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

Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation

The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.

Characterization of a Panel of Constitutive Promoters from Lactococcus cremoris for Fine-Tuning Gene Expression

Lactococcus cremoris (homotypic synonym: Lactococcus lactis) is receiving increasing attention as a prominent vehicle for the delivery of live vaccines. This can hardly be achieved without developing tools for the genetic manipulation of L. cremoris, and the paucity of studies on L. cremoris endogenous promoters has attracted our attention. Here, we report the discovery and characterization of 29 candidate promoters identified from L. cremoris subsp. cremoris NZ9000 by RNA sequencing analysis. Furthermore, 18 possible constitutive promoters were obtained by RT-qPCR screening from these 29 candidate promoters. Then, these 18 promoters were cloned and characterized by a reporter gene, gusA, encoding β-glucuronidase. Eventually, eight endogenous constitutive promoters of L. cremoris were obtained, which can be applied to genetic manipulation of lactic acid bacteria.

Genomic and transcriptomic analysis of genes involved in exopolysaccharide biosynthesis by Streptococcus thermophilus IMAU20561 grown on different sources of nitrogen

Exopolysaccharides (EPSs), which are produced by lactic acid bacteria, have been found to improve the texture and functionality of fermented dairy products. In a previous study, four nitrogen sources were identified as affecting the yield, molecular weight and structure of EPSs produced by Streptococcus thermophilus IMAU20561 in M17 medium. In this genomic and transcriptomics study, a novel eps gene cluster responsible for assembly of repeating units of EPS is reported. This eps cluster (22.3 kb), consisting of 24 open reading frames, is located in the chromosomal DNA. To explore the biosynthetic mechanisms in EPS, we completed RNA-seq analysis of S. thermophilus IMAU20561 grown in four different nitrogen sources for 5 h (log phase) or 10 h (stationary phase). GO functional annotation showed that there was a significant enrichment of differentially expressed genes (DEGs) involved in: amino acid biosynthesis and metabolism; ribonucleotide biosynthesis and metabolism; IMP biosynthesis and metabolism; and phosphorus metabolism. KEGG functional annotation also indicated enrichment of DEGs involved in amino acid biosynthesis, glycolysis, phosphotransferase system, fructose, and mannose metabolism. Our findings provide a better understanding the genetic traits of S. thermophilus, the biosynthetic pathways needed for the production of EPS, and a theoretical basis for screening dairy starter cultures.

New progress in the identifying regulatory factors of exopolysaccharide synthesis in lactic acid bacteria

The exopolysaccharides (EPSs) of lactic acid bacteria (LAB) have presented various bioactivities and beneficial characteristics, rendering their vast commercial value and attracting a broad interest of researchers. The diversity of EPS structures contributes to the changes of EPS functions. However, the low yield of EPS of LAB has severely limited these biopolymers' comprehensive studies and applications in different areas, such as functional food, health and medicine fields. The clarification of biosynthesis mechanism of EPS will accelerate the synthesis and reconstruction of EPS. In recent years, with the development of new genetic manipulation techniques, there has been significant progress in the EPS biosynthesis mechanisms in LAB. In this review, the structure of LAB-derived EPSs, the EPS biosynthesis basic pathways in LAB, the EPS biosynthetic gene cluster, and the regulation mechanism of EPS biosynthesis will be summarized. It will focus on the latest progress in EPS biosynthesis regulation of LAB and provide prospects for future related developments.

Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments

Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO₂ fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.

