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

The enhancement effect of mungbean on the physical, functional, and sensory characteristics of soy yoghurt

Vegetable drinks offer a convenient way to increase the daily intake of vegetables containing vitamins, antioxidants, and fiber. In this study, we discovered that mungbean milk serves as a carbohydrate source during fermentation using lactic acid bacteria (LAB) and enhances the nutritional value of vegetable yoghurt. Mungbean milk reduces pH while titratable acidity increases faster than soybean milk during fermentation. M0S, Soybean milk 100% with added sucrose exhibited the highest titratable acidity after 16 h of fermentation. The acetic acid content of all samples did not show significant changes during fermentation, but the lactic acid content increased. Proximate analysis showed no significant change during fermentation, regardless of the fermentation time and mixing ratio of mungbean to soybean milk. The sucrose content of samples except M0S decreased after 16 h of fermentation. Mungbean milk exhibited high antioxidant activity both before and after fermentation, while M0S showed the lowest antioxidant activity. The results of this study demonstrated the potential application of mungbean milk to improve fermented vegetable drinks using LAB functionally. Fermented mungbean milk yoghurt can be a valuable addition to a healthy and balanced diet for those who consume plant-based diets.

The potential of probiotics in the amelioration of hyperuricemia

Hyperuricemia is a common disease caused by metabolic disorders or the excessive intake of high-purine foods. Persistent hyperuricemia in extreme cases induces gout, and asymptomatic hyperuricemia is probably linked to other metabolic diseases, such as hypertension. The typical damage caused by asymptomatic hyperuricemia includes inflammation, oxidative stress and gut dysbiosis. Probiotics have broad potential applications as food additives, not as drug therapies, in the amelioration of hyperuricemia. In this review, we describe novel methods for potential hyperuricemia amelioration with probiotics. The pathways through which probiotics may ameliorate hyperuricemia are discussed, including the decrease in uric acid production through purine assimilation and XOD (xanthine oxidase) inhibition as well as enhanced excretion of uric acid production by promoting ABCG2 (ATP binding cassette subfamily G member 2) activity, respectively. Three possible probiotic-related therapeutic pathways for alleviating the syndrome of hyperuricemia are also summarized. The first mechanism is to alleviate the oxidation and inflammation induced by hyperuricemia through the inhibition of NLRP3 inflammasome, the second is to restore damaged intestinal epithelium barriers and prevent gut microbiota dysbiosis, and the third is to enhance the innate immune system by increasing the secretion of immunoglobulin A (sIgA) to resist the stimulus by hyperuricemia. We propose that future research should focus on superior strain resource isolation and insight into the cause-effect mechanisms of probiotics for hyperuricemia amelioration. The safety and effects of the application of probiotics in clinical use also need verification.

Proteomic perspectives on thermotolerant microbes: an updated review

INTRODUCTION

Thermotolerant microbes are a group of microorganisms that survive in elevated temperatures. The thermotolerant microbes, which are found in geothermal heat zones, grow at temperatures of or above 45°C. The proteins present in such microbes are optimally active at these elevated temperatures. Hence, therefore, serves as an advantage in various biotechnological applications. In the last few years, scientists have tried to understand the molecular mechanisms behind the maintenance of the structural integrity of the cell and to study the stability of various thermotolerant proteins at extreme temperatures. Proteomic analysis is the solution for this search. Applying novel proteomic tools determines the proteins involved in the thermostability of microbes at elevated temperatures.

METHODS

Advanced proteomic techniques like Mass spectrometry, nano-LC-MS, protein microarray, ICAT, iTRAQ, and SILAC could enable the screening and identification of novel thermostable proteins.

RESULTS

This review provides up-to-date details on the protein signature of various thermotolerant microbes analyzed through advanced proteomic tools concerning relevant research articles. The protein complex composition from various thermotolerant microbes cultured at different temperatures, their structural arrangement, and functional efficiency of the protein was reviewed and reported.

CONCLUSION

This review provides an overview of thermotolerant microbes, their enzymes, and the proteomic tools implemented to characterize them. This article also reviewed a comprehensive view of the current proteomic approaches for protein profiling in thermotolerant microbes.

Integrated Transcriptome and Proteome Analyses Reveal Protein Metabolism in Lactobacillus helveticus CICC22171

Lactobacillus helveticus is a homofermentative lactic acid bacterium. It is widely used in the fabrication of Swiss cheese and other dairy products. The aim of this study was to elucidate the mechanism by which L. helveticus utilizes protein. Lactobacillus helveticus CICC22171 were cultured in two different media with various nitrogen sources. The control contained 20 basic amino acids, while the experimental medium contained casein. De novo transcriptome and isobaric tags for relative and absolute quantification (iTRAQ) proteome analyses were applied to determine how L. helveticus utilizes protein. The casein underwent extracellular hydrolysis via ATP-binding cassette (ABC) transporter upregulation and Mn²⁺-associated cell envelope proteinase (CEP) downregulation. Sigma factors and EF-Tu were upregulated and Mg²⁺ was reduced in bacteria to accommodate DNA transcription and protein translation in preparation for proteolysis. Hydrolase activity was upregulated to digest intracellular polypeptides and control endopeptidase genes. In these bacteria, casein utilization affected glycolysis, trehalose phosphotransferase system (PTS), and key factors associated with aerobic respiration and reduced glucose consumption.

Bioactivities and ACE-inhibitory peptides releasing potential of lactic acid bacteria in fermented soy milk

Abstract

This study was designed to evaluate the bioactivities such as β-glucosidase activity, α-galactosidase activity, and the growth behavior of the Lactobacillus cultures in soy milk medium. Ten Lactobacillus cultures were considered in this study. L. fermentum (M2) and L. casei (NK9) were selected due to their better α-galactosidase, β-glucosidase activity and growth behavior in soy milk medium during fermentation. Further, soy milk fermented with M2 showed higher proteolytic activity (0.67 OD) and ACE-inhibitory (48.44%) than NK9 (proteolytic activity: 0.48 OD and ACE-inhibitory activity: 41.33%). Bioactive peptides produced during the fermentation of soy milk using the selected Lactobacillus cultures were also identified with potent ACE-inhibitory activity by MALDI-TOF spectrometry, and the identified ACE inhibitory peptide sequences from fermented soy milk were characterized using Biopep database.

Graphical abstract

Metaproteomics insights into traditional fermented foods and beverages

Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

Transcriptomic and proteomic profiling revealed global changes in Streptococcus thermophilus during pH-controlled batch fermentations

Understanding global changes of physiological processes at the molecular level during the growth of Streptococcus thermophilus is essential for the rational design of cultivation media and the optimization of bioprocesses. Transcriptomics and proteomics were combined to investigate the global changes at the transcript and protein level during the growth of S. thermophilus. The expression of 1396 genes (FDR ≤ 0.001) and 876 proteins (P < 0.05) changed significantly over time. The most remarkable growth phase dependent changes occurred in the late-lag phase and were related to heterofermentation, glycolysis, peptidoglycan biosynthesis, conversion between amino acids and stress response. The present results could provide theoretical guidance for high-cell-density culture, help design cultivation media, and help attain a high biomass of S. thermophilus.

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.

Using Raman spectroscopy and chemometrics to identify the growth phase of Lactobacillus casei Zhang during batch culture at the single-cell level

Background

As microbial cultures are comprised of heterogeneous cells that differ according to their size and intracellular concentrations of DNA, proteins, and other constituents, the detailed identification and discrimination of the growth phases of bacterial populations in batch culture is challenging. Cell analysis is indispensable for quality control and cell enrichment.

Methods

In this paper, we report the results of our investigation on the use of single-cell Raman spectrometry (SCRS) for real-time analysis and prediction of cells in different growth phases during batch culture of Lactobacillus (L.) casei Zhang. A targeted analysis of defined cell growth phases at the level of the single cell, including lag phase, log phase, and stationary phase, was facilitated by SCRS.

Results

Spectral shifts were identified in different states of cell growth that reflect biochemical changes specific to each cell growth phase. Raman peaks associated with DNA and RNA displayed a decrease in intensity over time, whereas protein-specific and lipid-specific Raman vibrations increased at different rates. Furthermore, a supervised classification model (Random Forest) was used to specify the lag phase, log phase, and stationary phase of cells based on SCRS, and a mean sensitivity of 90.7% and mean specificity of 90.8% were achieved. In addition, the correct cell type was predicted at an accuracy of approximately 91.2%.

Conclusions

To conclude, Raman spectroscopy allows label-free, continuous monitoring of cell growth, which may facilitate more accurate estimates of the growth states of lactic acid bacterial populations during fermented batch culture in industry.

Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures

Lactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. bulgaricus as a probiotic remain to be elucidated. In this study, we identified proteins of L. delbrueckii subsp. bulgaricus LBB.B5 that are produced in higher quantities in milk at growth-conducive and non-growth-conductive (refrigeration) temperatures compared to laboratory culture medium and further examined whether those L. delbrueckii subsp. bulgaricus cultures were affected differently in their capacity to survive transit through the murine digestive tract. This work provides novel insight into how a major, food-adapted microbe responds to its primary habitat. Such knowledge can be applied to improve starter culture and yogurt production and to elucidate matrix effects on probiotic performance.

