Combined transcriptomic and proteomic analysis of the response to bile stress in a centenarian-originated probiotic Lactobacillus salivarius Ren

Isolation of derivatives from the food-grade probiotic Lactobacillus johnsonii CNCM I-4884 with enhanced anti-Giardia activity

Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of G. intestinalis. Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic Lactobacillus johnsonii CNCM I-4884 inhibits G. intestinalis growth both in vitro and in vivo. This protective effect is largely mediated by bile salt hydrolase (BSH) enzymes, which convert conjugated bile acids (BAs) into free forms that are toxic to the parasite. The objective of this study was to use adaptive evolution to develop stress-resistant derivatives of L. johnsonii CNCM I-4884, with the aim of improving its anti-Giardia activity. Twelve derivatives with enhanced resistance to BAs and reduced autolysis were generated. Among them, derivative M11 exhibited the highest in vitro anti-Giardia effect with enhanced BSH activity. Genomic and proteomic analyses of M11 revealed two SNPs and the upregulation of the global stress response by SigB, which likely contributed to its increased BAs resistance and BSH overproduction. Finally, the anti-Giardia efficacy of M11 was validated in a murine model of giardiasis. In conclusion, our results demonstrate that adaptive evolution is an effective strategy to generate robust food-grade bacteria with improved health benefits.

Evaluation of the in vitro probiotic properties of Ligilactobacillus salivarius JCF5 and its impact on Jersey yogurt quality

BACKGROUND

Jersey milk, known for its high protein content, is an excellent base for yogurt production. Given that Jersey milk is derived from Jersey cows, this study was to isolate probiotics from Jersey cow feces and investigate their potential as alternative starter cultures for fermenting Jersey milk. Our goal was to develop new starter cultures specifically suited for Jersey yogurt production, while also contributing to the diversity of fermentation agents available for dairy products. This study aimed to evaluate the probiotic functions of Ligilactobacillus salivarius isolated from the feces of newborn Jersey calves after colostrum consumption and to investigate its impact as a starter culture on the quality of Jersey yogurt.

RESULTS

A lactic acid bacterial strain was screened through acid and bile salt tolerance tests and simulated gastrointestinal experiments. The strain survived up to 42.8% after 3 h of cultivation at pH 2, and its viable count after 3 h of cultivation in a medium containing 0.3% bile salt was 3 log(CFU mL-1). Additionally, the survival rates after 3 h of treatment with gastric and intestinal juices were 90.67 ± 0.41% and 84.97 ± 1.40%, respectively, indicating good acid and bile salt tolerance. Identification using 16S rDNA showed that the strain was L. salivarius JCF5. This strain improved the texture properties such as viscosity, elasticity and cohesiveness of yogurt when used in combination with commercial starter cultures.

CONCLUSION

Ligilactobacillus salivarius JCF5 is a promising probiotic strain for enhancing the quality of Jersey yogurt. © 2025 Society of Chemical Industry.

Active induction: a promising strategy for enhancing the bioactivity of lactic acid bacteria

Lactic acid bacteria (LAB), as key probiotic, play crucial roles in maintaining human health. However, their survival and functionality in diverse habitats depend on their ability to sense and respond to environmental stresses. Notably, active induction has emerged as a promising strategy for regulating the biological activity of LAB, potentially enhancing their health benefits. Therefore, this review summarizes the beneficial effects of active induction, including acid, bile, oxidation, ethanol, heat, cold, and radiation induction on the functional activities of LAB. In addition, omics methods, in silico analysis, and gene editing technologies have greatly facilitated the profound exploration of the stress regulatory network in LAB, thereby aiding the identification of active components and stress adaptors. Through these advancements, LAB provide health benefits by regulating stress-related genes and proteins, as well as inducing bioactive metabolite production. As a result, they could enhance stress tolerance, cross-protection, intestinal colonization, adhesion properties, and provide antialcohol and liver protection in vitro or in vivo. This study highlights the potential of active induction strategies in enhancing the functional role of LAB in food applications.

