Contribution of glutaminases to glutamine metabolism and acid resistance in Lactobacillus reuteri and other vertebrate host adapted lactobacilli

Enhancement of γ-aminobutyric acid in fermented cucumbers

The effects of brine acidification, glutamate addition, and starter culture on γ-aminobutyric acid (GABA) content of fermented cucumber were investigated. GABA is a nonprotein amino acid with antihypertensive, antianxiety, and immunomodulatory properties. It is produced during cucumber fermentation but is limited by the low intrinsic concentration of free glutamate. Glutamine is 10-fold more abundant than glutamate in fresh cucumber and could provide additional substrate if converted to glutamate by glutaminase. Cucumbers were fermented in triplicate in acidified (pH 4.7-4.8) or nonacidified (pH 6.6) cover brines with 2% (342 mM) sodium chloride (NaCl) and 0 or 10 mM added glutamate. Indigenous and starter culture-assisted fermentations were conducted for each treatment at 28°C. The starter culture included lactobacilli containing gene sequences that encode for glutaminase (Lactobacillus gasseri ATCC 33323) and glutamate decarboxylase (Lactiplantibacillus plantarum WCFS1 ATCC BAA-793). GABA, glutamate, and glutamine were quantified by liquid chromatography triple quadrupole mass spectrometry. Both indigenous and starter culture-assisted fermentations effectively metabolized intrinsic and added glutamate, resulting in 10.4 ± 2.2 mM to 14.9 ± 0.7 mM GABA in glutamate supplemented fermentations compared with only 1.1 ± 0.2 mM in indigenous ferments. No additional increases in glutamate or downstream formation of GABA were observed in nonacidified brines with or without starter cultures, indicating that glutaminase production by L. gasseri and the indigenous microbiota was minimal or absent under these conditions. Glutamate addition to reduced salt cucumber fermentations generated ready-to-eat pickles that can deliver clinically relevant levels of GABA in a typical serving size. PRACTICAL APPLICATION: Research was conducted to explore ways to increase the production of the health-promoting compound, γ-aminobutyric acid (GABA), in fermented cucumber pickles. Cucumbers were fermented in reduced salt cover brines with or without added glutamate and/or acetic acid. Both natural and starter culture-assisted fermentations effectively converted the intrinsic and added glutamate to GABA, producing ready-to-eat pickles that can deliver clinically relevant levels of GABA in a typical serving size.

Raw material-dependent changes in bacterial and compositional profiles are involved in insufficient pH decrease in natural lactic fermentation of Brassica rapa leaves

Sunki is an unsalted lactic fermented pickle made from red turnip leaves in the Kiso district, Japan. Accidental insufficient decrease in pH during sunki fermentation seriously reduces the product quality. To obtain insights into how the insufficient decrease occurs, we comprehensively analyzed differences in the microbiological and chemical properties of sunki made from three different turnip harvests and found a significant difference in their final pH. Microbiota and metabolome analyses revealed that the insufficient pH decrease showed strong relationships with the chemical composition (low lactic acid and high ammonia levels) and bacterial community structure (low Lactobacillus and high Limosilactobacillus). In vitro sunki fermentation experiments demonstrated that accumulated ammonia was associated with a decrease in glutamine and an increase in glutamic acid. Limosilactobacillus reuteri, a species of lactic acid bacteria possessing heterolactic metabolism, was suggested to be mainly responsible for insufficient decrease in pH related to accumulated ammonia during sunki fermentation.

Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning

Limosilactobacillus reuteri, a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied the independent component analysis (ICA) to 117 RNA-seq data sets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. Our findings indicate that the ICA provides a qualitative advancement and captures nuanced relationships within gene clusters that other methods may miss. This study uncovers the fundamental properties of L. reuteri's TRN and deepens our understanding of its arginine metabolism and the co-regulation of riboflavin metabolism and fatty acid conversion. It also sheds light on conditions that regulate genes within a specific biosynthetic gene cluster and allows for the speculation of the potential role of isoprenoid biosynthesis in L. reuteri's adaptive response to environmental changes. By integrating transcriptomics and machine learning, we provide a system-level understanding of L. reuteri's response mechanism to environmental fluctuations, thus setting the stage for modeling the probiotic transcriptome for applications in microbial food production.

