Metabolic and proteomic adaptation of Lactobacillus rhamnosus strains during growth under cheese-like environmental conditions compared to de Man, Rogosa, and Sharpe medium

Cultivable microbial diversity, peptide profiles, and bio-functional properties in Parmigiano Reggiano cheese

Introduction

Lactic acid bacteria (LAB) communities shape the sensorial and functional properties of artisanal hard-cooked and long-ripened cheeses made with raw bovine milk like Parmigiano Reggiano (PR) cheese. While patterns of microbial evolution have been well studied in PR cheese, there is a lack of information about how this microbial diversity affects the metabolic and functional properties of PR cheese.

Methods

To fill this information gap, we characterized the cultivable fraction of natural whey starter (NWS) and PR cheeses at different ripening times, both at the species and strain level, and investigated the possible correlation between microbial composition and the evolution of peptide profiles over cheese ripening.

Results and discussion

The results showed that NWS was a complex community of several biotypes belonging to a few species, namely, Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. lactis. A new species-specific PCR assay was successful in discriminating the cheese-associated species Lacticaseibacillus casei, Lacticaseibacillus paracasei, Lacticaseibacillus rhamnosus, and Lacticaseibacillus zeae. Based on the resolved patterns of species and biotype distribution, Lcb. paracasei and Lcb. zeae were most frequently isolated after 24 and 30 months of ripening, while the number of biotypes was inversely related to the ripening time. Peptidomics analysis revealed more than 520 peptides in cheese samples. To the best of our knowledge, this is the most comprehensive survey of peptides in PR cheese. Most of them were from β-caseins, which represent the best substrate for LAB cell-envelope proteases. The abundance of peptides from β-casein 38-88 region continuously increased during ripening. Remarkably, this region contains precursors for the anti-hypertensive lactotripeptides VPP and IPP, as well as for β-casomorphins. We found that the ripening time strongly affects bioactive peptide profiles and that the occurrence of Lcb. zeae species is positively linked to the incidence of eight anti-hypertensive peptides. This result highlighted how the presence of specific LAB species is likely a pivotal factor in determining PR functional properties.

Proteomics and Metabolomics Analysis Reveal the Regulation Mechanism of Linoleate Isomerase Activity and Function in Propionibacterium acnes

Conjugated linoleic acid (CLA) holds significant application prospects due to its anticancer, anti-atherosclerosis, lipid-lowering, weight-loss, and growth-promoting functions. The key to its efficient production lies in optimizing the biocatalytic performance of linoleic acid isomerase (LAI). Here, we constructed a Propionibacterium acnes mutant library and screened positive mutants with high linoleate isomerase activity. The proteomics and metabolomics were used to explore the mechanism in the regulation of linoleic acid isomerase activity. High-throughput proteomics revealed 104 differentially expressed proteins unique to positive mutant strains of linoleic acid isomerase of which 57 were upregulated and 47 were downregulated. These differentially expressed proteins were primarily involved in galactose metabolism, the phosphotransferase system, starch metabolism, and sucrose metabolism. Differential metabolic pathways were mainly enriched in amino acid biosynthesis, including glutamate metabolism, the Aminoacyl-tRNA biosynthesis pathway, and the ABC transporter pathway. The upregulated metabolites include dl-valine and Acetyl coA, while the downregulated metabolites include Glutamic acid and Phosphoenolpyruvate. Overall, the activity of linoleic acid isomerase in the mutant strain was increased by the regulation of key proteins involved in galactose metabolism, sucrose metabolism, and the phosphotransferase system. This study provides a theoretical basis for the development of high-yield CLA food.

Plasma branched-chain and aromatic amino acids correlate with the gut microbiota and severity of Parkinson's disease

Disturbances of circulating amino acids have been demonstrated in patients with Parkinson’s disease (PD). However, there have been no consistent results for branched-chain amino acids (BCAAs) and aromatic amino acids (AAAs), and related factors have not been explored. We aimed to explore plasma BCAA and AAA profiles in PD patients, and identify their correlations with clinical characteristics and the gut microbiota. Plasma BCAA (leucine, isoleucine, and valine) and AAA (tyrosine and phenylalanine) levels were measured in 106 PD patients and 114 controls. Fecal samples were collected from PD patients for microbiota sequencing and functional analysis. We found that plasma BCAAs and tyrosine were decreased in PD patients. BCAAs and AAAs were correlated with clinical characteristics and microbial taxa, and, in particular, they were negatively correlated with the Hoehn and Yahr stage. Compared with early PD patients, BCAA and AAA levels were even lower, and microbial composition was altered in advanced PD patients. Predictive functional analysis indicated that predicted genes numbers involved in BCAA biosynthesis were lower in advanced PD patients. What’s more, the fecal abundances of critical genes (ilvB, ilvC, ilvD, and ilvN) involved in BCAA biosynthesis were reduced and fecal BCAA concentrations were lower in advanced PD patients. In conclusion, the disturbances of plasma BCAAs and AAAs in PD patients may be related to the gut microbiota and exacerbated with PD severity. The microbial amino acid metabolism may serve as a potential mechanistic link.

Impact of NSLAB on Kazakh cheese flavor

Xinjiang is a multiethnic region of China. Traditionally, most ethnic minorities are known to produce and consume cheese. Nomadic people have been reported to use lactic acid bacteria (LAB) for decades to produce fermented dairy products as part of a balanced diet. Non-starter LAB (NSLAB) contribute to different degrees of ripening, depending on the cheese variety. In the present study, we screened three types of NSLAB with good proteolysis and autolytic abilities from traditional Kazakh cheese: Pediococcus acidilactici R3-5, Staphylococcus epidermidis R4-2, and Lactobacillus rhamnosus R9-6. A control (no NSLAB) was also included, resulting in four distinct types of cheese samples. We used gas chromatography-mass spectrometry and the electronic nose system to identify volatile compounds and analyze the effect of NSLAB on cheese flavor at the ripening stage. The physicochemical indicators changed significantly during the ripening of Kazakh cheese. Compared with the control, the protein content, free fatty acid content, pH, flavor compounds, and odor profiles of the test cheeses were significantly different. The major chemical differences among cheeses were the synthesis of some key volatile components (ethyl caprylate, ethyl caprate, myristyl carbonate, capric acid, caprylic acid, nonanal, and benzyl alcohol). NSLAB can be used as an adjunct starter to make Kazakh cheese and the use of NSLAB affected the cheese flavor quality positively.

Reliability of MALDI-TOF mass spectrometry to identify oral isolates of Streptococcus salivarius and Lactobacillus spp

OBJECTIVE

The aim of this study is to evaluate the performance of MALDI-TOF mass spectrometry in identifying bacteria isolated in the oral cavity known to be of probiotic interest.

DESIGN

We evaluated Bruker MALDI Biotyper for the identification of 92 clinical oral isolates of probiotic interest (31 Streptococcus salivarius and 61 Lactobacillus spp.) by comparing direct colony method with on-plate formic acid extraction. Isolates were previously identified by use of biochemical methods and molecular biology.

RESULTS

Using the manufacturer's suggested genus and species level cutoff scores, the direct colony method identified 42 (45.7%) isolates at the genus level and 35 (38%) at the species level while the on-plate extraction method correctly identified 90 (97.8%) isolates at the genus level and 82 (89.1%) at the species level. The difference between the two methods was statistically significant at the genus and species levels (P ≤ 0.0001). After dividing the isolates into two subgroups, the analysis was repeated. The direct colony method identified correctly all isolates of Streptococcus salivarius at the species level. In contrast, the direct colony method allowed the identification of only 11 (18%) lactobacilli at the genus level and 4 (6.6%) at the species level. The on-plate extraction method was statistically (P ≤ 0.0001) more efficient since 59 (96.7%) lactobacilli were identified at the genus level and 51 (83.6%) at the species level.

CONCLUSIONS

MALDI Biotyper can efficiently identify Streptococcus salivarius regardless of the preparative method but on-plate extraction is superior to direct colony method for the identification of lactobacilli.

Genomic analysis of a hop-resistance Lactobacillus brevis strain responsible for food spoilage and capable of entering into the VBNC state

BACKGROUND

Lactobacillus brevis is a major contaminant of spoiled beer. And it was able to enter VBNC state and cause false negative detection, which poses a major challenge to the brewing industry.

METHODS

The genomic DNA of L. brevis BM-LB13908 was extracted and purified to form a sequencing library that meets the quality requirements and was sequenced. The sequencing results were then screened and assembled to obtain the entire genome sequence of L. brevis. Predicted genes were annotated by GO database, KEGG pathway database and COG functional classification system.

RESULTS

The final assembly yielded 275 scaffolds of a total length of 2 840 080 bp with a G + C content of 53.35%. There were 2357, 701, 1519 predicted genes with corresponding GO functional, COG functional, and KEGG biological pathway annotations, respectively. The genome of L. brevis BM-LB13908 contains hop resistance gene horA and multiple genes related to the formation of VBNC state.

CONCLUSIONS

This report describes the draft genome sequence of L. brevis BM-LB13908, a spoilage strain isolated from finished beer sample. This study may support further study on L. brevis and other beer spoilage bacteria, and prevent and control beer spoilage caused by microorganisms.

Enhanced Exopolysaccharide Production by Lactobacillus rhamnosus in Co-Culture with Saccharomyces cerevisiae

Lactobacillus strains are known to produce exopolysaccharides (EPS) with recognized health benefits (i.e. prebiotic and immunomodulation) but production is limited by low yields. Co-culture has been shown to improve metabolite productivity, particularly bacteriocins and EPS. Although lactic acid bacteria (LAB) and yeasts are found in several fermented products, the molecular mechanisms linked to the microbial interactions and their influences on EPS biosynthesis are unclear. The aim of the present study was to investigate the effect of co-culture on EPS production by three Lactobacillus rhamnosus strains (ATCC 9595, R0011, and RW-9595M) in association with Saccharomyces cerevisiae. Fermentation, in both mono and co-culture, was carried out and the expression of key LAB genes was monitored. After 48 h, results revealed that EPS production was enhanced by 39%, 49%, and 42% in co-culture for R0011, ATCC 9595, and RW-9595M, respectively. Each strain showed distinctive gene expression profiles. For a higher EPS production, higher EPS operon expression levels were observed for RW-9595M in co-culture. The construction of gene co-expression networks revealed common correlations between the expression of genes related to the EPS operons, sugar metabolism, and stress during EPS production and microbial growth for the three strains. Our findings provide insight into the positive influence of inter-kingdom interactions in stimulating EPS biosynthesis, representing progress toward the development of a bio-ingredient with broad industrial applications.

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.

How Listeria monocytogenes Shapes Its Proteome in Response to Natural Antimicrobial Compounds

The goal of this study was to investigate the adaptation of L. monocytogenes Scott A cells to treatments with sublethal doses of antimicrobials (ethanol, citral, carvacrol, E-2-hexenal and thyme essential oil). The survival of L. monocytogenes cells was not affected by the antimicrobials at the concentrations assayed, with the exception of ethanol (1% v/v) and thyme essential oil (100 mg/L), which decreased cell viability from 8.53 ± 0.36 to 7.20 ± 0.22 log CFU/mL (P = 0.04). We subsequently evaluated how L. monocytogenes regulates and shapes its proteome in response to antimicrobial compounds. Compared to the control cells grown under optimal conditions, L. monocytogenes treated for 1 h with the antimicrobial compounds showed increased or decreased (≥ or ≤2-fold, respectively, P < 0.05) levels of protein synthesis for 223 protein spots. As shown multivariate clustering analysis, the proteome profiles differed between treatments. Adaptation and shaping of proteomes mainly concerned cell cycle control, cell division, chromosome, motility and regulatory related proteins, carbohydrate, pyruvate, nucleotide and nitrogen metabolism, cofactors and vitamins and stress response with contrasting responses for different stresses. Ethanol, citral (85 mg/l) or (E)-2-hexenal (150 mg/L) adapted cells increased survival during acid stress imposed under model (BHI) and food-like systems.

How the Fewest Become the Greatest. L. casei's Impact on Long Ripened Cheeses

Members of the Lactobacillus casei group, including species classified currently as L. casei, L. paracasei, and L. rhamnosus, are among the most frequently found species in raw milk, hard cooked, long-ripened cheeses. Starting from very low numbers in raw milk, they become dominant in the cheese during ripening, selected by physical and chemical changes produced by cheese making and ripening. Their presence at different stages of cheese making and ripening is crucial in defining product features. For these reasons, the scientific community has been more and more interested in studying these “tiny but mighty microbes” and their implications during cheese making and ripening. The present paper reviews the current literature on the effect of L. casei in cheeses, with particular reference to the case of Parmigiano Reggiano and Grana Padano, two of the most famous PDO (Protected Designation of Origin) Italian cheeses. Recent advances regarding the selection of new wild strains able to persist until the end of ripening and carrying out slow but crucial activities resulting in specific aromatic features, are also presented.

Proteome Response of Staphylococcus xylosus DSM 20266T to Anaerobiosis and Nitrite Exposure

The viability and competitiveness of Staphylococcus xylosus in meat mostly depend on the ability to adapt itself to rapid oxygen and nutrients depletion during meat fermentation. The utilization of nitrite instead of oxygen becomes a successful strategy for this strain to improve its performance in anaerobiosis; however, metabolic pathways of this strain underlying this adaptation, are partially known. The aim of this study was to provide an overview on proteomic changes of S. xylosus DSM 20266T cultured under anaerobiosis and nitrite exposure. Thus, two different cultures of this strain, supplemented or not with nitrite, were in vitro incubated in aerobiosis and anaerobiosis monitoring cell viability, pH, oxidation reduction potential and nitrite content. Protein extracts, obtained from cells, collected as nitrite content was depleted, were analyzed by 2DE/MALDI-TOF/TOF-MS. Results showed that DSM 20266T growth was significantly sustained by nitrite in anaerobiosis, whereas no differences were found in aerobiosis. Accordingly, nitrite content was depleted after 13 h only in anaerobiosis. At this time of sampling, a comparative proteomic analysis showed 45 differentially expressed proteins. Most differences were found between aerobic and anaerobic cultures without nitrite; the induction of glycolytic enzymes and glyoxylate cycle, the reduction of TCA enzymes, and acetate fermentation were found in anaerobiosis to produce ATP and maintain the cell redox balance. In anaerobic cultures the nitrite supplementation partially restored TCA cycle, and reduced the amount of glycolytic enzymes. These results were confirmed by phenotypic microarray that, for the first time, was carried out on cell previously adapted at the different growth conditions. Overall, metabolic changes were similar between aerobiosis and anaerobiosis NO₂-adapted cells, whilst cells grown under anaerobiosis showed different assimilation profiles by confirming proteomic data; indeed, these latter extensively assimilated substrates addressed at both supplying glucose for glycolysis or fueling alternative pathways to TCA cycle. In conclusion, metabolic pathways underlying the ability of S. xylosus to adapt itself to oxygen starvation were revealed; the addition of nitrite allowed S. xylosus to take advantage of nitrite to this condition, restoring some metabolic pathway underlying aerobic behavior of the strain.

Symposium review: Interaction of starter cultures and nonstarter lactic acid bacteria in the cheese environment

The microbiota of ripening cheese is dominated by lactic acid bacteria, which are either added as starters and adjunct cultures or originate from the production and processing environments (nonstarter or NSLAB). After curd formation and pressing, starters reach high numbers, but their viability then decreases due to lactose depletion, salt addition, and low pH and temperature. Starter autolysis releases cellular contents, including nutrients and enzymes, into the cheese matrix. During ripening, NSLAB may attain cell densities up to 8 log cfu per g after 3 to 9 mo. Depending on the species and strain, their metabolic activity may contribute to defects or inconsistency in cheese quality and to the development of typical cheese flavor. The availability of gene and genome sequences has enabled targeted detection of specific cheese microbes and their gene expression over the ripening period. Integrated systems biology is needed to combine the multiple perspectives of post-genomics technologies to elucidate the metabolic interactions among microorganisms. Future research should delve into the variation in cell physiology within the microbial populations, because spatial distribution within the cheese matrix will lead to microenvironments that could affect localized interactions of starters and NSLAB. Microbial community modeling can contribute to improving the efficiency and reduce the cost of food processes such as cheese ripening.

