Investigation of potential markers of acid resistance in Lactobacillus plantarum by comparative proteomics

Using metabolomics to understand stress responses in Lactic Acid Bacteria and their applications in the food industry

BACKGROUND

Lactic Acid Bacteria (LAB) are commonly used as starter cultures, probiotics, to produce lactic acid and other useful compounds, and even as natural preservatives. For use in any food product however, LAB need to survive the various stresses they encounter in the environment and during processing. Understanding these mechanisms may enable direction of LAB biochemistry with potential beneficial impact for the food industry.

AIM OF REVIEW

To give an overview of the use of LAB in the food industry and then generate a deeper biochemical understanding of LAB stress response mechanisms via metabolomics, and methods of screening for robust strains of LAB.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Uses of LAB in food products were assessed and factors which contribute to survival and tolerance in LAB investigated. Changes in the metabolic profiles of LAB exposed to stress were found to be associated with carbohydrates, amino acids and fatty acid levels and these changes were proposed to be a result of the bacteria trying to maintain cellular homeostasis in response to external conditions and minimise cellular damage from reactive oxygen species. This correlates with morphological analysis which shows that LAB can undergo cell elongation and shortening, as well as thinning and thickening of cell membranes, when exposed to stress. It is proposed that these innate strategies can be utilised to minimise negative effects caused by stress through selection of intrinsically robust strains, genetic modification and/or prior exposure to sublethal stress. This work demonstrates the utility of metabolomics to the food industry.

Evaluation of cholesterol transformation abilities and probiotic properties of Bacteroides dorei YGMCC0564

Hypercholesterolemia, a risk factor for cardiovascular disease (CVD), often requires therapeutic agents with varying degrees of side effects. This has created a need for safe and natural alternatives such as medications or functional foods that can improve lipid metabolism and reduce cholesterol levels. In recent years, Next-generation probiotics (NGPs) have recently emerged as a potential solution, offering distinct mechanisms compared to traditional probiotics. Among the NGPs, Bacteroides, a dominant bacterial genus in the human gut, has gained significant attention due to its prevalence, ability to break down plant polysaccharides, and production of short-chain fatty acids (SCFAs). Recent evidence has demonstrated that Bacteroides effectively reduces cholesterol levels, prevents obesity, and lowers the risk of CVD. However, research on Bacteroides is currently limited to a few species, leaving rooms for exploration of the beneficial functions of different species in this genus. In this study, we isolated 66 Bacteroides strains, including 9 distinct species, from healthy adults' fecal samples. By comparing their ability to assimilate cholesterol, we found that the transformation ability was not specific to any particular species. Notably, Bacteroides dorei YGMCC0564 revealed superior cholesterol-lowering capabilities and bile salt hydrolase (BSH) activity in vitro, surpassing that of Lactobacillus GG (LGG). YGMCC0564 exhibited favorable probiotic characteristics, including high survival rate in vitro simulation of gastrointestinal digestion, excellent adhesion ability, susceptibility to antibiotics, absence of hemolysis or virulence genes, and substantial production of SCFAs. The strain also demonstrated remarkable bile salt deconjugation activities and upregulation of the BT_416 gene associated with cholesterol, providing insights into a possible molecular mechanism underlying its cholesterol-reducing activity. These findings establish YGMCC0564 as a promising NPG candidate for improving cardiovascular health.

The regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7

BACKGROUND

Oro-gastrointestinal stress in the digestive tract is the main stress to which orally administered probiotics are exposed. The regulation of oro-gastrointestinal transit (OGT) stress on the adhesion and survival of probiotics under continuous exposure to simulated salivary-gastric juice-intestinal juice was researched in this study.