Optimization of growth of Levilactobacillus brevis SP 48 and in vitro evaluation of the effect of viable cells and high molecular weight potential postbiotics on Helicobacter pylori

Several Levilactobacillus brevis strains have the potential to be used as probiotics since they provide health benefits due to the interaction of live cells, and of their secreted products, with the host (tissues). Therefore, the development of simple fermentation processes that improve cell viability to reduce industrial production costs, and at the same time the characterization and biological evaluation of cell-free postbiotics that can further promote application, are of great interest. In the present study, small scale batch fermentations on semi defined media, deprived of animal derived raw materials, were used to optimize growth of L. brevis SP48, reaching 1.2 ± 0.4 × 1010 CFU/ml of viable cells after 16 h of growth. Displacement, competition, and inhibition assays compared the effect, on Helicobacter pylori, of L. brevis cells to that of its partially purified potentially postbiotic fraction rich in exopolysaccharides and proteins. The expression of pro and anti-inflammatory biochemical markers indicated that both samples activated antimicrobial defenses and innate immunity in a gastric model. Moreover, these compounds also acted as modulators of the inflammatory response in a gut in vitro model. These data demonstrate that the high molecular weight compounds secreted by L. brevis SP48 can contrast H. pylori and reduce inflammation related to intestinal bowel disease, potentially overcoming issues related to the preservation of probiotic viability.

Comparative transcriptome analysis for the biosynthesis of antioxidant exopolysaccharide in Streptococcus thermophilus CS6

BACKGROUND

Food grade Streptococcus thermophilus produces biological exopolysaccharides (EPSs) with great potential with respect to catering for higher health-promoting demands; however, how S. thermophilus regulates the biosynthesis of EPS is not completely understood, decelerating the application of these polymers. In our previous study, maltose, soy peptone and initial pH were three key factors of enhancing EPS yield in S. thermophilus CS6. Therefore, we aimed to investigate the regulating mechanisms of EPS biosynthesis in S. thermophilus CS6 via the method of comparative transcriptome and differential carbohydrate metabolism.

RESULTS

Soy peptone addition (58.6 g L^-1 ) and a moderate pH (6.5) contributed to a high bacterial biomass and a high EPS yield (407 mg L^-1 ). Maltose, soy peptone and initial pH greatly influenced lactose utilization in CS6. Soy peptone addition induced a high accumulation of mannose and arabinose in intracellular CS6, differential monosaccharide composition (mannose, glucose and arabinose) in EPS and high radical [2,2-diphenyl-1-picrylhydrazyl, superoxide and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] scavenging activities. Carbohydrate transportation, sugar activation and eps cluster-associated genes were differentially expressed to regulate EPS biosynthesis. Correlation analysis indicated high production of EPSs depended on high expression of lacS, galPMKUTE, pgm, gt2-5&4-1 and epsLM.

CONCLUSION

The production of antioxidant EPS in S. thermophilus CS6 depended on the regulation of galactose metabolism cluster and eps cluster. The present study recommends a new approach for enhancing EPS production by transcriptomic regulation for further food and health application of EPS. © 2022 Society of Chemical Industry.

Cysteine protected cells from H2O2-induced damage and promoted long-chain fatty acids synthesis in vivo to improve γ-aminobutyric acid production in Levilactobacillus brevis

Levilactobacillus brevis NPS-QW-145 isolated from kimchi is deficient in glutamate dehydrogenase-encoding gene (gdhA) to form glutamate, hence it required exogenous supplementation of glutamate/monosodium glutamate (MSG) for decarboxylation reaction to produce γ-aminobutyric acid (GABA). However, GABA conversion rate from MSG was relatively low. The individual effect of 20 amino acids on regulating GABA biosynthesis was investigated. Cysteine was selected to significantly improve GABA production from MSG. It was found that Lb. brevis was capable of producing H₂O₂, cysteine protected Lb. brevis against H₂O₂-induced oxidative damage to increase cell viability for the enhancement of GABA production. Moreover, cysteine promoted glucose consumption to produce acetyl-CoA for synthesizing long-chain fatty acids to significantly up-regulate GABA biosynthesis. These findings deciphered antioxidative capability of cysteine in Lb. brevis 145 and provided a theoretical basis for fatty acids synthesis-mediated GABA synthesis in Lb. brevis 145, and possibly in other lactic acid bacteria.

Overexpression of pdeR promotes biofilm formation of Paracoccus denitrificans by promoting ATP production and iron acquisition

Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria’s environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans, especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans, adding to our understanding of QS regulation in biofilm development.

