Effects of buffer salts on the freeze-drying survival rate of Lactobacillus plantarum LIP-1 based on transcriptome and proteome analyses

Proteo-Transcriptomic Analysis Reveals the Mechanisms Underlying Escherichia coli Phenotypic Shifts Under Blue Light

Bacteria can adapt their lifestyles, including microbial growth, metabolism, and biofilm formation, in response to light signaling. However, the molecular pathways through which blue light affects the lifestyle of Escherichia coli (E. coli) remain incomplete and poorly understood. To address this gap, transcriptomic and proteomic approaches were employed to analyze the physiological differences of E. coli under dark and blue light conditions. Our results indicate that, compared to dark conditions, blue light attenuates flagellar assembly, reduces cell motility and communication, and decreases biofilm formation in E. coli. In addition, this study elucidates the signaling pathways involved in the blue light-mediated regulation of E. coli behavior, providing a theoretical framework for understanding how E. coli responds to blue light signaling to modulate biofilm formation for the production of food chemicals.

A Closer Look at the Potential Mechanisms of Action of Protective Agents Used in the Drying of Microorganisms: A Review

Yeast, bacteria and sourdough are widely used in our daily lives, yet their drying and storage remains a significant challenge. A variety of techniques are used to improve the resistance of cells to thermal, dehydration, oxidative and osmotic stresses, which can occur at different stages of the process. The addition of protective agents prior to drying is a commonly used method, but the mechanisms that may lead to a change in viability following the addition of these agents, or more generally, the interaction between a protective agent and the drying process, are not yet fully understood. This review outlines seven main potential mechanisms, as highlighted in the literature, which can lead to internal or external modifications of the cells. The mechanisms in question are change of membrane fluidity, accumulation of compounds for osmoregulation, prior osmotic dehydration, prevention of oxidation, coating or encapsulation, enhancement in thermal resistance and change in drying kinetics. A comprehensive explanation of these mechanisms is provided. This review also highlights the connection between the mechanisms and the influence of the stresses occurring during drying and storage, which depend on the drying technique used and the operating conditions, the strains and the protective agents involved, on the importance of the different protection mechanisms. By gaining a deeper understanding of the mechanisms of action of protective agents, strategies to improve the quality of the microorganisms obtained after drying can be developed. One such strategy would be to combine several agents to achieve a synergistic effect.

Transcriptomic Analyses to Unravel Cronobacter sakazakii Resistance Pathways

The proliferation of antibiotic usage has precipitated the emergence of drug-resistant variants of bacteria, thereby augmenting their capacity to withstand pharmaceutical interventions. Among these variants, Cronobacter sakazakii (C. sakazakii), prevalent in powdered infant formula (PIF), poses a grave threat to the well-being of infants. Presently, global contamination by C. sakazakii is being observed. Consequently, research endeavors have been initiated to explore the strain's drug resistance capabilities, alterations in virulence levels, and resistance mechanisms. The primary objective of this study is to investigate the resistance mechanisms and virulence levels of C. sakazakii induced by five distinct antibiotics, while concurrently conducting transcriptomic analyses. Compared to the susceptible strains prior to induction, the drug-resistant strains exhibited differential gene expression, resulting in modifications in the activity of relevant enzymes and biofilm secretion. Transcriptomic studies have shown that the expression of glutathione S-transferase and other genes were significantly upregulated after induction, leading to a notable enhancement in biofilm formation ability, alongside the existence of antibiotic resistance mechanisms associated with efflux pumps, cationic antimicrobial peptides, and biofilm formation pathways. These alterations significantly influence the strain's resistance profile.

Carbon metabolism of a novel isolate from Lacticaseibacillus rhamnosus Probio-M9 derived through space mutant

AIMS

Carbon source is a necessary nutrient for bacterial strain growth. In industrial production, the cost of using different carbon sources varies greatly. Moreover, the complex environment in space may cause metabolic a series of changes in the strain, and this method has been successfully applied in some basic research. To date, space mutagenesis is still limited number of studies, particularly in carbon metabolism of probiotics.