Toward the identification of a type I toxin-antitoxin system in the plasmid DNA of dairy Lactobacillus rhamnosus

Plasmids carry genes that give bacteria beneficial traits and allow them to survive in competitive environments. In many cases, they also harbor toxin-antitoxin (TA) systems necessary for plasmid maintenance. TA systems are generally characterized by a stable “toxin”, a protein or peptide capable of killing the cell upon plasmid loss and by an unstable “antitoxin”, a protein or a non-coding RNA that inhibits toxin activity. Here we report data toward the identification of a RNA-regulated TA system in the plasmid DNA of L. rhamnosus isolated from cheese. The proposed TA system comprises two convergently transcribed RNAs: a toxin RNA encoding a 29 amino acid peptide named Lpt and an antitoxin non-coding RNA. Both toxin and antitoxin RNAs resulted upregulated under conditions mimicking cheese ripening. The toxicity of the Lpt peptide was demonstrated in E. coli by cloning the Lpt ORF under the control of an inducible promoter. Bioinformatics screening of the bacterial nucleotide database, shows that regions homologous to the Lpt TA locus are widely distributed in the Lactobacillus genus, particularly within the L. casei group, suggesting a relevant role of TA systems in plasmid maintenance of cheese microbiota.

Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay

Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. The close genetic relationship among those species, as well as the similarity of biochemical properties of the strains, hinders the development of an adequate selective method to identify these bacteria. Despite this being a hot topic, as demonstrated by the large amount of literature about it, the results of different proposed identification methods are often ambiguous and unsatisfactory. The aim of this study was to develop a more robust species-specific identification assay for differentiating the species of the L. casei group. A taxonomy-driven comparative genomic analysis was carried out to select the potential target genes whose similarity could better reflect genome-wide diversity. The gene mutL appeared to be the most promising one and, therefore, a novel species-specific multiplex PCR assay was developed to rapidly and effectively distinguish L. casei, L. paracasei and L. rhamnosus strains. The analysis of a collection of 76 wild dairy isolates, previously identified as members of the L. casei group combining the results of multiple approaches, revealed that the novel designed primers, especially in combination with already existing ones, were able to improve the discrimination power at the species level and reveal previously undiscovered intraspecific biodiversity.

Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening

Long ripened cheeses, such as Grana Padano (GP), a Protected Designation of Origin (PDO) Italian cheese, harbor a viable microbiota mainly composed of non-starter lactic acid bacteria (NSLAB), which contribute to the final characteristics of cheese. The NSLAB species Lactobacillus rhamnosus, Lb. casei and Lb. paracasei are frequently found in GP, and form a closely related taxonomic group (Lb. casei group), making it difficult to distinguish the three species through 16S rRNA sequencing. SpxB, a metabolic gene coding for pyruvate oxidase in Lb. casei group, was recently used to distinguish the species within this bacterial group, both in pure cultures and in cheese, where it could provide an alternative energy source through the conversion of pyruvate to acetate. The aim of this work was to study the evolution of the metabolically active microbiota during different stages of GP ripening, targeting 16S rRNA to describe the whole microbiota composition, and spxB gene to monitor the biodiversity within the Lb. casei group. Furthermore, activation of pyruvate oxidase pathway was measured directly in cheese by reverse transcription real time PCR (RT-qPCR). The results showed that Lb. casei group dominates throughout the ripening and high-throughput sequencing of spxB allowed to identify four clusters inside the Lb. casei group. The dynamics of the sequence types forming the clusters were followed during ripening. Pyruvate oxidase pathway was expressed in cheese, showing a decreasing trend over ripening time. This work highlights how the composition of the microbiota in the early manufacturing stages influences the microbial dynamics throughout ripening, and how targeting of a metabolic gene can provide an insight into the activity of strains relevant for dairy products.

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.

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.

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.

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

Lactic acid bacteria (LAB) are widely used as starter cultures in the manufacture of foods. Upon preparation, these cultures undergo various stresses resulting in losses of survival and fitness. In order to find conditions for the subsequent identification of proteomic biomarkers and their exploitation for preconditioning of strains, we subjected Lactobacillus (Lb.) paracasei subsp. paracasei TMW 1.1434 (F19) to different stress qualities (osmotic stress, oxidative stress, temperature stress, pH stress and starvation stress). We analysed the dynamics of its stress responses based on the expression of stress proteins using MALDI-TOF mass spectrometry (MS), which has so far been used for species identification. Exploiting the methodology of accumulating protein expression profiles by MALDI-TOF MS followed by the statistical evaluation with cluster analysis and discriminant analysis of principle components (DAPC), it was possible to monitor the expression of low molecular weight stress proteins, identify a specific time point when the expression of stress proteins reached its maximum, and statistically differentiate types of adaptive responses into groups. Above the specific result for F19 and its stress response, these results demonstrate the discriminatory power of MALDI-TOF MS to characterize even dynamics of stress responses of bacteria and enable a knowledge-based focus on the laborious identification of biomarkers and stress proteins. To our knowledge, the implementation of MALDI-TOF MS protein profiling for the fast and comprehensive analysis of various stress responses is new to the field of bacterial stress responses. Consequently, we generally propose MALDI-TOF MS as an easy and quick method to characterize responses of microbes to different environmental conditions, to focus efforts of more elaborate approaches on time points and dynamics of stress responses.

Stress Physiology of Lactic Acid Bacteria

Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

Proteome analysis of Lactobacillus plantarum strain under cheese-like conditions

As a food grade fermentation starter, Lactobacillus plantarum (L. plantarum) also named as the secondary starters during cheese ripening. In this study, the concentration of NaCl was screened as the main factor in the cheese-like conditions (15°C, pH5.2, 6% NaCl) to assess the potential properties of L. plantarum. A comprehensive proteome profile of L. plantarum strain was analyzed with iTRAQ proteomics methods fractionated by SCX chromatography. Proteins involved in carbohydrate transport and metabolism, cell envelope, peptide-glycan biosynthesis and lipid transport and metabolism were found significant changes. Meanwhile, the same trends were found in mRNA expression levels analyzed by RT-PCR. Some general transportation proteins related to ion transporters were detected as more abundant, which may reveal a rescue mechanism of the microbe in sodium-dependent glucose transfer. The understanding of L. plantarum proteome in salt tolerance could be useful to get strain adapted for specific applications.

BIOLOGICAL SIGNIFICANCE

The bacterial biota has a primary role in affecting cheese quality. Under cheese-like conditions, L. plantarum mainly increased the levels of enzymes that responsible for the flavour development during cheese ripening. However, the mechanisms of proteomic adaptation remain largely unclear in unraveling details of the salt tolerance of L. plantarum. This study revealed a dramatic change involved in carbohydrate transport and metabolism, cell envelope, peptide-glycan biosynthesis, lipid transport and metabolism, and glycolysis. Meanwhile, these pathways provide a comprehensive proteome profile of L. plantarum survived under cheese-like conditions. Furthermore, this study shows that iTRAQ proteomics provide more reliable information in describing the molecular rescue strategy of L. plantarum in sodium-dependent glucose transfer.

The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.

The spxB gene as a target to identify Lactobacillus casei group species in cheese

This study focused on the spxB gene, which encodes for pyruvate oxidase. The presence of spxB in the genome and its transcription could be a way to produce energy and allow bacterial growth during carbohydrate starvation. In addition, the activity of pyruvate oxidase, which produces hydrogen peroxide, could be a mechanism for interspecies competition. Because this gene seems to provide advantages for the encoding species for adaptation in complex ecosystems, we studied spxB in a large set of cheese isolates belonging to the Lactobacillus casei group. Through this study, we demonstrated that this gene is widely found in the genomes of members of the L. casei group and shows variability useful for taxonomic studies. In particular, the HRM analysis method allowed for a specific discrimination between Lactobacillus rhamnosus, Lactobacillus paracasei and L. casei. Regarding the coding region, the spxB functionality in cheese was shown for the first time by real-time PCR, and by exploiting the heterogeneity between the L. casei group species, we identified the bacterial communities encoding the spxB gene in this ecosystem. This study allowed for monitoring of the active bacterial community involved in different stages of ripening by following the POX pathway.

Lysozyme affects the microbial catabolism of free arginine in raw-milk hard cheeses

Lysozyme (LZ) is used in several cheese varieties to prevent late blowing which results from fermentation of lactate by Clostridium tyrobutyricum. Side effects of LZ on lactic acid bacteria population and free amino acid pattern were studied in 16 raw-milk hard cheeses produced in eight parallel cheese makings conducted at four different dairies using the same milk with (LZ+) or without (LZ-) addition of LZ. The LZ-cheeses were characterized by higher numbers of cultivable microbial population and lower amount of DNA arising from lysed bacterial cells with respect to LZ + cheeses. At both 9 and 16 months of ripening, Lactobacillus delbrueckii and Lactobacillus fermentum proved to be the species mostly affected by LZ. The total content of free amino acids indicated the proteolysis extent to be characteristic of the dairy, regardless to the presence of LZ. In contrast, the relative patterns showed the microbial degradation of arginine to be promoted in LZ + cheeses. The data demonstrated that the arginine-deiminase pathway was only partially adopted since citrulline represented the main product and only trace levels of ornithine were found. Differences in arginine degradation were considered for starter and non-starter lactic acid bacteria, at different cheese ripening stages.