IMPORTANCE

We have studied Limosilactobacillus reuteri, a beneficial probiotic microbe that plays a significant role in our health and production of sustainable foods, a type of foods that are nutritionally dense and healthier and have low-carbon emissions compared to traditional foods. Similar to how humans adapt their lifestyles to different environments, this microbe adjusts its behavior by modulating the expression of genes. We applied machine learning to analyze large-scale data sets on how these genes behave across diverse conditions. From this, we identified 35 unique patterns demonstrating how L. reuteri adjusts its genes based on 50 unique environmental conditions (such as various sugars, salts, microbial cocultures, human milk, and fruit juice). This research helps us understand better how L. reuteri functions, especially in processes like breaking down certain nutrients and adapting to stressful changes. More importantly, with our findings, we become closer to using this knowledge to improve how we produce more sustainable and healthier foods with the help of microbes.

Whole genome sequencing analysis of Limosilactobacillus reuteri from the intestinal tract of mice recovering from ulcerative colitis and preliminary study on anti-inflammatory effects of its derived peptides

Limosilactobacillus reuteri is an indigenous inhabitant of the animal gut known for its probiotic effects on the host. In our previous study, a large number of L. reuteri strains were isolated from the gastrointestinal tract of mice recovering from ulcerative colitis, from which we randomly selected L. reuteri RE225 for whole genome sequencing to explore its probiotic properties. The results of next-generation sequencing and third-generation single molecule sequencing showed that L. reuteri RE225 contained many genes encoding functional proteins associated with adhesion, anti-inflammatory and pathogen inhibition. And compared to other L. reuteri strains in NCBI, L. reuteri RE225 has unique gene families with probiotic functions. In order to further explore the probiotic effect of the L. reuteri RE225, the derived peptides were identified by LC-MS/MS, and the peptides with tumor necrosis factor-α binding ability were screened by reverse molecular docking and microscale thermophoresis. Finally, cell experiments demonstrated the anti-inflammatory ability of the peptides. Western blotting and qPCR analyses confirmed that the selected peptides might alleviate LPS-induced inflammation in NCM460 cells by inhibiting JAK2/STAT3 pathway activation.

Intestinal mucosal microbiota mediate amino acid metabolism involved in the gastrointestinal adaptability to cold and humid environmental stress in mice

Growing evidence has demonstrated that cold and humid environmental stress triggers gastrointestinal (GI) disorders. In this study, we explored the effects of intestinal microbiota homeostasis on the intestinal mucus barrier and GI disorders by cold and humid environmental stress. Moreover, the inner link between the intestinal mucosal microbiota and metabolites in mice with cold and humid environmental stress was interpreted by integrative analysis of PacBio HiFi sequencing microbial genomics and targeted metabolomics. In the current study, we found (1) after the cold and wet cold and humid environmental stress intervened in the intestinal microbiota disorder and homeostasis mice respectively, the bacterial culturing and fluorescein diacetate (FDA) microbial activity detection of intestinal microbiota including feces, intestinal contents, and intestinal mucosa suggested that the cold and humid environmental stress decreased the colony of culturable bacteria and microbial activity, in which intestinal microbiota disorder aggravated the injury of the intestinal mucus barrier and the GI symptoms related to cold and humid environmental stress; (2) the serum amino acid transferases such as glutamate pyruvic transa (GPT), and glutamic oxaloacetic transaminase (GOT) in cold and humid environmental stressed mice increased significantly, indicating that the intestinal microbiota adapted to cold and humid environmental stress by regulating the host's amino acid metabolism; (3) the integrative analysis of multi-omics illustrated a prediction model based on the microbiota Lactobacillus reuteri abundance and host amino acid level that can predict intestinal mucoprotein Muc2 with an adjusted R2 of 75.0%. In conclusion, the cold and humid environmental stress regulates the neurotransmitter amino acids metabolic function both in intestinal mucosal microbiota and host serum by adjusting the composition of the dominant bacterial population Lactobacillus reuteri, which contributes to the intestinal mucus barrier injury and GI disorders caused by cold and humid environmental stress.

The quest for the perfect loaf of sourdough bread continues: Novel developments for selection of sourdough starter cultures

Sourdough fermentation, one of the oldest unit operations in food production, is currently experiencing a revival in bread production at the household, artisanal, and the industrial level. The expanding use of sourdough fermentation in bread production and the adaptation of fermentation to large scale industrial bread production also necessitate the development of novel starter cultures. Developments in the last years also have expanded the tools that are used to assess the metabolic potential of specific strains, species or genera of the Lactobacillaceae and have identified multiple ecological and metabolic traits as clade-specific. This review aims to provide an overview on the clade-specific metabolic potential of members of the Lactobacillaceae for use in sourdough baking, and the impact of these clade-specific traits on bread quality. Emphasis is placed on carbohydrate metabolism, including the conversion of sucrose and starch to soluble polysaccharides, conversion of amino acids, and the metabolism of organic acids. The current state of knowledge to compose multi-strain starter cultures (synthetic microbial communities) that are suitable for back-slopping will also be discussed. Taken together, the communication outlines the current tools for selection of microbes for use in sourdough baking.

