on the growth and metabolomic profiles during milk fermentation and storage has been analyzed using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). The growth of B. lactis V9 can be significantly increased (p < 0.001) by co-cultivation with L. casei Zhang at the end of fermentation and storage 10 days, and valine, leucine and isoleucine biosynthesis may be a major contributor to the growth promotion of B. lactis V9. However, the growth of L. casei Zhang was not affected by co-cultivation with B. lactis V9. There were notable distinctions in volatile and non-volatile metabolomic profiles and pathways between the single and binary probiotics cultures; binary probiotics L. casei Zhang and B. lactis V9 significantly affected the volatile, non-volatile metabolic profiles compared to the single probiotics. The levels of acetic acid, hexanoic acid, butanoic acid and pentanoic acid were significantly higher (p < 0.05) in binary probiotics cultures compared to the single probiotic cultures at the storage 10 days, which indicates that binary probiotics had additive effects on the production of short-chain fatty acids during storage. This work provides a detailed insight into metabolomic profiles and growth that differ between the single and binary probiotics cultures, and it can be helpful to develop probiotic yogurt with high probiotic viability and distinct metabolomic profiles.

Different growth behaviors and metabolomic profiles in yogurts induced by multistrain probiotics of Lactobacillus casei Zhang and Bifidobacterium lactis V9 under different fermentation temperatures

The growth behaviors and metabolomic profiles in yogurts induced by multistrain probiotics of Lactobacillus casei Zhang (LCZ) and Bifidobacterium lactis V9 (V9) at the fermentation termination and 10 d of storage at 4°C under different fermentation temperatures (37°C and 42°C) were compared using metabolomics based on liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The growths of LCZ and V9 were affected by fermentation temperatures; the viable cell density of LCZ was higher at 37°C than that at 42°C; however, V9 was higher at 42°C. Multistrain probiotics had higher contribution to the changes in volatile and nonvolatile metabolomic profiles at 42°C than those at 37°C. At fermentation termination, there were 2 common enriched pathways increased by multistrain probiotics at 37°C and 42°C, which were biosynthesis of peptides and amino- and nucleotide-sugar metabolism. At 10 d of storage, 4 common increased enriched pathways were alanine, aspartate and glutamate metabolism; tyrosine metabolism; valine, leucine, and isoleucine degradation; and valine, leucine, and isoleucine biosynthesis. This work provided a detailed insight into different effects of different multistrain probiotics of LCZ and V9 fermentation temperatures on the growth behaviors and volatile and nonvolatile metabolomic profiles of yogurts.

Differential Analysis of Stress Tolerance and Transcriptome of Probiotic Lacticaseibacillus casei Zhang Produced from Solid-State (SSF-SW) and Liquid-State (LSF-MRS) Fermentations

The property differences between bacteria produced from solid-state and liquid-state fermentations have always been the focus of attention. This study analyzed the stress tolerance and transcriptomic differences of the probiotic Lacticaseibacillus casei Zhang produced from solid-state and liquid-state fermentations under no direct stress. The total biomass of L. casei Zhang generated from liquid-state fermentation with MRS medium (LSF-MRS) was 2.24 times as much as that from solid-state fermentation with soybean meal-wheat bran (SSF-SW) medium. Interestingly, NaCl, H2O2, and ethanol stress tolerances and the survival rate after L. casei Zhang agent preparation from SSF-SW fermentation were significantly higher than those from LSF-MRS fermentation. The global transcriptomic analysis revealed that in L. casei Zhang produced from SSF-SW fermentation, carbohydrate transport, gluconeogenesis, inositol phosphate metabolism were promoted, that pentose phosphate pathway was up-regulated to produce more NADPH, that citrate transport and fermentation was extremely significantly promoted to produce pyruvate and ATP, and that pyruvate metabolism was widely up-regulated to form lactate, acetate, ethanol, and succinate from pyruvate and acetyl-CoA, whereas glycolysis was suppressed, and fatty acid biosynthesis was suppressed. Moreover, in response to adverse stresses, some genes encoding aquaporins (GlpF), superoxide dismutase (SOD), nitroreductase, iron homeostasis-related proteins, trehalose operon repressor TreR, alcohol dehydrogenase (ADH), and TetR/AcrR family transcriptional regulators were up-regulated in L. casei Zhang produced from SSF-SW fermentation. Our findings provide novel insight into the differences in growth performance, carbon and lipid metabolisms, and stress tolerance between L. casei Zhang from solid-state and liquid-state fermentations.