METHODS AND RESULTS

HG-R7970-41 was isolated from bacterium suspension (Probio-M9) after space flight, which can produce capsular polysaccharide after space mutagenesis. Phenotype Microarray (PM) was used to evaluated the metabolism of HG-R7970-41 in 190 single carbon sources. RNA sequencing and total protein identification of two strains revealed their different carbon metabolism mechanisms. PM results demonstrated the metabolism of 10 carbon sources were different between Probio-M9 and HG-R7970-41. Transcriptomic and proteomic analyses revealed that this change in carbon metabolism of HG-R7970-41 mainly related to changes in phosphorylation and the glycolysis pathway. Based on the metabolic mechanism of different carbon sources and related gene cluster analysis, we found that the final metabolic activities of HG-R7970-41 and Probio-M9 were mainly regulated by PTS-specific membrane embedded permease, carbohydrate kinase and two rate-limiting enzymes (phosphofructokinase and pyruvate kinase) in the glycolysis pathway. The expanded culture test also confirmed that HG-R7970-41 had different metabolic characteristics from original strain.

CONCLUSIONS

These results suggested that space environment could change carbon metabolism of Probio-M9. The new isolate (HG-R7970-41) showed a different carbon metabolism pattern from the original strain mainly by the regulation of two rate-limiting enzymes.

Protective mechanism of milk fat globule membrane proteins on Lactobacillus acidophilus CICC 6074 under acid stress based on proteomic analysis

The prerequisite for lactic acid bacteria to perform their probiotic function is that they could survive the acid-stressed environment of production and application. In this experiment, the protective mechanism of milk fat globule membrane (MFGM) proteins on lactic acid bacteria under acid stress was investigated. Scanning electron microscopy and fluorescence probe were used to analyze the condition of the acid-treated bacteria, which showed that MFGM proteins could enhance the survival ability of Lactobacillus acidophilus CICC 6074 under acid stress by maintaining cell morphology, elevating intracellular pH and H+-ATPase activity. Furthermore, Tandem Mass Tags (TMT) proteomic analysis revealed that MFGM protein could exert protective effects on L. acidophilus CICC 6074 by regulating amino acid metabolism, ATPase activity, peptidoglycan synthesis, gene repair and heritage, etc. The results will provide a new approach for the protection and development of functional lactic acid bacteria.

Optimization of medium composition of Lactobacillus plantarum Y44 using Plackett-Burman and Box-Behnken designs

The biomass of Lactobacillus strains depends on the culture media and culture conditions. The purpose of this study was to optimize the culture medium composition and culture conditions of Lactobacillus plantarum Y44 to improve its biomass. The utilization of different carbon sources and nitrogen sources by L. plantarum Y44 was assessed by single factor experiment to screen out the economical carbon and nitrogen sources for L. plantarum Y44 growth. Through optimization experiments, the optimized culture medium for L. plantarum Y44 growth consists of soybean peptone 44.1 g/L, yeast extract 22.1 g/L, sucrose 35.6 g/L, hydrogen diamine citrate 2 g/L, anhydrous sodium acetate 8.5 g/L, dipotassium hydrogen phosphate 4 g/L, Tween-80 2 mL/L, manganese sulfate 0.25 g/L, and magnesium sulfate 0.58 g/L, and the initial pH 6.7. The concentration of viable bacteria cells of L. plantarum Y44 culturing in the optimized medium at 37 °C for 16 h was up to 3.363 × 1010 CFU/mL, as 6.11 times higher than that in the MRS medium.

Protection Mechanism of Metal Ion Pre-Stress on Lactobacillus acidophilus CICC 6074 under Acid Tolerance

The prerequisite for the probiotic effect of lactic acid bacteria is that they could survive the acid stress environment of production and application. In this experiment, the mechanism for the effect of different metal ion pre-stress on the acid-tolerant survival of Lactobacillus was investigated. Scanning electron microscopy, Fourier infrared spectroscopy, and flow cytometry were used to analyze the condition of bacteria after acid treatment, which revealed that different metal ion pre-stress could improve the survival ability of Lactobacillus acidophilus CICC 6074 under low acid conditions by improving cell morphology, mitigating cell membrane damage, and regulating surface protein expression. Furthermore, Tandem Mass Tags (TMT) proteomic analysis revealed that Mn2+ pre-stress showed relatively more superior protective effects on acid tolerance in L. acidophilus CICC 6074 through activation of DNA replication, RNA synthesis, S-layer protein secretion, H+-ATPase enzyme activity, etc. This study will provide new ideas and a theoretical basis for the development and application of lactic acid bacteria.

