Metabolic functions of the human gut microbiota: the role of metalloenzymes

In vivo evaluations of Lactobacillus-fermented Eucheuma spinosum polysaccharides on alleviating food allergy activity

In order to explore the in vivo anti-food allergy activity of Lactobacillus sakei subsp. sakei-fermented Eucheuma spinosum polysaccharides F1-ESP-3, an ovalbumin (OVA)-induced food allergy mouse model was established by ascites immunization and gavage. The weight, temperature, incidence of diarrhea, levels of allergic mediators and inflammatory factors in the serum of mice were analyzed. We analyzed the differentiation of mouse spleen lymphocytes and the proportion of sensitized mast cells by flow cytometry. The intestinal barrier status of mice was analyzed by intestinal pathological tissue sections and microbiota sequencing. The results showed that F1-ESP-3 could alleviate the food allergy symptoms of mice, such as hypothermia and loose stool; levels of OVA-specific immunoglobulin E, mast cell protease and histamine in the serum of sensitized mice and the proportion of dendritic cells and mast cells in mouse spleen were significantly reduced; in addition, F1-ESP-3 may protect the intestinal barrier and further improve the intestinal microenvironment of food-allergic mice by regulating the abundance of Bacteroidetes and Firmicutes. F1-ESP-3 can further improve the intestinal microenvironment of food-allergic mice by upregulating the levels of Lachnospiraceae, and may affect the signal pathways such as NOD-like receptor, MAPK, I kappa B and antigen processing and presentation.

Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages

SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.

Native gastrointestinal mucus: Critical features and techniques for studying interactions with drugs, drug carriers, and bacteria

Gastrointestinal mucus plays essential roles in modulating interactions between intestinal lumen contents, including orally delivered drug carriers and the gut microbiome, and underlying epithelial and immune tissues and cells. This review is focused on the properties of and methods for studying native gastrointestinal mucus and its interactions with intestinal lumen contents, including drug delivery systems, drugs, and bacteria. The properties of gastrointestinal mucus important to consider in its analysis are first presented, followed by a discussion of different experimental setups used to study gastrointestinal mucus. Applications of native intestinal mucus are then described, including experimental methods used to study mucus as a barrier to drug delivery and interactions with intestinal lumen contents that impact barrier properties. Given the significance of the microbiota in health and disease, its impact on drug delivery and drug metabolism, and the use of probiotics and microbe-based delivery systems, analysis of interactions of bacteria with native intestinal mucus is then reviewed. Specifically, bacteria adhesion to, motility within, and degradation of mucus is discussed. Literature noted is focused largely on applications of native intestinal mucus models as opposed to isolated mucins or reconstituted mucin gels.

The benefits of edible mushroom polysaccharides for health and their influence on gut microbiota: a review

The gut microbiome is a complex biological community that deeply affects various aspects of human health, including dietary intake, disease progression, drug metabolism, and immune system regulation. Edible mushroom polysaccharides (EMPs) are bioactive fibers derived from mushrooms that possess a range of beneficial properties, including anti-tumor, antioxidant, antiviral, hypoglycemic, and immunomodulatory effects. Studies have demonstrated that EMPs are resistant to human digestive enzymes and serve as a crucial source of energy for the gut microbiome, promoting the growth of beneficial bacteria. EMPs also positively impact human health by modulating the composition of the gut microbiome. This review discusses the extraction and purification processes of EMPs, their potential to improve health conditions by regulating the composition of the gut microbiome, and their application prospects. Furthermore, this paper provides valuable guidance and recommendations for future studies on EMPs consumption in disease management.

Assessing the Potential Biological Activities of Postbiotics Derived from Saccharomyces cerevisiae: An In Vitro Study

A new biotherapeutic strategy involves the use of microbial bioactive substances (postbiotics) that exhibit optimum compatibility and intimate contact with the immune system of the host. This study was aimed at investigating the potential biological activities of postbiotics derived from Saccharomyces cerevisiae (PTCC 5269) (PSC) under in vitro circumstances. Based on the outcomes, the synthesized PSC possessing a high level of phenolic (102.46 ± 0.25 mg GAE/g) and flavonoid (19.87 ± 75.32 mg QE/g) content demonstrated significant radical scavenging activity (87.34 ± 0.56%); antibacterial action towards Listeria monocytogenes, Streptococcus mutans, Salmonella typhi, and Escherichia coli (in order of effectiveness) in both in vitro and food models (whole milk and ground meat); probiotics' growth-promoting activity in the fermentation medium; α-glucosidase enzyme-inhibiting and cholesterol-lowering properties in a concentration- and pH-dependent manner; reduction in the cell viability (with the significant IC₅₀ values of 34.27 and 23.58 μg/mL after 24 and 48 h, respectively); suppressed the initial (G0/G1) phase of the cell's division; induced apoptosis; and increased the expression of PTEN gene, while the IkB, RelA, and Bcl-XL genes indicated diminished expression in treated SW480 cancer cells. These multiple health-promoting functions of PSC can be extended to medical, biomedical, and food scopes, as novel biotherapeutic approaches, in order to design efficient and optimized functional food formulations or/and supplementary medications to use as adjuvant agents for preventing or/and treating chronic/acute disorders.