RESULTS

Lactobacillus plantarum S7 had a higher survival rate after exposure to simulated OGT1 (containing 0.15% bile salt) stress and OGT2 (containing 0.30% bile salt) stress. The adhesion ability of L. plantarum S7 was significantly increased by OGT1 stress (P < 0.05) but was not changed significantly by OGT2 stress (P > 0.05), and this trend was also observed in terms of the thickness of the surface material of L. plantarum S7 cells. The expression of surface proteins of L. plantarum S7, such as the 30 S ribosomal proteins, mucus-binding protein and S-layer protein, was significantly downregulated by OGT stress (P < 0.05); meanwhile, the expression of moonlight proteins, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycorate kinase (PGK), beta-phosphoglucomutase (PGM1), GroEL and glucose-6-phosphate isomerase (PGI), was significantly upregulated (P < 0.05). However, the upregulation of GAPDH, PGK, PGM1 and PGI mediated by OGT1 stress was greater than those mediated by OGT2 stress. The quorum sensing pathway of L. plantarum S7 was changed significantly by OGT stress compared with no OGT stress cells (P < 0.05), and the expression of Luxs in the pathway was significantly upregulated by OGT1 stress (P < 0.05). The ABC transportation pathway was significantly altered by OGT1 stress (P < 0.05), of which the expression of the peptide ABC transporter substrate-binding protein and energy-coupling factor transporter ATP-binding protein EcfA was significantly upregulated by OGT stress (P < 0.05). The glycolide metabolism pathway was significantly altered by OGT1 stress compared with that in response to OGT2 stress (P < 0.05).

CONCLUSION

L. plantarum S7 had a strong ability to resist OGT stress, which was regulated by the proteins and pathways related to OGT stress. The adhesion ability of L. plantarum S7 was enhanced after continuous exposure to OGT1 stress, making it a potential probiotic with a promising future for application.

Whole genome sequence analysis and in-vitro probiotic characterization of Bacillus velezensis FCW2 MCC4686 from spontaneously fermented coconut water

In this study, the probiotic potential of B. velezensis FCW2, isolated from naturally fermented coconut water, was investigated by in vitro and genomic characterization. Our findings highlight key features of the bacterium which includes, antibacterial activity, high adhesive potential, aggregation capacity, production of nutrient secondary metabolites. In vivo safety assessment revealed no adverse effects on zebrafish. WGS data of B. velezensis FCW2 revealed a complete circular genome of 4,147,426 nucleotides and a GC content of 45.87%. We have identified 4059 coding sequence (CDS) genes that encode proteins involved in stress resistance, adhesion and micronutrient production. The genes responsible for producing secondary metabolites, exopolysaccharides, and other beneficial nutrients were identified. The KEGG and COG databases revealed that genes mainly involved amino acid metabolism, carbohydrate utilization, vitamin and cofactor metabolism, and biological adhesion. These findings suggest that B. velezensis FCW2 could be a putative probiotic in the development of fermented foods.

Genomic and metabolic properties of Staphylococcus gallinarum FCW1 MCC4687 isolated from naturally fermented coconut water towards GRAS assessment

Staphylococcus gallinarum FCW1 was isolated from naturally fermented coconut-water and identified by biochemical and molecular methods. Probiotic characterization and safety assessment were conducted through a series of in vitro tests. A high survival rate was observed when the strain was tested for resistance to bile, lysozyme, simulated gastric and intestinal fluid, phenol, and different temperature and salt concentrations. The strain showed antagonism against some pathogens, was susceptible to all antibiotics tested except penicillin, and showed no hemolytic and DNase activity. Hydrophobicity, autoaggregation, biofilm formation, and antioxidation tests indicated that the strain possessed a high adhesive and antioxidant ability. Enzymatic activity was used to evaluate the metabolic capacities of the strain. In-vivo experiment on zebrafish was performed to check its safety status. The whole-genome sequencing indicated that the genome contained 2,880,305 bp with a GC content of 33.23%. The genome annotation confirmed the presence of probiotic-associated genes and genes for oxalate degradation, sulfate reduction, acetate metabolism, and ammonium transport in the FCW1 strain, adding to the theory that this strain may be helpful in treating kidney stones. This study revealed that the strain FCW1 might be an excellent potential probiotic in developing fermented coconut beverages and treating and preventing kidney stone disease.

Assessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis

Lacticaseibacillus rhamnosus is a generalist that can adapt to different ecological niches, serving as a valuable source of probiotics. The genome of L. rhamnosus X253 contains one chromosome and no plasmids, with a size of 2.99 Mb. Both single-copy orthologous gene-based phylogenetic analysis and average nucleotide identity indicated that dairy-derived L. rhamnosus X253 was most closely related to the human-intestine-derived strain L. rhamnosus LOCK908, rather than other dairy strains. The adaptation of L. rhamnosus X253 and the human-intestine-derived strain L. rhamnosus GG to different ecological niches was explained by structural variation analysis and COG annotation. Hemolytic assays, API ZYM assays, and antimicrobial susceptibility tests were performed to validate risk-related sequences such as virulence factors, toxin-encoding genes, and antibiotic-resistance genes in the genomes of L. rhamnosus X253 and GG. The results showed that L. rhamnosus GG was able to use L-fucose, had a higher tolerance to bile salt, and adhered better to CaCo-2 cells. In contrast, L. rhamnosus X253 was capable of utilizing D-lactose, withstood larger quantities of hydrogen peroxide, and possessed excellent antioxidant properties. This study confirmed the safety and probiotic properties of L. rhamnosus X253 via complete genome and phenotype analysis, suggesting its potential as a probiotic.

Whole genome sequence of Lactiplantibacillus plantarum MC5 and comparative analysis of eps gene clusters

Introduction

Probiotic Lactiplantibacillus plantarum MC5 produces large amounts of exopolysaccharides (EPS), and its use as a compound fermentor can greatly improve the quality of fermented milk.

Methods

To gain insight into the genomic characteristics of probiotic MC5 and reveal the relationship between its EPS biosynthetic phenotype and genotype, we analyzed the carbohydrate metabolic capacity, nucleotide sugar formation pathways, and EPS biosynthesis-related gene clusters of strain MC5 based on its whole genome sequence. Finally, we performed validation tests on the monosaccharides and disaccharides that strain MC5 may metabolize.

Results

Genomic analysis showed that MC5 has seven nucleotide sugar biosynthesis pathways and 11 sugar-specific phosphate transport systems, suggesting that the strain can metabolize mannose, fructose, sucrose, cellobiose, glucose, lactose, and galactose. Validation results showed that strain MC5 can metabolize these seven sugars and produce significant amounts of EPS (> 250 mg/L). In addition, strain MC5 possesses two typical eps biosynthesis gene clusters, which include the conserved genes epsABCDE, wzx, and wzy, six key genes for polysaccharide biosynthesis, and one MC5-specific epsG gene.

Discussion

These insights into the mechanism of EPS-MC5 biosynthesis can be used to promote the production of EPS through genetic engineering.

Functional genomics of the lactic acid bacterium Limosilactobacillus fermentum LAB-1: metabolic, probiotic and biotechnological perspectives

A genome-based systematic analysis was conducted to characterize the metabolic, probiotic, fitness, and safety properties of Limosilactobacillus fermentum LAB-1, a lactic acid bacterium demonstrating strong antimicrobial effects against clinical pathogens. Gene functional characterization revealed a large number of genes for carbohydrate metabolism and a heterofermentative system for carbon dissimilation. Genes for intact pyruvate oxidation, pentose phosphate, and PRPP biosynthetic pathways were identified. Substantial carbohydrate-active enzymes and transporters were also predicted. Metabolic reconstruction revealed complete sets of enzymes for arginine, lysine, methionine, threonine, proline, and ornithine biosynthesis. The bacterium harbors a diverse range of peptidases, and a large variety of peptide and amino acid uptake systems. It encodes restriction-modification and CRISPR-Cas systems for protection against phage infections and carries a wide spectrum of stress proteins for adaptation in the gut and industrial conditions. Genes related to the biosynthesis of B-group and K vitamins were identified allowing its application for novel bio-enriched food production. Other beneficial traits of probiotic and industrial importance such as production of flavor compounds, exopolysaccharide, acetoin, and butanediol were identified. Three antimicrobial peptides were predicted which showed >98% sequence-identity to experimentally validated bacteriocins. Negative traits such as transmissible antibiotic resistance, pathogenicity or virulence appeared to be absent suggesting the strain to be considered safe. The genome analysis will allow precisely targeted laboratory research and full exploitation of the probiotic potentials towards functional-food, biotechnology and health-related applications.