The Space Environment Activates Capsular Polysaccharide Production in Lacticaseibacillus rhamnosus Probio-M9 by Mutating the wze (ywqD) Gene

The study of microorganisms in outer space has focused mainly on investigating phenotypic changes in microbial pathogens induced by factors encountered in space. This study aimed to investigate the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Probio-M9 cells were exposed to space in a spaceflight. Interestingly, our results showed that a substantial proportion of space-exposed mutants (35/100) exhibited a ropy phenotype, characterized by their larger colony sizes and an acquired ability to produce capsular polysaccharide (CPS), compared with the original Probio-M9 or the ground control isolates without space exposure. Whole-genome sequencing analyses on both the Illumina and PacBio platforms revealed a skewed distribution of single nucleotide polymorphisms (12/89 [13.5%]) toward the CPS gene cluster, particularly in the wze (ywqD) gene. The wze gene encodes a putative tyrosine-protein kinase that regulates CPS expression through substrate phosphorylation. Transcriptomics analysis of two space-exposed ropy mutants revealed increased expression in the wze gene relative to a ground control isolate. Finally, we showed that the acquired ropy phenotype (CPS-producing ability) and space-induced genomic changes could be stably inherited. Our findings confirmed that the wze gene directly influences the capacity for CPS production in Probio-M9, and space mutagenesis is a potential strategy for inducing stable physiological changes in probiotics. IMPORTANCE This work investigated the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Interestingly, the space-exposed bacteria became capable of producing capsular polysaccharide (CPS). Some probiotic-derived CPSs have nutraceutical potential and bioactive properties. They also enhance the survival of probiotics through the gastrointestinal transit and ultimately strengthen the probiotic effects. Space mutagenesis seems to be a promising strategy for inducing stable changes in probiotics, and the obtained high-CPS-yielding mutants are valuable resources for future 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.

Characterization, High-Density Fermentation, and the Production of a Directed Vat Set Starter of Lactobacilli Used in the Food Industry: A Review

Lactobacilli have been widely concerned for decades. Bacteria of the genus Lactobacillus have been commonly employed in fermented food to improve the appearance, smell, and taste of food or prolong its shelf-life. They comprise 261 species (by March 2020) that are highly diverse at the phenotypic, ecological, and genotypic levels. Some Lactobacilli strains have been documented to be essential probiotics, which are defined as a group of living microorganisms that are beneficial to the health of the host when ingested in sufficiency. However, the characterization, high-density fermentation, and the production of a directed vat set (DVS) starter of Lactobacilli strains used in the food industry have not been systematically reported. This paper mainly focuses on reviewing Lactobacilli as functional starter cultures in the food industry, including different molecular techniques for identification at the species and strain levels, methods for evaluating Lactobacilli properties, enhancing their performance and improving the cell density of Lactobacilli, and the production techniques of DVS starter of Lactobacilli strains. Moreover, this review further discussed the existing problems and future development prospects of Lactobacilli in the food industry. The viability and stability of Lactobacilli in the food industry and gastrointestinal environment are critical challenges at the industrial scale. The new production equipment and technology of DVS starter of Lactobacilli strains will have the potential for large-scale application, for example, developing low-temperature spray drying, freezing granulation drying, and spray freeze-drying.