Matrix metalloproteinases are key targets of acupuncture in the treatment of ulcerative colitis

The aim of this study was to elucidate the key targets of acupuncture in the colon of ulcerative colitis (UC) mice model using full-length transcriptome sequencing. 2.5% dextran sodium sulfate (DSS)-induced colitis mice were treated with or without acupuncture. Intestinal pathology was observed, and full transcriptome sequencing and bioinformatic analysis were performed. The results demonstrated that acupuncture treatment reduced the UC symptoms, disease activity index score, and histological colitis score and increased body weight, colon length, and the number of intestinal goblet cells. In addition, acupuncture can also decrease the expression of necrotic biomarker phosphorylates mixed lineage kinase domain-like pseudo kinase (p-MLKL). Full-length transcriptome analysis indicated that acupuncture reversed the expression of 987 of the 1918 upregulated differentially expressed genes (DEGs), and 632 of the 1351 downregulated DEGs induced by DSS. DEGs regulated by acupuncture were mainly involved in inflammatory responses and intestinal barrier pathways. The protein-protein interaction network analysis revealed that matrix metalloproteinases (MMPs) are important genes regulated by acupuncture. Gene set enrichment analysis revealed that extracellular matrix (ECM)-receptor interaction was an important target of acupuncture. In addition, alternative splicing analysis suggested that acupuncture improved signaling pathways related to intestinal permeability, the biological processes of xenobiotics, sulfur compounds, and that monocarboxylic acids are closely associated with MMPs. Overall, our transcriptome analysis results indicate that acupuncture improves intestinal barrier function in UC through negative regulation of MMPs expression.

Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.

Effects of microbial-derived biotics (meta/pharma/post-biotics) on the modulation of gut microbiome and metabolome; general aspects and emerging trends

Potential effects of metabiotics (probiotics effector molecules or signaling factors), pharmabiotics (pro-functional metabolites produced by gut microbiota (GMB)) and postbiotics (multifunctional metabolites and structural compounds of food-grade microorganisms) on GMB have been rarely reviewed. These multifunctional components have several promising capabilities for prevention, alleviation and treatment of some diseases or disorders. Correlations between these essential biotics and GMB are also very interesting and important in human health and nutrition. Furthermore, these natural bioactives are involved in modulation of the immune function, control of metabolic dysbiosis and regulation of the signaling pathways. This review discusses the potential of meta/pharma/post-biotics as new classes of pharmaceutical agents and their effective mechanisms associated with GMB-host cell to cell communications with therapeutic benefits which are important in balance and the integrity of the host microbiome. In addition, cutting-edge findings about bioinformatics /metabolomics analyses related to GMB and these essential biotics are reviewed.

Cell-free supernatant of probiotic bacteria exerted antibiofilm and antibacterial activities against Pseudomonas aeruginosa: A novel biotic therapy

Aim: This study aims to verify the antibacterial and antibiofilm action of cell-free spent medium (CFSM) from four lactic acid bacteria with potential probiotic characteristics (Lactiplantibacillus plantarum, Lactobacillus acidophilus, Lactobacillus johnsonii, and Lactobacillus delbrueckii) against two Pseudomonas aeruginosa strains. Main methods: The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the CFSM, antibacterial activity by analysing the formation of inhibition zones, and inhibition of planktonic cultures were determined. Whether an increase in the concentration of CFSM influenced the growth of pathogenic strains and the anti-adhesive activity of the CFSM in biofilm formation (crystal violet and MTT assays) were determined, which were all corroborated by using scanning electron microscopy. Key findings: The relationship between the MIC and MBC values showed a bactericidal or bacteriostatic effect for all the cell-free spent media (CFSMs) tested for P. aeruginosa 9027™ and 27853™ strains. The CFSM supplemental doses of 18 or 22%, 20 or 22%, 46 or 48%, and 50 or 54% of L. acidophilus, L. delbrueckii, L. plantarum, and L. johnsonii, respectively, could completely inhibit the growth of both pathogen strains. The antibiofilm activity of the CFSM in three biofilm conditions (pre-coated, co-incubated, and preformed) demonstrated values ranging between 40% and 80% for biofilm inhibition, and similar results were observed for cell viability. Significance: This work provides strong evidence that the postbiotic derived from different Lactobacilli could be practical as an adjuvant therapy for reducing the use of antibiotics, being a good candidate to overcome the growing challenge of hospital infections due to this pathogen.

Beyond cellulose: pharmaceutical potential for bioactive plant polysaccharides in treating disease and gut dysbiosis

Polysaccharides derived from plants, algae, or fungi serve as the major components of some human diets. Polysaccharides have been shown to exhibit diverse biological activities in improving human health, and have also been proposed to function as potent modulators of gut microbiota composition, thus playing a bi-directional regulatory role in host health. Here, we review a variety of polysaccharide structures potentially linked to biological functions, and cover current research progress in characterizing their pharmaceutical effects in various disease models, including antioxidant, anticoagulant, anti-inflammatory, immunomodulatory, hypoglycemic, and antimicrobial activities. We also highlight the effects of polysaccharides on modulating gut microbiota via enrichment for beneficial taxa and suppression of potential pathogens, leading to increased microbial expression of carbohydrate-active enzymes and enhanced short chain fatty acid production. This review also discusses polysaccharide-mediated improvements in gut function by influencing interleukin and hormone secretion in host intestinal epithelial cells.

Dextran-Sulfate-Sodium-Induced Colitis-Ameliorating Effect of Aqueous Phyllanthus emblica L. Extract through Regulating Colonic Cell Gene Expression and Gut Microbiomes

The anti-inflammation effect of aqueous Phyllanthus emblica L. extract (APE) and its possible underlying mechanism in dextran sulfate sodium (DSS)-induced mice chronic colonic inflammation were studied. APE treatment significantly improved the colitic symptoms, including ameliorating the shortening of the colon, increasing the DSS-induced body weight loss, reducing the disease activity index, and reversing the condition of colon tissue damage of mucus lost and goblet cell reduction. Overproduction of serum pro-inflammatory cytokines were suppressed by the treatment of APE. Gut microbiome analysis showed that APE remodeled the structure of gut bacteria in phylum and genus levels, upregulating the abundance of phylum Bacteroidetes, family Muribaculaceae, and genus Bacteroides and downregulating the abundance of phylum Firmicutes. The reshaped gut microbiome caused metabolic functions and pathway change with enhanced queuosine biosynthesis and reduced polyamine synthesis pathway. Colon tissue transcriptome analysis further elucidated APE-inhibited mitogen-activated protein kinase (MAPK), cytokine-cytokine receptor interaction, and tumor necrosis factor (TNF) signaling pathways and the expressions of the genes that promote the progress of colorectal cancer. It turned out that APE reshaped the gut microbiome and inhibited MAPK, cytokine-cytokine receptor interaction, and TNF signaling pathways as well as the colorectal-cancer-related genes to exert its colitis protective effect.

Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases"

The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.

Postbiotics against Obesity: Perception and Overview Based on Pre-Clinical and Clinical Studies

Overweight and obesity are significant global public health concerns that are increasing in prevalence at an alarming rate. Numerous studies have demonstrated the benefits of probiotics against obesity. Postbiotics are the next generation of probiotics that include bacteria-free extracts and nonviable microorganisms that may be advantageous to the host and are being increasingly preferred over regular probiotics. However, the impact of postbiotics on obesity has not been thoroughly investigated. Therefore, the goal of this review is to gather in-depth data on the ability of postbiotics to combat obesity. Postbiotics have been reported to have significant potential in alleviating obesity. This review comprehensively discusses the anti-obesity effects of postbiotics in cellular, animal, and clinical studies. Postbiotics exert anti-obesity effects via multiple mechanisms, with the major mechanisms including increased energy expenditure, reduced adipogenesis and adipocyte differentiation, suppression of food intake, inhibition of lipid absorption, regulation of lipid metabolism, and regulation of gut dysbiosis. Future research should include further in-depth studies on strain identification, scale-up of postbiotics, identification of underlying mechanisms, and well-defined clinical studies. Postbiotics could be a promising dietary intervention for the prevention and management of obesity.

Beyond probiotics: a narrative review on an era of revolution

Whether knowingly or unknowingly, humans have been consuming probiotic microorganisms through traditionally fermented foods for generations. Bacteria, like lactic acid bacteria, are generally thought to be harmless and produce many metabolites that are beneficial for human health. Probiotics offer a wide range of health benefits; however, their therapeutic usage is limited because they are living organisms. As a result, the focus on the health advantages of microbes has recently shifted from viable live probiotics to non-viable microbes made from probiotics. These newly emerging non-viable microbes include paraprobiotics, postbiotics, psychobiotics, nutribiotics, and gerobiotics. Their metabolites can boost physiological health and reveal the therapeutic effects of probiotics. This new terminology in microbes, their traits, and their applications are summarized in the present review.

Dual Regulation of Sulfonated Lignin to Prevent and Treat Type 2 Diabetes Mellitus

With the rapid increase of diabetes cases in the world, there is an increasing demand for slowing down and managing diabetes and its effects. It is considered that a viable prophylactic treatment for type 2 diabetes mellitus (T2DM) is to reduce carbohydrate digestibility by controlling the activities of α-amylase and α-glucosidase to control postprandial hyperglycemia and promote the growth of intestinal beneficial bacteria. In this work, the effects of sulfonated lignin with different sulfonation degrees (0.8 mmol/g, SL₁; 2.9 mmol/g, SL₂) on the inhibition of α-amylase and α-glucosidase and the proliferation of intestinal beneficial bacteria in vitro were investigated. The results showed that both SL₁ and SL₂ can inhibit the activity of α-amylase and α-glucosidase. The inhibition capacity (IC₅₀, 32.35 μg/mL) of SL₂ with a low concentration (0-0.5 mg/mL) to α-amylase was close to that of acarbose to α-amylase (IC₅₀, 27.33 μg/mL). Compared with the control groups, the bacterial cell concentrations of Bifidobacteria adolescentis and Lactobacillus acidophilus cultured with SL₁ and SL₂ increased in varying degrees (8-36%), and the produced short-chain fatty acids were about 1.2 times higher. This work demonstrates the prospect of sulfonated lignin as a prebiotic for the prevention and treatment of T2DM, which provides new insights for opening up a brand new field of lignin.

S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota

Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme

Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.

Postbiotics as the key mediators of the gut microbiota-host interactions

The priority of the Sustainable Development Goals for 2022 is to reduce all causes related to mortality. In this regard, microbial bioactive compounds with characteristics such as optimal compatibility and close interaction with the host immune system are considered a novel therapeutic approach. The fermentation process is one of the most well-known pathways involved in the natural synthesis of a diverse range of postbiotics. However, some postbiotics are a type of probiotic response behavior to environmental stimuli that usually play well-known biological roles. Also, postbiotics with unique structure and function are key mediators between intestinal microbiota and host cellular processes/metabolic pathways that play a significant role in maintaining homeostasis. By further understanding the nature of parent microbial cells, factors affecting their metabolic pathways, and the development of compatible extraction and identification methods, it is possible to achieve certain formulations of postbiotics with special efficiencies, which in turn will significantly improve the performance of health systems (especially in developing countries) toward a wide range of acute/chronic diseases. The present review aims to describe the fundamental role of postbiotics as the key mediators of the microbiota-host interactions. Besides, it presents the available current evidence regarding the interaction between postbiotics and host cells through potential cell receptors, stimulation/improvement of immune system function, and the enhancement of the composition and function of the human microbiome.

Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins

Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α₃X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.