Enhancing the application of probiotics in probiotic food products from the perspective of improving stress resistance by regulating cell physiological function: A review

Probiotic foods are foods containing probiotics, including dairy and non-dairy products, that exert significant beneficial impacts on human health. Benefiting from the rapid progress in systems biology, diverse types of probiotics with prominent health-promoting functionalities are unraveled, albeit such functions could be substantially influenced by the stress environments. Here, we conducted a comprehensive review to characterize the state-of-the-art research on probiotic foods and specific probiotics employed in their production. We summarized the detrimental effects of various environmental stresses, including those encountered during industrial fermentation and storage (in vitro), as well as in vivo conditions such as digestion and intestinal colonization, on the biological functions of probiotics. Furthermore, this review outlines the recent advancements in elucidating the mechanisms of stress resistance, which are expected to enhance targeted probiotic applications and optimize their functional properties. Additionally, we summarized various strategies aimed at improving stress tolerance by regulating cell physiological function, specifically adaptive laboratory evolution, preadaptation treatment, exogenous supplementation, and molecular biological manipulation. This review underscores the significance of enhancing our understanding of stress tolerance mechanisms at a systems level and developing efficacious anti-stress strategies to enhance the application of probiotics while maximizing their biological functionalities.

Evaluation of Probiotic Potential and Functional Properties of Lactobacillus Strains Isolated from Dhan, Traditional Algerian Goat Milk Butter

Goat milk butter, locally known as "Dhan", from the Sfisfa region of Algeria, holds significant cultural and economic value. This study investigates the probiotic properties of lactic acid bacteria (LAB) present in Dhan, focusing particularly on Lactobacillus strains. Molecular identification using 16S rRNA revealed a dominance of Levilactobacillus brevis and Lactiplantibacillus plantarum, forming a substantial part of the bacterial profile. Three LAB isolates (DC01-A, DC04, and DC06) were selected from fresh samples, and rigorous analyses were performed to evaluate their probiotic properties. Safety assessments confirmed the absence of gelatinase, DNase, and haemolytic activities in all isolates. The isolates demonstrated high tolerance to bile salts and acidic conditions, along with the ability to survive simulated gastrointestinal digestion. Notably, strain DC06 exhibited exceptional survival at low pH (1.5) and high bile salt concentrations (0.15-0.3%). All isolates showed substantial growth in MRS medium with 2% phenol, although growth was significantly decreased at 5% phenol. Furthermore, our strains exhibited high adhesion rates to various solvents, demonstrating their potential for strong interaction with cell membranes. Specifically, adhesion to chloroform was observed at 98.26% for DC01-A, 99.30% for DC04, and 99.20% for DC06. With xylene, the adhesion rates were 75.94% for DC01-A, 61.13% for DC04, and 76.52% for DC06. The LAB strains demonstrated impressive growth in ethanol concentrations up to 12%, but their tolerance did not exceed this concentration. They also exhibited robust growth across temperatures from 10 °C to 37 °C, with strains DC04 and DC06 able to proliferate at 45 °C, though none survived at 50 °C. Additionally, the isolates showed significant resistance to oxidative stress induced by hydrogen peroxide (H2O2) and displayed medium to high autolytic activity, with rates of 50.86%, 37.53%, and 33.42% for DC01-A, DC04, and DC06, respectively. The cell-free supernatant derived from strain DC04 exhibited significant antimicrobial activity against the tested pathogens, while strain DC06 demonstrated moderate antioxidant activity with the highest DPPH scavenging rate at 68.56%, compared to the probiotic reference strain LGG at 61.28%. These collective findings not only suggest the probiotic viability of LAB strains found in Dhan but also highlight the importance of traditional food practises in contributing to health and nutrition. Consequently, this study supports the potential of traditional Dhan butter as a functional food and encourages further exploration of its health benefits.

Genomic and transcriptomic analysis of Ligilactobacillus salivarius IBB3154-in search of new promoters for vaccine construction

IMPORTANCE

The genome of the strain Ligilactobacillus salivarius IBB3154 was sequenced, and transcriptome analysis was carried out at two different temperatures, allowing the determination of gene expression levels in response to environmental changes (temperature). Genes with higher expression at 42°C were identified. The use of a reporter gene (β- glucuronidase) did not confirm the transcriptomic results; it was found that the promoters of the genes sasA1 and sasA2 were active in the presence of bile salts. This opens up new opportunities for the overexpression of genes of other bacterial species in Ligilactobacillus cells in the intestinal environment.