Probiotic bacteria from 10 different traditional Iranian cheeses: Isolation, characterization, and investigation of probiotic potential

In this study, 10 different traditional Iranian cheeses, which are still consumed by people in rural areas of Iran, were examined to isolate new strains of probiotic bacteria. Isolated bacteria were identified by 16s rRNA gene amplification and subjected to series of in vitro tests to find out their probiotic potential. A total of 2345 colonies were collected and 465 of them were confirmed as lactic acid bacteria (LAB), of which Lactiplantibacillus plantarum, Lactobacillus bulgaricus, and Lacticaseibacillus casei were the top three isolated bacteria. Among the different species of LAB isolated in this study, Lactip. plantarum was the most isolated species, and seven isolates had the significant criteria for being a probiotic strain than other isolates indicating the most adaptable properties of this species. Lactiplantibacillus plantarum was the most resistant bacteria in the bile resistance test and was also the most durable bacteria in gastrointestinal conditions, for example, acidic environment (pH = 2.5) and trypsin. In contrast, Lacticaseibacillus casei was the most susceptible bacterial strain. Lactobacillus rhamnosus showed the most antibacterial effect against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. This study showed that probiotic strains isolated from local cheeses could be considered as suitable biopreservatives and used as specific starter cultures for the production of functional cheeses.

Incidence of virulence determinants and antibiotic resistance in lactic acid bacteria isolated from food products

Background: Lactic acid bacteria (LAB) confer beneficial health effects in humans. However, the safety of these bacteria and their potential to spread resistance in the environment must be evaluated. Materials & methods: Fifty-three LAB were isolated from different food samples and assessed for the prevalence of virulence determinants and antibiotic resistance profile. Results: Multiple resistance was reported for Lactobacillus brevis MIM04, having revealed phenotypic resistance to vancomycin (MIC >128 μg/ml), ampicillin, cefotaxime, oxacillin and gentamicin. Virulence traits (cylA, gelE, esp and agg) were detected using specific primers. Enterococcus faecium CHE32, Lactobacillus plantarum CHE37 and E. faecium MLK68 lack virulence genes, possess antimicrobial activity and survive in low pH and bile salt conditions. Conclusion: Isolated LAB revealed probiotic properties.

Lactiplantibacillus plantarum-Nomad and Ideal Probiotic

Probiotics are increasingly recognized as capable of positively modulating several aspects of human health. There are numerous attributes that make an ideal probiotic. Lactiplantibacillus plantarum (Lp) exhibits an ecological and metabolic flexibility that allows it to thrive in a variety of environments. The present review will highlight the genetic and functional characteristics of Lp that make it an ideal probiotic and summarizes the current knowledge about its potential application as a prophylactic or therapeutic intervention.

Response of Lactiplantibacillus plantarum NMGL2 to Combinational Cold and Acid Stresses during Storage of Fermented Milk as Analyzed by Data-Independent Acquisition Proteomics

To understand the mechanism of tolerance of lactic acid bacteria (LAB) during cold storage of fermented milk, 31 LAB strains were isolated from traditional fermented products, and Lactiplantibacillus plantarum NMGL2 was identified with good tolerance to both cold and acid stresses. Data-independent acquisition proteomics method was employed to analyze the response of Lpb. plantarum NMGL2 to the combinational cold and acid stresses during storage of the fermented milk made with the strain at 4 °C for 21 days. Among the differentially expressed proteins identified, 20 low temperature-resistant proteins and 10 acid-resistant proteins were found. Protein interaction analysis showed that the low temperature-resistant proteins associated with acid-resistant proteins were Hsp1, Hsp2, Hsp3, CspC, MurA1, MurC, MurD, MurE1, and MurI, while the acid-resistant proteins associated with low temperature-resistant proteins were DnaA, DnaK, GrpE, GroEL, and RbfA. The overall metabolic pathways of Lpb. plantarum NMGL2 in response to the stresses were determined including increased cell wall component biosynthesis, extracellular production of abundant glycolipids and glycoproteins, increased expression of F₁F_o-ATPase, activation of glutamate deacidification system, enhanced expression of proteins and chaperones associated with cell repairing caused by the acidic and cold environment into the correct proteins. The present study for the first time provides further understanding of the proteomic pattern and metabolic changes of Lpb. plantarum in response to combinational cold and acid stresses in fermented milk, which facilitates potential application of Lpb. plantarum in fermented foods with enhanced survivability.

Updates on understanding of probiotic lactic acid bacteria responses to environmental stresses and highlights on proteomic analyses

Probiotics are defined as live microorganisms that improve the health of the host when administered in adequate quantities. Nonetheless, probiotics encounter extreme environmental conditions during food processing or along the gastrointestinal tract. This review discusses different environmental stresses that affect probiotics during food preparation, storage, and along the alimentary canal, including high temperature, low temperature, low and alkaline pH, oxidative stress, high hydrostatic pressure, osmotic pressure, and starvation. The understanding of how probiotics deal with environmental stress and thrive provides useful information to guide the selection of the strains with enhanced performance in specific situations, in food processing or during gastrointestinal transit. In most cases, multiple biological functions are affected upon exposure of the cell to environmental stress. Sensing of sublethal environmental stress can allow for adaptation processes to occur, which can include alterations in the expression of specific proteins.

Probiotic Validation of a Non-native, Thermostable, Phytase-Producing Bacterium: Streptococcus thermophilus

Phytate-linked nutritional deficiency disorders have plagued poultry for centuries. The application of exogenous phytases in poultry feed has served as a solution to this problem. However, they are linked to certain limitations which include thermal instability during prolonged feed processing. Therefore, in this study, Streptococcus thermophilus 2412 based phytase stability was assessed at higher temperatures up to 90 °C. This was followed by probiotic validation of the same bacterium in an in vitro intestinal model. Bacterial phytase showed thermostability up to 70 °C with a recorded activity of 9.90 U. The bacterium was viable in the intestinal lumen as indicated by the cell count of 6.10 log(CFU/mL) after 16 h. It also showed acid tolerance with a stable cell count of 5.01 log(CFU/mL) after 16 h of incubation at pH 2. The bacterium displayed bile tolerance yielding a cell count of 6.36 log(CFU/mL) in the presence of 0.3% bile. Bacterial susceptibility was observed toward all tested antibiotics with a maximum zone of 20 mm against clindamycin. The maximum antagonistic activity was observed against Staphylococcus aureus, Serratia marcescens, and Escherichia coli with inhibition zone diameters up to 10 mm. The above characteristics prove that S. thermophilus 2412 can be used as an effective phytase-producing poultry probiotic.

Whole genome sequence analysis and in vitro probiotic characteristics of a Lactobacillus strain Lactobacillus paracasei ZFM54

AIM

The aim was to identify a Lactobacillus strain with potential probiotic characteristics by whole-genome sequence analysis and in vitro experimental studies.

METHODS AND RESULTS

The whole-genome sequencing was carried out using PacBio RSII sequencing method and Illumina's paired-end sequencing technology. Gene prediction and annotation were achieved using GlimmerVersion 3.02 and NCBI prokaryotic Genome Annotation Pipeline. Identification was done by biochemical tests and 16S rRNA sequence analysis. mega 6 software was used to build phylogenetic tree. Antagonism against pathogen was determined by agar well diffusion method. Resistance and stability to bile, simulated gastric acid, different salt concentration and thermostability were investigated. Hydrophobicity assay, aggregation assay and anti-oxidation assay were performed to check further probiotic traits. Finally antibiotic susceptibility and acute oral toxicity of the strain in mice were investigated to check its safety status. The strain showed >99% similarity to Lactobacillus paracasei which was further confirmed by biochemical tests. It significantly inhibited pathogens in agar well diffusion assay. It showed tolerance to simulated gastric acid (pH 3), 0·3% bile salt and 10% NaCl. Significant hydrophobic, aggregation and anti-oxidizing activities were observed. No resistance to antibiotics tested was observed and no adverse effects during acute oral toxicity in mice were detected.

