Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium

Effect of direct arginine supplementation on growth of Lacticaseibacillus rhamnosus GG

OBJECTIVES

The study aimed to examine the effect of direct arginine (Arg) supplementation on Lacticaseibacillus rhamnosus GG (LRG) growth.

METHODS

The probiotic LRG ATCC 53103 was routinely cultured in MRS broth and adjusted to 107 CFU/ml. l-Arg at 0.25 % and 0.5 % w/v. was directly supplemented to MRS broth containing LRG. Then, LRG with/without supplemented Arg was characterised to determine growth curves for 72 h under a CO2-driven, environment-controlled spectrophotometer. Whereas, end-point McFarland spectrophotometric, metabolic assays (XTT and WST-8), colony forming units (CFU) assessment, live/dead bacterial confocal imaging, and viable DNA quantification were undertaken after 24 h CO2 incubation to determine LRG growth with/without supplemented Arg.

RESULTS

Growth curve analysis revealed similar absorbance profiles with LRG and LRG+0.25 % Arg with no overlaps to LRG+0.5 % Arg; with a similar trend observed as per end-point McFarland spectrophotometric assessment. The % viability estimated by metabolic assays with LRG and LRG+0.25 % Arg was significantly lower than LRG+0.5 % Arg (p < 0.05). As per CFU assessment, CFU/ml for LRG+0.25 % Arg and LRG+0.5 % Arg was significantly higher than LRG control (p < 0.05). LRG live-dead proportions determined using confocal imaging denote no differences between the groups (p > 0.05), with live cell proportions significantly higher than the dead cells (p < 0.05). However, LRG cellular density appeared to increase with increasing concentrations of Arg. Additionally, the viable cells quantified with PMA-qPCR significantly increased with increasing concentrations of Arg (p < 0.05).

CONCLUSION

Direct supplementation of 0.5 % Arg to LRG enhances LRG growth, demonstrating a promising synbiotic potential. CLINICAL SIGNIFICANCE (48 WORDS): Primary caries prevention is initiated at biofilms using biotic strategies that modulate the microbiome matrix to maintain ecological homeostasis. The results of the present study establish a deliverable synbiotic of Arg and probiotic Lacticaseibacillus rhamnosus GG, demonstrating a promising synergism between interventions in the milieu targeted for high caries-risk individuals.

The effect of arginine on the growth of probiotics

OBJECTIVE(S)

The study objective was to examine the effect of arginine (Arg) supplementation on the growth of probiotics.

METHODS

Lacticaseibacillus rhamnosus GG, Lactiplantibacillus plantarum, and Lactobacillus acidophilus were identified as potential probiotics. L. rhamnosus GG and L. plantarum were selected for further experimentation. The probiotics were co-treated with 0.9 % NaCl (negative control), 0.5 % Arg, and 1.0 % Arg in a 1:1 ratio for 24 h at 5 % CO2, 37 °C. The probiotics were tested for growth profiles, spectroscopic turbidity assay, metabolic assays (XTT and WST-8), live/dead cell assessment using confocal laser scanning microscopy (CLSM), and colony forming units (CFU).

RESULTS

The growth profiles of L. rhamnosus GG and L. plantarum were found to be similar, whereas L. acidophilus showed minimal or no transition from the initial lag phase. In the turbidity assay, the end-point absorbance for L. rhamnosus GG with 1.0 % Arg was significantly lower than 0.9 % NaCl and 0.5 % Arg (p < 0.05). For metabolic assays and CFU, increasing concentrations of Arg increased the viable cells for L. rhamnosus GG (p < 0.05), but decreased viability for L. plantarum (p < 0.05). Metabolic assays with dual-species bacterial suspensions indicated that Arg co-treatment inhibited viable proportions compared to control (p < 0.05). The dead cell proportion was significantly lower than live cell proportion for all tested interventions and probiotics (p < 0.05).

CONCLUSION

Increasing concentrations of Arg promote the growth of L. rhamnosus GG, while conversely inhibiting the growth of L. plantarum. Therefore, the effect of prebiotic Arg on probiotics is concentration-dependent, leading to a selective promotion or inhibition of growth.

CLINICAL SIGNIFICANCE

The present study results show that Arg supplementation can selectively enhance the growth of L. rhamnosus GG while inhibit the growth of L. plantarum. This underscores the need to consider strain-specific responses in probiotic formulations when developing Arg-based synbiotics for modulating biofilms and creating ecologically homeostatic biofilm microenvironments.

Growth phase matters: Boosting immunity via Lacticasebacillus-derived membrane vesicles and their interactions with TLR2 pathways

Lipid bi-layered particles known as membrane vesicles (MVs), produced by Gram-positive bacteria are a communication tool throughout the entire bacterial growth. However, the MVs characteristics may vary across all stages of maternal culture growth, leading to inconsistencies in MVs research. This, in turn, hinders their employment as nanocarriers, vaccines and other medical applications. In this study, we aimed to comprehensively characterize MVs derived from Lacticaseibacillus rhamnosus CCM7091 isolated at different growth stages: early exponential (6 h, MV6), late exponential (12 h, MV12) and late stationary phase (48 h, MV48). We observed significant differences in protein content between MV6 and MV48 (data are available via ProteomeXchange with identifier PXD041580), likely contributing to their different immunomodulatory capacities. In vitro analysis demonstrated that MV48 uptake rate by epithelial Caco-2 cells is significantly higher and they stimulate an immune response in murine macrophages RAW 264.7 (elevated production of TNFα, IL-6, IL-10, NO). This correlated with increased expression of lipoteichoic acid (LTA) and enhanced TLR2 signalling in MV48, suggesting that LTA contributes to the immunomodulation. In conclusion, we showed that Lacticaseibacillus rhamnosus CCM7091-derived MVs from the late stationary phase boost the immune response the most effectively, which pre-destines them for therapeutical application as nanocarriers.

COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling

Metabolism governs cell performance in biomanufacturing, as it fuels growth and productivity. However, even in well-controlled culture systems, metabolism is dynamic, with shifting objectives and resources, thus limiting the predictive capability of mechanistic models for process design and optimization. Here, we present Cellular Objectives and State Modulation In bioreaCtors (COSMIC)-dFBA, a hybrid multi-scale modeling paradigm that accurately predicts cell density, antibody titer, and bioreactor metabolite concentration profiles. Using machine-learning, COSMIC-dFBA decomposes the instantaneous metabolite uptake and secretion rates in a bioreactor into weighted contributions from each cell state (growth or antibody-producing state) and integrates these with a genome-scale metabolic model. A major strength of COSMIC-dFBA is that it can be parameterized with only metabolite concentrations from spent media, although constraining the metabolic model with other omics data can further improve its capabilities. Using COSMIC-dFBA, we can predict the final cell density and antibody titer to within 10% of the measured data, and compared to a standard dFBA model, we found the framework showed a 90% and 72% improvement in cell density and antibody titer prediction, respectively. Thus, we demonstrate our hybrid modeling framework effectively captures cellular metabolism and expands the applicability of dFBA to model the dynamic conditions in a bioreactor.

Inorganic phosphate modifies stationary phase fitness and metabolic pathways in Lactiplantibacillus paraplantarum CRL 1905

Inorganic phosphate (Pi) concentration modulates polyphosphate (polyP) levels in diverse bacteria, affecting their physiology and survival. Lactiplantibacillus paraplantarum CRL 1905 is a lactic acid bacterium isolated from quinoa sourdough with biotechnological potential as starter, for initiating fermentation processes in food, and as antimicrobial-producing organism. The aim of this work was to evaluate the influence of the environmental Pi concentration on different physiological and molecular aspects of the CRL 1905 strain. Cells grown in a chemically defined medium containing high Pi (CDM + P) maintained elevated polyP levels up to late stationary phase and showed an enhanced bacterial survival and tolerance to oxidative stress. In Pi sufficiency condition (CDM-P), cells were ~ 25% longer than those grown in CDM + P, presented membrane vesicles and a ~ 3-fold higher capacity to form biofilm. Proteomic analysis indicated that proteins involved in the "carbohydrate transport and metabolism" and "energy production and conversion" categories were up-regulated in high Pi stationary phase cells, implying an active metabolism in this condition. On the other hand, stress-related chaperones and enzymes involved in cell surface modification were up-regulated in the CDM-P medium. Our results provide new insights to understand the CRL 1905 adaptations in response to differential Pi conditions. The adjustment of environmental Pi concentration constitutes a simple strategy to improve the cellular fitness of L. paraplantarum CRL 1905, which would benefit its potential as a microbial cell factory.

Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.

Evaluation of microbial communities of Chinese Feng-flavor Daqu with effects of environmental factors using traceability analysis

Analysis of the changes of microorganisms during Chinese Feng-flavor Daqu fermentation, and the specific contribution of different environmental factors to Daqu microorganisms. High throughput sequencing technology and SourceTracker software were used to analyze the microbial diversity of Feng-flavor Daqu before and after fermentation. 85 fungal and 105 bacterial were detected in the newly pressed Feng-flavor Daqu, while 33 fungal and 50 bacterial in the mature Daqu, and 202 fungal and 555 bacterial in the environmental samples. After fermentation, the microbial community structure of Daqu changed and decreased significantly. 94.7% of fungi come from raw materials and 1.8% from outdoor ground, 60.95% of bacteria come from indoor ground, 20.44% from raw materials, and 8.98% from tools. By comparing the changes of microorganisms in Daqu before and after fermentation, the microorganisms in mature Daqu may mainly come from not only the enhanced strains but also the environment.The source of main microorganisms in Feng-flavor Daqu and the influence of environmental factors on the quality of Daqu were clarified, which provided a basis for improving the quality of Feng-flavor Daqu.

The effect of synbiotic-fluoride therapy on multi-species biofilm

OBJECTIVES

The study objective was to examine the effect of synbiotic-fluoride (SF) therapy within a multi-species cariogenic biofilm model system comprising of S. mutans, S. sanguinis, and S. gordonii.

METHODS

The SF therapy was prepared using 2% L-arginine (Arg), 0.2% NaF and probiotic L. rhamnosus GG (LRG). The 8 treatment groups were: Group 1: No treatment, Group 2: 2% Arg, Group 3: 0.2% NaF, Group 4: LRG, Group 5: 2% Arg+0.2% NaF, Group 6: 2% Arg+LRG, Group 7: 0.2% NaF+LRG, and Group 8: SF therapy (2% Arg+0.2% NaF +LRG). Multi-species biofilm model over 96 h comprising Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii was utilized. The biofilms received cariogenic challenge and SF therapy 2 × /day. The extracellular matrix components were analyzed for carbohydrates, proteins, and extra-cellular DNA (eDNA). The live/dead cells were imaged and quantified using confocal microscopy. The viable/dead bacterial concentrations were estimated using propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR). The gene expressions for gtfB, sagP, arcA, argG, and argH were measured using real-time reverse transcriptase qPCR.

RESULTS

Carbohydrates and protein content with SF therapy were higher than non-LRG containing groups, while eDNA content was lower than other groups (p<0.05). Live bacterial proportions determined using confocal imaging with SF therapy were the lowest (p<0.05). The 2% Arg+LRG and SF therapy showed higher viable L. rhamnosus GG than 0.2% NaF+LRG (p<0.05). The dead S. mutans with SF therapy were higher than the other groups (p<0.05) with no difference from 2% Arg+0.2% NaF and 2% Arg+LRG (p>0.05). The SF therapy significantly downregulates gtfB and upregulates sagP, arcA, argG, argH gene expression (p<0.05).

CONCLUSION

Synbiotic-fluoride therapy effectuates multi-fold changes in the multi-species biofilm matrix and cellular components leading to superior ecological homeostasis than its individual contents, prebiotics (arginine), probiotic (L. rhamnosus GG), and fluorides (NaF).

CLINICAL SIGNIFICANCE

The ecological-based synbiotic-fluoride caries-preventive therapy aids in maintaining biofilm homeostasis to preempt/restore dysbiosis thereby sustaining dynamic-diverse health-associated microbial stability significant as a preventive regimen for high caries-risk patients.

Intestinal epithelial cell-derived components regulate transcriptome of Lactobacillus rhamnosus GG

Introduction

Intestinal epithelial cells (IECs) provide the frontline responses to the gut microbiota for maintaining intestinal homeostasis. Our previous work revealed that IEC-derived components promote the beneficial effects of a commensal and probiotic bacterium, Lactobacillus rhamnosus GG (LGG). This study aimed to elucidate the regulatory effects of IEC-derived components on LGG at the molecular level.

Methods

Differential gene expression in LGG cultured with IEC-derived components at the timepoint between the exponential and stationary phase was studied by RNA sequencing and functional analysis.

Results

The transcriptomic profile of LGG cultured with IEC-derived components was significantly different from that of control LGG, with 231 genes were significantly upregulated and 235 genes significantly down regulated (FDR <0.05). The Clusters of Orthologous Groups (COGs) and Gene Ontology (GO) analysis demonstrated that the predominant genes enriched by IEC-derived components are involved in nutrient acquisition, including transporters for amino acids, metals, and sugars, biosynthesis of amino acids, and in the biosynthesis of cell membrane and cell wall, including biosynthesis of fatty acid and lipoteichoic acid. In addition, genes associated with cell division and translation are upregulated by IEC-derived components. The outcome of the increased transcription of these genes is supported by the result that IEC-derived components significantly promoted LGG growth. The main repressed genes are associated with the metabolism of amino acids, purines, carbohydrates, glycerophospholipid, and transcription, which may reflect regulation of metabolic mechanisms in response to the availability of nutrients in bacteria.

Discussion

These results provide mechanistic insight into the interactions between the gut microbiota and the host.

Sangyod rice bran extract enhances Lacticaseibacillus paracasei growth during the exponential phase and antibacterial activity of L. paracasei supernatant against zoonotic and foodborne pathogens

Background and Aim: Prebiotics are a group of nutrients or compounds that are degraded by the gut microbiota, including Lacticaseibacillus paracasei. The probiotic plays an important role in adhesion to the gut and is able to produce antimicrobial substances to inhibit pathogens. This study aimed to investigate the effects of Sangyod rice bran extract on the growth promotion of L. paracasei. Furthermore, antibacterial activity of the extract and L. paracasei supernatants cultured in De Man, Rogosa and Sharpe (MRS) medium plus the extract against zoonotic and foodborne pathogens was investigated. Materials and Methods: Antibacterial activity of the crude extract and the oil from Sangyod rice bran against the pathogens, including Bacillus cereus, Staphylococcus aureus, Escherichia coli, Avian pathogenic E. coli, and Pseudomonas aeruginosa was investigated using broth microdilution assay. The effects of the crude extract and the oil on the growth and adhesion of L. paracasei were further determined. The antibacterial activity of L. paracasei supernatant cultured in the medium supplemented with the extract and the oil against the pathogens was determined by agar well diffusion assay, followed by the broth microdilution assay. Finally, the chemical constituents and antioxidant activity of the crude extract and the oil from Sangyod rice bran were investigated. Results: The crude extract and the oil from Sangyod rice bran enhanced L. paracasei growth during the exponential phase. Furthermore, the crude extract at 0.25 mg/mL significantly enhanced the adhesion of L. paracasei to the surface compared with the control. Both minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values of the crude extract against B. cereus and S. aureus were 0.5 and 1.0 mg/mL, respectively. All pathogens were sensitive to the supernatant of L. paracasei with similar MIC and MBC ranging from 12.5% v/v to 50% v/v. However, the MIC and MBC values of L. paracasei supernatant grown in MRS medium plus the crude extract and oil were not significantly different compared to the supernatant obtained from MRS alone. The crude extract had free radical scavenging activities with IC50 values at 0.61 mg/mL. Conclusion: The results suggested the potential benefits of the crude extract from Sangyod rice bran for inducing the growth and the adhesion of L. paracasei and inhibiting zoonotic and foodborne pathogens.

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

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

The production and biochemical characterization of α-carbonic anhydrase from Lactobacillus rhamnosus GG

Abstract

We report the production and biochemical characterization of an α-carbonic anhydrase (LrhCA) from gram-positive probiotic bacteria Lactobacillus rhamnosus GG. CAs form a family of metalloenzymes that catalyze hydration of CO₂/interconversion between CO₂ and water to bicarbonate ions and protons. They are divided into eight independent gene families (α, β, γ, δ, ζ, η, θ, and ι). Interestingly, many pathogens have been identified with only β- and/or γ-CAs, which can be targeted with CA-specific inhibitors (CAIs) acting as anti-pathogen drugs. Since it is important to study the potential off-target effects of CAIs for both the human body and its commensal bacteria, we took L. rhamnosus GG as our study subject. To date, only a single α-CA has been identified in L. rhamnosus GG, which was successfully produced and biochemically characterized. LrhCA showed moderate catalytic activity with the following kinetic parameters: k_cat of 9.86 × 10⁵ s⁻¹ and k_cat/K_M of 1.41 × 10⁷ s⁻¹ M⁻¹. Moderate inhibition was established with 11 of the 39 studied sulfonamides. The best inhibitors were 5-((4-aminophenyl)sulfonamido)-1,3,4-thiadiazole-2-sulfonamide, 4-(2-hydroxymethyl-4-nitrophenyl-sulfonamidoethyl)-benzenesulfonamide, and benzolamide with K_i values of 319 nM, 378 nM, and 387 nM, respectively. The other compounds showed weaker inhibitory effects. The K_i of acetazolamide, a classical CAI, was 733 nM. In vitro experiments with acetazolamide showed that it had no significant effect on cell growth in L. rhamnosus GG culture. Several sulfonamides, including acetazolamide, are in use as clinical drugs, making their inhibition data highly relevant to avoid any adverse off-target effects towards the human body and its probiotic organisms.

Key points

• The α-carbonic anhydrase from Lactobacillus rhamnosus GG (LrhCA) is 24.3 kDa.

• LrhCA has significant catalytic activity with a kcat of 9.9 × 105 s-1.

• Acetazolamide resulted in a marginal inhibitory effect on cell growth.

Investigating Differential Expressed Genes of Limosilactobacillus reuteri LR08 Regulated by Soybean Protein and Peptides

Soybean protein and peptides have the potential to promote the growth of Lactobacillus, but the mechanisms involved are not well understood. The purpose of this study is to investigate differentially expressed genes (DEGs) of Limosilactobacillus reuteri (L. reuteri) LR08 responding to soybean protein and peptides using transcriptome. The results showed that both digested protein (dpro) and digested peptides (dpep) could enhance a purine biosynthesis pathway which could provide more nucleic acid and ATP for bacteria growth. Moreover, dpep could be used instead of dpro to promote the ABC transporters, especially the genes involved in the transportation of various amino acids. Interestingly, dpro and dpep played opposite roles in modulating DEGs from the acc and fab gene families which participate in fatty acid biosynthesis. These not only provide a new direction for developing nitrogen-sourced prebiotics in the food industry but could also help us to understand the fundamental mechanism of the effects of dpro and dpep on their growth and metabolisms and provides relevant evidence for further investigation.

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

Background

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

Results

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

Conclusions

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

Supplementary Information

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

Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response

Under starvation conditions, bacteria tend to slow down their translation rate by reducing rRNA synthesis, but the way they accomplish that may vary in different bacteria. In Mycobacterium species, transcription of rRNA is activated by the RNA polymerase (RNAP) accessory transcription factor CarD, which interacts directly with RNAP to stabilize the RNAP-promoter open complex formed on rRNA genes. The functions of CarD have been extensively studied, but the mechanisms that control its expression remain obscure. Here, we report that the level of CarD was tightly regulated when mycobacterial cells switched from nutrient-rich to nutrient-deprived conditions. At the translational level, an antisense RNA of carD (AscarD) was induced in a SigF-dependent manner to bind with carD mRNA and inhibit CarD translation, while at the post-translational level, the residual intracellular CarD was quickly degraded by the Clp protease. AscarD thus worked synergistically with Clp protease to decrease the CarD level to help mycobacterial cells cope with the nutritional stress. Altogether, our work elucidates the regulation mode of CarD and delineates a new mechanism for the mycobacterial starvation response, which is important for the adaptation and persistence of mycobacterial pathogens in the host environment.

Untargeted LC-QTOF-MS/MS based metabolomics approach for revealing bioactive components in probiotic fermented coffee brews

Amidst trends in non-dairy probiotic foods and functional coffees, we recently developed a fermented coffee brew containing high live counts of the probiotics Lacticaseibacillus rhamnosus GG and Saccharomyces boulardii CNCM-I745. However, probiotic fermentation did not alter levels of principal coffee bioactive components based on targeted analyses. Here, to provide therapeutic justification compared to other non-fermented coffee brews, we aimed to discover postbiotics in coffee brews fermented with L. rhamnosus GG and/or S. boulardii CNCM-I745. By using an untargeted LC-QTOF-MS/MS based metabolomics approach coupled with validated multivariate analyses, 37 differential metabolites between fermentation treatments were putatively annotated. These include the production of postbiotics such as 2-isopropylmalate by S. boulardii CNCM-I745, and aromatic amino acid catabolites (indole-3-lactate, p-hydroxyphenyllactate, 3-phenyllactate), and hydroxydodecanoic acid by L. rhamnosus GG. Overall, LC-QTOF based untargeted metabolomics can be an effective approach to uncover postbiotics, which may substantiate additional potential functionalities of probiotic fermented foods compared to their non-fermented counterparts.

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.

Growth, survival, and metabolic activities of probiotics Lactobacillus rhamnosus GG and Saccharomyces cerevisiae var. boulardii CNCM-I745 in fermented coffee brews

Amidst rising demand for non-dairy probiotic foods, and growing interest in coffees with added functionalities, it would be opportune to ferment coffee brews with probiotics. However, challenges exist in maintaining probiotic viability in high-moisture food products. Here, we aimed to enhance the viability of the probiotic bacteria, Lactobacillus rhamnosus GG, in coffee brews by co-culturing with the probiotic yeast, Saccharomyces cerevisiae var. boulardii CNCM-I745. The yeast significantly enhanced the viability of L. rhamnosus GG, as bacterial populations beyond 7 Log CFU/mL were maintained throughout 14 weeks of storage at 4 and 25 °C. In contrast, the single culture of L. rhamnosus GG suffered viability losses below 6 Log CFU/mL within 10 weeks at 4 °C, and 3 weeks at 25 °C. Growth and survival of S. boulardii CNCM-I745 remained unaffected by the presence of L. rhamnosus GG. Volatile profiles of coffee brews were altered by probiotic metabolic activities, but co-culturing led to suppressed generation of diacetyl and ethanol compared to single cultures. Probiotic fermentation did not alter principal coffee bioactive compounds and antioxidant capacities; however, declines in peroxyl radical scavenging capacities were observed after ambient storage. Overall, we illustrate that yeasts are effective in enhancing probiotic bacterial viability in coffee brews, which may be useful in developing shelf stable probiotic food products.

Microencapsulation of Lactobacillus casei and Lactobacillus rhamnosus in pectin and pectin-inulin microgel particles: Effect on bacterial survival under storage conditions

The main objective of the research was to evaluate the performance of synbiotic delivery systems using pectin microgels on the protection of two probiotic strains (Lactobacillus casei ATCC 393 and Lactobacillus rhamnosus strain GG [ATCC 53103]) to simulated gastrointestinal digestion (GD) and storage conditions (4 ± 1 °C) in a 42 days trial. Microgel particles were prepared by ionotropic gelation method and three variables were evaluated: incubation time (24 and 48 h), free vs encapsulated cells, and presence or absence of prebiotic (commercial and Jerusalem artichoke inulin). Results demonstrated an encapsulation efficiency of 96 ± 4% into particles with a mean diameter between 56 and 118 μm. The viability of encapsulated cells after 42 days storage stayed above 7 log units, being encapsulated cells in pectin-inulin microgels more resistant to GD compared to non-encapsulated cells or without prebiotics. In all cases incubation time influenced the strains' survival.

Combined effect of arginine and fluoride on the growth of Lactobacillus rhamnosus GG

The objectives of the in vitro study were: (1) to investigate the effect of combining L-arginine (Arg) and NaF on the growth of Lactobacillus rhamnosus GG (LRG); and (2) to identify an optimum synergistic concentration for the synbiotic (Arg + LRG)-fluoride (SF) therapy. 1% Arg + 2000-ppm NaF (A-SF) and 2% Arg + 2000-ppm NaF (B-SF) demonstrated antagonism against LRG (FIC > 4.0). Both XTT (2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) and WST-8 (2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt) assays showed that A-SF and B-SF enhanced the growth of LRG when compared to 2000-ppm NaF and LRG control. Colony forming units, bacterial weight, and biofilm thickness of A-SF and B-SF were significantly higher than 2000-ppm NaF and LRG control. Biofilm imaging depicted that 2000-ppm NaF inhibited biofilm formation; while 1%/2% Arg, A-SF, and B-SF increased biofilm growth of LRG. Lactic acid formation was the lowest for 2000-ppm NaF, followed by A-SF and then B-SF. The SF buffer potential after 24 h was the highest for B-SF, and then A-SF. Biofilm pH for B-SF was closest to neutral. Fluoride, Arg and LRG bioavailability remained unaffected in B-SF. The relative gene expression for arcA, argG, and argH was significantly higher for B-SF than the respective controls. In conclusion, combining 2% Arg, 2000-ppm NaF, and LRG provides an optimum synbiotic-fluoride synergism.

A Fast, Efficient and Easy to Implement Method to Purify Bacterial Pili From Lacticaseibacillus rhamnosus GG Based on Multimodal Chromatography

Pili are polymeric proteins located at the cell surface of bacteria. These filamentous proteins play a pivotal role in bacterial adhesion with the surrounding environment. They are found both in Gram-negative and Gram-positive bacteria but differ in their structural organization. Purifying these high molecular weight proteins is challenging and has certainly slowed down their characterization. Here, we propose a chromatography-based protocol, mainly relying on multimodal chromatography (core bead technology using Capto Core 700 resin), to purify sortase-dependent SpaCBA pili from the probiotic strain Lacticaseibacillus rhamnosus GG (LGG). Contrary to previously published methods, this purification protocol does not require specific antibodies nor complex laboratory equipment, including for the multimodal chromatography step, and provides high degree of protein purity. No other proteins were detectable by SDS-PAGE and the 260/280 nm ratio (∼0.6) of the UV spectrum confirmed the absence of any other co-purified macromolecules. One can obtain ∼50 μg of purified pili, starting from 1 L culture at OD_600nm ≈ 1, in 2–3 working days. This simple protocol could be useful to numerous laboratories to purify pili from LGG easily. Therefore, the present work should boost specific studies dedicated to LGG SpaCBA pili and the characterization of the interactions occurring with their protein partners at the molecular level. Moreover, this straightforward purification process might be extended to the purification of sortase-dependant pili from other Gram-positive bacteria.

Synbiotics in caries prevention: A scoping review

The scoping review aimed to examine the evidence on the role of synbiotics in caries prevention. PubMed, SCOPUS, and Web of Science databases search were performed. Any in vitro study, clinical trial, systematic review with/without meta-analysis, umbrella review/meta-evaluation, narrative review addressing the role of synbiotics in caries prevention were included in the scoping review. Data were extracted from the included studies using pre-approved registered protocol. Twenty-eight records were identified, of which 5 in vitro studies, 1 quasi-experimental clinical trial and 1 narrative review were included in the present review. No controlled clinical trials or systematic reviews on the role of synbiotics in caries prevention could be identified. Except 1, all in vitro studies examined the combined effect of saccharides and lactobacilli spp. as potential synbiotics on the growth of Streptococcus mutans. However, the proposed synbiotics in 4 in vitro studies either did not qualify or remained ambiguous of its eligibility as a potential synbiotic for caries prevention. One recent in vitro study explored the possibility of L-arginine and Lactobacillus rhamnosus GG synbiotic for caries prevention. The quasi-experimental clinical study without a control arm did not explicitly mention the intervention composition and thus, its synbiotic potential remains unclear. A narrative review highlighted the potential of combining arginine (prebiotic) with arginolytic bacteria (probiotic) as a synbiotic, which appears promising for caries prevention. The eligibility of the proposed synbiotics as a true synbiotic needs to be carefully addressed. Due to a lack of controlled clinical studies on synbiotics for caries prevention, evidence on their caries-preventive potential is weak. Future studies are needed to examine the combination of amino acids (esp. arginine) with probiotics as a potential synbiotic against cariogenic pathogens.

Effect of a novel synbiotic on Streptococcus mutans

We examined the effect of L-arginine - (i) on the growth of L. rhamnosus GG (LrG) and (ii) combined LrG synbiotic on the growth of cariogenic S. mutans. Viability of LrG was assessed using MTT/XTT assays, confocal imaging with ADS activity measurement. The effect of L-arginine (0.5%/1%/2%) (2×/24 h) with LrG on S. mutans was evaluated by measuring the colony forming units, biofilm biomass, real-time qPCR and confocal imaging. The pH of the spent media was measured immediately and 24 h post-treatment with assessment of lactic acid. The LrG viability was highest with 2% L-arginine (p < 0.001). Confocal imaging showed that 2% L-arginine increased biofilm thickness of LrG. The 2% L-arginine and LrG synbiotic significantly inhibited the growth of S. mutans (p < 0.001) reducing the viable counts (p = 0.002) and biofilm biomass (p < 0.001). The pH of spent media was the highest when treated with 2% L-arginine and LrG synbiotic (p < 0.001) with no difference between post-treatment and 24 h post-treatment (p > 0.05). Conversely, the 2% L-arginine and LrG synbiotic showed the lowest lactic acid production (p < 0.001). This study demonstrated that L-arginine enhanced the growth of LrG. The 2% L-arginine and LrG synbiotic synergistically inhibits the growth of S. mutans with significant potential to develop as an anti-caries regimen.

Identification of putative adhesins and carbohydrate ligands of Lactobacillus paracasei using a combinatorial in silico and glycomics microarray profiling approach

Commensal bacteria must colonize host mucosal surfaces to exert health-promoting properties, and bind to gastrointestinal tract (GIT) mucins via their cell surface adhesins. Considerable effort has been directed towards discovery of pathogen adhesins and their ligands to develop anti-infective strategies; however, little is known about the lectin-like adhesins and associated carbohydrate ligands in commensals. In this study, an in silico approach was used to detect surface exposed adhesins in the human commensal Lactobacillus paracasei subsp. paracasei, a promising probiotic commonly used in dairy product fermentation that presents anti-microbial activity. Of the 13 adhesin candidates, 3 sortase-dependent pili clusters were identified in this strain and expression of the adhesin candidate genes was confirmed in vitro. Mass spectrometry analysis confirmed the presence of surface adhesin elongation factor Tu and the chaperonin GroEL, but not pili expression. Whole cells were subsequently incubated on microarrays featuring a panel of GIT mucins from nine different mammalian species and two human-derived cell lines and a library of carbohydrate structures. Binding profiles were compared to those of two known pili-producing lactobacilli, L. johnsonii and L. rhamnosus and all Lactobacillus species displayed overlapping but distinct signatures, which may indicate different abilities for regiospecific GIT colonization. In addition, L. paracasei whole cells favoured binding to α-(2 → 3)-linked sialic acid and α-(1 → 2)-linked fucose-containing carbohydrate structures including blood groups A, B and O and Lewis antigens x, y and b. This study furthers our understanding of host-commensal cross-talk by identifying potential adhesins and specific GIT mucin and carbohydrate ligands and provides insight into the selection of colonization sites by commensals in the GIT.

Lactobacillus rhamnosus GG Genomic and Phenotypic Stability in an Industrial Production Process

Lactobacillus rhamnosus GG is one of the most widely marketed and studied probiotic strains. In L. rhamnosus GG, the spaCBA-srtC1 gene cluster encodes pili, which are important for some of the probiotic properties of the strain. A previous study showed that the DNA sequence of the spaCBA-srtC1 gene cluster was not present in some L. rhamnosus GG variants isolated from liquid dairy products. To examine the stability of the L. rhamnosus GG genome in an industrial production process, we sequenced the genome of samples of L. rhamnosus GG (DSM 33156) collected at specific steps of the industrial production process, including the culture collection stock, intermediate fermentations, and final freeze-dried products. We found that the L. rhamnosus GG genome sequence was unchanged throughout the production process. Consequently, the spaCBA-srtC1 gene locus was intact and fully conserved in all 31 samples examined. In addition, different production batches of L. rhamnosus GG exhibited consistent phenotypes, including the presence of pili in final freeze-dried products, and consistent characteristics in in vitro assays of probiotic properties. Our data show that L. rhamnosus GG is highly stable in this industrial production process.IMPORTANCE Lactobacillus rhamnosus GG is one of the best-studied probiotic strains. One of the well-characterized features of the strain is the pili encoded by the spaCBA-srtC1 gene cluster. These pili are involved in persistence in the gastrointestinal tract and are important for the probiotic properties of L. rhamnosus GG. Previous studies demonstrated that the L. rhamnosus GG genome can be unstable under certain conditions and can lose the spaCBA-srtC1 gene cluster. Since in vitro studies have shown that the loss of the spaCBA-srtC1 gene cluster decreases certain L. rhamnosus GG probiotic properties, we assessed both the genomic stability and phenotypic properties of L. rhamnosus GG throughout an industrial production process. We found that neither genomic nor phenotypic changes occurred in the samples. Therefore, we demonstrate that L. rhamnosus GG retains the spaCBA-srtC1 cluster and exhibits excellent genomic and phenotypic stability in the specific industrial process examined here.

Ribosomal protein L4 of Lactobacillus rhamnosus LRB alters resistance to macrolides and other antibiotics

Lactobacillus rhamnosus is an important lactic acid bacterium that is predominantly used as a probiotic supplement. This bacterium secretes immunomodulatory and antibacterial peptides that are necessary for the probiotic trait. This organism also occupies diverse ecological niches, such as gastrointestinal tracts and the oral cavity. Several studies have shown that L. rhamnosus is prone to spontaneous genome rearrangement irrespective of the ecological origins. We previously characterized an oral isolate of L. rhamnosus, LRB, which is genetically closely related to the widely used probiotic strain L. rhamnosus LGG. In this study, we isolated a nontargeted mutant that was particularly sensitive to acid stress. Using next generation sequencing, we further mapped the putative mutations in the genome and found that the mutant had acquired a deletion of 75 base pairs in the rplD gene that encodes the large ribosomal subunit L4. The mutant had a growth defect at 37°C and at ambient temperature. Further antibiotic sensitivity analyses indicated that the mutant is relatively more resistant to erythromycin and chloramphenicol; two antibiotics that target the 50S subunit. In contrast, the mutant was more sensitive to tetracycline, which targets the 30S subunit. Thus, it appears that nontargeted mutations could significantly alter the antibiotic resistance profile of L. rhamnosus. Our study raises concern that probiotic use of L. rhamnosus should be carefully monitored to avoid unintended consequences.

Characterization of a stress tolerance-defective mutant of Lactobacillus rhamnosus LRB

Lactobacillus rhamnosus is a lactic acid bacterium that survives diverse ecological niches, including the human oral cavity and gastrointestinal tract. L. rhamnosus is an acidogenic bacterium that produces copious amounts of lactic acid. The organism is also considered as aciduric, since it can survive prolonged exposure to an acidic environment. For a probiotic bacterium such as L. rhamnosus, it is necessary to understand how this organism survives acid stress. In this study we used L. rhamnosus LRB to isolate one spontaneous mutant that was sensitive to acid stress. The mutant, which we named RBM1, also displayed sensitivity to a wide range of stresses including osmotic, thermal, and others. Using whole genome sequencing, we mapped the putative mutations in the mutant strain. It appears that three single nucleotide substitutions occurred in the mutant as compared to the wild-type LRB strain. Among those, the most relevant mutation occurred in the ftsH gene that created a single amino acid change in the protein. We performed a comparative proteomic study to understand the molecular basis for stress sensitivity and found that ~15% of the proteome is altered in the mutant strain. Our study suggests that generation of spontaneous mutants during L. rhamnosus colonization could drastically affect bacterial physiology and survival under stress conditions.

Construction of Synthetic Microbiota for Reproducible Flavor Compound Metabolism in Chinese Light-Aroma-Type Liquor Produced by Solid-State Fermentation

Natural microbiota plays an essential role in flavor compounds used in traditional food fermentation; however, the fluctuation in natural microbiota results in inconsistency in food quality. Thus, it is critical to reveal the core microbiota for flavor compound production and to construct a synthetic core microbiota for use in constant food fermentation. Here, we reveal the core microbiota based on their flavor production and cooccurrence performance, using Chinese light-aroma-type liquor as a model system. Five genera, Lactobacillus, Saccharomyces, Pichia, Geotrichum, and Candida, were identified to be the core microbiota. The synthetic core microbiota of these five genera presented a reproducible dynamic profile similar to that in the natural microbiota. A Monte Carlo test showed that the effects of five environmental factors (lactic acid, ethanol, and acetic acid contents, moisture, and pH) on the synthetic microbiota distribution were highly significant (P < 0.01), similar to those effects on a natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ > 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. This work is of great significance for the tractable and constant production of various fermented foods.IMPORTANCE The transformation from natural fermentation to synthetic fermentation is essential in constructing a constant food fermentation process, which is the premise for stably making high-quality food. According to flavor-producing and cooccurring functions in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light-aroma-type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compound production in the in vitro system. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota but also be beneficial for constructing a tractable and reproducible food fermentation process.

Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex

Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR-Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR-Cas systems in plant-pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR-Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR-Cas types I-E and II-C were found, with I-E being the most common. The presence of the same CRISPR-Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I-E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage-insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR-Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer-protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR-Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy.

Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress

Prolonged heat stress is one of the harsh conditions Lactobacillus casei strains encounter as non-starter lactic acid bacteria in dairy product manufacture. To understand the physiological and molecular mechanisms through which Lb. casei GCRL163 adapts to persistent elevated temperature, label-free quantitative proteomics of cell-free extracts was used to characterize the global responses of the strain cultured anaerobically in bioreactors at 30 to 45°C, pH 6.5, together with GC-MS for fatty acid methyl ester analysis at different growth phases. At higher growth temperatures, repression of energy-consuming metabolic pathways, such as fatty acid, nucleotide and amino acid biosynthesis, was observed, while PTS- and ABC-type transporter systems associated with uptake of nitrogen and carbon sources were up-regulated. Alkaline shock protein Asp23_2 was only detected at 45°C, expressed at high abundance, and presumptive α-L-fucosidase only at 40 and 45°C, with highly increased abundance (log2-fold change of 7) at 45°C. We identified a novel SecB homolog as a protein export chaperone putatively involved in posttranslational translocation systems, which was down-regulated as growth temperature increased and where the modelled 3D-structure shared architectural similarities with the Escherichia coli SecB protein. Membrane lipid analyses revealed temporal changes in fatty acid composition, cyclization of oleic acid to cyclopropane and novel cyclopentenyl moieties, and reduced synthesis of vaccenic acid, at higher temperatures. An 18kDa α-crystallin domain, Hsp20 family heat shock protein was more highly up-regulated in response to heat stress compared to other molecular chaperones, suggesting this protein could be a useful biomarker of prolonged heat stress in Lb. casei GCRL163.

Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275

In a previous study, incorporation of high exopolysaccharide (EPS) producing dairy starter bacterium Streptococcus thermophilus ASCC 1275 was found to improve functionality of low fat mozzarella cheese and yogurt. This bacterium in its eps gene cluster has a unique pair of chain length determining genes, epsC- epsD, when compared to other sequenced S. thermophilus strains. Hence, the aim of this study was to understand the regulatory mechanism of EPS production in this bacterium using transcriptomic analysis to provide opportunities to improve the yield of EPS. As sugars are considered as one of the major determinants of EPS production, after preliminary screening, we selected three sugars, glucose, sucrose and lactose to identify the EPS producing mechanism of this bacterium in M17 medium. Complete RNA-seq analysis was performed using Illumina HiSeq 2000 sequencing system on S. thermophilus 1275 grown in three different sugars at two-time points, 5 h (log phase) and 10 h (stationary phase) to recognize the genes involved in sugar uptake, UDP-sugar formation, EPS assembly and export of EPS outside the bacterial cell. S. thermophilus 1275 was found to produce high amount of EPS (∼430 mg/L) in sucrose (1%) supplemented M17 medium when compared to other two sugars. Differential gene expression analysis revealed the involvement of phosphoenolpyruvate phosphotransferase system (PEP-PTS) for glucose and sucrose uptake, and lacS gene for lactose uptake. The pathways for the formation of UDP-glucose and UDP-galactose were highly upregulated in all the three sugars. In the presence of sucrose, eps1C1D2C2D were found to be highly expressed which refers to high EPS production. Protein homology study suggested the presence of Wzx/Wzy-dependent EPS synthesis and transport pathway in this bacterium. KEGG pathway and COG functional enrichment analysis were also performed to support the result. This is the first report providing the transcriptomic insights into the EPS production mechanism of a common dairy bacterium, S. thermophilus.

Two-step production of anti-inflammatory soluble factor by Lactobacillus reuteri CRL 1098

We have demonstrated previously that a soluble factor (LrS) produced by Lactobacillus (L.) reuteri CRL 1098 modulates the inflammatory response triggered by lipopolysaccharide. In this study, the production of LrS by L. reuteri CRL 1098 was realized through two steps: i) bacterial biomass production, ii) LrS production, where the bacterial biomass was able to live but did not proliferate. Therefore, the simultaneous evaluation of the effect of different factors on the growth and LrS production was performed. Biomass production was found to be dependent mainly on culture medium, while LrS production with anti-inflammatory activity depended on culture conditions of the biomass such as pH, agitation and growth phase. The L. reuteri CRL 1098 biomass and LrS production in the optimized culture media designed for this work reduced the complete process cost by approximately 95%, respectively to laboratory scale cost.

Potential of Lactobacillus plantarum ccm 3627 and Lactobacillus brevis ccm 1815 for fermentation of cereal substrates

Lactobacillus is the most representative strain in a group of lactic acid bacteria, which perform an essential role in the preservation and production of wholesome foods. Lactic acid fermentation is the oldest traditional method for preparation of fermented vegetables, meat products, dairy products and cereal foods. Cereal grains are considered to be one of the most important sources of dietary proteins, carbohydrates, vitamins, minerals and fibre for people. The main exploitation of cereals is to prepare sourdough, which is a mixture of wheat, rye or other cereal flour with water and contains yeasts and lactobacilli. The basic biochemical changes that occur in sourdough bread fermentation are acidification of the dough with organic acids produced by the lactobacilli and leavening with carbon dioxide produced by the yeast and the lactobacilli. Acidification perhaps initiate enzymatic processes of proteins and phytates degradation. Lactobacilli produce various enzymes which make flavour precursors, improve of mineral bioavailability or degrade celiac active peptides, because some species of lactobacilli produce specific peptidases during growth, which are capable to hydrolyze hardly cleavable, celiac-active proline-rich peptides. Microbial fermentation with selected strains of lactobacilli may be new alternative approach for modification of gluten by hydrolysis. In this paper are described growth characteristics and intracellular aminopeptidases activities of Lactobacillus plantarum CCM 3627 and Lactobacillus brevis CCM 1815. Work was focused on characterization of the lactobacilli for potential usage as a starter culture in further fermentation experiments.

Fermentation of Dietetic Fiber from Green Bean and Prickly Pear Shell by Pure and Mixture Culture of Lactobacillus acidophilus LA-5 and Bifidobacterium bifidum 450B

The aim of this study was to evaluate the fermentation of dietary fiber from green bean (Phaseolus vulgaris) and prickly pear shell (Opuntia ficus-indica) by Lactobacillus acidophilus LA-5 and Bifidobacterium bifidum 450B growing as mono-culture and co-culture, the fermentation products, and proteins expressed during this process. The analysis of the fermentation profile showed a major growth of bacteria in the culture media of each dietary fiber supplemented with glucose, and particularly B. bifidum 450B at 48 h showed the highest growth. In the case of the co-culture, the growth was lower indicating the possible negative interaction between L. acidophilus LA-5 and B. bifidum 450B and may be due to the less amount of carbohydrates and the high content of non-soluble fiber that affected the nutrients availability for the bacterial strains. The pH changes indicated the presence of short-chain fatty acids (SCFAs), being acetate (46-100%) the main SCFA. Changes in the proteome concerned proteins that are involved in carbohydrate and other carbohydrate pathways. The characterization of the bacteria according to the growth, metabolites, and proteins expressed allows understanding the response to the change of environmental conditions and could be useful to understand L. acidophilus LA-5 and B. bifidum 450B strains' adaptation to specific applications.

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.

Proteomic analysis of an engineered isolate of Lactobacillus plantarum with enhanced raffinose metabolic capacity

Lactic acid bacteria that can produce alpha-galactosidase are a promising solution for improving the nutritional value of soy-derived products. For their commercial use in the manufacturing process, it is essential to understand the catabolic mechanisms that facilitate their growth and performance. In this study, we used comparative proteomic analysis to compare catabolism in an engineered isolate of Lactobacillus plantarum P-8 with enhanced raffinose metabolic capacity, with the parent (or wild-type) isolate from which it was derived. When growing on semi-defined medium with raffinose, a total of one hundred and twenty-five proteins were significantly up-regulated (>1.5 fold, P < 0.05) in the engineered isolate, whilst and one hundred and six proteins were significantly down-regulated (<−1.5 fold, P < 0.05). During the late stages of growth, the engineered isolate was able to utilise alternative carbohydrates such as sorbitol instead of raffinose to sustain cell division. To avoid acid damage the cell layer of the engineered isolate altered through a combination of de novo fatty acid biosynthesis and modification of existing lipid membrane phospholipid acyl chains. Interestingly, aspartate and glutamate metabolism was associated with this acid response. Higher intracellular aspartate and glutamate levels in the engineered isolate compared with the parent isolate were confirmed by further chemical analysis. Our study will underpin the future use of this engineered isolate in the manufacture of soymilk products.