Key Stress Response Mechanisms of Probiotics During Their Journey Through the Digestive System: A Review

The survival of probiotic microorganisms during their exposure to harsh environments plays a critical role in the fulfillment of their functional properties. In particular, transit through the human gastrointestinal tract (GIT) is considered one of the most challenging habitats that probiotics must endure, because of the particularly stressful conditions (e.g., oxygen level, pH variations, nutrient limitations, high osmolarity, oxidation, peristalsis) prevailing in the different sections of the GIT, which in turn can affect the growth, viability, physiological status, and functionality of microbial cells. Consequently, probiotics have developed a series of strategies, called "mechanisms of stress response," to protect themselves from these adverse conditions. Such mechanisms may include but are not limited to the induction of new metabolic pathways, formation/production of particular metabolites, and changes of transcription rates. It should be highlighted that some of such mechanisms can be conserved across several different strains or can be unique for specific genera. Hence, this review attempts to review the state-of-the-art knowledge of mechanisms of stress response displayed by potential probiotic strains during their transit through the GIT. In addition, evidence whether stress responses can compromise the biosafety of such strains is also discussed.

Understanding the Probiotic Bacterial Responses Against Various Stresses in Food Matrix and Gastrointestinal Tract: A Review

Probiotic bacteria are known to have ability to tolerate inhospitable conditions experienced during food preparation, food storage, and gastrointestinal tract of consumer. As probiotics are living cells, they are adversely affected by the harsh environment of the carrier matrix as well as low pH, bile salts, oxidative stress, osmotic pressure, and commensal microflora of the host. To overcome the unfavorable environments, many probiotics switch on the cell-mediated protection mechanisms, which helps them to survive, acclimatize and remain operational in the harsh circumstances. In this review, we provide comprehensive understanding on the different stresses experienced by the probiotic when added in carrier food as well as during human gastrointestinal tract transit. Under such situation how these health beneficial bacteria protect themselves by activation of several defense systems and get adapted to the lethal environments.

Increased heat tolerance and transcriptome analysis of Salmonella enterica Enteritidis PT 30 heat-shocked at 42 ℃

In this study, we compared the heat tolerance parameter (D_65℃) values of Salmonella enterica serovar Enteritidis PT 30 (S. Enteritidis ) heat adapted at different degrees (at 42 ℃ for 20-180 min) and cultivated using two methods. The treated group with the highest D_65℃ value (LP-42 ℃-60 min) and the untreated groups (Control-TSB and Control-TSA) were subjected to transcriptome analysis. Heat-adaptation increased the D_65℃ values of S. Enteritidis by 24.5-60.8%. The D_65℃ values of the LP-42 ℃-60 min group (1.85 ± 0.13 min, 7.7% higher) was comparable to that of the Control-TSA. A total of 483 up- and 443 downregulated genes of S. enteritidis were identified in the LP-42 ℃-60 min group (log₂fold change > 1, adjusted p-value < 0.05). Among these genes, 5 co-expressed and 15 differentially expressed genes in the LP-42 ℃-60 min and Control-TSA grops possibly contributed to the high D_65℃ values of S. Enteritidis . The Rpo regulon was involved in the heat adaptation of S. Enteritidis , as evidenced by the significant upregulation of rpoS, rpoN, and rpoE. KEGG enrichment pathways, such as biosynthesis of secondary metabolites, tricarboxylic acid, and ribosomes were identified and mapped to reveal the molecular mechanisms of S. enteritidis during heat adaptation. This study quantified the enhanced heat tolerance of S. Enteritidis heat adapted at different degrees of heat-adaptation. The results of this study may serve as a basis for elucidating the molecular mechanisms underlying the enhanced heat tolerance at the transcriptome level.

