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Nephrolithiasis is a medical condition characterized by the existence or development of calculi, commonly referred to as stones within the renal system, and poses significant health challenges. Calcium phosphate and calcium oxalate are the predominant constituents of renal calculi and are introduced into the human body primarily via dietary sources. The presence of oxalates can become particularly problematic when the delicate balance of the normal flora residing within the gastrointestinal tract is disrupted. Within the human gut, species of Oxalobacter, Lactobacillus, and Bifidobacterium coexist in a symbiotic relationship. They play a pivotal role in mitigating the risk of stone formation by modulating certain biochemical pathways and producing specific enzymes that can facilitate the breakdown and degradation of oxalate salts. The probiotic potential exhibited by these bacteria is noteworthy, as it underscores their possible utility in the prevention of nephrolithiasis. Investigating the mechanisms by which these beneficial microorganisms exert their effects could lead to novel therapeutic strategies aimed at reducing the incidence of kidney stones. The implications of utilizing probiotics as a preventive measure against kidney stone formation represent an intriguing frontier in both nephrology and microbiome research, meriting further investigation to unlock their full potential. [ABSTRACT FROM AUTHOR]

Iprodione is a pesticide that belongs to the dicarboximide fungicide family. This pesticide was designed to combat various agronomical pests; however, its use has been restricted due to its environmental toxicity and risks to human health. In this study, we explored the proteomic changes in the Pseudomonas sp. C9 strain when exposed to iprodione, to gain insights into the affected metabolic pathways and enzymes involved in iprodione tolerance and biodegradation processes. As a result, we identified 1472 differentially expressed proteins in response to iprodione exposure, with 978 proteins showing significant variations. We observed that the C9 strain upregulated the expression of efflux pumps, enhancing its tolerance to iprodione and other harmful compounds. Peptidoglycan-binding proteins LysM, glutamine amidotransferase, and protein Ddl were similarly upregulated, indicating their potential role in altering and preserving bacterial cell wall structure, thereby enhancing tolerance. We also observed the presence of hydrolases and amidohydrolases, essential enzymes for iprodione biodegradation. Furthermore, the exclusive identification of ABC transporters and multidrug efflux complexes among proteins present only during iprodione exposure suggests potential counteraction against the inhibitory effects of iprodione on downregulated proteins. These findings provide new insights into iprodione tolerance and biodegradation by the Pseudomonas sp. C9 strain. [ABSTRACT FROM AUTHOR]

Autochthonic recalcitrant organic carbon is the most stable component in karst aquatic systems. Still, the processes of its generation and transformation remain unclear, which hinders the study of the mechanisms and quantitative calculations of carbon sinks in karst aquatic systems. This study collected water samples from the Li River, a typical surface karst river in Southwest China. Through in situ microbial cultivation and the chromophoric dissolved organic matter (CDOM) spectrum, changes in organic carbon components and their contents during the transformation of autochthonic dissolved organic carbon (Auto-DOC) to autochthonic dissolved recalcitrant organic carbon (Auto-RDOC) were analyzed to investigate the inert transformation processes of endogenous organic carbon. This study found that microbial carbon pumps (MCPs) promote the tyrosine-like component condensed into microbial-derived fulvic and humic components via heterotrophic bacteria metabolism, forming Auto-RDOC. During the dry season, the high level of Auto-DOC provides abundant organic substrates for heterotrophic bacteria, resulting in significantly higher Auto-RDOC production compared to the rainy season. This study provides fundamental information on the formation mechanisms of Auto-DOC in karst aquatic systems, which contributes to the assessment of carbon sinks in karst aquatic systems. [ABSTRACT FROM AUTHOR]

YqeK is a bacterial HD-domain metalloprotein that hydrolyzes the putative second messenger diadenosine tetraphosphate (Ap4A). Elevated Ap4A levels are primarily observed upon exposure of bacteria to factors such as heat or oxidative stress and cause pleiotropic effects, including antibiotic sensitivity and disrupted biofilm formation. Ap4A thus plays a central role in bacterial physiology and metabolism, and its hydrolysis by YqeK is intimately linked to the ability of these microbes to cope with stress. Although YqeK is reported to hydrolyze Ap4A under aerobic conditions, all four existing crystal structures reveal an active site that consists of a diiron center, portraying a cryptic chemical nature for the active metallocofactor. This study examines two YqeK proteins from two ecologically diverse parent organisms: the obligate anaerobe Clostridium acetobutylicum and the facultative aerobe Bacillus halodurans. Both enzymes utilize Fe-based cofactors for catalysis, while under ambient or oxidative conditions, Bh YqeK hydrolyzes Ap4A more efficiently compared to Ca YqeK. This redox-dependent activity difference stems from the following two molecular mechanisms: the incorporation of mixed-metal, Fe-based bimetallic cofactors, in which the second metal is redox inert (i.e., Fe–Zn) and the upshift of the Fe–Fe cofactor reduction potentials. In addition, three strictly conserved, positively charged residues vicinal to the active site are critical for tuning Ap4A hydrolysis. In conclusion, YqeK is an Fe-dependent phosphohydrolase that appears to have evolved to permit Ap4A hydrolysis under different environmental niches (aerobic vs. anaerobic) by expanding its cofactor configuration and O2 tolerance. [ABSTRACT FROM AUTHOR]

Bicarbonate and CO2 are essential substrates for carboxylation reactions in bacterial central metabolism. In Staphylococcus aureus, the bicarbonate transporter, MpsABC (membrane potential-generating system) is the only carbon concentrating system. An mpsABC deletion mutant can hardly grow in ambient air. In this study, we investigated the changes that occur in S. aureus when it suffers from CO2/bicarbonate deficiency. Electron microscopy revealed that ΔmpsABC has a twofold thicker cell wall thickness compared to the parent strain. The mutant was also substantially inert to cell lysis induced by lysostaphin and the non-ionic surfactant Triton X-100. Mass spectrometry analysis of muropeptides revealed the incorporation of alanine into the pentaglycine interpeptide bridge, which explains the mutant's lysostaphin resistance. Flow cytometry analysis of wall teichoic acid (WTA) glycosylation patterns revealed a significantly lower α-glycosylated and higher ß-glycosylated WTA, explaining the mutant's increased resistance towards Triton X-100. Comparative transcriptome analysis showed altered gene expression profiles. Autolysin-encoding genes such as sceD, a lytic transglycosylase encoding gene, were upregulated, like in vancomycin-intermediate S. aureus mutants (VISA). Genes related to cell wall-anchored proteins, secreted proteins, transporters, and toxins were downregulated. Overall, we demonstrate that bicarbonate deficiency is a stress response that causes changes in cell wall composition and global gene expression resulting in increased resilience to cell wall lytic enzymes and detergents. [ABSTRACT FROM AUTHOR]

The control of metabolic networks is incompletely understood, even for glycolysis in highly studied model organisms. Direct real-time observations of metabolic pathways can be achieved in cellular systems with 13C NMR using dissolution Dynamic Nuclear Polarization (dDNP NMR). The method relies on a short-lived boost of NMR sensitivity using a redistribution of nuclear spin states to increase the alignment of the magnetic moments by more than four orders of magnitude. This temporary boost in sensitivity allows detection of metabolism with sub-second time resolution. Here, we hypothesized that dDNP NMR would be able to investigate molecular phenotypes that are not easily accessible with more conventional methods. The use of dDNP NMR allows real-time insight into carbohydrate metabolism in a Gram-positive bacterium (Lactoccocus lactis), and comparison to other bacterial, yeast and mammalian cells shows differences in the kinetic barriers of glycolysis across the kingdoms of life. Nevertheless, the accumulation of non-toxic precursors for biomass at kinetic barriers is found to be shared across the kingdoms of life. We further find that the visualization of glycolysis using dDNP NMR reveals kinetic characteristics in transgenic strains that are not evident when monitoring the overall glycolytic rate only. Finally, dDNP NMR reveals that resting Lactococcus lactis cells use the influx of carbohydrate substrate to produce acetoin rather than lactate during the start of glycolysis. This metabolic regime can be emulated using suitably designed substrate mixtures to enhance the formation of the C4 product acetoin more than 400-fold. Overall, we find that dDNP NMR provides analytical capabilities that may help to clarify the intertwined mechanistic determinants of metabolism and the optimal usage of biotechnologically important bacteria. [ABSTRACT FROM AUTHOR]