The future of functional food: Emerging technologies application on prebiotics, probiotics and postbiotics

This review was the first to gather literature about the effect of emerging technologies on probiotic, prebiotic, and postbiotic products. Applying emerging technologies to probiotic products can increase probiotic survival and improve probiotic properties (cholesterol attachment, adhesion to Caco-2 cells, increase angiotensin-converting enzyme (ACE) inhibitory, antioxidant, and antimicrobial activities, and decrease systolic blood pressure). Furthermore, it can optimize the fermentation process, produce or maintain compounds of interest (bacteriocin, oligosaccharides, peptides, phenolic compounds, flavonoids), improve bioactivity (vitamin, aglycones, calcium), and sensory characteristics. Applying emerging technologies to prebiotic products did not result in prebiotic degradation. Still, it contributed to higher concentrations of bioactive compounds (citric and ascorbic acids, anthocyanin, polyphenols, flavonoids) and health properties (antioxidant activity and inhibition of ACE, α-amylase, and α-glucosidase). Emerging technologies may also be applied to obtain postbiotics with increased health effects. In this way, current studies suggest that emerging food processing technologies enhance the efficiency of probiotics and prebiotics in food. The information provided may help food industries to choose a more suitable technology to process their products and provide a basis for the most used process parameters. Furthermore, the current gaps are discussed. Emerging technologies may be used to process food products resulting in increased probiotic functionality, prebiotic stability, and higher concentrations of bioactive compounds. In addition, they can be used to obtain postbiotic products with improved health effects compared to the conventional heat treatment.

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Urease catalyzes the hydrolysis of urea to form ammonia and carbamate, inducing an overall pH increase that affects both human health and agriculture. Inhibition, mutagenesis, and kinetic studies have provided insights into its enzymatic role, but there have been debates on the substrate binding mode as well as the reaction mechanism. In the present study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) calculations on urease that mainly investigate the binding mode of urea and the mechanism of the urease-catalyzed hydrolysis reaction. Comparison between the experimental data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that urea hydrolysis via a complex with bidentate-bound urea is much more favorable than via that with monodentate-bound urea for both nucleophilic attack and the subsequent proton transfer steps. We also indicate that the bidentate coordination of urea fits the active site with a closed conformation of the mobile flap and can facilitate the stabilization of transition states and intermediates by forming multiple hydrogen bonds with certain active site residues.

The role of microbiota-derived postbiotic mediators on biofilm formation and quorum sensing-mediated virulence of Streptococcus mutans: A perspective on preventing dental caries

Dental caries is not only one of the most prevalent diseases worldwide, but also a public health problem, undoubtedly. Among the various types of cariogenic bacteria, Streptococcus mutans is considered to be the major etiological pathogen of dental caries. The present study aimed to assess the influence of microbiota-derived postbiotic mediators (PMs) on the pathogenesis of dental caries. Within this aim, the antibacterial (agar diffusion method) and antibiofilm (crystal violet assay) characteristics of PMs derived from Lactiplantibacillus plantarum EIR/IF-1, Lactiplantibacillus curvatus EIR/DG-1, and Lactiplantibacillus curvatus EIR/BG-2 against S. mutans (ATCC 25175) were analyzed. According to the results, PM of the strain EIR/IF-1, isolated from infant feces showed the highest inhibitory effect (pH-dependent). Besides, sub-MIC doses of all PMs eliminated the biofilm formation following the co-incubation and pre-treatment assays. The reduction of cell viability and notable changes in biofilm formation was also confirmed both on glass coverslips and ex vivo human tooth surfaces by confocal laser scanning microscopy and scanning electron microscopy. Moreover, sub-MIC values of PMs down-regulated the expression of gtfC, comA, and comX, without any significant growth inhibition. Organic acids, fatty acids, and vitamins in PMs were also reported. Overall, these findings indicated the possible preventive roles of microbiota-derived PMs for the pathogenesis of dental caries.

Edible fungal polysaccharides, the gut microbiota, and host health

The plasticity of the gut microbiota (GM) creates an opportunity to reshape the biological output of gut microbes by manipulating external factors. It is well known that edible fungal polysaccharides (EFPs) can reach the distal intestine and be assimilated to reshape the GM. The GM has unique devices that utilize various EFPs and produce oligosaccharides, which can selectively promote the growth of beneficial bacteria and are fermented into short-chain fatty acids that interact closely with intestinal cells. Here we review EFPs-based interventions for the GM, particularly the key microorganisms, functions, and metabolites. In addition, we discuss the bi-directional causality between GM imbalance and diseases, and the beneficial effects of EFPs on host health via GM. This review can offer a valuable reference for the design of edible fungal polysaccharide- or oligosaccharide-based nutrition interventions or drug development for maintaining human health by targeted regulation of the GM.

The Relationship Between Mucosal Microbiota, Colitis, and Systemic Inflammation in Chronic Granulomatous Disorder

PURPOSE

Chronic granulomatous disorder (CGD) is a primary immunodeficiency which is frequently complicated by inflammatory colitis and is associated with systemic inflammation. Herein, we aimed to investigate the role of the microbiome in the pathogenesis of colitis and systemic inflammation.

METHODS

We performed 16S rDNA sequencing on mucosal biopsy samples from each segment of 10 CGD patients' colons and conducted compositional and functional pathway prediction analyses.

RESULTS

The microbiota in samples from colitis patients demonstrated reduced taxonomic alpha-diversity compared to unaffected patients, even in apparently normal bowel segments. Functional pathway richness was similar between the colitic and non-colitic mucosa, although metabolic pathways involved in butyrate biosynthesis or utilization were enriched in patients with colitis and correlated positively with fecal calprotectin levels. One patient with very severe colitis was dominated by Enterococcus spp., while among other patients Bacteroides spp. abundance correlated with colitis severity measured by fecal calprotectin and an endoscopic severity score. In contrast, Blautia abundance is associated with low severity scores and mucosal health. Several taxa and functional pathways correlated with concentrations of inflammatory cytokines in blood but not with colitis severity. Notably, dividing patients into "high" and "low" systemic inflammation groups demonstrated clearer separation than on the basis of colitis status in beta-diversity analyses.