Exopolysaccharide-Producing Lacticaseibacillus rhamnosus Space Mutant Improves the Techno-Functional Characteristics of Fermented Cow and Goat Milks

Lacticaseibacillus rhamnosus Probio-M9 (Probio-M9) is increasingly used as a co-fermentation culture in fermented milk production. Recently, a capsular polysaccharide (CPS)- and exopolysaccharide (EPS)-producing mutant of Probio-M9, HG-R7970-3, was generated by space mutagenesis. This study compared the performance of cow and goat milk fermentation between the non-CPS/-EPS-producing parental strain (Probio-M9) and the CPS/EPS producer (HG-R7970-3), and the stability of products fermented by the two bacteria. Our results showed that using HG-R7970-3 as the fermentative culture could improve the probiotic viable counts, physico-chemical, texture, and rheological properties in both cow and goat milk fermentation. Substantial differences were also observed in the metabolomics profiles between fermented cow and goat milks produced by the two bacteria. Comparing with Probio-M9-fermented cow and goat milks, those fermented by HG-R7970-3 were enriched in a number of flavor compounds and potential functional components, particularly acids, esters, peptides, and intermediate metabolites. Moreover, HG-R7970-3 could improve the post-fermentation flavor retention capacity. These new and added features are of potential to improve the techno-functional qualities of conventional fermented milks produced by Probio-M9, and these differences are likely imparted by the acquired CPS-/EPS-producing ability of the mutant. It merits further investigation into the sensory quality and in vivo function of HG-R7970-3-fermented milks.

Limosilactobacillus reuteri Regulating Intestinal Function: A Review

Probiotics have extensive use in daily life, due to the function of the changing intestinal metabolism and material conversion processes, wherein they remodel the intestinal microbiota, regulate the intestinal function and affect the organism’s health. Limosilactobacillus reuteri (L. reuteri), originally discovered in breast milk and currently reported to be present within the gut of almost all vertebrates and mammals, is an intestinal probiotic with prebiotic efficacy. Most L. reuteri have good intestinal colonization and bacteriocin secretion abilities, which can increase the expression of the mucin (mucoprotein) genes 2 MUC2 and MUC13, which in turn promote the development and maturation of intestinal organoids, and augment mucin secretion. In enteritis patients, L. reuteri downregulates α Tumor necrosis factor-α, (TNF-α), Interleukin-6 (IL-6), IL-8, and IL-12 expression to attenuate inflammation. It also induces the host’s production of immunoglobulin A (IGA), which manipulates the intestinal microbial community, inhibiting the growth of pathogens. L. reuteri has been widely used in daily life. with in-depth studies having been conducted on the prebiotic effects of L. reuteri. However, the complexity of its application in a clinical setting is still unclear because the pathogenesis of various diseases still requires a large amount of data and theoretical support.

Heat, cold, acid, and bile salt induced differential proteomic responses of a novel potential probiotic Lactococcus garvieae C47 isolated from camel milk

Probiotics encounter various stresses during food processing and digestion. This study evaluated the differential proteomic responses of a newly identified potential probiotic lactic acid bacteria, Lactococcus garvieae, isolated from camel milk. Lc. garvieae C47 was exposed to heat, cold, acid, and bile conditions, and stress-responsive proteins were identified. The proteomic analysis was done using 2D-IEF SDS PAGE and nano-LC-MS/MS. Out of 91 differentially expressed proteins, 20 upregulated and 27 downregulated proteins were shared among the stresses. The multivariate data analysis revealed abundance of elongation factor Ts (spot C42), uridine phosphorylase, fructose-bisphosphate aldolase, peptidase T, cobalt ECF transporter T component CbiQ, UDP-N-acetylmuramate-l-alanine ligase, uncharacterized protein, aspartokinase, chaperone protein DnaK, IGP synthase cyclase subunit, probable nicotinate-nucleotide adenylyltransferase, NADH-quinone oxidoreductase, holo-[acyl-carrier-protein] synthase, l-lactate dehydrogenase, and uncharacterized protein. The maximum number of differentially expressed proteins belonged to carbohydrate and protein metabolism, which indicates Lc. garvieae shifts towards growth and energy metabolism for resistance against stress conditions.