Antimicrobial activity against Staphylococcus aureus and genome features of Lactiplantibacillus plantarum LR-14 from Sichuan pickles

The persistence of Staphylococcus aureus within biofilm can lead to contamination of medical devices and life-threatening infections. Luckily, lactic acid bacteria (LAB) have an inhibitory effect on the growth of these bacteria. This study aims to select LAB strains from fermented vegetables, and analyze their potential inhibition activities against S. aureus. In total, 45 isolates of LAB were successfully isolated from Sichuan pickles, and the CFS of Lactiplantibacillus plantarum LR-14 exerted the strongest inhibitory effect against S. aureus. Moreover, S. aureus cells in planktonic and biofilm states both wrinkled and damaged when treated with the CFS of L. plantarum LR-14. In addition, whole genome sequencing analysis indicates that L. plantarum LR-14 contains various functional genes, including predicted extracellular polysaccharides (EPS) biosynthesis genes, and genes participating in the synthesis and metabolism of fatty acid, implying that L. plantarum LR-14 has the potential to be used as a probiotic with multiple functions.

Fermentability of Maitake polysaccharides processed by various hydrothermal conditions and fermented with probiotic (Lactobacillus)

Maitake polysaccharides, after hydrothermal processing, were fermented with Lactobacillus acidophilus CCFM202 (L.A.) and Lactobacillus plantarum CCFM6392 (L.P.). The degradation of molecular weight of polysaccharides by hydrothermal processing under acidic conditions was obviously enhanced, which turned part of the water-insoluble-polysaccharides (WIP) into water-soluble-polysaccharides (WSPs). The pH value of water-soluble-polysaccharides (WSPs) and water-insoluble-polysaccharides (WIPs) were intensely dropped (4- 5) after 24 h fermentation. The optical density (O.D.) was increased (1.4- 2.3) due to bacterial growth, and short-chain fatty acids also followed this trend. LA-WSP predominantly produced acetic acid, 3- 4 folds to lactic acid, while LP-WIP groups produced dominant butyric acid (15- 17 folds). Hydrothermal processing induced the growth of L.A. and L.P., where the highest abundance was 2.5 × 10⁴. From the Venn diagram, WSP-1 produced the most elevated metabolites (874). Therefore, experimental results show a significant impact on making WSPs fragments, whereas temperature and pH influence the WSPs degradation, withstand to higher fermentation efficacy.

Functional Characterization and Whole-Genome Analysis of an Aflatoxin-Degrading Rhodococcus pyridinivorans Strain

Simple Summary

The microbiological degradation of AFB₁ has been a promising approach to control AFB₁ contamination. Here, we characterize a Rhodococcus pyridinivorans strain that can efficiently degrade AFB₁. The AFB₁-degrading capacity of this bacterial strain was characterized, and the completed genome was sequenced and analyzed. Further proteomic analyses of this strain identified a total of 723 proteins in an extracellular component that showed the strongest capacity to degrade AFB₁ (degradation rate 83.7%). Multiple potential AFB₁-degrading enzymes, and enzymes that are reported to respond to AFB₁ treatment, have been identified accordingly. These findings provide a genomic, proteomic, and experimental approach for characterizing an efficient AFB₁-degrading bacterial strain with great potential for use in the remediation of AFB₁ contamination.

Abstract

Aflatoxin B₁ (AFB₁) is one of the most toxic, naturally occurring carcinogen compounds and is produced by specific strains of fungi. Crop contamination with AFB₁ can cause huge economic losses and serious health problems. Many studies have examined the microbiological degradation of AFB₁, especially the use of efficient AFB₁-degrading microorganisms, to control AFB₁ contamination. Here, we reported the identification of a new Rhodococcus pyridinivorans strain (4-4) that can efficiently degrade AFB₁ (degradation rate 84.9%). The extracellular component of this strain showed the strongest capacity to degrade AFB₁ (degradation rate 83.7%). The effects of proteinase K, SDS, temperature, pH, incubation time, and AFB₁ concentration on the AFB₁ degradation ability of the extracellular component were investigated. We sequenced the complete genome of this strain, encoding 5246 protein-coding genes and 169 RNA genes on a circular chromosome and two plasmids. Comparative genomic analysis revealed high homology with other Rhodococcus strains with high AFB₁-degradation ability. Further proteomic analyses of this strain identified a total of 723 proteins in the extracellular component, including multiple potential AFB₁-degrading enzymes, along with enzymes that are reported to response to AFB₁ treatment. Overall, the results demonstrate that R. pyridinivorans 4-4 would be an excellent candidate for the biodegradation and detoxification of AFB₁ contamination.