Genome-Scale Metabolic Modeling Combined with Transcriptome Profiling Provides Mechanistic Understanding of Streptococcus thermophilus CH8 Metabolism

Streptococcus thermophilus is a lactic acid bacterium adapted toward growth in milk and is a vital component of starter cultures for milk fermentation. Here, we combine genome-scale metabolic modeling and transcriptome profiling to obtain novel metabolic insights into this bacterium. Notably, a refined genome-scale metabolic model (GEM) accurately representing S. thermophilus CH8 metabolism was developed. Modeling the utilization of casein as a nitrogen source revealed an imbalance in amino acid supply and demand, resulting in growth limitation due to the scarcity of specific amino acids, in particular sulfur amino acids. Growth experiments in milk corroborated this finding. A subtle interdependency of the redox balance and the secretion levels of the key metabolites lactate, formate, acetoin, and acetaldehyde was furthermore identified with the modeling approach, providing a mechanistic understanding of the factors governing the secretion product profile. As a potential effect of high expression of arginine biosynthesis genes, a moderate secretion of ornithine was observed experimentally, augmenting the proposed hypothesis of ornithine/putrescine exchange as part of the protocooperative interaction between S. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in yogurt. This study provides a foundation for future community modeling of food fermentations and rational development of starter strains with improved functionality.

IMPORTANCEStreptococcus thermophilus is one the main organisms involved in the fermentation of milk and, increasingly, also in the fermentation of plant-based foods. The construction of a functional high-quality genome-scale metabolic model, in conjunction with in-depth transcriptome profiling with a focus on metabolism, provides a valuable resource for the improved understanding of S. thermophilus physiology. An example is the model-based prediction of the most significant route of synthesis for the characteristic yogurt flavor compound acetaldehyde and identification of metabolic principles governing the synthesis of other flavor compounds. Moreover, the systematic assessment of amino acid supply and demand during growth in milk provides insights into the key challenges related to nitrogen metabolism that is imposed on S. thermophilus and any other organism associated with the milk niche.

Screening and Molecular Identification of Lactic Acid Bacteria Producing β-Glucan in Boza and Cider

The goal of this study was screening and molecular identification of Lactic Acid Bacteria (LAB) producing β-glucan from different species isolated from boza and cider compared to a standard strain for Lactobacillus rhamnosus NRRL 1937 (LGG). From 48 unknown isolates, four LAB strains were selected. Based on the NCBI database, their nomenclature was A3, B6, and C9 for Limosilactobacillus fermentum SH1, SH2, and SH3 along with D6 for Leuconostoc mesenteroides SH4. Also, their similarity values were 100%, 99.8%, 100%, and 100%, respectively. The potential of Exopolysaccharide (EPS) (as β-glucan) production for selected LAB strains by gtf gene, conventional PCR and gene expression using both LGG as a control and LAB 16S rRNA gene as a house-keeping gene was investigated. In addition, EPS (mg/100 mL), cell mass (mg/100 mL), pH, total carbohydrate%, total protein% and β-glucan% by the HPLC for all selected LAB isolates were studied. All results of genetic and chemical tests proved the superiority of B6 treatment for L. fermentum SH2. The results showed the superiority of B6 treatment in gtf gene expression (14.7230 ± 0.070-fold) followed by C9 and A3 treatments, which were 10.1730 ± 0.231-fold and 8.6139 ± 0.320-fold, respectively. while D6 treatment recorded the lowest value of gene expression (0.8566 ± 0.040-fold) compared to the control LGG (one-fold). The results also demonstrated that B6 treatment was superior to the other treatments in terms of EPS formation, with a value of 481 ± 1.00 mg/100 mL, followed by the C9 treatment at 440 ± 2.00 mg/100 mL, compared to the LGG (control) reaching 199.7 ± 3.51 mg/100 mL. Also, the highest % of quantitative and qualitative β-glucan in EPS was observed in B6 followed by C9, D6 and A3 which were 5.56 ± 0.01%, 4.46 ± 0.01%, 0.25 ± 0.008% and 0.12 ± 0.008%, respectively compared to control (0.31 ± 0.01%). Finally, the presented results indicate the importance of screening the local LAB isolates to obtain a superior strain for β-glucan production which will be introduced in a subsequent study under optimum conditions.

Effect of amino acids on free exopolysaccharide biosynthesis by Streptococcus thermophilus 937 in chemically defined medium

Free exopolysaccharide (f-EPS) produced by Streptococcus thermophilus improves the texture and functionality of fermented dairy foods. Our previous study showed a major improvement in f-EPS production of Strep. thermophilus 937 by increasing the concentrations of histidine, isoleucine, and glutamate to 15 mM in an optimized chemically defined medium. The aim of this study was to elucidate the effect of His, Ile, and Glu on the growth, f-EPS biosynthesis pathway, and carbohydrate metabolism profiles of Strep. thermophilus 937. The growth kinetics; transcript levels of key genes in the EPS biosynthesis pathway; enzyme activity involved in sugar nucleotide synthesis; concentrations of lactic acid, lactose, and galactose; and extracellular and intracellular pH were analyzed in chemically defined media with different initial histidine, isoleucine, and glutamate concentrations. The results showed that f-EPS production and viable cell counts of Strep. thermophilus 937 increased 2-fold after the concentrations of His, Ile, and Glu were increased. Additionally, increasing the concentrations of His, Ile, and Glu upregulated transcription of EPS biosynthesis genes and increased the activity of key enzymes in sugar nucleotide synthesis. Moreover, the consumption of lactose increased and secretion of galactose decreased, indicating that increasing the concentration of His, Ile, and Glu could enhance f-EPS production by maintaining viable cell counts, promoting sugar nucleotide synthesis, and increasing the transcript levels of the eps gene cluster. Our results provide a better understanding of the effect of AA on EPS biosynthesis in Strep. thermophilus.

Effect of zero-valent iron and granular activated carbon on nutrient removal and community assembly of photogranules treating low-strength wastewater

Traditional wastewater treatment processes with high energy consumption and greenhouse gas emissions are not suitable for rural areas with low sewage strength and wide distribution. In this study, a microalgae-bacteria synergistic photogranules system was developed under the impetus of green chemical additives to address these challenges. The results showed that zero-valent iron (ZVI) or granular activated carbon (GAC) addition made successful photogranulation treating low-strength wastewater with excellent settleability and stability performance (settling velocity: 14-22 m h^-1; integrity coefficient: 0.81-6.62%), while systems without light or additives failed due to the bio-granules disintegration caused by the overgrowth of predators or phototrophic species. A better nutrient removal performance (TN < 15 mg L^-1, TP < 0.4 mg L^-1) was observed in photogranules systems, and stoichiometric and biological analysis found that the divisions of nitrogen removal by microalgae and bacteria were different for photogranules between GAC and ZVI additions. As a physical enhancer, GAC can be used as the nucleus of photogranules regenerating after granules disintegration rather than affecting the community succession process. However, ZVI addition strengthened the sedimentation ability and stability of photogranules through chemical and biological effects, focusing on enhancing bacterial community diversity, enriching biofilm formation bacteria and inhibiting the overgrowth of filamentous cyanobacteria. Notably, the photogranules process with ZVI addition could be operated under non-aeration conditions without compromising removal efficiency. There existed an ideal distribution of microalgae and bacterial functional species in the photogranules, which seemed to be essential for its self-sustained synergistic symbiosis and stability. Consequently, this work might provide engineering alternatives for realizing carbon neutrality and environmental sustainability of the decentralized wastewater treatment process for low-strength wastewater in rural areas.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Structure, physicochemical characterization, and antioxidant activity of the highly arabinose-branched exopolysaccharide EPS-M2 from Streptococcus thermophilus CS6

Streptococcus thermophilus CS6 could produce the high exopolysaccharide (EPS) level in optimized skimmed milk medium. However, physicochemical properties and structure of these polymers have not been fully characterized. In this study, two purified fractions (EPS-M1 and EPS-M2) exhibited good rheology, thermostability and antioxidant activity. Further monosaccharide composition, molecular weight and NMR analysis indicated EPS-M2 was composed of galactose, arabinose and glucose (5:2.5:1) with an average molecular weight of 2.22 × 10⁴ Da and its suggested repeating unit was →6)-[α-L-Araf-(1 → 3)]-β-D-Galp-(1 → 4)-β-D-Galp-(1 → 6)-[α-L-Araf-(1 → 5)-{α-L-Araf-(1 → 3)}-α-L-Araf-(1 → 3)]-β-D-Galp-(1 → 4)-β-D-Galp-(1 → 6)-[β-D-Galp-(1 → 5)-α-L-Araf-(1 → 5)-α-L-Araf-(1 → 3)]-β-D-Galp-(1 → 6)-[β-D-Galp-(1 → 5)-α-L-Araf-(1 → 5)-{α-L-Araf-(1 → 3)}-α-L-Araf-(1 → 3)]-β-D-Galp-(1→. High EPS production relied on the expression of eps gene cluster and key enzymes of nucleotide sugar metabolism. Overall, EPS-M2 from a potential functional starter S. thermophilus CS6 provided opportunities for natural thickener, stabilizer, and antioxidant agent exploration in the food industry.

Lactic Acid Bacteria Exopolysaccharides Producers: A Sustainable Tool for Functional Foods

Lactic acid bacteria (LAB) used in the food industry, mainly for the production of dairy products, are able to synthetize exopolysaccharides (EPS). EPS play a central role in the assessment of rheological and sensory characteristics of dairy products since they positively influence texture and organoleptic properties. Besides these, EPS have gained relevant interest for pharmacological and nutraceutical applications due to their biocompatibility, non-toxicity and biodegradability. These bioactive compounds may act as antioxidant, cholesterol-lowering, antimicrobial and prebiotic agents. This review provides an overview of exopolysaccharide-producing LAB, with an insight on the factors affecting EPS production, their dairy industrial applications and health benefits.

Structural characterisation of EPS of Streptococcus thermophilus S-3 and its application in milk fermentation

The application of Streptococcus thermophilus S-3 into yogurt production was studied and the structural properties of the generated exopolysaccharides (EPS-S3) were characterized. The proposed structure of EPS-S3 was obtained. EPS-S3 contained a high ratio of N-Acetyl-galactosamine with the Mw of 574 kDa, which was higher than that of AR333 (314 kD) leading to higher apparent viscosity. Streptococcus thermophilus strain S-3 was co-cultured with Lactobacillus delbrueckii for yogut production which highly increased the acidifying rate and post-acidification rate. The quality of the co-cultured yogurts in terms of apparent viscosity, syneresis capacity, water holding capacity and rheological properties were much better than that by using Lactobacillus bulgaricus only. The production mechanism of EPS-S3 from gene regulated level was also discussed which is helpful to facilitate the application of Streptococcus thermophilus strain into milk production.

Comparative Peptidomic and Metatranscriptomic Analyses Reveal Improved Gamma-Amino Butyric Acid Production Machinery in Levilactobacillus brevis Strain NPS-QW 145 Cocultured with Streptococcus thermophilus Strain ASCC1275 during Milk Fermentation