Antimicrobial dosing can be a complex challenge. Although a solid rationale exists for a link between antibiotic exposure and outcome, conflicting data suggest a poor correlation between pharmacokinetic/pharmacodynamic targets and infection control. Different reasons may lead to this discrepancy: poor tissue penetration by β-lactams due to inflammation and inadequate tissue perfusion; different bacterial response to antibiotics and biofilms; heterogeneity of the host's immune response and drug metabolism; bacterial tolerance and acquisition of resistance during therapy. Consequently, either a fixed dose of antibiotics or a fixed target concentration may be doomed to fail. The role of biomarkers in understanding and monitoring host response to infection is also incompletely defined. Nowadays, with the ever-growing stream of data collected in hospitals, utilizing the most efficient analytical tools may lead to better personalization of therapy. The rise of artificial intelligence and machine learning has allowed large amounts of data to be rapidly accessed and analyzed. These unsupervised learning models can apprehend the data structure and identify homogeneous subgroups, facilitating the individualization of medical interventions. This review aims to discuss the challenges of β-lactam dosing, focusing on its pharmacodynamics and the new challenges and opportunities arising from integrating machine learning algorithms to personalize patient treatment. [ABSTRACT FROM AUTHOR]

The propagation of antibiotic resistance in environments, particularly aquatic environments that serve as primary pathways for antibiotic resistance genes (ARGs), poses significant health risks. The impact of nutrients, as key determinants of bacterial growth and metabolism, on the propagation of ARGs, particularly extracellular ARGs (eARGs), remains poorly understood. In this study, we collected microorganisms from the Yangtze River and established a series of microcosms to investigate how variations in nutrient levels and delivery frequency affect the relative abundance of intracellular ARGs (iARGs) and eARGs in bacterial communities. Our results show that the relative abundance of 7 out of 11 representative eARGs in water exceeds that of iARGs, while 8 iARGs dominate in biofilms. Notably, iARGs and eARGs consistently exhibited opposite responses to nutrient variation. When nutrient levels increased, iARGs in the water also increased, with the polluted group (COD = 333.3 mg/L, COD:N:P = 100:3:0.6, m/m) and the eutrophic group (COD = 100 mg/L, COD:N:P = 100:25:5, m/m) showing 1.2 and 3.2 times higher levels than the normal group (COD = 100 mg/L, COD:N:P = 100:10:2, m/m), respectively. In contrast, eARGs decreased by 6.7% and 8.4% in these groups. On the other hand, in biofilms, higher nutrient levels led to an increase in eARGs by 1.5 and 1.7 times, while iARGs decreased by 17.5% and 50.1% in the polluted and eutrophic groups compared to the normal group. Moreover, while increasing the frequency of nutrient delivery (from 1 time/10 d to 20 times/10 d) generally did not favor iARGs in either water or biofilm, it selectively enhanced eARGs in both. To further understand these dynamics, we developed an ARGs-nutrient model by integrating the Lotka–Volterra and Monod equations. The results highlight the complex interplay of bacterial growth, nutrient availability, and mechanisms such as horizontal gene transfer and secretion influencing ARGs' propagation, driving the opposite trend between these two forms of ARGs. This contrasting response between iARGs and eARGs contributes to a dynamic balance that stabilizes bacterial resistance levels amid nutrient fluctuations. This study offers helpful implications regarding the persistence of bacterial resistance in the environment. [ABSTRACT FROM AUTHOR]

Objectives: To develop a system for the rapid detection of Acinetobacter baumannii 173-p1 antibiotic resistance (to ensure reliable fixation of bacteria on a cantilever without losing their nanomotion, to show that nanomotion is due to bacterial metabolism, to compare the nanomotion of bacteria in suspension form and inside of the biofilms), to study the sensitivity/resistance of A. baumannii 173-p1 to antibiotics (lincomycin, ceftriaxone and doxycycline) using the oscillation method of atomic force microscopy and to evaluate the sensitivity and speed of the method in comparison with the classical disk diffusion method. Methods: The oscillation mode of atomic force microscopy, scanning electron microscopy and the classical disk diffusion method were used for a complex parallel study of A. baumannii 173-p1 antibiotic resistance, which included testing of fixing agents (poly-L-lysine, rosin and fibronectin), comparison of bacterial metabolism in a set of media (normal saline solution, meat-peptone broth and lysogeny broth) and assessment of antibiotic sensitivity/resistance per se. Results: A method for express testing of Acinetobacter baumannii antibiotic resistance using AFM was developed; it is shown that bacterial nanomotion directly correlates with bacteria metabolic activity and that bacterial nanomotion is more easily detected in suspension form, rather than in biofilms. Conclusion: The express testing method gave results that are completely comparable with the classical disk diffusion test and with the results of morphology studies by the SEM method, but it significantly exceeded them in speed, allowing a conclusion to be made on the sensitivity/resistance of bacteria less than an hour after the start of the diagnostics. [ABSTRACT FROM AUTHOR]

The rise of antibiotic tolerance in bacteria harboring genetic elements conferring resistance to antibiotics poses an increasing threat to public health. However, the primary factors responsible for the emergence of antibiotic tolerance and the fundamental molecular mechanisms involved remain poorly comprehended. Here, we demonstrate that the commonly utilized food additive Benzaldehyde (BZH) possesses the capacity to induce a significant level of fluoroquinolone tolerance in vitro among resistant Escherichia coli. Our findings from animal models reveal that the pre-administration of BZH results in an ineffective eradication of bacteria through ciprofloxacin treatment, leading to similar survival rates and bacterial loads as observed in the control group. These results strongly indicate that BZH elicits in vivo tolerance. Mechanistic investigations reveal several key factors: BZH inhibits the formation of bacterial flagella and releases proton motive force (PMF), which aids in expelling antibiotics from within cells to reducing their accumulation inside. In addition, BZH suppresses bacterial respiration and inhibits the production of reactive oxygen species (ROS). Moreover, exogenous pyruvate successfully reverses BZH-induced tolerance and restores the effectiveness of antibiotics, highlighting how crucial the pyruvate cycle is in combating antibiotic tolerance. The present findings elucidate the underlying mechanisms of BZH-induced tolerance and highlight potential hazards associated with the utilization of BZH. [ABSTRACT FROM AUTHOR]

Microbial infections pose a significant global health threat, affecting millions of individuals and leading to substantial mortality rates. The increasing resistance of microorganisms to conventional treatments requires the development of novel antimicrobial agents. Pyrroloquinoline quinone (PQQ), a natural medicinal drug involved in various cellular processes, holds promise as a potential antimicrobial agent. In the present study, our aim was, for the first time, to explore the antimicrobial activity of PQQ against 29 pathogenic microbes, including 13 fungal strains, 8 Gram-positive bacteria, and 8 Gram-negative bacteria. Our findings revealed potent antifungal properties of PQQ, particularly against Syncephalastrum racemosum, Talaromyces marneffei, Candida lipolytica, and Trichophyton rubrum. The MIC values varied between fungal strains, and T. marneffei exhibited a lower MIC, indicating a greater susceptibility to PQQ. In addition, PQQ exhibited notable antibacterial activity against Gram-positive and -negative bacteria, with a prominent inhibition observed against Staphylococcus epidermidis, Proteus vulgaris, and MRSA strains. Remarkably, PQQ demonstrated considerable biofilm inhibition against the MRSA, S. epidermidis, and P. vulgaris strains. Transmission electron microscopy (TEM) studies revealed that PQQ caused structural damage and disrupted cell metabolism in bacterial cells, leading to aberrant morphology, compromised cell membrane integrity, and leakage of cytoplasmic contents. These findings were further affirmed by shotgun proteomic analysis, which revealed that PQQ targets several important cellular processes in bacteria, including membrane proteins, ATP metabolic processes, DNA repair processes, metal-binding proteins, and stress response. Finally, detailed molecular modeling investigations indicated that PQQ exhibits a substantial binding affinity score for key microbial targets, including the mannoprotein Mp1P, the transcriptional regulator TcaR, and the endonuclease PvuRTs1I. Taken together, our study underscores the effectiveness of PQQ as a broad-spectrum antimicrobial agent capable of combating pathogenic fungi and bacteria, while also inhibiting biofilm formation and targeting several critical biological processes, making it a promising therapeutic option for biofilm-related infections. [ABSTRACT FROM AUTHOR]