Differential proteome and cellular adhesion analyses of the probiotic bacterium Lactobacillus acidophilus NCFM grown on raffinose - an emerging prebiotic

Whole cell and surface proteomes were analyzed together with adhesive properties of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) grown on the emerging prebiotic raffinose, exemplifying a synbiotic. Adhesion of NCFM to mucin and intestinal HT-29 cells increased three-fold after culture with raffinose versus glucose, as also visualized by scanning electron microscopy. Comparative proteomics using 2D-DIGE showed 43 unique proteins to change in relative abundance in whole cell lysates from NCFM grown on raffinose compared to glucose. Furthermore, 14 unique proteins in 18 spots of the surface subproteome underwent changes identified by differential 2DE, including elongation factor G, thermostable pullulanase, and phosphate starvation inducible stress-related protein increasing in a range of +2.1 - +4.7 fold. By contrast five known moonlighting proteins decreased in relative abundance by up to -2.4 fold. Enzymes involved in raffinose catabolism were elevated in the whole cell proteome; α-galactosidase (+13.9 fold); sucrose phosphorylase (+5.4 fold) together with metabolic enzymes from the Leloir pathway for galactose utilization and the glycolysis; β-galactosidase (+5.7 fold); galactose (+2.9/+3.1 fold) and fructose (+2.8 fold) kinases. The insights at the molecular and cellular levels contributed to the understanding of the interplay of a synbiotic composed of NCFM and raffinose with the host.

Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili

Mapping of the microbial molecules underlying microbiota-host interactions is key to understand how microbiota preserve mucosal homeostasis. A pivotal family of such bacterial molecules are pili. Pili are proteinaceous cell wall appendages with a well-documented role in adhesion, whilst their role in immune interaction with the host is less established. Gram-positive pili are often posttranslationally modified by sortase-specific cleavage reactions and the formation of intramolecular peptide bonds. Here we report glycosylation as a new level of posttranslational modification of sortase-dependent pili of a beneficial microbiota species and its role in immune modulation. We focused on the SpaCBA pili of the model probiotic and beneficial human gut microbiota isolate Lactobacillus rhamnosus GG. A unique combination of molecular techniques, nanoscale mechanical and immunological approaches led to the identification of mannose and fucose residues on the SpaCBA pili. These glycans on the pili are recognized by human dendritic cells via the C-type lectin receptor DC-SIGN, a key carbohydrate-dependent immune tailoring pattern recognition receptor. This specific lectin-sugar interaction is moreover of functional importance and modulated the cytokine response of dendritic cells. This provides insight into the direct role bacterial glycoproteins can play in the immunomodulation of the host. Modification of the complex heterotrimeric pili of a model probiotic and microbiota isolate with mannose and fucose is of importance for the functional interaction with the host immune lectin receptor DC-SIGN on human dendritic cells. Our findings shed light on the yet underappreciated role of glycoconjugates in bacteria-host interactions.

Identification of Oxygen-Responsive Transcripts in the Silage Inoculant Lactobacillus buchneri CD034 by RNA Sequencing

The Lactobacillus buchneri CD034 strain, known to improve the ensiling process of green fodder and the quality of the silage itself was transcriptionally analyzed by sequencing of transcriptomes isolated under anaerobic vs. aerobic conditions. L. buchneri CD034 was first cultivated under anaerobic conditions and then shifted to aerobic conditions by aeration with 21% oxygen. Cultivations already showed that oxygen was consumed by L. buchneri CD034 after aeration of the culture while growth of L. buchneri CD034 was still observed. RNA sequencing data revealed that irrespective of the oxygen status of the culture, the most abundantly transcribed genes are required for basic cell functions such as protein biosynthesis, energy metabolism and lactic acid fermentation. Under aerobic conditions, 283 genes were found to be transcriptionally up-regulated while 198 genes were found to be down-regulated (p-value < 0.01). Up-regulated genes i. a. play a role in oxygen consumption via oxidation of pyruvate or lactate (pox, lctO). Additionally, genes encoding proteins required for decomposition of reactive oxygen species (ROS) such as glutathione reductase or NADH peroxidase were also found to be up-regulated. Genes related to pH homeostasis and redox potential balance were found to be down-regulated under aerobic conditions. Overall, genes required for lactic acid fermentation were hardly affected by the growth conditions applied. Genes identified to be differentially transcribed depending on the aeration status of the culture are suggested to specify the favorable performance of the strain in silage formation.

Ecologically and geologically relevant isotope signatures of C, N, and S: okenone producing purple sulfur bacteria Part I

Purple sulfur bacteria (PSB) are known to couple the carbon, nitrogen, and sulfur cycling in euxinic environments. This is the first study with multiple strains and species of okenone-producing PSB to examine the carbon (C), nitrogen (N), and sulfur (S) metabolisms and isotopic signatures in controlled laboratory conditions, investigating what isotopic fractionations might be recorded in modern environments and the geologic record. PSB play an integral role in the ecology of euxinic environments and produce the unique molecular fossil okenane, derived from the diagenetic alteration of the carotenoid pigment okenone. Cultures of Marichromatium purpuratum 1591 (Mpurp1591) were observed to have carbon isotope fractionations ((13)ε biomass - CO2), via RuBisCO, ranging from -16.1 to -23.2‰ during exponential and stationary phases of growth. Cultures of Thiocapsa marina 5653 (Tmar5653) and Mpurp1591 had a nitrogen isotope fractionation ((15)ε biomass - NH 4) of -15‰, via glutamate dehydrogenase, measured and recorded for the first time in PSB. The δ(34) SVCDT values and amount of stored elemental sulfur for Mpurp1591 cells grown autotrophically and photoheterotrophically were dependent upon their carbon metabolic pathways. We show that PSB may contribute to the isotopic enrichments observed in modern and ancient anoxic basins. In a photoheterotrophic culture of Mpurp1591 that switched to autotrophy once the organic substrate was consumed, there were bulk biomass δ(13)C values that span a broader range than recorded across the Late Devonian, Permian-Triassic, Triassic-Jurassic, and OAE2 mass extinction boundaries. This finding stresses the complexities in interpreting and assigning δ(13)C values to bulk organic matter preserved in the geologic record.

Immunomodulation properties of multi-species fermented milks

Dairy propionibacteria (PAB) are used as a ripening starter in combination with Lactic acid bacteria (LAB) for dairy products such as Swiss-type cheese. LAB and PAB have also been studied for their probiotic properties but little is still known about their individual and/or synergistic beneficial effects within dairy matrices. In the context of a rising incidence of Inflammatory Bowel Diseases, it has become crucial to evaluate the immunomodulatory potential of bacteria ingested in large numbers via dairy products. We therefore selected different strains and combinations of technological LAB and PAB. We determined their immunomodulatory potential by IL-10 and IL-12 induction, in human peripheral blood mononuclear cells, on either single or mixed cultures, grown on laboratory medium or directly in milk. Milk was fermented with selected anti-inflammatory strains of LAB or PAB/LAB mixed cultures and the resulting bacterial fractions were also evaluated for these properties, together with starter viability and optimum technological aspects. The most promising fermented milks were evaluated in the context of TNBS- or DSS-induced colitis in mice. The improvement in inflammatory parameters evidenced an alleviation of colitis symptoms as a result of fermented milk consumption. This effect was clearly strain-dependent and modulated by growth within a fermented dairy product. These findings offer new tools and perspectives for the development of immunomodulatory fermented dairy products for targeted populations.