Identification of Two Myrosinases from a Leclercia adecarboxylata Strain and Investigation of Its Tolerance Mechanism to Glucosinolate Hydrolysate

Glucosinolates (GSLs), secondary metabolites synthesized by cruciferous plants, can be hydrolyzed by myrosinase into compounds, such as isothiocyanates (ITCs), with various bioactivities. Thus, myrosinase plays an important role in the utilization of GSLs. We isolated a bacterial strain, which was identified as Leclercia adecarboxylata, from the rhizosphere soil of rape seedlings and identified two myrosinase genes and an ITC hydrolase gene. Both myrosinases are intracellular and have 658 amino acid residues. Via molecular docking and chemical modification assays investigating the active sites of the myrosinases, arginine was found to be essential for their catalytic activity. Transcriptomic analysis of the response to sinigrin revealed significant up-regulation of some genes involved in allyl-ITC detoxification, with metallo-β-lactamase 3836 having the highest fold change. Thus, we discovered two myrosinases from L. adecarboxylata and demonstrated that the mechanism of tolerance of the bacterium to allyl-ITC likely involved metallo-β-lactamase activity.

Effect of oleic acid on the viability of different freeze-dried Lactiplantibacillus plantarum strains

Freeze drying is one of the most convenient ways to preserve microorganisms, but in the freeze-drying process, strains will inevitably suffer varying degrees of damage under different conditions. The deterioration of cell membrane integrity is one of the main forms of damage. The type and ratio of fatty acids in the cell membrane affect its characteristics. Therefore, it is worth investigating whether certain fatty acids can increase freeze-drying resistance. In this study, we found that adding a low concentration of oleic acid to a cryoprotectant could increase survival rate of strains of Lactiplantibacillus plantarum following freeze drying, and the optimal concentration of oleic acid was determined to be 0.001%. When 0.001% oleic acid was added to phosphate-buffered saline, the freeze-drying survival rate of L. plantarum increased by up to 6.63 times. Adding 0.001% oleic acid to sorbitol, the survival rate of L. plantarum increased by as much as 3.65 times. The 0.001% oleic acid-sucrose cryoprotectant resulted in a freeze-drying survival rate of L. plantarum of about 90%, a 2.26-fold improvement compared with sucrose alone. Although the effect of oleic acid depends on the cryoprotectants used and the strain treated, addition of oleic acid showed significant improvement overall. Further experiments showed that adding a low concentration of oleic acid to the cryoprotectants improved the freeze-drying survival rate of L. plantarum by maintaining cell membrane integrity and lactate dehydrogenase activity. Our findings provide a new strategy for safeguarding bacterial viability in commonly used cryoprotectants by the addition of a common food ingredient, which may be extensively applied in the food industry.

Improving the freeze-drying survival rate of Lactobacillus plantarum LIP-1 by increasing biofilm formation based on adjusting the composition of buffer salts in medium

Lactic acid bacteria can improve their resistance to adverse environments through the formation of biofilm. This study found that adding different buffer salts in culture medium had a great impact on the freeze-drying survival rate of the Lactobacillus plantarum LIP-1, which could be linked to biofilm formation. Transcriptome data showed that potassium ions in buffer salt increased the expression of the luxS gene in the LuxS/autoinducer-2 (AI-2) quorum sensing system and increase synthesis of the quorum sensing signal AI-2. The AI-2 signal molecules up-regulated the cysE gene, which helps to promote biofilm formation. By adding a biofilm inhibitor, d-galactose, and performing a real-time quantitative polymerase chain reaction experiment, we found that d-galactose could down-regulated the luxS and cysE genes, reduced biofilm formation, and decreased the freeze-drying survival rate. The results of this study showed that promoting biofilm formation using appropriate buffer salts may lead to better freeze-drying survival rates.