Graphene Quantum Dots (GQDs) have shown the potential for antimicrobial photodynamic treatment, due to their particular physicochemical properties. Here, we investigated the activity of three differently functionalized GQDs—Blue Luminescent GQDs (L-GQDs), Aminated GQDs (NH2-GQDs), and Carboxylated GQDs (COOH-GQDs)—against E. coli. GQDs were administrated to bacterial suspensions that were treated with blue light. Antibacterial activity was evaluated by measuring colony forming units (CFUs) and metabolic activities, as well as reactive oxygen species stimulation (ROS). GQD cytotoxicity was then assessed on human colorectal adenocarcinoma cells (Caco-2), before setting in an in vitro infection model. Each GQD exhibits antibacterial activity inducing ROS and impairing bacterial metabolism without significantly affecting cell morphology. GQD activity was dependent on time of exposure to blue light. Finally, GQDs were able to reduce E. coli burden in infected Caco-2 cells, acting not only in the extracellular milieu but perturbating the eukaryotic cell membrane, enhancing antibiotic internalization. Our findings demonstrate that GQDs combined with blue light stimulation, due to photodynamic properties, have a promising antibacterial activity against E. coli. Nevertheless, we explored their action mechanism and toxicity on epithelial cells, fixing and standardizing these infection models. [ABSTRACT FROM AUTHOR]

The application of phosphorus-solubilizing bacteria is an effective method for increasing the available phosphorus content and inhibiting wheat uptake of heavy metals. However, further research is needed on the mechanism by which phosphorus-solubilizing bacteria inhibit cadmium (Cd) uptake in wheat roots and its impact on the expression of root-related genes. Here, the effects of strain Klebsiella aerogenes M2 on Cd absorption in wheat and the expression of root-related Cd detoxification and immobilization genes were determined. Compared with the control, strain M2 reduced (64.1–64.6%) Cd uptake by wheat roots. Cd fluorescence staining revealed that strain M2 blocked the entry of exogenous Cd into the root interior and enhanced the immobilization of Cd by cell walls. Forty-seven genes related to Cd detoxification, including genes encoding peroxidase, chalcone synthase, and naringenin 3-dioxygenase, were upregulated in the Cd+M2 treatment. Strain M2 enhanced the Cd resistance and detoxification activity of wheat roots through the regulation of flavonoid biosynthesis and antioxidant enzyme activity. Moreover, strain M2 regulated the expression of genes related to phenylalanine metabolism and the MAPK signaling pathway to enhance Cd immobilization in roots. These results provide a theoretical basis for the use of phosphorus-solubilizing bacteria to remediate Cd-contaminated fields and reduce Cd uptake in wheat. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) are a group of microorganisms which are beneficial and well-characterized with respect to the flavor and texture of food products via fermentation. The accumulated literature has suggested that dietary intake of fermented foods rich in LAB is related to different health-promoting benefits; however, in recent years, emerging evidence suggests a contribution of LAB to blood lipid regulation and cardiovascular health via certain mechanisms. Different potential mechanisms for the lipid regulatory effects of LAB may include the interaction of hydroxymethylglutaryl-CoA (HMG-CoA) reductase and bile salt hydrolase activity and bile salt metabolism; gut microbiome modulation; and regulation of mRNA expression of genes related to fat metabolism in animal models and human studies. This review comprehensively aims to answer whether/how LAB influence blood lipids in both animal models and human studies while also uncovering the underlying mechanisms linking LAB to lipid metabolism. [ABSTRACT FROM AUTHOR]

Bacteriocins is the name given to products of the secondary metabolism of many bacterial genera that must display antimicrobial activity. Although there are several bacteriocins described today, it has not been possible to reach a consensus on the method of classification for these biomolecules. In addition, many of them are not yet authorized for therapeutic use against multi-drug-resistant microorganisms due to possible toxic effects. However, recent research has achieved considerable progress in the understanding, classification, and elucidation of their mechanisms of action against microorganisms, which are of medical and biotechnological interest. Therefore, in more current times, protocols are already being conducted for their optimal use, in the hopes of solving multiple health and food conservation problems. This review aims to synthetize the information available nowadays regarding bacteriocins, and their classification, while also providing an insight into the future possibilities of their usage for both the pharmaceutical, food, and biotechnological industry. [ABSTRACT FROM AUTHOR]

Solventogenic Clostridium species are important for establishing the sustainable industrial bioproduction of fuels and important chemicals such as acetone and butanol. The inherent versatility of these species in substrate utilization and the range of solvents produced during acetone butanol–ethanol (ABE) fermentation make solventogenic Clostridium an attractive choice for biotechnological applications such as the production of fuels and chemicals. The functional qualities of these microbes have thus been identified to be related to complex regulatory networks that play essential roles in modulating the metabolism of this group of bacteria. Yet, solventogenic Clostridium species still struggle to consistently achieve butanol concentrations exceeding 20 g/L in batch fermentation, primarily due to the toxic effects of butanol on the culture. Genomes of solventogenic Clostridium species have a relatively greater prevalence of genes that are intricately controlled by various regulatory molecules than most other species. Consequently, the use of genetic or metabolic engineering strategies that do not consider the underlying regulatory mechanisms will not be effective. Several regulatory factors involved in substrate uptake/utilization, sporulation, solvent production, and stress responses (Carbon Catabolite Protein A, Spo0A, AbrB, Rex, CsrA) have been identified and characterized. In this review, the focus is on newly identified regulatory factors in solventogenic Clostridium species, the interaction of these factors with previously identified molecules, and potential implications for substrate utilization, solvent production, and resistance/tolerance to lignocellulose-derived microbial inhibitory compounds. Taken together, this review is anticipated to highlight the challenges impeding the re-industrialization of ABE fermentation, and inspire researchers to generate innovative strategies for overcoming these obstacles. [ABSTRACT FROM AUTHOR]

Cardiovascular diseases accompanying metabolic syndrome comprise one of the leading causes of death worldwide. The medical community undertakes attempts to improve treatment options and minimize cardiovascular diseases' numerous consequences and exacerbations. In parallel with pharmacotherapies provided by physicians, nutritionists are developing strategies for diet therapy and prevention based on lifestyle changes, with high success rates. Consumption of specified food compounds included in various products with proven protective properties can be helpful in this regard. Due to the wide possibilities of diet in metabolic health promotion, it seems necessary to systematize information about the metabolically protective and cardioprotective properties of fiber, probiotic bacteria, plant sterols, folic acid, vitamins B12, C, and E, PUFAs, lycopene, polyphenols, arginine, CoQ10, and allicin. The aim of this review was to present the food compounds with potential use in cardiometabolic prevention and diet therapy based on the latest available literature. [ABSTRACT FROM AUTHOR]

Conjugation of carbohydrates to nanomaterials has been extensively studied and recognized as an alternative in the biomedical field. Dendrimers synthesized with mannose at the end group and with entrapped zero-valent copper/silver could be a potential candidate against bacterial proliferation. This study is aimed at investigating the bactericidal activity of metal-glycodendrimers. The Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) reaction was used to synthesize a new mannosylated dendrimer containing 12 mannopyranoside residues in the periphery. The enterotoxigenic Escherichia coli fimbriae 4 (ETEC:F4) viability, measured at 600 nm, showed the half-inhibitory concentration (IC50) of metal-free glycodendrimers (D), copper-loaded glycodendrimers (D:Cu) and silver-loaded glycodendrimers (D:Ag) closed to 4.5 × 101, 3.5 × 101 and to 1.0 × 10−2 µg/mL, respectively, and minimum inhibitory concentration (MIC) of D, D:Cu and D:Ag of 2.0, 1.5 and 1.0 × 10−4 µg/mL, respectively. The release of bacteria contents onto broth and the inhibition of ETEC:F4 biofilm formation increased with the number of metallo-glycodendrimer materials, with a special interest in silver-containing nanomaterial, which had the highest activity, suggesting that glycodendrimer-based materials interfered with bacteria-bacteria or bacteria–polystyrene interactions, with bacteria metabolism and can disrupt bacteria cell walls. Our findings identify metal–mannose-dendrimers as potent bactericidal agents and emphasize the effect of entrapped zero-valent metal against ETEC:F4. [ABSTRACT FROM AUTHOR]

In lactic acid bacteria, the global transcriptional regulator CcpA regulates carbon metabolism by repressing and activating the central carbon metabolism pathway, thus decreasing or increasing the yield of certain metabolites to maximize carbon flow. However, there are no reports on the deregulation of the inhibitory effects of CcpA on the metabolism of secondary metabolites. In this study, we identified a single-base mutant strain of Lactococcus lactis N8-2 that is capable of metabolizing 2,3-butanediol. It has been established that CcpA dissociates from the catabolite responsive element (cre) site due to a mutation, leading to the activation of derepression and expression of the 2,3-butanediol dehydrogenase gene cluster (butB and butA). Transcriptome analysis and quantitative polymerase chain reaction (Q-PCR) results showed significant upregulation of transcription of butB and butA compared to the unmutated strain. Furthermore, micro-scale thermophoresis experiments confirmed that CcpA did not bind to the mutated cre. Furthermore, in a bacterial two-plasmid fluorescent hybridization system, it was similarly confirmed that the dissociation of CcpA from cre eliminated the repressive effect of CcpA on downstream genes. Finally, we investigated the differing catalytic capacities of the 2,3-butanediol dehydrogenase gene cluster in L. lactis N8-1 and L. lactis N8-2 for 2,3-butanediol. This led to increased expression of butB and butA, which were deregulated by CcpA repression. This is the first report on the elimination of the deterrent effect of CcpA in lactic acid bacteria, which changes the direction of enzymatic catalysis and alters the direction of carbon metabolism. This provides new perspectives and strategies for metabolizing 2,3-butanediol using bacteria in synthetic biology. [ABSTRACT FROM AUTHOR]

KDO (2-keto-3-deoxy-D-manno-octulosonate) is a landmark molecule of the Gram-negative outer membrane. Mutants without KDO formation are known to be barely viable. Arabinose 5-phosphate (A5P) is a precursor of KDO biosynthesis and is normally derived from ribulose 5-phosphate by A5P isomerases, encoded by kdsD and gutQ genes in E. coli K-12. We created a kdsD gutQ-deficient double mutant of strain BW25113 and confirmed that these cells are A5P auxotrophs. Fructose 6-phosphate aldolase (FSA) is known to utilize (among other donors such as dihydroxyacetone or hydroxyacetone) glycolaldehyde (GoA) as a donor compound and to provide A5P in vitro when glyceraldehyde 3-phosphate is the acceptor. We show here that this FSA function in vivo fully reverses the growth defect and the A5P deficiency in kdsD gutQ double mutants. Expression of both plasmid-encoded fsaA, fsaAA129S, or fsaB genes as well as a chromosomally integrated form of fsaAA129S led to maximal OD600 values of >2.2 when GoA was added exogenously (together with glucose as a C source) at a concentration of 100 µM (Ks values in the range of 4–10 µM). Thus, a novel bio-orthogonal bypass to overcome an A5P deficiency was opened. Lower GoA concentrations led to lower growth yields. Interestingly, mutant strains with recombinant fsa genes showed considerable growth yields even without exogenous GoA addition, pointing to yet unknown endogenous GoA sources in E. coli metabolism. This is a further example of the usefulness of FSA in rewiring central metabolic pathways in E. coli. [ABSTRACT FROM AUTHOR]

Clostridioides difficile is a clinically and agriculturally important organism with diverse metabolic capabilities. Commercially available media types to cultivate C. difficile typically include multiple growth substrates and often selective agents. Under these conditions, it is difficult to determine what the bacteria utilized and which products are derived from which substrates. These experiments compared a commercial broth (Reinforced Clostridium Medium/RCM) to simpler, defined, carbonate-based media types influenced by Robert Hungate. Peptides (tryptone peptone), amino acids (casamino acids), and/or glucose were added to evaluate the growth of C. difficile strains 9689, BAA-1870, and 43597, and the metabolism of the type strain 9689. C. difficile grew to the greatest optical density in the rich RCM broth but produced less ammonia than the tryptone-containing media types. C. difficile utilized all glucose in RCM and T+G media in addition to performing amino acid fermentations, though the volatile fatty acids produced were not necessarily consistent across media type. When cultured in CAA-containing media, 9689 performed very little metabolism and did not grow regardless of supplementation with glucose. These data demonstrated that C. difficile could metabolize substrates and grow in defined, anaerobic, and carbonate-buffered media. Hungate-style media appear to be an acceptable choice for reliable culturing of C. difficile. [ABSTRACT FROM AUTHOR]

Simple Summary: Gut health depends on a complex network interaction between the host and the mucosal-associated microbiota, and it is modulated by dietary inputs. To gain knowledge on this interaction and shed light on the nutritional impacts at this level, this study assessed the effect of dietary protein quality on the modulation of different gut health parameters. Fish performance and gut microbiome abundance were correlated with amino acid intake and the functional prediction of bacteria metabolism. The results indicate that different protein qualities modulate the relationship between bacteria functional pathways and amino acid intake. Dietary protein quality plays a key role in maintaining intestinal mucosal integrity, but also modulates the growth of luminal microorganisms. This work assessed the effect of dietary protein sources on the performance, gut morphology, and microbiome in Nile tilapia. Four isonitrogenous and isolipidic diets comprising equivalent amounts of the protein supply derived from either PLANT, ANIMAL, INSECT, or BACTERIAL (bacterial biomass) sources were fed to triplicate groups of fish (IBW: 12 g) for 46 days. Fish fed the ANIMAL and BACTERIAL diets showed significantly higher weight gains than those fed the PLANT and INSECT diets (p < 0.05). Relative abundance at the phylum level showed that Bacteroidetes, Fusobacteria, and Proteobacteria were the more abundant phyla in tilapia's intestine, while Cetobacterium was the most representative genus in all treatments. Interesting patterns were observed in the correlation between amino acid intake and genus and species abundance. Metabolism prediction analysis showed that BACTERIAL amine and polyamine degradation pathways are modulated depending on diets. In conclusion, different protein sources modulate the relationship between bacteria functional pathways and amino acid intake. [ABSTRACT FROM AUTHOR]

High concentrations of nitrite in marine aquaculture wastewater not only pose a threat to the survival and immune systems of aquatic organisms but also contribute to eutrophication, thereby impacting the balance of coastal ecosystems. Compared to traditional physical and chemical methods, utilizing microorganism-mediated biological denitrification is a cost-effective and efficient solution. However, the osmotic pressure changes and salt-induced enzyme precipitation in high-salinity seawater aquaculture environments may inhibit the growth and metabolism of freshwater bacterial strains, making it more suitable to select salt-tolerant marine microorganisms for treating nitrite in marine aquaculture wastewater. In this study, a salt-tolerant nitrite-degrading bacterium, designated as DM6, was isolated from the seawater (salinity of 25–30‰) of Portunus trituberculatus cultivation. The molecular identification of strain DM6 was conducted using 16S rRNA gene sequencing technology. The impacts of various environmental factors on the nitrite degradation performance of strain DM6 were investigated through single-factor and orthogonal experiments, with the selected conditions considered to be the key factors affecting the denitrification efficiency of microorganisms in actual wastewater treatment. PCR amplification of key genes involved in the nitrite metabolism pathway of strain DM6 was conducted, including denitrification pathway-related genes narG, narH, narI, nirS, and norB, as well as assimilation pathway-related genes nasC, nasD, nasE, glnA, gltB, gltD, gdhB, and gdhA. The findings indicated that strain DM6 is classified as Pseudomonas aeruginosa and exhibits efficient nitrite degradation even under a salinity of 35‰. The optimal nitrite degradation efficiency of DM6 was observed when using sodium citrate as the carbon source, a C/N ratio of 20, a salinity of 13‰, pH 8.0, and a temperature of 35 °C. Under these conditions, DM6 could completely degrade an initial nitrite concentration of 156.33 ± 1.17 mg/L within 36 h. Additionally, the successful amplification of key genes involved in the nitrite denitrification and assimilation pathways suggests that strain DM6 may possess both denitrification and assimilation pathways for nitrite degradation simultaneously. Compared to freshwater strains, strain DM6 demonstrates higher salt tolerance and exhibits strong nitrite degradation capability even at high concentrations. However, it may be more suitable for application in the treatment of wastewater from marine aquaculture systems during summer, high-temperature, or moderately alkaline conditions. [ABSTRACT FROM AUTHOR]

Prunella vulgaris L. (PV) is a widely distributed plant species, known for its versatile applications in both traditional and contemporary medicine, as well as in functional food development. Despite its broad-spectrum antimicrobial utility, the specific mechanism of antibacterial action remains elusive. To fill this knowledge gap, the present study investigated the antibacterial properties of PV extracts against methicillin-resistant Staphylococcus aureus (MRSA) and assessed their mechanistic impact on bacterial cells and cellular functions. The aqueous extract of PV demonstrated greater anti-MRSA activity compared to the ethanolic and methanolic extracts. UPLC-ESI-MS/MS tentatively identified 28 phytochemical components in the aqueous extract of PV. Exposure to an aqueous extract at ½ MIC and MIC for 5 h resulted in a significant release of intracellular nucleic acid (up to 6-fold) and protein (up to 10-fold) into the extracellular environment. Additionally, this treatment caused a notable decline in the activity of several crucial enzymes, including a 41.51% reduction in alkaline phosphatase (AKP), a 45.71% decrease in adenosine triphosphatase (ATPase), and a 48.99% drop in superoxide dismutase (SOD). Furthermore, there was a decrease of 24.17% at ½ MIC and 27.17% at MIC in tricarboxylic acid (TCA) cycle activity and energy transfer. Collectively, these findings indicate that the anti-MRSA properties of PV may stem from its ability to disrupt membrane and cell wall integrity, interfere with enzymatic activity, and impede bacterial cell metabolism and the transmission of information and energy that is essential for bacterial growth, ultimately resulting in bacterial apoptosis. The diverse range of characteristics exhibited by PV positions it as a promising antimicrobial agent with broad applications for enhancing health and improving food safety and quality. [ABSTRACT FROM AUTHOR]

The low-temperature environment significantly inhibits the growth and metabolism of denitrifying bacteria, leading to an excessive concentration of ammonia nitrogen and total nitrogen in sewage treatment plants during the cold season. In this study, an efficient denitrifying strain of heterotrophic nitrification–aerobic denitrification (HN–AD) bacteria named HS2 was isolated and screened from industrial sewage of a chemical factory in Inner Mongolia at 8 °C. The strain was confirmed to be Achromobacter spiritinus, a colorless rod-shaped bacterium. When cultured with sodium succinate as the carbon source, a carbon-to-nitrogen ratio of 20–30, a shaking rate of 150–180 r/min, and an initial pH of 6–10, the strain HS2 exhibited excellent nitrogen removal at 8 °C. Through the results of whole-genome sequencing, gene amplification, and gas product detection, the strain HS2 was determined to possess key enzyme genes in both nitrification and denitrification pathways, suggesting a HN–AD pathway of NH4+-N → NH2OH → NO2−N → NO → N2O → N2. At 8 °C, the strain HS2 could completely remove ammonia nitrogen from industrial sewage with an initial concentration of 127.23 mg/L. Microbial species diversity analysis of the final sewage confirmed Achromobacter sp. as the dominant genus, which indicated that the low-temperature denitrifying strain HS2 plays an important role in nitrogen removal in actual low-temperature sewage. [ABSTRACT FROM AUTHOR]

Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections. [ABSTRACT FROM AUTHOR]

Lichens are not only fungal–algal symbiotic associations but also matrices for association with bacteria, and the bacterial diversity linked to lichens has been receiving more attention in studies. This study compares the diversity and possible metabolism of lichen-associated bacteria from saxicolous foliose and fruticose taxa Alectoria, Canoparmelia, Crocodia, Menegazzia, Usnea, and Xanthoparmelia from the Venezuelan Guiana Shield and the South African Highveld Plateau. We used DNA extractions from the lichen thalli to amplify the eukaryotic 18S rRNA gene (rDNA) and the V3–V4 region of the bacterial 16S rDNA, of which amplicons were then Sanger- and MiSeq-sequenced, respectively. The V3–V4 sequences of the associated bacteria were grouped into operational taxonomic units (OTUs) ascribed to twelve bacterial phyla previously found in the rock tripe Umbilicaria lichens. The bacterial OTUs emphasized the uniqueness of each region, while, at the species and higher ranks, the regional microbiomes were shown to be somewhat similar. Nevertheless, regional biomarker OTUs were screened to predict relevant metabolic pathways, which implicated different regional metabolic features. [ABSTRACT FROM AUTHOR]

Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment. [ABSTRACT FROM AUTHOR]

Satureja bachtiarica is an endemic plant from the Lamiaceae family, growing in the Zagros mountain range in Iran. Even if S. bachtiarica is reported to possess many biological activities, little is known about its chemical composition. For this reason, in the present research, a phytochemical investigation of this species was carried out. To have a preliminary metabolite profile of S. bachtiarica, the n-BuOH extract was analyzed using LC-ESI/LTQOrbitrap/MS/MS in negative ion mode, allowing the identification of specialized metabolites belonging to flavonoid, monoterpene, indol, phenylpropanoid, phenolic, lignan, coumarin, biphenyl, and triterpene classes. The LC-MS/MS analysis guided the isolation of compounds, and their structures were characterized using spectroscopic methods including 1D- and 2D-NMR experiments and HRMSn analysis. In this way, a compound never reported before belonging to the biphenyl class was identified. Total flavonoid content of the extract along with the antioxidant activity were assessed. Based on the traditional uses of S. bachtiarica suggesting potential antibacterial properties, an evaluation of the biofilm inhibitory activity of the extract and isolated compounds against mature biofilms of Acinetobacter baumannii, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Staphylococcus aureus, as well as their influence on the metabolism of sessile bacterial cells, was conducted. The results evidenced that some compounds including parmentin B, biphenyls, and 1-(1H-indole-3-carboxylate)-β-D-glucopyranoside might inhibit some changes occurring in the bacterial cells, which increases their virulence. In particular, biphenyl derivatives at a concentration of 80 μg/mL were capable of limiting remarkably the mature biofilms of A. baumannii and L. monocytogenes remarkably at a percentage ranging between 52.76% and 75.02%, and they reached an inhibition percentage of 69.28 % against E. coli. Biphenyl derivatives were also effective in exerting an inhibitory action against the mature biofilm of P. aeruginosa (inhibition ranging from 59.38% to 81.08%) and Staphylococcus aureus (inhibition percentage reached 82.94%). Of note, the biphenyl derivatives resulted in being capable of acting on the metabolism of the cells within the biofilm of all five pathogens. [ABSTRACT FROM AUTHOR]

Tuberculosis remains a serious challenge to human health worldwide. para-Aminosalicylic acid (PAS) is an important anti-tuberculosis drug, which requires sequential activation by Mycobacterium tuberculosis (M. tuberculosis) dihydropteroate synthase and dihydrofolate synthase (DHFS, FolC). Previous studies showed that loss of function mutations of a thymidylate synthase coding gene thyA caused PAS resistance in M. tuberculosis, but the mechanism is unclear. Here we showed that deleting thyA in M. tuberculosis resulted in increased content of tetrahydrofolate (H4PteGlu) in bacterial cells as they rely on the other thymidylate synthase ThyX to synthesize thymidylate, which produces H4PteGlu during the process. Subsequently, data of in vitro enzymatic activity experiments showed that H4PteGlu hinders PAS activation by competing with hydroxy dihydropteroate (H2PtePAS) for FolC catalysis. Meanwhile, over-expressing folC in ΔthyA strain and a PAS resistant clinical isolate with known thyA mutation partially restored PAS sensitivity, which relieved the competition between H4PteGlu and H2PtePAS. Thus, loss of function mutations in thyA led to increased H4PteGlu content in bacterial cells, which competed with H2PtePAS for catalysis by FolC and hence hindered the activation of PAS, leading to decreased production of hydroxyl dihydrofolate (H2PtePAS-Glu) and finally caused PAS resistance. On the other hand, functional deficiency of thyA in M. tuberculosis pushes the bacterium switch to an unidentified dihydrofolate reductase for H4PteGlu biosynthesis, which might also contribute to the PAS resistance phenotype. Our study revealed how thyA mutations confer PAS resistance in M. tuberculosis and provided new insights into studies on the folate metabolism of the bacterium. [ABSTRACT FROM AUTHOR]

Brucella, a zoonotic facultative intracellular pathogenic bacterium, poses a significant threat both to human health and to the development of the livestock industry. Alanine racemase (Alr), the enzyme responsible for alanine racemization, plays a pivotal role in regulating virulence in this bacterium. Moreover, Brucella mutants with alr gene deletions (Δalr) exhibit potential as vaccine candidates. However, the mechanisms that underlie the detrimental effects of alr knockouts on Brucella pathogenicity remain elusive. Here, initially, we conducted a bioinformatics analysis of Alr, which demonstrated a high degree of conservation of the protein within Brucella spp. Subsequent metabolomics studies unveiled alterations in amino acid pathways following deletion of the alr gene. Furthermore, alr deletion in Brucella suis S2 induced decreased resistance to stress, antibiotics, and other factors. Transmission electron microscopy of simulated macrophage intracellular infection revealed damage to the cell wall in the Δalr strain, whereas propidium iodide staining and alkaline phosphatase and lactate dehydrogenase assays demonstrated alterations in cell membrane permeability. Changes in cell wall properties were revealed by measurements of cell surface hydrophobicity and zeta potential. Finally, the diminished adhesion capacity of the Δalr strain was shown by immunofluorescence and bacterial enumeration assays. In summary, our findings indicate that the alr gene that regulates amino acid metabolism in Brucella influences the properties of the cell wall, which modulates bacterial adherence capability. This study is the first demonstration that Alr impacts virulence by modulating bacterial metabolism, thereby providing novel insights into the pathogenic mechanisms of Brucella spp. [ABSTRACT FROM AUTHOR]

Ga(III) can mimic Fe(III) in the biological system due to its similarities in charge and ionic radius to those of Fe(III) and can exhibit antimicrobial activity by disrupting the acquisition and metabolism of Fe in bacterial cells. For example, Ga(NO3)3 has been proven to be effective in treating chronic lung infections by Pseudomonas aeruginosa (P. aeruginosa) in cystic fibrosis patients in a recent phase II clinical trial. However, Ga(NO3)3 is an ionic compound that can hydrolyze to form insoluble hydroxides at physiological pH, which not only reduces its bioavailability but also causes potential renal toxicity when it is used as a systemic drug. Although complexion with suitable chelating agents has offered a varying degree of success in alleviating the hydrolysis of Ga(III), the use of nanotechnology to deliver this metallic ion should constitute an ultimate solution to all the above-mentioned problems. Thus far, the development of Ga-based nanomaterials as metalloantibiotics is an underexploited area of research. We have developed two different synthetic routes for the preparation of biocompatible Ga2(HPO4)3 NPs and shown that both the PVP- or PEG-coated Ga2(HPO4)3 NPs exhibit potent antimicrobial activity against P. aeruginosa. More importantly, such polymer-coated NPs do not show any sign of Ga-resistant phenotype development after 30 passes, in sharp contrast to Ga(NO3)3, which can rapidly develop Ga-resistant phenotypes of P. aeruginosa, indicating the potential of using Ga2(HPO4)3 NPs a new antimicrobial agent in place of Ga(NO3)3. [ABSTRACT FROM AUTHOR]

Background: Imbalance in the intestinal microbiota can lead to chronic low-grade inflammation. Diet may influence this association. In this study, we aimed to evaluate the interaction between Akkermansia muciniphila (A. muciniphila) and dietary patterns using a proinflammatory index. Methods: We conducted a cross-sectional study with school-aged children. We quantified the relative abundance (RA) of A. muciniphila in feces using a polymerase chain reaction. We collected dietary information through employing a food frequency questionnaire and generated dietary patterns using principal component analysis. We generated a proinflammatory index from serum levels of interleukin-6, interleukin-10, tumor necrosis factor alpha, and adiponectin validated by receptor operating characteristic curves. We evaluated the association between A. muciniphila and the proinflammatory index using logistic regression, including an interaction term with dietary patterns. Results: We found that children with a low RA of A. muciniphila and a high intake of simple carbohydrates and saturated fats had increased odds of being high on the proinflammatory index. However, when the consumption of this dietary pattern is low, children with a low RA of A. muciniphila had decreased odds of being high on the proinflammatory index. Conclusions: Our results suggest that the simultaneous presence of A. muciniphila and diet have a more significant impact on the presence of being high on the proinflammatory index compared to both factors separately. [ABSTRACT FROM AUTHOR]

New antibiotics are unquestionably needed to fight the emergence and spread of multidrug-resistant bacteria. To date, antibiotics targeting bacterial central metabolism have been poorly investigated. By determining the minimal inhibitory concentration (MIC) of desmethylphosphinothricin (Glu-γ-PH), an analogue of glutamate with a phosphinic moiety replacing the γ-carboxyl group, we previously showed its promising antibacterial activity on Escherichia coli. Herein, we synthetized and determined the growth inhibition exerted on E. coli by an L-Leu dipeptide derivative of Glu-γ-PH (L-Leu-D,L-Glu-γ-PH). Furthermore, we compared the growth inhibition obtained with this dipeptide with that exerted by the free amino acid, i.e., Glu-γ-PH, and by their phosphonic and non-desmethylated analogues. All the tested compounds were more effective when assayed in a chemically-defined minimal medium. The dipeptide L-Leu-D,L-Glu-γ-PH had a significantly improved antibacterial activity (2 μg/mL), at a concentration between the non-desmethytaled (0.1 μg/mL) and the phosphonic (80 μg/mL) analogues. Also, in Bacillus subtilis, the dipeptide L-Leu-D,L-Glu-γ-PH displayed an activity comparable to that of the antibiotic amoxicillin. This work highlights the antibacterial relevance of the phosphinic pharmacophore and proposes new avenues for the development of novel antimicrobial drugs containing the phosphinic moiety. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa is a ubiquitous nosocomial opportunistic pathogen that harbors many virulence determinants. Part of P. aeruginosa success colonizing a variety of habitats resides in its metabolic robustness and plasticity, which are the basis of its capability of adaptation to different nutrient sources and ecological conditions, including the infected host. Given this situation, it is conceivable that P. aeruginosa virulence might be, at least in part, under metabolic control, in such a way that virulence determinants are produced just when needed. Indeed, it has been shown that the catabolite repression control protein Crc, which together with the RNA chaperon Hfq regulates the P. aeruginosa utilization of carbon sources at the post-transcriptional level, also regulates, directly or indirectly, virulence-related processes in P. aeruginosa. Among them, Crc regulates P. aeruginosa cytotoxicity, likely by modulating the activity of the Type III Secretion System (T3SS), which directly injects toxins into eukaryotic host cells. The present work shows that the lack of Crc produces a Type III Secretion-defective phenotype in P. aeruginosa. The observed impairment is a consequence of a reduced expression of the genes encoding the T3SS, together with an impaired secretion of the proteins involved. Our results support that the impaired T3SS activity of the crc defective mutant is, at least partly, a consequence of a defective protein export, probably due to a reduced proton motive force. This work provides new information about the complex regulation of the expression and the activity of the T3SS in P. aeruginosa. Our results highlight the need of a robust bacterial metabolism, which is defective in the ∆crc mutant, to elicit complex and energetically costly virulence strategies, as that provided by the T3SS. [ABSTRACT FROM AUTHOR]

Simple Summary: Wild Daurian ground squirrels (Spermophilus dauricus) breed only a few months out of the year, a behavior known as seasonal breeding. Despite the gut microbiota being an essential "organ" of animals, little is understood about how they relate to seasonal breeding. In the present investigation, metagenomic sequencing techniques were employed to examine the diversity of gut microbiota in wild Daurian ground squirrels across different breeding seasons. The findings indicate notable variations in the gut microbiota's structure and function among wild Daurian ground squirrels during different seasons. This study may provide an in-depth discussion of how seasonal reproduction affects gut microbes and aid in analyzing how changes in gut microbes act on the host. This study could provide new insights into the seasonal reproductive behavior of animals as well as a new theoretical basis for the study of gut microbiology. The Spermophilus dauricus, the wild Daurian ground squirrel, is known to exhibit seasonal breeding behavior. Although the importance of gut microbiota in animal digestion, metabolism, and immunity is well-established, the correlation between gut microbiota and seasonal breeding in this species remains inadequately explored. In the present study, using metagenomic sequencing technology, the compositions and functions of the gut microbiota of wild Daurian ground squirrels in different breeding seasons were explored. The dominant gut microbial phyla were Firmicutes and Bacteroidetes. The Firmicutes were predominant in the breeding season, whereas Bacteroidetes were predominant in the non-breeding season. At the genus level, Lactobacillus accumulated during the breeding season, whereas Odoribacter and Alistipes increased during the non-breeding season. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genome) annotations indicated that genes in gut samples were highly associated with metabolic functions. The differential expression gene analysis showed that genes related to the phosphotransferase system, cysteine, and methionine metabolism were highly expressed during the breeding season, whereas the non-breeding season upregulated genes were enriched in starch and sucrose metabolism and bacterial chemotaxis pathways. In conclusion, this study could provide a reference for investigating gut microbiota in seasonal breeding animals and offer new insight into gut microbial function. [ABSTRACT FROM AUTHOR]

Sialic acids (SAs) are α-keto-acid sugars with a nine-carbon backbone present at the non-reducing end of human milk oligosaccharides and the glycan moiety of glycoconjugates. SAs displayed on cell surfaces participate in the regulation of many physiologically important cellular and molecular processes, including signaling and adhesion. Additionally, sialyl-oligosaccharides from human milk act as prebiotics in the colon by promoting the settling and proliferation of specific bacteria with SA metabolism capabilities. Sialidases are glycosyl hydrolases that release α-2,3-, α-2,6- and α-2,8-glycosidic linkages of terminal SA residues from oligosaccharides, glycoproteins and glycolipids. The research on sialidases has been traditionally focused on pathogenic microorganisms, where these enzymes are considered virulence factors. There is now a growing interest in sialidases from commensal and probiotic bacteria and their potential transglycosylation activity for the production of functional mimics of human milk oligosaccharides to complement infant formulas. This review provides an overview of exo-alpha-sialidases of bacteria present in the human gastrointestinal tract and some insights into their biological role and biotechnological applications. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the ability of lactic acid bacteria to remove cholesterol in simulated gastric and intestinal fluids. The findings showed that the amount of cholesterol removed was dependent on the biomass, viability, and bacterial strain. Some cholesterol binding was stable and not released during gastrointestinal transit. The presence of cholesterol affected the fatty acid profile of bacterial cells, potentially influencing their metabolism and functioning. However, adding cholesterol did not significantly impact the survival of lactic acid bacteria during gastrointestinal transit. Storage time, passage, and bacterial culture type did not show significant effects on cholesterol content in fermented dairy products. Variations in cell survival were observed among lactic acid bacteria strains in simulated gastric and intestinal fluids, depending on the environment. Higher milk protein content was found to be more protective for bacterial cells during gastrointestinal transit than fat content. Future research should aim to better understand the impact of cholesterol on lactic acid bacteria metabolism and identify potential health benefits. [ABSTRACT FROM AUTHOR]

Chlamydia infection represents an important cause for concern for public health worldwide. Chlamydial infection of the genital tract in females is mostly asymptomatic at the early stage, often manifesting as mucopurulent cervicitis, urethritis, and salpingitis at the later stage; it has been associated with female infertility, spontaneous abortion, ectopic pregnancy, and cervical cancer. As an obligate intracellular bacterium, Chlamydia depends heavily on host cells for nutrient acquisition, energy production, and cell propagation. The current review discusses various strategies utilized by Chlamydia in manipulating the cell metabolism to benefit bacterial propagation and survival through close interaction with the host cell mitochondrial and apoptotic pathway molecules. [ABSTRACT FROM AUTHOR]

Antibiotic tolerance has become an increasingly serious crisis that has seriously threatened global public health. However, little is known about the exogenous factors that can trigger the development of antibiotic tolerance, both in vivo and in vitro. Herein, we found that the addition of citric acid, which is used in many fields, obviously weakened the bactericidal activity of antibiotics against various bacterial pathogens. This mechanistic study shows that citric acid activated the glyoxylate cycle by inhibiting ATP production in bacteria, reduced cell respiration levels, and inhibited the bacterial tricarboxylic acid cycle (TCA cycle). In addition, citric acid reduced the oxidative stress ability of bacteria, which led to an imbalance in the bacterial oxidation–antioxidant system. These effects together induced the bacteria to produce antibiotic tolerance. Surprisingly, the addition of succinic acid and xanthine could reverse the antibiotic tolerance induced by citric acid in vitro and in animal infection models. In conclusion, these findings provide new insights into the potential risks of citric acid usage and the relationship between antibiotic tolerance and bacterial metabolism. [ABSTRACT FROM AUTHOR]

Simple Summary: Intrauterine growth retardation (IUGR) hurts the postnatal growth and development of weanling piglets. Equol (Eq), a primary bioactive metabolite of daidzein, derives from intestinal bacterial metabolism and exerts numerous biological benefits. Nevertheless, no evidence is available to discover whether dietary Eq treatment exerts positive influences on the growth performance, redox status, intestinal health and skeletal muscle development of piglets with IUGR. Therefore, the aim of this study was to evaluate the influences of Eq supplementation on growth performance, redox status, intestinal health and skeletal muscle development. Here, twenty IUGR piglets and ten normal-birth-weight (NBW) female weanling piglets were used in this study and the results showed that Eq treatment enhanced antioxidant capacity and intestinal health, and facilitated skeletal muscle development, thus promoting the growth performance of IUGR piglets. Our findings provide significant implications for improving the growth performance of IUGR piglets and highlighting feasible applications in pig production. Animals with intrauterine growth retardation (IUGR) usually undergo injured postnatal growth and development during the early period after birth. Equol (Eq), an isoflavan produced by gut bacteria in response to daidzein intake, has various health benefits. Therefore, the objective of this study was to evaluate whether Eq supplementation can influence the growth performance, redox status, intestinal health and skeletal muscle development of weanling piglets with IUGR. A total of 10 normal-birth-weight (NBW) newborn female piglets and 20 newborn female piglets with IUGR were selected. After weaning at the age of 21 d, 10 NBW piglets and 10 IUGR piglets were allocated to the NBW group and IUGR group, respectively, and offered a basal diet. The other 10 IUGR piglets were allocated to the IUGR + Eq group and offered a basal diet with 50 mg of Eq per kg of diet. The whole trial lasted for 21 d. At the end of the feeding trial, all piglets were sacrificed for the collection of serum, intestinal tissues and skeletal muscles. Supplementation with Eq increased the average daily gain (ADG), average daily feed intake (ADFI), duodenal villus height to crypt depth ratio (V/C), jejunal villus height and V/C, but reduced the duodenal crypt depth in neonatal piglets with IUGR. Meanwhile, Eq supplementation elevated the activities of superoxide dismutase (SOD) and catalase (CAT) in the serum and duodenum and the activity of SOD in the jejunum, but lowered malondialdehyde (MDA) content in the serum, jejunum and ileum of piglets with IUGR. In addition, supplementation with Eq reduced diamine oxidase (DAO) activity and the levels of D-lactate and endotoxin in serum, and the tumor necrosis factor-α (TNF-α) level in jejunum and ileum, whereas the concentration of serum immunoglobulin G (IgG) and the mRNA levels of intestinal barrier-related markers in jejunum and ileum of IUGR piglets were increased. Furthermore, supplementation with Eq elevated the percentage of fast-fibers and was accompanied with higher mRNA expression of myosin heavy chain IIb (MyHC IIb) and lower mRNA levels in MyHC I in the longissimus thoracis (LT) muscle of IUGR piglets. In summary, Eq supplementation can promote antioxidant capacity, maintain intestinal health and facilitate skeletal muscle development, thus resulting in the higher growth performance of IUGR piglets. [ABSTRACT FROM AUTHOR]

The urgent necessity to fight antimicrobial resistance is universally recognized. In the search of new targets and strategies to face this global challenge, a promising approach resides in the study of the cellular response to antimicrobial exposure and on the impact of global cellular reprogramming on antimicrobial drugs' efficacy. The metabolic state of microbial cells has been shown to undergo several antimicrobial-induced modifications and, at the same time, to be a good predictor of the outcome of an antimicrobial treatment. Metabolism is a promising reservoir of potential drug targets/adjuvants that has not been fully exploited to date. One of the main problems in unraveling the metabolic response of cells to the environment resides in the complexity of such metabolic networks. To solve this problem, modeling approaches have been developed, and they are progressively gaining in popularity due to the huge availability of genomic information and the ease at which a genome sequence can be converted into models to run basic phenotype predictions. Here, we review the use of computational modeling to study the relationship between microbial metabolism and antimicrobials and the recent advances in the application of genome-scale metabolic modeling to the study of microbial responses to antimicrobial exposure. [ABSTRACT FROM AUTHOR]

The gut microbiome is made up of bacteria, fungi, viruses and archaea, all of which are closely related with human health. As the main component of enterovirus, the role of bacteriophages (phages) in chronic liver disease has been gradually recognized. Chronic liver diseases, including alcohol-related liver disease and nonalcoholic fatty liver disease, exhibit alterations of the enteric phages. Phages shape intestinal bacterial colonization and regulate bacterial metabolism. Phages adjoining to intestinal epithelial cells prevent bacteria from invading the intestinal barrier, and mediate intestinal inflammatory response. Phages are also observed increasing intestinal permeability and migrating to peripheral blood and organs, likely contributing to inflammatory injury in chronic liver diseases. By preying on harmful bacteria, phages can improve the gut microbiome of patients with chronic liver disease and thus act as an effective treatment method. [ABSTRACT FROM AUTHOR]

Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells. [ABSTRACT FROM AUTHOR]

Parkinson's disease, one of the most common neurodegenerative diseases, may not only affect the motor system, but also the physiology of the gastrointestinal tract. Delayed gastric emptying, impaired motility and altered intestinal bacteria are well-established consequences of the disease, which can have a pronounced effect on the absorption of orally administered drugs. In contrast, no studies have been performed into the composition of intestinal fluids. It is not unlikely that Parkinson's disease also affects the composition of intestinal fluids, a critical factor in the in vitro and in silico simulation of drug dissolution, solubilization and absorption. In the current study, duodenal fluids were aspirated from Parkinson's disease (PD) patients and age-matched healthy controls (healthy controls, HC) consecutively in fasted and fed conditions. The fluids were then characterized for pH, buffer capacity, osmolality, total protein, phospholipids, bile salts, cholesterol and lipids. In a fasted state, the intestinal fluid composition was highly similar in PD patients and healthy controls. In general, the same was true for fed-state fluids, apart from a slightly slower and less pronounced initial change in factors directly affected by the meal (i.e., buffer capacity, osmolality, total protein and lipids) in PD patients. The absence of a fast initial increase for these factors immediately after meal intake, as was observed in healthy controls, might result from slower gastric emptying in PD patients. Irrespective of the prandial state, a higher relative amount of secondary bile salts was observed in PD patients, potentially indicating altered intestinal bacterial metabolism. Overall, the data from this study indicate that only minor disease-specific adjustments in small intestinal fluid composition should be considered when simulating intestinal drug absorption in PD patients. [ABSTRACT FROM AUTHOR]

Antibiotic tolerance poses a threat to current antimicrobial armamentarium. Bacteria at a tolerant state survive in the presence of antibiotic treatment and account for persistence, relapse and recalcitrance of infections. Antibiotic treatment failure may occur due to antibiotic tolerance. Persistent infections are difficult to treat and are often associated with poor prognosis, imposing an enormous burden on the healthcare system. Effective strategies targeting antibiotic-tolerant bacteria are therefore highly warranted. In this study, small molecule compound SA-558 was identified to be effective against Staphylococcus aureus that are tolerant to being killed by conventional antibiotics. SA-558 mediated electroneutral transport across the membrane and led to increased ATP and ROS generation, resulting in a reduction of the population of antibiotic-tolerant bacteria. In a murine chronic infection model, of which vancomycin treatment failed, we demonstrated that SA-558 alone and in combination with vancomycin caused significant reduction of MRSA abundance. Our results indicate that SA-558 monotherapy or combinatorial therapy with vancomycin is an option for managing persistent S. aureus bacteremia infection and corroborate that bacterial metabolism is an important target for counteracting antibiotic tolerance. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria possess a remarkable ability to adapt to fluctuating host environments and cause infection. Disturbing bacterial central metabolism through inhibition of 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) has the potential to hinder bacterial adaptation, representing a new antibacterial strategy. DXPS functions at a critical metabolic branchpoint to produce the metabolite DXP, a precursor to pyridoxal-5-phosphate (PLP), thiamin diphosphate (ThDP) and isoprenoids presumed essential for metabolic adaptation in nutrient-limited host environments. However, specific roles of DXPS in bacterial adaptations that rely on vitamins or isoprenoids have not been studied. Here we investigate DXPS function in an adaptation of uropathogenic E. coli (UPEC) to d-serine (d-Ser), a bacteriostatic host metabolite that is present at high concentrations in the urinary tract. UPEC adapt to d-Ser by producing a PLP-dependent deaminase, DsdA, that converts d-Ser to pyruvate, pointing to a role for DXPS-dependent PLP synthesis in this adaptation. Using a DXPS-selective probe, butyl acetylphosphonate (BAP), and leveraging the toxic effects of d-Ser, we reveal a link between DXPS activity and d-Ser catabolism. We find that UPEC are sensitized to d-Ser and produce sustained higher levels of DsdA to catabolize d-Ser in the presence of BAP. In addition, BAP activity in the presence of d-Ser is suppressed by β-alanine, the product of aspartate decarboxylase PanD targeted by d-Ser. This BAP-dependent sensitivity to d-Ser marks a metabolic vulnerability that can be exploited to design combination therapies. As a starting point, we show that combining inhibitors of DXPS and CoA biosynthesis displays synergy against UPEC grown in urine where there is increased dependence on the TCA cycle and gluconeogenesis from amino acids. Thus, this study provides the first evidence for a DXPS-dependent metabolic adaptation in a bacterial pathogen and demonstrates how this might be leveraged for development of antibacterial strategies against clinically relevant pathogens. [ABSTRACT FROM AUTHOR]

Oxidative stress causes various diseases, such as type II diabetes and dyslipidemia, while antioxidants in foods may prevent a number of diseases and delay aging by exerting their effects in vivo. Phenolic compounds are phytochemicals such as flavonoids which consist of flavonols, flavones, flavanonols, flavanones, anthocyanidins, isoflavones, lignans, stilbenoids, curcuminoids, phenolic acids, and tannins. They have phenolic hydroxyl groups in their molecular structures. These compounds are present in most plants, are abundant in nature, and contribute to the bitterness and color of various foods. Dietary phenolic compounds, such as quercetin in onions and sesamin in sesame, exhibit antioxidant activity and help prevent cell aging and diseases. In addition, other kinds of compounds, such as tannins, have larger molecular weights, and many unexplained aspects still exist. The antioxidant activities of phenolic compounds may be beneficial for human health. On the other hand, metabolism by intestinal bacteria changes the structures of these compounds with antioxidant properties, and the resulting metabolites exert their effects in vivo. In recent years, it has become possible to analyze the composition of the intestinal microbiota. The augmentation of the intestinal microbiota by the intake of phenolic compounds has been implicated in disease prevention and symptom recovery. Furthermore, the "brain–gut axis", which is a communication system between the gut microbiome and brain, is attracting increasing attention, and research has revealed that the gut microbiota and dietary phenolic compounds affect brain homeostasis. In this review, we discuss the usefulness of dietary phenolic compounds with antioxidant activities against some diseases, their biotransformation by the gut microbiota, the augmentation of the intestinal microflora, and their effects on the brain–gut axis. [ABSTRACT FROM AUTHOR]

Silver nanoparticles have been a recent focus of many researchers in dentistry, and their potential uses and benefits have drawn attention in dentistry and medicine. The fabrication and utilization of nanoscale substances and structures are at the core of the rapidly developing areas of nanotechnology. They are often used in the dental industry because they prevent bacteria from making nanoparticles, oxides, and biofilms. They also stop the metabolism of bacteria. Silver nanoparticles (AgNPs) are a type of zero-dimensional material with different shapes. Dentistry has to keep up with changing patient needs and new technology. Silver nanoparticles (AgNPs) can be used in dentistry for disinfection and preventing infections in the oral cavity. One of the most interesting metallic nanoparticles used in biomedical applications is silver nanoparticles (AgNPs). The dental field has found promising uses for silver nanoparticles (AgNPs) in the elimination of plaque and tartar, as well as the elimination of bacterial and fungal infections in the mouth. The incorporation of AgNPs into dental materials has been shown to significantly enhance patients' oral health, leading to their widespread use. This review focuses on AgNP synthesis, chemical properties, biocompatibility, uses in various dental fields, and biomaterials used in dentistry. With an emphasis on aspects related to the inclusion of silver nanoparticles, this descriptive review paper also intends to address the recent developments of AgNPs in dentistry. [ABSTRACT FROM AUTHOR]

The World Health Organization has cautioned that antimicrobial resistance (AMR) will be responsible for an estimated 10 million deaths annually by 2050. To facilitate prompt and accurate diagnosis and treatment of infectious disease, we investigated the potential of amino acids for use as indicators of bacterial growth activity by clarifying which amino acids are taken up by bacteria during the various growth phases. In addition, we examined the amino acid transport mechanisms that are employed by bacteria based on the accumulation of labeled amino acids, Na+ dependence, and inhibitory effects using a specific inhibitor of system A. We found that 3H-L-Ala accurately reflects the proliferative activity of Escherichia coli K-12 and pathogenic EC-14 in vitro. This accumulation in E. coli could be attributed to the amino acid transport systems being different from those found in human tumor cells. Moreover, biological distribution assessed in infection model mice with EC-14 using 3H-L-Ala showed that the ratio of 3H-L-Ala accumulated in infected muscle to that in control muscle was 1.20. By detecting the growth activity of bacteria in the body that occurs during the early stages of infection by nuclear imaging, such detection methods may result in expeditious diagnostic treatments for infectious diseases. [ABSTRACT FROM AUTHOR]