Influence of nitrogen sources on the tolerance of Lacticaseibacillus rhamnosus to heat stress and oxidative stress

It has been found that 32 genes related to nitrogen source metabolism in Lacticaseibacillus rhamnosus are downregulated under both heat stress and oxidative stress. In this study, the influence of different nitrogen sources within the growth medium on the tolerance of L. rhamnosus to heat stress and oxidative stress was investigated. Tryptone-free MRS was found to enhance the tolerance of L. rhamnosus hsryfm 1301 to heat stress and oxidative stress during the whole growth period, and this result was universal for all L. rhamnosus species analyzed. The strongest strengthening effect occurred when the OD₆₀₀ value reached 2.0, at which the survival rates under heat stress and oxidative stress increased 130-fold and 40-fold, respectively. After supplementing phenylalanine, isoleucine, glutamate, valine, histidine, or tryptophan into the tryptone-free MRS, the tolerance of L. rhamnosus to heat stress and oxidative stress exhibited a sharp drop. The spray drying survival rate of L. rhamnosus hsryfm 1301 cultured in the tryptone-free MRS rose to 75% (from 30%), and the spray dried powder also performed better in the experimentally simulated gastrointestinal digestion. These results showed that decreasing the intake of amino acids is an important mechanism for L. rhamnosus to tolerate heat stress and oxidative stress. When L. rhamnosus is cultured for spray drying, the concentration of the nitrogen source's components should be an important consideration.

Unraveling the mechanism of raffinose utilization in Ligilactobacillus salivarius Ren by transcriptomic analysis

In the gastrointestinal tract, some dietary carbohydrates, such as xylose, raffinose and arabinose, are able to stimulate the growth of Lactobacillus and Bifidobacterium. In this study, the growth rate of Ligilactobacillus salivarius Ren in raffinose was 0.91 ± 0.03 h-1, which was higher than that in glucose (0.83 ± 0.01 h-1). However, limited information is available on specific transporters and glycoside hydrolases responsible for raffinose uptake and catabolism in L. salivarius. Transcriptomic analysis revealed the differential expression of 236 genes (∣log2FoldChange∣ > 0.8) in response to raffinose, which were mainly associated with raffinose transport, raffinose hydrolysis, galactose metabolism and pyruvate metabolism. Notably, gene rafP encoding lactose/raffinose permease was 101.86-fold up-regulated. Two α-galactosidase gene galA1 and galA2 were 117.82-fold and 2.66-fold up-regulated, respectively. To further investigate the role of these genes in raffinose utilization, insertional inactivation was performed using the pORI28-pTRK669 system. The growth assay of these mutants in modified MRS containing 2% (w/v) raffinose indicated that RafP played an important role in raffinose transport and GalA1 was the primary enzyme involved in raffinose hydrolysis. To our knowledge, this is the first report on the molecular mechanism of raffinose utilization in L. salivarius.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03280-6.

Integrated transcriptomic and proteomic analysis reveals the response mechanisms of Alicyclobacillus acidoterrestris to heat stress

Alicyclobacillus acidoterrestris can survive pasteurization and is implicated in pasteurized fruit juice spoilage. However, the mechanisms underlying heat responses remain largely unknown. Herein, gene transcription changes of A. acidoterrestris under heat stress were detected by transcriptome, and an integrated analysis with proteomic and physiological data was conducted. A total of 911 differentially expressed genes (DEGs) was observed. The majority of DEGs and differentially expressed proteins (DEPs) were exclusively regulated at the mRNA and protein level, respectively, whereas only 59 genes were regulated at both levels and had the same change trends. Comparative analysis of the functions of the specifically or commonly regulated DEGs and DEPs revealed that the heat resistance of A. acidoterrestris was primarily based on modulating peptidoglycan and fatty acid composition to maintain cell envelope integrity. Low energy consumption strategies were established with attenuated glycolysis, decreased ribosome de novo synthesis, and activated ribosome hibernation. Terminal oxidases, cytochrome bd and aa₃, in aerobic respiratory chain were upregulated. Meanwhile, the MarR family transcriptional regulator was upregulated, reactive oxygen species (ROS) was discovered, and the concentration of superoxide dismutase (SOD) increased, indicating that the accompanied oxidative stress was induced by high temperature. Additionally, DNA and protein damage repair systems were activated. This study provided a global perspective on the response mechanisms of A. acidoterrestris to heat stress, with implications for better detection and control of its contamination in fruit juice.

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes.