Molecular analysis of the glutamate decarboxylase locus in Streptococcus thermophilus ST110

Optimization of fermentation conditions for the production of γ-aminobutyric acid by Lactobacillus hilgardii GZ2 from traditional Chinese fermented beverage system

γ-Aminobutyric acid (GABA) is a crucial neurotransmitter with wide application prospects. In this study, we focused on a GABA-producing strain from a traditional Chinese fermented beverage system. Among the six isolates, Lactobacillus hilgardii GZ2 exhibited the greatest ability to produce GABA in the traditional Chinese fermented beverage system. To increase GABA production, we optimized carbon sources, nitrogen sources, temperature, pH, and monosodium glutamate and glucose concentrations and conducted fed-batch fermentation. The best carbon and nitrogen sources for GABA production and cell growth were glucose, yeast extract and tryptone. Gradual increases in GABA were observed as the glucose and monosodium glutamate concentrations increased from 10 g/L to 50 g/L. During fed-batch fermentation, lactic acid was used to maintain the pH at 5.56, and after feeding with 0.03 g/mL glucose and 0.4 g/mL sodium glutamate for 72 h, the GABA yield reached 239 g/L. This novel high-GABA-producing strain holds great potential for the industrial production of GABA, as well as the development of health-promoting functional foods and medical fields.

Phenotypic, Technological, Safety, and Genomic Profiles of Gamma-Aminobutyric Acid-Producing Lactococcus lactis and Streptococcus thermophilus Strains Isolated from Cow's Milk

Gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) can be used as starters in the development of GABA-enriched functional fermented foods. In this work, four GABA-producing strains each of Lactococcus lactis and Streptococcus thermophilus species were isolated from cow's milk, and their phenotypic, technological, and safety profiles determined. Genome analysis provided genetic support for the majority of the analyzed traits, namely, GABA production, growth in milk, and the absence of genes of concern. The operon harboring the glutamate decarboxylase gene (gadB) was chromosomally encoded in all strains and showed the same gene content and gene order as those reported, respectively, for L. lactis and S. thermophilus. In the latter species, the operon was flanked (as in most strains of this species) by complete or truncated copies of insertion sequences (IS), suggesting recent acquisition through horizontal gene transfer. The genomes of three L. lactis and two S. thermophilus strains showed a gene encoding a caseinolytic proteinase (PrtP in L. lactis and PrtS in S. thermophilus). Of these, all but one grew in milk, forming a coagulum of good appearance and an appealing acidic flavor and taste. They also produced GABA in milk supplemented with monosodium glutamate. Two L. lactis strains were identified as belonging to the biovar. diacetylactis, utilized citrate from milk, and produced significant amounts of acetoin. None of the strains showed any noticeable antibiotic resistance, nor did their genomes harbor transferable antibiotic resistance genes or genes involved in toxicity, virulence, or pathogenicity. Altogether these results suggest that all eight strains may be considered candidates for use as starters or components of mixed LAB cultures for the manufacture of GABA-enriched fermented dairy products.

A comprehensive investigation into the production of gamma-aminobutyric acid by Limosilactobacillus fermentum NG16, a tuna gut isolate

Gamma-aminobutyric acid (GABA), a four-carbon non-protein amino acid, is widely known to have multiple physiological functions. The present study aimed to investigate the cultivation parameters for GABA production by a lactic acid bacteria (LAB) strain isolated from a tuna gut sample. Among 60 tuna gut LAB, only 7 Limosilactobacillus fermentum isolates, i.e. NG01, NG12, NG13, NG14, NG16, NG23, and NG27, were capable of GABA fermentation, with NG16 being the most potent GABA producer. The GABA production by isolate NG16 was therefore thoroughly characterised. The optimal batch culture conditions for GABA production were an initial cell density of 5×106 CFU mL−1, a monosodium glutamate concentration of 2%, an initial pH of 7, a fermentation temperature of 35 °C, and an incubation time of 96 h. Under this cultivation conditions, NG16 produced a maximum GABA yield of 25.52 ± 0.41 mM.

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects

Recent studies have shown that the gut microbiota modulates the physical and psychological functions of the host through several modes of action. One of them is mediating the production of active neurotransmitters, such as serotonin and gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the central nervous system. Here, we analyzed the relationship between fecal GABA concentration and microbial composition in more than 70 human participants. The gut microbiome composition was analyzed using next-generation sequencing based on 16S ribosomal RNA. High-performance liquid chromatography was used to evaluate the neurotransmitters GABA and glutamate. The GABA level was detected in a broad range (0-330 µg/g feces). The participants' samples were classified into high (>100 µg/g), medium (10-100 µg/g), and low (<10 µg/g) groups, based on fecal GABA concentration. The results reveal that the microbiome of the high-GABA samples had lower alpha diversity than the other samples. Beta diversity analysis showed significant (p < 0.05) separation between the high-GABA samples and others. Furthermore, we surveyed the abundance of specific GABA producer biomarkers among the microbiomes of tested samples. The family Bifidobacteriaceae exhibited high abundance in the microbiome of the high-GABA group. This study demonstrated that Bifidobacterium abundance was associated with high fecal GABA content in healthy human subjects. These results may aid the development of potential probiotics to improve microbial GABA production, which can support the maintenance of the physical and psychiatric health of the host.