Genomics of Weissella cibaria with an examination of its metabolic traits

Weissella is a genus of lactic acid bacteria (LAB) consisting of species formerly included in the Leuconostoc paramesenteroides group. Similar to other LAB, they are commonly found in fermented foods but have also been isolated from environmental and human samples. Currently there are 20 recognized species. Herein, three Weissella cibaria genomes were sequenced using Illumia Mi-Seq and Roche 454 technologies. Annotation was performed using the Prokka and JGI IMG pipelines. A thorough analysis of the genomics of the W. cibaria strains was performed, in addition to brief comparative analyses of the genus Weissella as a whole. Genomic sequence data from the newly sequenced W. cibaria strains and data available in GenBank for other Weissella strains was used (n = 10; four Weissella cibaria, one Weissella ceti, one Weissella confusa, one Weissella halotolerans, two Weissella koreensis and one Weissella paramesenteroides). The genomes had sizes varying from 1.3 to 2.4 Mb. DNA G+C contents ranged from 35 to 45 mol%. The core- and pan-proteome at genus and species levels were determined. The genus pan-proteome was found to comprise 4712 proteins. Analysis of the four W. cibaria genomes indicated that the core-proteome, consisting of 729 proteins, constitutes 69 % of the species pan-proteome. This large core-set may explain the divergent niches in which this species has been found. In W. cibaria, in addition to a number of phosphotransferase systems conferring the ability to assimilate plant-associated polysaccharides, an extensive proteolytic system was identified.

Transcriptomic clues to understand the growth of Lactobacillus rhamnosus in cheese

Background

Lactobacillus rhamnosus is a non-starter lactic acid bacterium that plays a significant role during cheese ripening, leading to the formation of flavor. In long-ripened cheeses it persists throughout the whole time of ripening due to its capacity to adapt to changing environmental conditions. The versatile adaptability of L. rhamnosus to different ecosystems has been associated with the capacity to use non-conventional energy sources, regulating different metabolic pathways. However, the molecular mechanisms allowing the growth of L. rhamnosus in the cheese dairy environment are still poorly understood. The aim of the present study was to identify genes potentially contributing to the growth ability of L. rhamnosus PR1019 in cheese-like medium (CB) using a transcriptomic approach, based on cDNA-amplified fragment length polymorphism (cDNA-AFLP) and quantitative real-time reverse transcription-PCR (qPCR).

Results

Using three primer combinations, a total of 89 and 98 transcript-derived fragments were obtained for L. rhamnosus PR1019 grown in commercial MRS medium and CB, respectively. The cDNA-AFLP results were validated on selected regulated genes by qPCR. In order to investigate the main adaptations to growth in a cheese-mimicking system, we focused on 20 transcripts over-expressed in CB with respect to MRS. It is worth noting the presence of transcripts involved in the degradation of pyruvate and ribose. Pyruvate is a intracellular metabolite that can be produced through different metabolic routes starting from the carbon sources present in cheese, and can be released in the cheese matrix with the starter lysis. Similarly the ribonucleosides released with starter lysis could deliver ribose that represents a fermentable carbohydrate in environments, such as cheese, where free carbohydrates are lacking.

Both pyruvate degradation and ribose catabolism induce a metabolite flux toward acetate, coupled with ATP production via acetate kinase. Taking into account these considerations, we suggest that the energy produced through these pathways may concur to explain the great ability of L. rhamnosus PR1019 to grow on CB.

Conclusions

By a transcriptomic approach we identified a set of genes involved in alternative metabolic pathways in L. rhamnosus that could be responsible for L. rhamnosus growth in cheese during ripening.

Fermentation and proteome profiles of Lactobacillus plantarum strains during growth under food-like conditions

This study aimed at investigating the proteomic adaptation of Lactobacillus plantarum strains. Cultivation of L. plantarum strains under food-like conditions (wheat flour hydrolyzed, whey milk, tomato juice) affected some metabolic traits (e.g., consumption of carbohydrates and synthesis of organic acids) compared to de Man, Rogosa and Sharpe (MRS) broth. The analysis of the fermentation profile showed that the highest number of carbon sources metabolized by L. plantarum strains was found using cells cultivated in media containing low concentration of glucose or no glucose at all. The proteomic maps of the strains were comparatively determined after growth on MRS broth and under food-like conditions. The amount of proteins depended on strain and, especially, on culture conditions. Proteins showing decreased or increased amounts under food-like conditions were identified using MALDI-TOF-MS/MS or LC-nano-ESI-MS/MS. Changes of the proteome concerned proteins that are involved in carbohydrate transport and metabolism, energy metabolism, Sec-dependent secretion system, stress response, nucleotide metabolism, regulation of nitrogen metabolism, and protein biosynthesis. A catabolic repression by glucose on carbohydrate transport and metabolism was also found. The characterization of the proteomes in response to changing environmental conditions could be useful to get L. plantarum strains adapted for specific applications.

BIOLOGICAL SIGNIFICANCE

Microbial cell performance during food biotechnological processes has become one of the greatest concerns all over the world. L. plantarum is a lactic acid bacterium with a large industrial application for fermented foods or functional foods (e.g., probiotics). The present study compared the fermentation and proteomic profiling of L. plantarum strains during growth under food-like conditions and under optimal laboratory conditions (MRS broth). This study provides specific mechanisms of proteomic adaptation involved in the microbial performances (carbohydrates utilization, energy metabolism, stress resistance, etc.) affecting the main biotechnological tracts of L. plantarum strains. The finding of this study provides evidences that may be exploited to get strains adapted for specific applications in food biotechnology.

Effects of the peptide pheromone plantaricin A and cocultivation with Lactobacillus sanfranciscensis DPPMA174 on the exoproteome and the adhesion capacity of Lactobacillus plantarum DC400

This study aimed at investigating the extracellular and cell wall-associated proteins (exoproteome) of Lactobacillus plantarum DC400 when cultivated on modified chemically defined medium (CDM) supplemented with the chemically synthesized pheromone plantaricin A (PlnA) or cocultured with L. plantarum DPPMA20 or Lactobacillus sanfranciscensis DPPMA174. Compared to monoculture, two-dimensional gel electrophoresis (2-DE) analysis showed that the exoproteome of L. plantarum DC400 was affected by PlnA and cocultivation with strains DPPMA20 and, especially, DPPMA174. The highest similarity of the 2-DE maps was found between DC400 cells cultivated in monoculture and in coculture with strain DPPMA20. Almost all extracellular proteins (22 spots) and cell wall-associated proteins (40 spots) which showed decreased or increased levels of synthesis during growth in CDM supplemented with PlnA and/or in coculture with strain DPPMA20 or DPPMA174 were identified. On the basis of the sequences in the Kyoto Encyclopedia of Genes and Genomes database, changes to the exoproteome concerned proteins involved in quorum sensing (QS), the transport system, stress response, carbohydrate metabolism and glycolysis, oxidation/reduction processes, the proteolytic system, amino acid metabolism, cell wall and catabolic processes, and cell shape, growth, and division. Cultivation with PlnA and cocultivation with strains DPPMA20 and, especially, DPMMA174 markedly increased the capacity of L. plantarum DC400 to form biofilms, to adhere to human Caco-2 cells, and to prevent the adhesion of potential intestinal pathogens. These phenotypic traits were in part related to oversynthesized moonlighting proteins (e.g., DnaK and GroEL, pyruvate kinase, enolase, and glyceraldehyde-3-phosphate dehydrogenase) in response to QS mechanisms and interaction with L. plantarum DPPMA20 and, especially, L. sanfranciscensis DPPMA174.

Perspectives on the contribution of lactic acid bacteria to cheese flavor development

It has been known since the 1960s that lactic acid bacteria are essential for the development of cheese flavor. In the ensuing 50 years significant research has been directed at understanding the microbiology, genetics and biochemistry of this process. This review briefly covers the current status of cheese flavor development and then provides our vision for approaches which will enhance our understanding of this process. The long-term goal of this area of research is to enable technology (i.e. cultures and enzymes) that results in consistent rapid development of cheese variety-specific characteristic flavors.