Metabolomic analysis of significant changes in Lactobacillus casei Zhang during culturing to generation 4,000 under conditions of glucose restriction

Lactic acid bacteria are being consumed more frequently as awareness of their health benefits has increased. The industrial production of lactic acid bacteria requires a comprehensive understanding of their survival stress, especially regarding changes in metabolic substances in a glucose-limited environment. In the present study, a metabolomic approach was applied to investigate Lactobacillus casei Zhang using cultures from a common ancestor that were permitted to evolve under conditions with normal or glucose-restricted media for up to 4,000 generations. Metabolomic analyses of intracellular and extracellular differential metabolites under De Man, Rogosa and Sharpe broth (2% vol/vol glucose; Oxoid Ltd., Basingstoke, UK) and glucose-restricted (0.02% vol/vol glucose in De Man, Rogosa and Sharpe broth) conditions were performed at generations 0, 2,000, and 4,000 and revealed 23 different metabolites. Myristic acid, ergothioneine, Lys-Thr, and palmitamide contents exhibited significant reductions between 0 and 4,000 generations, whereas nicotinate, histidine, palmitic acid, l-lysine, urocanate, thymine, and other substances increased. The dynamics of the pathways involved in AA metabolism, including glycine, serine, and threonine metabolism, histidine metabolism, lysine degradation, and arginine and proline metabolism, were also a focus of the present study. There were also changes in several other metabolic pathways, including vitamin B₆, thiamine, nicotinate, and nicotinamide, according to generation time. Additionally, in the present study we screened for key metabolites involved in the glucose-restricted response and provided a theoretical basis for comprehensively revealing the regulatory mechanisms associated with L. casei Zhang glucose restriction at the metabolic level. These findings also provide novel ideas and methods for analyzing the glucose-restricted stress response at the metabolic level.

Characterization of the Adaptive Amoxicillin Resistance of Lactobacillus casei Zhang by Proteomic Analysis

Amoxicillin is one of the most commonly prescribed antibiotics for bacterial infections and gastrointestinal disorders. To investigate the adaptation of Lactobacillus (L.) casei Zhang to amoxicillin stress, an iTRAQ-based comparative proteomic analysis was performed to compare the protein profiles between the parental L. casei Zhang and its amoxicillin-resistant descendent strains. Our results revealed a significant increase in the relative expression of 38 proteins (>2.0-folds, P < 0.05), while the relative expression of 34 proteins significantly decreased (<-2.0-folds, P < 0.05). The amoxicillin-resistant descendent strain exhibited marked alterations in carbohydrate and amino acid metabolism. Moreover, certain components involving in membrane metabolism were activated. The differences in the proteomic profiles between the two strains might explain the enhanced stress resistance of the adapted bacteria.

Adaptation of Lactobacillus casei Zhang to Gentamycin Involves an Alkaline Shock Protein

Lactobacillus (L. casei) Zhang is a koumiss-originated probiotic strain, which was used as a model in a long-term antibiotics-driven evolution experiment to reveal bacterial evolutionary dynamics; and we isolated gentamycin-resistant L. casei Zhang descendents. To decipher the gentamycin resistance mechanism, here we cultivated the parental L. casei Zhang and its descendent cells in an antibiotics-containing environment to compare their global protein expression profiles using the iTRAQ-based proteomic approach. A total of 72 proteins were significantly up-regulated (>2.0-fold, P < 0.05), whilst 32 proteins were significantly down-regulated <−2.0-fold, P < 0.05) in the descendent line. The gentamycin-resistant descendent line showed elevated expression in some carbohydrates, amino acids, and purine metabolic pathways. Several stress-related proteins were also differentially expressed. Among them, one alkaline shock protein, asp23, was up-regulated most in the gentamycin-resistant strain (21.9-fold increase compared with the parental strain). The asp23 gene disruption mutant was significantly more sensitive to gentamycin compared with the wild type, suggesting an important role of this gene in developing the gentamycin-resistant phenotype in L. casei. Our report has described the adaptation of a probiotic strain that has acquired antibiotics resistance through long-term antibiotics exposure at the proteome level, and we revealed a novel mechanism of gentamycin resistance.