CONCLUSIONS

Lactobacillus paracasei ZFM 54, a new and safe Lactobacillus strain was identified with numerous probiotic-associated genes and characteristics confirmed by experimental studies.

SIGNIFICANCE AND IMPACT OF THE STUDY

A new probiotic strain has been identified which is highly stable, safe and suitable to be used in health and food industries.

Simulated gastrointestinal conditions increase adhesion ability of Lactobacillus paracasei strains isolated from kefir to Caco-2 cells and mucin

Gastrointestinal conditions along the digestive tract are the main stress to which probiotics administrated orally are exposed because they must survive these adverse conditions and arrive alive to the intestine. Adhesion to epithelium has been considered one of the key criteria for the characterization of probiotics because it extends their residence time in the intestine and as a consequence, can influence the health of the host by modifying the local microbiota or modulating the immune response. Nevertheless, there are very few reports on the adhesion properties to epithelium and mucus of microorganisms after passing through the gastrointestinal tract. In the present work, we evaluate the adhesion ability in vitro of L. paracasei strains isolated from kefir grains after acid and bile stress and we observed that they survive simulated gastrointestinal passage in different levels depending on the strain. L. paracasei CIDCA 8339, 83120 and 83123 were more resistant than L. paracasei CIDCA 83121 and 83124, with a higher susceptibility to simulated gastric conditions. Proteomic analysis of L. paracasei subjected to acid and bile stress revealed that most of the proteins that were positively regulated correspond to the glycolytic pathway enzymes, with an overall effect of stress on the activation of the energy source. Moreover, it is worth to remark that after gastrointestinal passage, L. paracasei strains have increased their ability to adhere to mucin and epithelial cells in vitro being this factor of relevance for maintenance of the strain in the gut environment to exert its probiotic action.

Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872

The article provides an overview of the genomic features of Lactobacillus fermentum strain 3872. The genomic sequence reported here is one of three L. fermentum genome sequences completed to date. Comparative genomic analysis allowed the identification of genes that may be contributing to enhanced probiotic properties of this strain. In particular, the genes encoding putative mucus binding proteins, collagen-binding proteins, class III bacteriocin, as well as exopolysaccharide and prophage-related genes were identified. Genes related to bacterial aggregation and survival under harsh conditions in the gastrointestinal tract, along with the genes required for vitamin production were also found.

Functional proteomics within the genus Lactobacillus

Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains.

Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

Physiological and proteomic analysis of Lactobacillus casei in response to acid adaptation

The aim of this study was to investigate the acid tolerance response (ATR) in Lactobacillus casei by a combined physiological and proteomic analysis. To optimize the ATR induction, cells were acid adapted for 1 h at different pHs, and then acid challenged at pH 3.5. The result showed that acid adaptation improved acid tolerance, and the highest survival was observed in cells adapted at pH 4.5 for 1 h. Analysis of the physiological data showed that the acid-adapted cells exhibited higher intracellular pH (pHi), intracellular NH4+ content, and lower inner permeability compared with the cells without adaptation. Proteomic analysis was performed upon acid adaptation to different pHs (pH 6.5 vs. pH 4.5) using two-dimensional electrophoresis. A total of 24 proteins that exhibited at least 1.5-fold differential expression were identified. Four proteins (Pgk, LacD, Hpr, and Galm) involved in carbohydrate catabolism and five classic stress response proteins (GroEL, GrpE, Dnak, Hspl, and LCAZH_2811) were up-regulated after acid adaptation at pH 4.5 for 1 h. Validation of the proteomic data was performed by quantitative RT-PCR, and transcriptional regulation of all selected genes showed a positive correlation with the proteomic patterns of the identified proteins. Results presented in this study may be useful for further elucidating the acid tolerance mechanisms and may help in formulating new strategies to improve the industrial performance of this species during acid stress.