Glutamate Decarboxylase from Lactic Acid Bacteria-A Key Enzyme in GABA Synthesis

Glutamate decarboxylase (l-glutamate-1-carboxylase, GAD; EC 4.1.1.15) is a pyridoxal-5’-phosphate-dependent enzyme that catalyzes the irreversible α-decarboxylation of l-glutamic acid to γ-aminobutyric acid (GABA) and CO₂. The enzyme is widely distributed in eukaryotes as well as prokaryotes, where it—together with its reaction product GABA—fulfils very different physiological functions. The occurrence of gad genes encoding GAD has been shown for many microorganisms, and GABA-producing lactic acid bacteria (LAB) have been a focus of research during recent years. A wide range of traditional foods produced by fermentation based on LAB offer the potential of providing new functional food products enriched with GABA that may offer certain health-benefits. Different GAD enzymes and genes from several strains of LAB have been isolated and characterized recently. GABA-producing LAB, the biochemical properties of their GAD enzymes, and possible applications are reviewed here.

Gamma-aminobutyric acid (GABA) production in milk fermented by specific wild lactic acid bacteria strains isolated from artisanal Mexican cheeses

Purpose

The purpose of this study was to screen wild GABA-producing lactic acid bacteria (LAB) isolated from artisanal Mexican cheeses and to evaluate the fermentation conditions for the enhancement of the GABA yield in fermented milk.

Methods

A qualitative test was carried out to select the GABA-producing LAB and the GABA was quantified by reversed-phase high-performance liquid chromatography in fermented milk (FM). Two inoculum concentrations (107 and 109 CFU/mL), two incubation temperatures (30 and 37 °C), three glutamate concentrations (1, 3, and 5 g/L), and three pyridoxal 5′-phosphate (PLP) concentrations (0, 100, and 200 μM) were assessed to establish suitable conditions to enhance the GABA yield in FM.

Results

Results showed that, from a total of 94 LAB strains, fermented milk with two Lactococcus lactis strains (L-571 or L-572) presented the highest GABA production. However, 37 °C of incubation and 109 CFU/mL and 3 g/L of glutamate significantly led the highest GABA yield in FM with L-571. Further studies are needed to establish the optimum conditions for producing GABA by this strain, and in vivo studies may reveal its potential use as GABA-producing culture.

Conclusion

These results highlight the importance of wild LAB strains in order to generate new alternatives and opportunities in the development of functional foods containing GABA.

Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

Streptococcus thermophilus plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of S. thermophilus strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 S. thermophilus genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and in vitro survival capacity in the gastrointestinal tract. CS9 possesses a special eps gene cluster containing significant traces of HGT, while the eps gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new S. thermophilus strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.

Deciphering the crucial roles of transcriptional regulator GadR on gamma-aminobutyric acid production and acid resistance in Lactobacillus brevis

Background

In lactic acid bacteria (LAB), acid stress leads to decreases of cell vitality and fermentation yield. Glutamate decarboxylase (GAD) system is regarded as one of the essential acid-resistance mechanisms in LAB. However, the regulation of GAD system is not well identified in the genus Lactobacillus. Although potential transcriptional regulator gene located upstream of GAD system genes was found in several Lactobacillus species, such as Lactobacillus (L.) brevis, the contribution of the regulator to acid resistance of the genus Lactobacillus has not been experimentally determined.

Results

The potential transcriptional regulator gene gadR was disrupted by homologous recombination in L. brevis ATCC 367, leading to the decreased expression of gadC and gadB. The inactivation of GadR completely eliminated γ-aminobutyric acid (GABA) production and decreased the glutamate-dependent acid resistance. Moreover, expression of gadC and gadB in the presence of glutamate was increased and glutamate also stimulated the expression of gadR. In addition, L. brevis D17, a strain screened from acidic fermented grains of Chinese liquor production, had much higher expression level of gadR than the typical strain L. brevis ATCC 367. Under the pH-controlled and mixed-feed fermentation, L. brevis D17 achieved a titer of 177.74 g/L and a productivity of 4.94 g/L/h of GABA within 36 h. However, the L. brevis ATCC 367 only achieved a titer of 6.44 g/L and 0.18 g/L/h of GABA although the same fermentation control approach was employed.