We identified the proteins synthesized by Lactobacillus delbrueckii subsp. bulgaricus strain LBB.B5 in laboratory culture medium (MRS) at 37°C and milk at 37 and 4°C. Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry. A total of 635 proteins were recovered from all cultures, among which 72 proteins were milk associated (unique or significantly more abundant in milk). LBB.B5 responded to milk by increasing the production of proteins required for purine biosynthesis, carbohydrate metabolism (LacZ and ManM), energy metabolism (TpiA, PgK, Eno, SdhA, and GapN), amino acid synthesis (MetE, CysK, LBU0412, and AspC) and transport (GlnM and GlnP), and stress response (Trx, MsrA, MecA, and SmpB). The requirement for purines was confirmed by the significantly improved cell yields of L. delbrueckii subsp. bulgaricus when incubated in milk supplemented with adenine and guanine. The L. delbrueckii subsp. bulgaricus-expressed proteome in milk changed upon incubation at 4°C for 5 days and included increased levels of 17 proteins, several of which confer functions in stress tolerance (AddB, UvrC, RecA, and DnaJ). However, even with the activation of stress responses in either milk or MRS, L. delbrueckii subsp. bulgaricus did not survive passage through the murine digestive tract. These findings inform efforts to understand how L. delbrueckii subsp. bulgaricus is adapted to the dairy environment and its implications for its health-benefiting properties in the human digestive tract.

IMPORTANCELactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. bulgaricus as a probiotic remain to be elucidated. In this study, we identified proteins of L. delbrueckii subsp. bulgaricus LBB.B5 that are synthesized in higher quantities in milk at growth-conducive and non-growth-conductive (refrigeration) temperatures compared to laboratory culture medium and further examined whether those L. delbrueckii subsp. bulgaricus cultures were affected differently in their capacity to survive transit through the murine digestive tract. This work provides novel insight into how a major, food-adapted microbe responds to its primary habitat. Such knowledge can be applied to improve starter culture and yogurt production and to elucidate matrix effects on probiotic performance.

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.

Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans

Lactic acid bacteria (LAB) are the most common beer-spoilage bacteria regardless of beer type, and thus pose significant problems for the brewery industry. The aim of this study was to investigate the genetic mechanisms involved in the ability of the hard-to-culture beer-spoilage bacterium Lactobacillus acetotolerans to enter into the viable putative non-culturable (VPNC) state. A genome-wide transcriptional analysis of beer-spoilage L. acetotolerans strains BM-LA14526, BM-LA14527, and BM-LA14528 under normal, mid-term and VPNC states were performed using RNA-sequencing (RNA-seq) and further bioinformatics analyses. GO function, COG category, and KEGG pathway enrichment analysis were conducted to investigate functional and related metabolic pathways of the differentially expressed genes. Functional and pathway enrichment analysis indicated that heightened stress response and reduction in genes associated with transport, metabolic process, and enzyme activity might play important roles in the formation of the VPNC state. This is the first transcriptomic analysis on the formation of the VPNC state of beer spoilage L. acetotolerans.

Functional beverage from fermented soymilk with improved amino nitrogen, β-glucosidase activity and aglycone content using Bacillus subtilis starter

The bioactivity of soymilk was enhanced by fermentation with three strains of β-glucosidaseproducing Bacillus subtilis for 36 h at 37oC. The results indicated that protease, cellulase, and β-glucosidase activities were significantly (p<0.05) increased with increasing fermentation time. In addition, the amino-type nitrogen content in B. subtilis-fermented soymilk was increased to 121.1-140.7 mg% after 36 h of fermentation. Among the isoflavones in soymilk, the contents of β-glucosides or acetyl-glucosides were decreased, while aglycone content was increased by fermentation. In particular, the soymilk fermented with B. subtilis HJ18-9 had highest β-glucosidase activity and the largest increase in aglycone content. The total aerobic and anaerobic cell counts were increased with increasing fermentation time. Therefore, this study suggests that soy beverages fermented with β-glucosidase-producing B. subtilis have the potential to enhance the health and nutritional status of consumers.

Study on the Influence of Tea Extract on Probiotics in Skim Milk: From Probiotics Propagation to Metabolite

In this study, the influence of tea extract (TE) on the growth of probiotics in skim milk was examined. Lactobacillus plantarum ST-III, Bifidobacterium bifidum Bb02, Lactobacillus acidophilus NCFM, and Lactobacillus rhamnosus GG were used in this study. The introduction of TE in milk significantly stimulated the propagation and acidification of L. rhamnosus GG and L. acidophilus NCFM. The antioxidant capacities and the total free amino acid contents of all fermented milk products were enhanced by the addition of TE; however, there were different antioxidant properties and free amino acid contents of fermented milk samples fermented by different bacteria. With a 9% (w/w) level, the fermentation with L. rhamnosus GG and L. acidophilus NCFM showed larger numbers of viable cells and faster acidifying rates, as well as excellent antioxidant capacity and abundant free amino acids.  The stimulative effects of TE on probiotics can be considered for industrial purposes and has practical implications for commercial applications.