Differences between Kazak Cheeses Fermented by Single and Mixed Strains Using Untargeted Metabolomics

Mixed fermentation improves the flavor quality of food. Untargeted metabolomics were used to evaluate the impact of mixed fermentation and single-strain fermentation on the volatile and non-volatile compound profiles of Kazak cheese. Lacticaseibacillus paracasei SMN-LBK and Kluyveromyces marxianus SMN-S7-LBK were used to make mixed-fermentation cheese (M), while L. paracasei SMN-LBK was applied in single-strain-fermentation cheese (S). A higher abundances of acids, alcohols, and esters were produced via mixed fermentation. Furthermore, 397 differentially expressed non-volatile metabolites were identified between S and M during ripening. The flavor compounds in mixed-fermentation cheese mainly resulted from ester production (ethyl butanoate, ethyl acetate, ethyl octanoate, and ethyl hexanoate) and amino acid biosynthesis (Asp, Glu, Gln, and Phe). The metabolites were differentially expressed in nitrogen metabolism, D-glutamine and D-glutamate metabolism, phenylalanine metabolism, D-alanine metabolism, and other metabolic pathways. The amount of flavor compounds was increased in M, indicating that L. paracasei SMN- LBK and K. marxianus SMN-S7-LBK had synergistic effects in the formation of flavor compounds. This study comprehensively demonstrated the difference in metabolites between mixed-fermentation and single-strain-fermentation cheese and provided a basis for the production of Kazak cheese with diverse flavor characteristics.

Biological characteristics and whole-genome analysis of the potential probiotic, Lactobacillus reuteri S5

Lactic acid bacteria are microorganisms used for probiotic purposes and form major parts of human and mammalian intestinal microbiota, exerting important health-promoting effects on the host. Here, we evaluated L. reuteri strain S5 isolated from the intestines of healthy white feather broilers. L. reuteri S5 grew best after 20 h of incubation in MRS medium. Lactic acid production was 1.42 mmol L^-1 at 24 h, which was well tolerated. Activities of T-AOC, GSH-Px and T-SOD in the cell-free fermentation supernatant of L. reuteri S5 were higher than those in the bacteria, and the strain showed good hydrophobicity in vitro. The dominant carbon and nitrogen sources of L. reuteri S5 were glucose and soybean meal. A high-quality complete genome map of L. reuteri S5 was obtained using a Pacbio nanopore third-generation sequencing platform. The results showed that L. reuteri S5 possesses a complete primary metabolic pathway, encoding the main functional enzymes of the glycolysis pathway and pentose phosphate pathway. The genome contains genes encoding antioxidants and conferring tolerance to inorganic salt ions, acids and bile salts. This study shows that L. reuteri S5 is a probiotic strain with excellent probiotic characteristics and has great potential for the development of feed additives to promote animal health.

Amino Acids in Microbial Metabolism and Function

Amino acids (AAs) not only serve as building blocks for protein synthesis in microorganisms but also play important roles in their metabolism, survival, inter-species crosstalk, and virulence. Different AAs have their distinct functions in microbes of the digestive tract and this in turn has important impacts on host nutrition and physiology. Deconjugation and re-conjugation of glycine- or taurine- conjugated bile acids in the process of their enterohepatic recycling is a good example of the bacterial adaptation to harsh gut niches, inter-kingdom cross-talk with AA metabolism, and cell signaling as the critical control point. It is also a big challenge for scientists to modulate the homeostasis of the pools of AAs and their metabolites in the digestive tract with the aim to improve nutrition and regulate AA metabolism related to anti-virulence reactions. Diversity of the metabolic pathways of AAs and their multi-functions in modulating bacterial growth and survival in the digestive tract should be taken into consideration in recommending nutrient requirements for animals. Thus, the concept of functional amino acids can guide not only microbiological studies but also nutritional and physiological investigations. Cutting edge discoveries in this research area will help to better understand the mechanisms responsible for host-microbe interactions and develop new strategies for improving the nutrition, health, and well-being of both animals and humans.