The high-gamma-amino butyric acid (GABA)-producing bacterium Levilactobacillus brevis strain NPS-QW 145, along with Streptococcus thermophilus (one of the two starter bacteria used to make yogurt for its proteolytic activity), enhances GABA production in milk. However, a mechanistic understanding of how Levilactobacillus brevis cooperates with S. thermophilus to stimulate GABA production has been lacking. Comparative peptidomic and metatranscriptomic analyses were carried out to unravel the casein and lactose utilization patterns during milk fermentation with the coculture. We found that particular peptides hydrolyzed by S. thermophilus ASCC1275 were transported and biodegraded with peptidase in Lb. brevis 145 to meet the growth needs of the latter. In addition, amino acid synthesis and metabolism in Lb. brevis 145 were activated to further support its growth. Glucose, as a result of lactose hydrolysis by S. thermophilus 1275, but not available lactose in milk, was metabolized as the main carbon source by Lb. brevis 145 for ATP production. In the stationary phase, under acidic conditions due to the accumulation of lactic acid produced by S. thermophilus 1275, the expression of genes involved in pyridoxal phosphate (coenzyme of glutamic acid decarboxylase) metabolism and glutamic acid decarboxylase (Gad) in Lb. brevis 145 was induced for GABA production.SIGNIFICANCE A huge market for GABA-rich milk as a dietary therapy for the management of hypertension is anticipated. The novelty of this work lies in applying peptide profiles supported by metatranscriptomics to elucidate (i) the pattern of casein hydrolysis by S. thermophilus 1275, (ii) the supply of peptides and glucose by S. thermophilus 1275 to Lb. brevis 145, (iii) the transportation of peptides in Lb. brevis and the degradation of peptides by this organism, which was reported to be nonproteolytic, and (iv) GABA production by Lb. brevis 145 under acidic conditions. Based on the widely reported contribution of lactic acid bacteria (LAB) and GABA to human health, the elucidation of interactions between the two groups of bacterial communities in the production of GABA-rich milk is important for promoting the development of functional dairy food and may provide new insight into the development of industrial GABA production.

Proteomic analysis reveals potential factors associated with enhanced EPS production in Streptococcus thermophilus ASCC 1275

Streptococcus thermophilus ASCC 1275 has two chain length determining genes - epsC and epsD- in its eps gene cluster, and produces two times more EPS in sucrose medium than that in glucose and lactose. Hence, we investigated the influence of sugars (glucose, sucrose and lactose), at log phase (5 h) and stationary phase (10 h), on the global proteomics of S. thermophilus 1275 to understand the differentially expressed proteins (DEPs) during EPS production using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. Among 98 DEPs in sucrose medium, most of them were mapped into EPS biosynthesis pathway and other related metabolisms. There was an upregulation of several proteins involved in sugar transport (phosphoenolpyruvate (PEP) phosphotransferase system), EPS assembly (epsG1D) and amino acid metabolism (methionine, cysteine/arginine metabolism) in sucrose medium. This study showed that increased EPS production in S. thermophilus 1275 requires a well-co-ordinated regulation of pathway involved in both EPS assembly and amino acid metabolism along with the availability of sugars. Thus, it provided valuable insights into the biosynthesis and regulation of EPS in S. thermophilus 1275, and potential gene targets for understanding high-EPS strains.

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958^T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.

Genomic and phenotypic analyses of exopolysaccharide biosynthesis in Streptococcus thermophilus S-3

Streptococcus thermophilus, one of the most important industrial lactic acid bacteria, is widely used as a starter culture in the dairy industry. Streptococcus thermophilus S-3 isolated from Chinese traditional dairy products has shown great potential for the production of larger amounts of exopolysaccharides (EPS), which significantly affect the organoleptic properties of fermented milk products. To understand the relationship between the genotype and phenotype of S. thermophilus S-3 in terms of EPS biosynthesis, its genome of strain S-3 was sequenced and the genes related to carbohydrate utilization, nucleotide sugars synthesis, and EPS biosynthesis were investigated. The genomic analysis revealed that S. thermophilus S-3 can use sucrose, mannose, glucose, galactose, and lactose. Phenotypic analysis showed that S-3 prefers fermenting lactose to fermenting glucose or galactose. The genetic analysis of nucleotide sugars and EPS biosynthesis revealed that S-3 can synthesize uridine diphosphate (UDP)-glucose, deoxythymidine diphosphate-glucose, deoxythymidine diphosphate-rhamnose, UDP-galactose, UDP-N-acetylgalactosamine, and UDP-N-acetylglucosamine. A high yield of EPS from S-3 cultivated with lactose rather than glucose as the carbon source was correlated with high transcriptional levels of the genes associated with metabolism of these nucleotide sugars and EPS biosynthesis. Our results provide a better understanding of EPS biosynthesis in S. thermophilus and can facilitate enhanced EPS production by lactic acid bacteria fermentation via genetic and metabolic engineering approaches.