CONCLUSION

The microbiome is abnormal in CGD-associated colitis and altered functional characteristics probably contribute to pathogenesis. Furthermore, the relationship between the mucosal microbiome and systemic inflammation, independent of colitis status, implies that the microbiome in CGD can influence the inflammatory phenotype of the condition.

Listeria monocytogenes biofilm inhibition on food contact surfaces by application of postbiotics from Lactobacillus curvatus B.67 and Lactobacillus plantarum M.2

Owing to their preservative and antimicrobial effects, postbiotics (metabolic byproducts of probiotics) are promising natural components for the food industry. Therefore, the present study aimed to investigate the efficacy of postbiotics collected from isolated Lactobacillus curvatus B.67 and Lactobacillus plantarum M.2 against Listeria monocytogenes pathogens in planktonic cells, motility, and biofilm states. The analysis of the metabolite composition of the postbiotics revealed various organic acids, along with a few well-known bacteriocin-encoding genes with potential antimicrobial effects. Postbiotics maintained their residual antimicrobial activity over the pH range 1-6 but lost all activity at neutral pH (pH 7). Full antimicrobial activity (100%) was observed during heat treatment, even under the autoclaving condition.Minimum inhibitory concentration (MICs) of L. curvatus B.67 and L. plantarum M.2 against L. monocytogenes were 80 and 70 mg/mL, respectively. However, four sub-MICs of the postbiotics (1/2, 1/4, 1/8, and 1/16 MIC) were tested for inhibition efficacy against L. monocytogenes during different experiment in this study. Swimming motility, biofilm formation, and expression levels of target genes related to biofilm formation, virulence, and quorum-sensing were significantly inhibited with increasing postbiotics concentration. Postbiotics from L. plantarum M.2 exhibited a higher inhibitory effect than the postbiotics from L. curvatus B.67. Nonetheless, both these postbiotics from Lactobacillus spp. could be used as effective bio-interventions for controlling L. monocytogenes biofilm in the food industry.

Novel 4-Hydroxybenzyl Adducts in Human Hemoglobin: Structures and Mechanisms of Formation

Humans are exposed to large numbers of electrophiles from their diet, the environment, and endogenous physiological processes. Adducts formed at the N-terminal valine of hemoglobin are often used as biomarkers of human exposure to electrophilic compounds. We previously reported the formation of hemoglobin N-terminal valine adducts (added mass, 106.042 Da) in the blood of human smokers and nonsmokers and identified their structure as 4-hydroxybenzyl-Val. In the present work, mass spectrometry-based proteomics was utilized to identify additional sites for 4-hydroxybenzyl adduct formation at internal nucleophilic amino acid side chains within hemoglobin. Hemoglobin isolated from human blood was treated with para-quinone methide (para-QM) followed by global nanoLC-MS/MS and targeted nanoLC-MS/MS to identify amino acid residues containing the 4-hydroxybenzyl modification. Our experiments revealed the formation of 4-hydroxybenzyl adducts at the αHis20, αTyr24, αTyr42, αHis45, βSer72, βThr84, βThr87, βSer89, βHis92, βCys93, βCys112, βThr123, and βHis143 residues (in addition to N-terminal valine) through characteristic MS/MS spectra. These amino acid side chains had variable reactivity toward para-QM with αHis45, αTyr42, βCys93, βHis92, and βSer72 forming the largest numbers of adducts upon exposure to para-QM. Two additional mechanisms for formation of 4-hydroxybenzyl adducts in humans were investigated: exposure to 4-hydroxybenzaldehyde (4-HBA) followed by reduction and UV-mediated reactions of hemoglobin with tyrosine. Exposure of hemoglobin to a 5-fold molar excess of 4-HBA followed by reduction with sodium cyanoborohydride produced 4-hydroxybenzyl adducts at several amino acid side chains of which αHis20, αTyr24, αTyr42, αHis45, βSer44, βThr84, and βHis92 were verified in targeted mass spectrometry experiments. Similarly, exposure of human blood to ultraviolet radiation produced 4-hydroxybenzyl adducts at αHis20, αTyr24, αTyr42, αHis45, βSer44, βThr84, and βSer89. Overall, our results reveal that 4-hydroxybenzyl adducts form at multiple nucleophilic sites of hemoglobin and that para-QM is the most likely source of these adducts in humans.

The relationship between gut microbiota and proteolytic activity in irritable bowel syndrome

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disease that affects 3.8-9.2% of the world population. It affects the physiology and psychology of patients and increases the burden on families, the healthcare system, society, and economic development. Presently, a large number of studies have shown that compared to healthy individuals, the composition and diversity of gut microbiota in IBS patients have changed, and the proteolytic activity (PA) in fecal supernatant and colonic mucosa of IBS patients has also increased. These findings indicate that the imbalance of intestinal microecology and intestinal protein hydrolysis is closely related to IBS. Furthermore, the intestinal flora is a key substance that regulates the PA and is associated with IBS. The current review described the intestinal microecology and intestinal proteolytic activity of patients with IBS and also discussed the effect of intestinal flora on PA. In summary, this study proposed a pivotal role of gut microbiota and PA in IBS, respectively, and provided an in-depth insight into the diagnosis and treatment targets of IBS as well as the formulation of new treatment strategies for other digestive diseases and protease-related diseases.

Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review

Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.

Changes in digoxin pharmacokinetics associated with hepatic P-glycoprotein upregulation in rats with non-alcoholic fatty liver disease

BACKGROUND & OBJECTIVES

Upregulation of hepatic P-glycoprotein (P-gp) expression has been reported in patients with non-alcoholic fatty liver disease (NAFLD) and rodent models thereof. Here, we explored the changes hepatic P-gp expression and activity in a NAFLD rat model and the effects thereof on the pharmacokinetics of digoxin (a probe substrate of P-gp).

METHODS

Rats were fed a 1% (w/w) orotic acid-containing diet for 20 days to induce NAFLD; control rats received a normal diet. P-gp expression and biliary digoxin excretion were examined. The pharmacokinetics of digoxin were evaluated after it had been administered intravenously (10 μg·kg^-1 ) and orally (200 μg·kg^-1 ) to control and NAFLD rats.

RESULTS

The total areas under the plasma concentration-time curves (AUCs) of digoxin after intravenous and oral administration were significantly smaller (by 39.1% and 73.0%, respectively) in NAFLD rats because of faster biliary digoxin excretion, reflecting elevations of hepatic P-gp expression and activity. Notably, the steady-state volume of distribution rose by 98.2%, while extent of oral bioavailability fell by 55.5% in NAFLD rats.

CONCLUSION

This is the first study to report digoxin pharmacokinetic changes caused by hepatic P-gp upregulation in NAFLD. Further studies are needed to explore the clinical impact of enhanced P-gp-mediated biliary excretion on pharmacotherapies using P-gp substrates in patients with NAFLD.

Signaling pathways in intestinal homeostasis and colorectal cancer: KRAS at centre stage

The intestinal epithelium acts as a physical barrier that separates the intestinal microbiota from the host and is critical for preserving intestinal homeostasis. The barrier is formed by tightly linked intestinal epithelial cells (IECs) (i.e. enterocytes, goblet cells, neuroendocrine cells, tuft cells, Paneth cells, and M cells), which constantly self-renew and shed. IECs also communicate with microbiota, coordinate innate and adaptive effector cell functions. In this review, we summarize the signaling pathways contributing to intestinal cell fates and homeostasis functions. We focus especially on intestinal stem cell proliferation, cell junction formation, remodelling, hypoxia, the impact of intestinal microbiota, the immune system, inflammation, and metabolism. Recognizing the critical role of KRAS mutants in colorectal cancer, we highlight the connections of KRAS signaling pathways in coordinating these functions. Furthermore, we review the impact of KRAS colorectal cancer mutants on pathway rewiring associated with disruption and dysfunction of the normal intestinal homeostasis. Given that KRAS is still considered undruggable and the development of treatments that directly target KRAS are unlikely, we discuss the suitability of targeting pathways downstream of KRAS as well as alterations of cell extrinsic/microenvironmental factors as possible targets for modulating signaling pathways in colorectal cancer.

The Interactions between Polyphenols and Microorganisms, Especially Gut Microbiota

This review presents the comprehensive knowledge about the bidirectional relationship between polyphenols and the gut microbiome. The first part is related to polyphenols' impacts on various microorganisms, especially bacteria, and their influence on intestinal pathogens. The research data on the mechanisms of polyphenol action were collected together and organized. The impact of various polyphenols groups on intestinal bacteria both on the whole "microbiota" and on particular species, including probiotics, are presented. Moreover, the impact of polyphenols present in food (bound to the matrix) was compared with the purified polyphenols (such as in dietary supplements) as well as polyphenols in the form of derivatives (such as glycosides) with those in the form of aglycones. The second part of the paper discusses in detail the mechanisms (pathways) and the role of bacterial biotransformation of the most important groups of polyphenols, including the production of bioactive metabolites with a significant impact on the human organism (both positive and negative).

Comparative Studies of Inhibitory and Antioxidant Activities, and Organic Acids Compositions of Postbiotics Produced by Probiotic Lactiplantibacillus plantarum Strains Isolated From Malaysian Foods

Despite inflammation being a protective natural defense against imbalance stressors in the body, chronic inflammation could lead to the deterioration of immune response, low production, and poor performance in livestock as well as severe economic losses to the farmers. Postbiotics produced by Lactiplantibacillus plantarum has been reported recently to be a natural source of antioxidant, promoting growth performance, anti-inflammation, and immune responses. However, the effects of fermentation media on the compositions of L. plantarum postbiotic have not been reported elsewhere. Hence, a comparative study was conducted to compare the volatile compounds, organic acid composition, and antioxidant and antimicrobial activities of postbiotics produced by six strains of L. plantarum cultivated by using formulated media and the commercial de Man, Rogosa, and Sharpe (MRS) medium as a control. Postbiotics RG14, RI11, and UL4 produced by using formulated media exhibited higher inhibitory activity against Pediococcus acidilactici 446, Escherichia coli E-30, Salmonella enterica CS3, and vancomycin-resistant Enterococci except for Listeria monocytogenes LS55. As for the antioxidant activity, hydroxyl radical scavenging activity was enhanced in formulated media, whereas reducing power activity was the highest in postbiotic RI11. Three organic acids, namely, acetic acid, caproic acid, and lactic acid, were detected in the postbiotic produced by various L. plantarum strains. The concentration of acetic acid was influenced by the fermentation media, whereas caproic acid was detected as the highest in postbiotic RG11. Lactic acid was the predominant compound detected in all the postbiotics and had the significantly highest concentration in postbiotic RS5 when produced by using the MRS medium. Intermediary and pyrrole compounds were the other main compounds that were detected by using GC-MS. Positive correlations were found between organic acid production and inhibitory activity, as well as antioxidant activity exhibited by postbiotics. In conclusion, the compositions and functional characteristics of postbiotics produced by the six strains of L. plantarum were strain-dependent and affected greatly by the fermentation medium. The effects of postbiotic composition on the functional characteristics of postbiotics were elucidated in this study to warrant their applications as a promising beneficial natural growth promoter for the livestock industry.

Human gut microbiota and its association with pathogenesis and treatments of neurodegenerative diseases

Human gut microbiota consists of various microorganisms whose numbers are similar to those of human cells. Human gut microbes and the brain form bidirectional communications through the brain-gut-axis, and play a central role in normal physiological processes and in pathogenesis of many human diseases. Accumulating evidence has demonstrated the crucial effect of gut microbes in proper brain functions and under disease conditions. Here we first focus on revealing current knowledge of the role of gut microbes in neural development and functions. We then summarize mutual relationships between gut microbes and human diseases, in particular neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease and Multiple sclerosis. Finally, we highlight ongoing studies in exploring gut microbes in treatments of human diseases. Applying gut microbes as a means in treatment of human diseases is becoming a promising research direction, and has a great potential in clinical practice.

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics

Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.

Effects of ecologically relevant concentrations of cadmium on locomotor activity and microbiota in zebrafish

Cadmium (Cd) is widely spread in the aquatic environment, and its impact on humans and the ecosystem is an important issue in public health. However, its effects on zebrafish microbiota are still poorly understood. In this study, the potential developmental neurotoxicity and microbiota dysbiosis of ecologically relevant concentrations of Cd (0, 1.25, 2.5 and 5 μg/L) was evaluated by waterborne exposure for 7 days. The data showed that exposure to 5 μg/L of Cd significantly decreased survival rates and impaired locomotor activities. Uptake of Cd was enhanced with the increase of the concentration and duration of exposure. High-throughput sequencing analysis revealed a significant change in the richness and diversity of the microbiota of Cd-treated zebrafish. At the phylum level, the abundance of Proteobacteria increased, while that Firmicutes was significantly decreased after exposure to 5 μg/L Cd. At the genus level, there were significant changes in the abundances of several bacteria involved in the regulation of neurodegenerative diseases (Pseudomonas, Ruminococcaceae, Blautia, Bacteroides, Lactobacillus, Lachnospiraceae, and Phascolarctobacterium) in the Cd-treatment groups, as compared to the control group. In addition, the mRNA expression profiles of bdnf and genes involved in serotonin signaling and metabolism were changed in the Cd exposure groups. Together, these data suggest that Cd could be harmful to zebrafish health by inducing the microbiota changes, and the microbiota could serve as a potential target to protect against the adverse effects of Cd toxicity.

Differences in Intestinal Metabolism of Ginseng Between Normal and Immunosuppressed Rats

BACKGROUND AND OBJECTIVE

Ginseng is usually consumed as a dietary supplement for health care in the normal state or prescribed as a herbal medicine in pathologic conditions. Although metabolic studies of ginseng are commonly performed on healthy organisms, the metabolic characteristics in pathologic organisms remain unexplored. This study aimed to uncover the difference in intestinal metabolism of ginseng between normal and cyclophosphamide-induced immunosuppressed rats and further discuss the potential mechanisms involved.

METHODS

Twelve Sprague-Dawley rats (6-8 weeks old) were randomly divided into two groups: the normal group (NG) and immunosuppressed group (ISG). Rats in the NG and ISG groups were intraperitoneally administered normal saline and cyclophosphamide injections (40 mg/kg) on the 1st, 2nd, 3rd and 10th days; on the 12th day, all rats were intragastrically administered ginseng water extract (900 mg/kg). The difference in intestinal metabolism of ginseng was compared using an ultra-high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry-based metabolomics approach, and the diversities of gut microbiota were analyzed by 16S rRNA gene sequencing between the two groups.

RESULTS

The intestinal metabolomic characteristics of ginseng were significantly different between the normal and immunosuppressed rats, with the ginsenoside F₂ (F₂), 20S-ginsenoside Rg₃ (20(S)-Rg₃), pseudo-ginsenoside Rt₅ (Pseudo-Rt₅), ginsenoside Rd (Rd), ginsenoside Rh₁ (Rh₁), 20S-ginsenoside Rg₁ (20(S)-Rg₁), ginsenoside compound K (CK), ginsenoside Rg₂ (Rg₂) and 20S-panaxatriol (S-PPT) more abundant in immunosuppressed ones (P < 0.05). Additionally, the composition of gut microbiota was remarkably altered in the two groups, with some specific bacterial communities such as Bacteroides spp., Eubacterium spp. and Lachnospiraceae_UCG-010 spp. increased and Bifidobacterium spp. decreased in immunosuppressed rats compared with normal ones.

CONCLUSION

The intestinal metabolism of ginseng in immunosuppressed rats was significantly different from that in normal ones, which might be partly attributed to the changes in the intensity of specific gut bacteria. The outcomes of this study could provide scientific data for rationalization of ginseng use as both a dietary supplement and herbal medicine.

Postbiotics produced by lactic acid bacteria: The next frontier in food safety

There are many critical challenges in the use of primary and secondary cultures and their biological compounds in food commodities. An alternative is the application of postbiotics from the starter and protective lactic acid bacteria (LAB). The concept of postbiotics is relatively new and there is still not a recognized definition for this term. The word "postbiotics" is currently used to refer to bioactive compounds, which did not fit to the traditional definitions of probiotics, prebiotics, and paraprobiotics. Therefore, the postbiotics may be presently defined as bioactive soluble factors (products or metabolic byproducts), produced by some food-grade microorganisms during the growth and fermentation in complex microbiological culture (in this case named cell-free supernatant), food, or gut, which exert some benefits to the food or the consumer. Many LAB are considered probiotic and their postbiotic compounds present similar or additional health benefits to the consumer; however, this review aimed to address the most recent applications of the postbiotics with food safety purposes. The potential applications of postbiotics in food biopreservation, food packaging, and biofilm control were reviewed. The current uses of postbiotics in the reduction and biodegradation of some food safety-related chemical contaminants (e.g., biogenic amines) were considered. We also discussed the safety aspects, the obstacles, and future perspectives of using postbiotics in the food industry. This work will open up new insights for food applications of postbiotics prepared from LAB.

Cecal microbiome composition and metabolic function in probiotic treated broilers

Probiotics have become increasingly popular in the poultry industry as a promising nutritional intervention to promote the modulation of intestinal microbial communities and their metabolic activities as a means of improving health and performance. This study aimed to determine the influence of different probiotic formulations on the taxonomic and metabolic profiling of cecal microbial communities, as well as to define associations between cecal microbiota and growth parameters in 21 and 42-day-old broilers. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Dietary inclusion of SYNBIO, YEAST, SINGLE2, and SINGLE3 into the diets supported a significant stimulation of BW and BWG by 7 days of age. Besides, SYNBIO reduced the overall mortality rate by 42d (p<0.05). No significant variation was observed among different probiotic-based formulations for cecal microbiota composition. However, there was a treatment-specific effect on the metabolic profiles, with a particular beneficial metabolic adaptation by the microbiota when supplemented by SYNBIO and SINGLE2. Furthermore, the population of Lactobacillales was identified to be strongly associated with lower Enterobacteriales colonization, higher BW means, and lower mortality rate of growing broilers. Overall, the results emphasize that probiotic supplementation may enhance the microbial energy metabolism in the ceca of young broilers.

Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation

Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.

d-glutamate and Gut Microbiota in Alzheimer's Disease

Background: An increasing number of studies have shown that the brain–gut–microbiota axis may significantly contribute to Alzheimer’s disease (AD) pathogenesis. Moreover, impaired memory and learning involve the dysfunction neurotransmission of glutamate, the agonist of the N-methyl-d-aspartate receptor and a major excitatory neurotransmitter in the brain. This systematic review aimed to summarize the current cutting-edge research on the gut microbiota and glutamate alterations associated with dementia. Methods: PubMed, the Cochrane Collaboration Central Register of Controlled Clinical Trials, and Cochrane Systematic Reviews were reviewed for all studies on glutamate and gut microbiota in dementia published up until Feb 2020. Results: Several pilot studies have reported alterations of gut microbiota and metabolites in AD patients and other forms of dementia. Gut microbiota including Bacteroides vulgatus and Campylobacter jejuni affect glutamate metabolism and decrease the glutamate metabolite 2-keto-glutaramic acid. Meanwhile, gut bacteria with glutamate racemase including Corynebacterium glutamicum, Brevibacterium lactofermentum, and Brevibacterium avium can convert l-glutamate to d-glutamate. N-methyl-d-aspartate glutamate receptor (NMDAR)-enhancing agents have been found to potentially improve cognition in AD or Parkinson’s disease patients. These findings suggest that d-glutamate (d-form glutamate) metabolized by the gut bacteria may influence the glutamate NMDAR and cognitive function in dementia patients. Conclusions: Gut microbiota and glutamate are potential novel interventions to be developed for dementia. Exploring comprehensive cognitive functions in animal and human trials with glutamate-related NMDAR enhancers are warranted to examine d-glutamate signaling efficacy in gut microbiota in patients with AD and other neurodegenerative dementias.

Harnessing the gut microbiome in the fight against anthelminthic drug resistance

Intestinal helminth parasites present major challenges to the welfare of humans and threaten the global food supply. While the discovery of anthelminthic drugs empowered our ability to offset these harms to society, the alarming rise of anthelminthic drug resistance mitigates contemporary efforts to treat and control intestinal helminthic infections. Fortunately, emerging research points to potential opportunities to combat anthelminthic drug resistance by harnessing the gut microbiome as a resource for discovering novel therapeutics and informing responsible drug administration. In this review, we highlight research that demonstrates this potential and provide rationale to support increased investment in efforts to uncover and translationally utilize knowledge about how the gut microbiome mediates intestinal helminthic infection and its outcomes.

Allosteric control of metal-responsive transcriptional regulators in bacteria

Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.

Unambiguous Characterization of p-Cresyl Sulfate, a Protein-Bound Uremic Toxin, as Biomarker of Heart and Kidney Disease

p-Cresyl sulfate is one of the bound uremic toxins whose level increases in the sera of patients with the severity of chronic kidney disease and is therefore used as a standard for clinical investigations. Our first attempts to obtain p-cresyl sulfate led exclusively to the product of sulfonation of the aromatic ring instead of sulfation on the OH moiety. Nevertheless, this initial discouraging result allowed us to handle both p-cresyl sulfate and 2-hydroxy-5-methylbenzenesulfonic acid obtained by different synthetic pathways. Interestingly, the comparison between the two isomers pointed out that the two molecules show the same fragmentation pattern and are indistinguishable by mass spectrometry. They cannot be separated on several commercially available columns. The only difference between the two compounds is a 10-fold higher ionization yield under negative ion electrospray ionization. NMR spectral studies definitely confirmed the different molecular structures. We present here an unambiguous biomimetic synthetic route for p-cresyl sulfate and the spectroscopic characterization of both the compounds by nuclear magnetic resonance and mass spectrometry.

Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples

New strategies are required for the discovery of unknown bioactive molecules produced by gut microbiota in the human host. Herein, we utilize a chemoselective probe immobilized to magnetic beads for analysis of carbonyls in human fecal samples. We identified 112 metabolites due to femtomole analysis and an increased mass spectrometric sensitivity by up to six orders of magnitude.