Potentially synbiotic fermented beverage with aqueous extracts of quinoa (Chenopodium quinoa Willd) and soy

The aim of this study was to develop a potentially synbiotic beverage fermented with Lactobacillus casei LC-1 based on aqueous extracts of soy and quinoa with added fructooligosaccharides (FOS). Five formulations with differing proportions of soy and quinoa extracts were tested. The viability of the microorganism, the pH, and the acidity of all formulations were monitored until the 28th day of storage at 5 ℃. The chemical composition of the extracts and beverages and the rheological and sensory properties of the final products were analyzed. Although an increase in acidity and a decrease in pH were observed during the 28 days of storage, the viability of the probiotic microorganism was maintained at 108 CFU·mL−1 in all formulated beverages throughout the storage period. An increase in viscosity and consistency in the formulations with higher concentrations of quinoa (F1 and F2) was observed. Formulation F4 (70% soy and 30% quinoa extracts) showed the least hysteresis. Formulations F4 and F5 (100% soy extract) had the best sensory acceptance while F4 resulted in the highest intention to purchase from a group of 80 volunteers. For chemical composition, F3 (50% soy and 50% quinoa extracts) and F4 showed the best results compared to similar fermented beverages. The formulation F4 was considered the best beverage overall.

Proteomic comparison of the probiotic bacterium Lactobacillus casei Zhang cultivated in milk and soy milk

Soy milk is regarded as a substitute for milk and has become popular in varied diets throughout the world. It has been shown that a newly characterized probiotic bacterium (Lactobacillus casei Zhang) actually grows faster in soy milk than in bovine milk. To elucidate the mechanism involved, we carried out a proteomic analysis to characterize bacterial proteins that varied upon growth in soy milk and bovine milk at 3 different growth phases, and compare their expression under these conditions. A total of 104 differentially expressed spots were identified from different phases using a peptide mass fingerprinting assay. Functional analysis revealed that a major part of these identified proteins is associated with transport and metabolism of carbohydrates, nucleotides, and amino acids as well. The results from our proteomic analysis were clarified by real-time quantitative PCR assay, which showed that Lb. casei Zhang loci involved in purine and pyrimidine biosynthesis were transcriptionally enhanced during growth in soy milk at lag phase (pH 6.4), whereas the loci involved in carbohydrate metabolism were upregulated in bovine milk. Particularly, our results showed that l-glutamine might play an important role in the growth of Lb. casei Zhang in soy milk and bovine milk, perhaps by contributing to purine, pyrimidine, and amino sugar metabolism.

Comparative analysis of the gene expression profile of probiotic Lactobacillus casei Zhang with and without fermented milk as a vehicle during transit in a simulated gastrointestinal tract

Studies have found that the survival of probiotics could be strongly enhanced with dairy products as delivery vehicles, but the molecular mechanism by which this might occur has seldom been mentioned. In this study, microarray technology was used to detect the gene expression profile of Lactobacillus casei Zhang with and without fermented milk used as a delivery vehicle during transit in simulated gastrointestinal juice. Numerous genes of L. casei Zhang in strain suspension were upregulated compared to those from L. casei Zhang in fermented milk. These data might indicate that L. casei Zhang is stimulated directly without the protection of fermented milk, and the high-level gene expression observed here may be a stress response at the transcriptional level. A large proportion of genes involved in translation and cell division were downregulated in the bacteria that were in strain suspension during transit in simulated intestinal juice. This may impede protein biosynthesis and cell division and partially explain the lower viability of L. casei Zhang during transit in the gastrointestinal tract without the delivery vehicle.