Molecular Analysis of Glutamate Decarboxylases in Enterococcus avium

Enterococcus avium (E. avium) is a common bacterium inhabiting the intestines of humans and other animals. Most strains of this species can produce gamma-aminobutyric acid (GABA) via the glutamate decarboxylase (GAD) system, but the presence and genetic organization of their GAD systems are poorly characterized. In this study, our bioinformatics analyses showed that the GAD system in E. avium strains was generally encoded by three gadB genes (gadB1, gadB2, and gadB3), together with an antiporter gene (gadC) and regulator gene (gadR), and these genes are organized in a cluster. This finding contrasts with that for other lactic acid bacteria. E. avium SDMCC050406, a GABA producer isolated from human feces, was employed to investigate the contribution of the three gadB genes to GABA biosynthesis. The results showed that the relative expression level of gadB3 was higher than those of gadB1 and gadB2 in the exponential growth and stationary phases, and this was accompanied by the synchronous transcription of gadC. After heterologous expression of the three gadB genes in Escherichia coli BL21 (DE3), the K_m value of the purified GAD3 was 4.26 ± 0.48 mM, a value lower than those of the purified GAD1 and GAD2. Moreover, gadB3 gene inactivation caused decreased GABA production, accompanied by a reduction in resistance to acid stress. These results indicated that gadB3 plays a crucial role in GABA biosynthesis and this property endowed the strain with acid tolerance. Our findings provided insights into how E. avium strains survive the acidic environments of fermented foods and throughout transit through the stomach and gut while maintaining cell viability.

Characterization of γ-glutamyl cysteine ligases from Limosilactobacillus reuteri producing kokumi-active γ-glutamyl dipeptides

γ-Glutamyl cysteine ligases (Gcls) catalyze the first step of glutathione synthesis in prokaryotes and many eukaryotes. This study aimed to determine the biochemical properties of three different Gcls from strains of Limosilactobacillus reuteri that accumulate γ-glutamyl dipeptides. Gcl1, Gcl2, and Gcl3 were heterologously expressed in Escherichia coli and purified by affinity chromatography. Gcl1, Gcl2, and Gcl2 exhibited biochemical with respect to the requirement for metal ions, the optimum pH and temperature of activity, and the kinetic constants for the substrates cysteine and glutamate. The substrate specificities of the three Gcls to 14 amino acids were assessed by liquid chromatography-mass spectrometry. All three Gcls converted ala, met, glu, and gln into the corresponding γ-glutamyl dipeptides. None of the three were active with val, asp, and his. Gcl1 and Gcl3 but not Gcl2 formed γ-glu-leu, γ-glu-ile, and γ-glu-phe; Gcl3 exhibited stronger activity with gly, pro, and asp when compared to Gcl2. Phylogenetic analysis of Gcl and the Gcl-domain of GshAB in lactobacilli demonstrated that most of Gcls were present in heterofermentative lactobacilli, while GshAB was identified predominantly in homofermentative lactobacilli. This distribution suggests a different ecological role of the enzyme in homofermentative and heterofermentative lactobacilli. In conclusion, three Gcls exhibited similar biochemical properties but differed with respect to their substrate specificity and thus the synthesis of kokumi-active γ-glutamyl dipeptides. KEY POINTS: • Strains of Limosilactobacillus reuteri encode for up to 3 glutamyl cysteine ligases. • Gcl1, Gcl2, and Gcl3 of Lm. reuteri differ in their substrate specificity. • Gcl1 and Gcl3 produce kokumi-active dipeptides.

Metabolic network of ammonium in cereal vinegar solid-state fermentation and its response to acid stress

Shanxi aged vinegar (SAV), a Chinese traditional vinegar, is produced by various microorganisms. Ammonium is an important nitrogen source for microorganisms and a key intermediate for the utilization of non-ammonium nitrogen sources. In this work, an ammonium metabolic network during SAV fermentation was constructed through the meta-transcriptomic analysis of in situ samples, and the potential mechanism of acid affecting ammonium metabolism was revealed. The results showed that ammonium was enriched as the acidity increased. Meta-transcriptomic analysis showed that the conversion of glutamine to ammonia is the key pathway of ammonium metabolism in vinegar and that Lactobacillus and Acetobacter are the dominant genera. The construction and analysis of the metabolic network showed that amino acid metabolism, nucleic acid metabolism, pentose phosphate pathway and energy metabolism were enhanced to resist acid damage to the intracellular environment and cell structures. The enhancement of nitrogen assimilation provides nitrogen for metabolic pathways that resist acid cytotoxicity. In addition, the concentration gradient allows ammonium to diffuse outside the cell, which causes ammonium to accumulate during fermentation.

Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism

Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.