Conclusions

GadR is a positive transcriptional regulator controlling GABA conversion and acid resistance in L. brevis. L. brevis strains with hyper-expressing of gadR are excellent candidates for GABA production in industrial scale.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1157-2) contains supplementary material, which is available to authorized users.

Production of γ-aminobutyric acid (GABA) by lactic acid bacteria strains isolated from traditional, starter-free dairy products made of raw milk

γ-Aminobutyric acid (GABA), an amino acid not used in protein synthesis, intervenes in several physiological functions and has both diuretic and calming effects in humans. Lactic acid bacteria (LAB) strains that produce GABA could be exploited for the manufacture of health-promoting GABA-enriched dairy products. In this study, 262 LAB strains isolated from traditional dairy products made from raw milk without starter cultures were screened for GABA production in culture media supplemented with 1% monosodium glutamate (MSG) using an enzymatic (GABase) method. About half of the strains (123) were found to be GABA producers. Of these, 24, among which were 16 Lactococcus lactis subsp. lactis and three Streptococcus thermophilus strains, produced >1 mM of GABA (range 1.01-2.81 mM) and were selected for further characterisation. GABA production was confirmed in most strains by culturing in 5 mM MSG followed by HPLC quantification. A majority of the strains were confirmed to be GABA producers by this method, although lower production levels were recorded. Using species-specific primers, the gene encoding glutamate decarboxylase (GAD) was PCR-amplified in all but one of the GABA producers analysed. Amplicons sequences were compared to one another and to those held in databases. Except for one Lactobacillus brevis strain, none of the 24 GABA producers investigated produced toxic biogenic amines, such as tyramine, histamine or cadaverine. They were therefore considered safe. Either alone, in mixtures, or in combination with industrial starter or adjunct cultures, these strains might be useful in the development of health-oriented dairy products.

High γ-aminobutyric acid production from lactic acid bacteria: Emphasis on Lactobacillus brevis as a functional dairy starter

γ-Aminobutyric acid (GABA) and GABA-rich foods have shown anti-hypertensive and anti-depressant activities as the major functions in humans and animals. Hence, high GABA-producing lactic acid bacteria (LAB) could be used as functional starters for manufacturing novel fermented dairy foods. Glutamic acid decarboxylases (GADs) from LAB are highly conserved at the species level based on the phylogenetic tree of GADs from LAB. Moreover, two functionally distinct GADs and one intact gad operon were observed in all the completely sequenced Lactobacillus brevis strains suggesting its common capability to synthesize GABA. Difficulties and strategies for the manufacture of GABA-rich fermented dairy foods have been discussed and proposed, respectively. In addition, a genetic survey on the sequenced LAB strains demonstrated the absence of cell envelope proteinases in the majority of LAB including Lb. brevis, which diminishes their cell viabilities in milk environments due to their non-proteolytic nature. Thus, several strategies have been proposed to overcome the non-proteolytic nature of Lb. brevis in order to produce GABA-rich dairy foods.

Complete Genome Sequence of Streptococcus thermophilus Strain B59671, Which Naturally Produces the Broad-Spectrum Bacteriocin Thermophilin 110

Streptococcus thermophilus strain B59671 is a Gram-positive lactic acid bacterium that naturally produces a broad-spectrum bacteriocin, thermophilin 110, and is capable of producing gamma-aminobutyric acid (GABA). The complete genome sequence for this strain contains 1,821,173 nucleotides, 1,936 predicted genes, and an average G+C content of 39.1%.

Potential of a lactic acid bacterial starter culture with gamma-aminobutyric acid (GABA) activity for production of fermented sausage

The ability of lactic acid bacterial starter cultures to produce gamma-aminobutyric acid (GABA) during sausage fermentation was studied. Among 305 strains of lactic acid bacteria isolated from kimchi samples, 11 strains were selected as starter candidates based on the following criteria: growth speed, pH lowering ability, and biogenic amine productivity including GABA-producing activity. During in vitro tests, the Y8 (Lactobacillus brevis), O52, and KA20 strains produced 39.00 ± 1.36, 49.73 ± 3.80, and 64.59 ± 0.61 mg/kg of GABA, respectively. Interestingly, although isolate Y8 showed low productivity in vitro, the GABA content it produced during in situ tests (61.30 ± 2.61 mg/kg) was similar to that produced by isolate PM3 (L. brevis) used as positive control (69.64 ± 2.20 mg/kg). Therefore, isolate Y8 was selected as the best functional starter culture for the production of fermented sausage because it exhibited rapid growth, safety, and abundant GABA productivity.

Application of Baechu-Kimchi Powder and GABA-Producing Lactic Acid Bacteria for the Production of Functional Fermented Sausages

This study was carried out to determine the physicochemical, microbiological, and quality characteristics of a new type of fermented sausage manufactured by incorporating Baechu-kimchi powder and gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB). The LAB count was at the maximum level by day nine of ripening in inoculated sausages, accompanied by a rapid decrease in the pH. The addition of kimchi powder decreased the lightness (L*) and increased the redness (a*) and, yellowness (b*) values, while also significantly increasing the hardness and chewiness of the sausage (p<0.05). Moreover, although the thiobarbituric acid reactive substances values increased in all samples during the study period, this increase was lower in the kimchi-treated samples, indicating a reduction in lipid oxidation. Overall, our results show that the addition of Baechu-kimchi powder to sausages reduced the off-flavor properties and improved the taste profile of the fermented sausage in sensory evaluations. The GABA content of all fermented sausages increased from 17.42-25.14 mg/kg on the third day of fermentation to 60.95-61.47 mg/kg on the thirtieth day. These results demonstrate that Baechu-kimchi powder and GABA-producing LAB could be functional materials in fermented sausage to improve quality characteristics.

Proteolytic Activity and Production of γ-Aminobutyric Acid by Streptococcus thermophilus Cultivated in Microfiltered Pasteurized Milk

A set of 191 strains of Streptococcus thermophilus were preliminarily screened for the presence of the genes codifying for cell envelope-associated proteinase (prtS) and for glutamate decarboxylase (gadB) responsible for γ-aminobutyric acid (GABA) production. The growth and proteolytic activity of the gadB-positive strains (9 presenting the prtS gene and 11 lacking it) were studied in microfiltered pasteurized milk. Degradation of both caseins (capillary electrophoresis) and soluble nitrogen fractions (HPLC) and changes in the profile of free amino acids (FAAs; ion-exchange chromatography) were evaluated at inoculation and after 6 and 24 h of incubation at 41 °C. None of the strains was capable of hydrolyzing caseins and β-lactoglobulin, and only two hydrolyzed part of α-lactalbumin, these proteins being present in their native states in pasteurized milk. Contrarily, most strains were able to hydrolyze peptones and peptides. For initial growth, most strains relied on the FAAs present in milk, whereas, after 6 h, prtS⁺ strains released variable amounts of FAA. One prtS⁺ strain expressed a PrtS^- phenotype, and two prtS^- strains showed a rather intense proteolytic activity. Only five strains (all prtS⁺) produced GABA, in variable quantities (up to 100 mg/L) and at different rates, depending on the acidification strength. Addition of glutamate did not induce production of GABA in nonproducing strains that, however, unexpectedly were shown to adopt the degradation of arginine into citrulline and ornithine as an alternative acid resistance system and likely as a source of ATP.

Characterization of a glutamate decarboxylase (GAD) gene from Lactobacillus zymae

Lactic acid bacteria (LAB) were isolated from Kimchi, a Korean traditional fermented vegetable food. LAB accumulating GABA (γ-aminobutyric acid) in the culture media were screened by TLC analysis. One isolate, GU240, produced the highest amount of GABA among the 3,000 isolates and identified as a Lactobacillus zymae strain. Glutamate decarboxylase (GAD) gene was cloned and over-expressed in E. coli BL21(DE3) using pET26b(+). The recombinant GAD was purified by using a Ni-NTA column. Its size was 53 kDa by SDS-PAGE. Maximum GAD activity was at pH 4.5 and 41 °C and the activity was dependent on pyridoxal 5'-phosphate. Km and Vmax of LzGAD were 1.7 mM and 0.01 mM/min, respectively, when glutamate was used as a substrate.

gadA gene locus in Lactobacillus brevis NCL912 and its expression during fed-batch fermentation

Normally, Lactobacillus brevis has two glutamate decarboxylase (GAD) genes; gadA and gadB. Using PCR, we cloned the gadA gene from L. brevis strain NCL912, a high yield strain for the production of gamma-aminobutyric acid (GABA). However, despite using 61 different primer pairs, including degenerate primers from conserved regions, we were unable to use PCR to clone gadB from the NCL912 strain. Furthermore, we could not clone it by genomic walking over 3000 bp downstream of the aldo-keto reductase gene, a single-copy gene that is located 1003 bp upstream of gadB in L. brevis ATCC367. Altogether, the data suggest that L. brevis NCL912 does not contain a gadB gene. By genomic walking, we cloned regions upstream and downstream of the gadA gene to obtain a 4615 bp DNA fragment that included the complete gadA locus. The locus contained the GAD gene (gadA) and the glutamate:GABA antiporter gene (gadC), which appear to be transcribed in an operon (gadCA), and a transcriptional regulator (gadR) of gadCA. During whole fed-batch fermentation, the expression of gadR, gadC and gadA was synchronized and correlated well with GABA production. The gadA locus we cloned from NCL912 has reduced homology compared with gadA loci of other L. brevis strains, and these differences might explain the ability of NCL912 to produce higher levels of GABA in culture.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS.