Comparison of metabolic response between the planktonic and air-dried Escherichia coli to electrolysed water combined with ultrasound by 1H NMR spectroscopy

Purification and characterization of betacyanin monomers from Hylocereus polyrhizus peel: A comparative study of their antioxidant and antidiabetic activities with mechanistic insights

Betacyanins have garnered escalating research interest for their promising bioactivities. However, substantial challenges in purification and separation have impeded a holistic comprehension of the distinct bioactivities of individual betacyanins and their underlying mechanisms. Herein, betanin and phyllocactin monomers with purity exceeding 95% were successfully obtained from Hylocereus polyrhizus peel using a feasible protocol. These monomers were subsequently employed for comparative bioactivity assessments to uncover underlying mechanisms and illuminate structure-activity relationships. Interestingly, phyllocactin exhibited superior antioxidant activities and 36.1% stronger inhibitory activity on α-glucosidase compared to betanin. Mechanistic studies have revealed that they function as mixed-type inhibitors of α-amylase and competitive inhibitors of α-glucosidase, with interactions predominantly driven by hydrogen bonding. Notably, phyllocactin demonstrated a greater binding affinity with enzymes than betanin, thereby substantiating its heightened inhibitory activity. Overall, our results highlight novel bioactivities of betacyanin monomers and provide profound insights into the intricate interplay between structures and properties.

Glycogen plays a key role in survival of Salmonella Typhimurium on dry surfaces and in low-moisture foods

Salmonella enterica is known to survive in desiccate environments and is often associated with low-moisture foods (LMFs). In this work, S. Typhimurium ATCC 14028 was found to survive better by achieving the least reductions (3.17 ± 0.20 Log CFU reduction) compared to S. Tennessee ATCC 10722 (3.82 ± 0.13 Log CFU reduction) and S. Newport ATCC 6962 (6.03 ± 0.36 Log CFU reduction) after 30 days on surfaces with a relative humidity of 49% at ambient temperature. A metabolomic analysis revealed that S. Typhimurium was still active in energy metabolism after 24 h in the desiccate environment and glycogen, an energy reserve, was drastically reduced. We followed up on the glycogen levels over 30 days and found indeed a sharp decline on the first day. However, the glycogens detected on day 7 were significantly higher (P < 0.05) and thereafter remained stable above the original levels until day 30. The expression levels of both glycogen anabolism- and catabolism-related genes (csrA, glgA, glgC, glgX) were significantly up-regulated at all tested points (P < 0.05). The glgA and glgC insertion mutants displayed weaker survivability on both dry surfaces and in representative LMFs (flour and milk powder) compared to the wild-type strain. This work highlights the role of glycogen during different periods of desiccation, which may bring novel insight into mitigating Salmonella by disrupting glycogen metabolism.

Itaconic acid and dimethyl itaconate exert antibacterial activity in carbon-enriched environments through the TCA cycle

Itaconic acid (IA), a metabolite generated by the tricarboxylic acid (TCA) cycle in eukaryotic immune cells, and its derivative dimethyl itaconate (DI) exert antibacterial functions in intracellular environments. Previous studies suggested that IA and DI only inhibit bacterial growth in carbon-limited environments; however, whether IA and DI maintain antibacterial activity in carbon-enriched environments remains unknown. Here, IA and DI inhibited the bacteria with minimum inhibitory concentrations of 24.02 mM and 39.52 mM, respectively, in a carbon-enriched environment. The reduced bacterial pathogenicity was reflected in cell membrane integrity, motility, biofilm formation, AI-2/luxS, and virulence. Mechanistically, succinate dehydrogenase (SDH) activity and fumaric acid levels decreased in the IA and DI treatments, while isocitrate lyase (ICL) activity was upregulated. Inhibited TCA circulation was also observed through untargeted metabolomics. In addition, energy-related aspartate metabolism and lysine degradation were suppressed. In summary, these results indicated that IA and DI reduced bacterial pathogenicity while exerting antibacterial functions by inhibiting TCA circulation. This study enriches knowledge on the inhibition of bacteria by IA and DI in a carbon-mixed environment, suggesting an alternative method for treating bacterial infections by immune metabolites.

High temperature stress induced oxidative stress, gut inflammation and disordered metabolome and microbiome in tsinling lenok trout

Tsinling lenok trout (Brachymystax lenok tsinlingensis Li) is a species of cold-water salmon that faces serious challenges due to global warming. High temperature stress has been found to damage the gut integrity of cold-water fish, impacting their growth and immunity. However, limited research exists on the causal relationship between gut microbial disturbance and metabolic dysfunction in cold-water fish induced by high temperature stress. To address this gap, we conducted a study to investigate the effects of high temperature stress (24 °C) on the gut tissue structure, antioxidant capacity, gut microorganisms, and metabolome reactions of tsinling lenok trout. Our analysis using 16 S rDNA gene sequencing revealed significant changes in the gut microbial composition and metabolic profile. Specifically, the abundance of Firmicutes and Gemmatimonadetes decreased significantly with increasing temperature, while the abundance of Bacteroidetes increased significantly. Metabolic analysis revealed a significant decrease in the abundance of glutathione, which is synthesized from glutamate and glycine, under high temperature stress. Additionally, there was a notable reduction in the levels of adenosine, inosine, xanthine, guanosine, and deoxyguanosine, which are essential for DNA/RNA synthesis. Conversely, there was a significant increase in the abundance of D-glucose 6 P. Furthermore, high temperature stress adversely affects intestinal structure and barrier function. Our findings provide valuable insights into the mechanism of high temperature stress in cold-water fish and serve as a foundation for future research aimed at mitigating the decline in production performance caused by such stress.

Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways

The toxic reactive oxygen species (toxROS) is the reactive oxygen species (ROS) beyond the normal concentration of cells, which has inactivation and disinfection effects on foodborne bacteria. However, foodborne bacteria can adapt and survive by physicochemical regulation of antioxidant systems, especially through central carbon metabolism (CCM), which is a significant concern for food safety. It is thus necessary to study the antioxidant regulation mechanisms of CCM in foodborne bacteria under toxROS stresses. Therefore, the purpose of this review is to provide an update and comprehensive overview of the reconfiguration of CCM fluxes in foodborne bacteria that respond to different toxROS stresses. In this review, two key types of toxROS including exogenous toxROS (exo-toxROS) and endogenous toxROS (endo-toxROS) are introduced. Exo-toxROS are produced by disinfectants, such as H₂O₂ and HOCl, or during food non-thermal processing such as ultraviolet (UV/UVA), cold plasma (CP), ozone (O₃), electrolyzed water (EW), pulsed electric field (PEF), pulsed light (PL), and electron beam (EB) processing. Endo-toxROS are generated by bioreagents such as antibiotics (aminoglycosides, quinolones, and β-lactams). Three main pathways for CCM in foodborne bacteria under the toxROS stress are also highlighted, which are glycolysis (EMP), pentose phosphate pathway (PPP), and tricarboxylic acid cycle (TCA). In addition, energy metabolisms throughout these pathways are discussed. Finally, challenges and future work in this area are suggested. It is hoped that this review should be beneficial in providing insights for future research on bacterial antioxidant CCM defence under both exo-toxROS stresses and endo-toxROS stresses.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Gene Networks and Pathways Involved in Escherichia coli Response to Multiple Stressors

Stress response helps microorganisms survive extreme environmental conditions and host immunity, making them more virulent or drug resistant. Although both reductionist approaches investigating specific genes and systems approaches analyzing individual stress conditions are being used, less is known about gene networks involved in multiple stress responses. Here, using a systems biology approach, we mined hundreds of transcriptomic data sets for key genes and pathways involved in the tolerance of the model microorganism Escherichia coli to multiple stressors. Specifically, we investigated the E. coli K-12 MG1655 transcriptome under five stresses: heat, cold, oxidative stress, nitrosative stress, and antibiotic treatment. Overlaps of transcriptional changes between studies of each stress factor and between different stressors were determined: energy-requiring metabolic pathways, transport, and motility are typically downregulated to conserve energy, while genes related to survival, bona fide stress response, biofilm formation, and DNA repair are mainly upregulated. The transcription of 15 genes with uncharacterized functions is higher in response to multiple stressors, which suggests they may play pivotal roles in stress response. In conclusion, using rank normalization of transcriptomic data, we identified a set of E. coli stress response genes and pathways, which could be potential targets to overcome antibiotic tolerance or multidrug resistance.

Metabolic Responses of "Big Six" Escherichia coli in Wheat Flour to Thermal Treatment Revealed by Nuclear Magnetic Resonance Spectroscopy

Escherichia coli outbreaks linked to wheat flour consumption have kept emerging in recent years, which necessitated an antimicrobial step being incorporated into the flour production process. The objectives of this in vivo study were to holistically evaluate the sanitizing efficacy of thermal treatment at 60 and 70°C against the "big six" E. coli strains (O26:H11, O45:H2, O103:H11, O111, O121:H19, and O145) in wheat flour and to assess the strain-specific metabolic responses using nuclear magnetic resonance (NMR) spectroscopy. The 70°C treatment temperature indiscriminatingly inactivated all strains by over 4.3-log CFU/g within 20 min, suggesting the high sanitization effectiveness of this treatment temperature, whereas the treatment at 60°C inactivated the strains to various degrees during the 1-h process. The most resistant strains at 60°C, O26 and O45, were characterized by amino acid and sugar depletion, and their high resistance was attributed to the dual effects of activated heat shock protein (HSP) synthesis and promoted glycolysis. O121 also demonstrated these metabolic changes, yet its thermal resistance was largely impaired by the weakened membrane structure and diminished osmotic protection due to phosphorylcholine exhaustion. In contrast, O111, O145, and O103 presented a substantial elevation of metabolites after stress at 60°C; their moderate thermal resistance was mainly explained by the accumulation of amino acids as osmolytes. Overall, the study enhanced our understanding of the metabolic responses of big six E. coli to heat stress and provided a model for conducting NMR-based metabolomic studies in powdered food matrices. IMPORTANCE "Big six" Escherichia coli strains have caused several outbreaks linked to wheat flour consumption in the last decade, revealing the vital importance of adopting an antimicrobial treatment during the flour production process. Therefore, the present study was carried out to evaluate the efficacy of a typical sanitizing approach, thermal treatment, against the big six strains in wheat flour along with the underlying antimicrobial mechanisms. Findings showed that thermal treatment at 60 and 70°C could markedly mitigate the loads of all strains in wheat flour. Moreover, activated heat shock protein synthesis combined with expedited glycolysis and enhanced osmotic protection were identified as two major metabolic alteration patterns in the E. coli strains to cope with the heat stress. With the responses of big six in wheat flour to thermal treatment elucidated, scientific basis for incorporating a thermal inactivation step in wheat flour production was provided.

Metabolomic analyses on microbial primary and secondary oxidative stress responses

Food safety is veryimportant in our daily life. In food processing or disinfection, microorganisms are commonly exposed to oxidative stress perturbations. However, microorganisms can adapt and respond to physicochemical interventions, leading to difficulty and complexity for food safety assurance. Therefore, understanding the response mechanisms of microbes and providing an overview of the responses under oxidative stress conditions are beneficial for ensuring food safety for the industry. The current review takes the metabolomics approach to reveal small metabolite signatures and key pathway alterations during oxidative stress at the molecular and technical levels. These alterations are involved in primary oxidative stress responses due to inactivation treatments such as using hypochlorite (HOCl), hydrogen peroxide (H₂ O₂ ), electrolyzed water (EW), irradiation, pulsed light (PL), electron beam (EB), and secondary oxidative stress responses due to exposures to excessive conditions such as heat, pressure, acid, and alkaline. Details on the putative origin of exogenous or endogenous reactive oxygen species (ROS) are discussed, with particular attention paid to their effects on lipid, amino acid, nucleotide, and carbohydrate metabolism. In addition, mechanisms on counteracting oxidative stresses, stabilization of cell osmolality as well as energy provision for microbes to survive are also discussed.

Metabolite release and rheological properties of sponge cake after in vitro digestion and the influence of a flour replacer rich in dietary fibre

The present study aimed to better understand the metabolite release and rheological characteristics of sponge cake after in vitro digestion and the effect of Eucheuma as a fibre-rich flour replacer. Overall, 22 compounds including amino acids, saccharides, fatty acids, and other metabolites were identified based on nuclear magnetic resonance spectra. Principal component analysis and orthogonal projection to latent structures-discriminant analysis showed that Eucheuma reduced the release of amino acids and fatty acids. The released glucose from the EP20 sample (20% replacement of flour with Eucheuma) decreased by 35.4% in intestinal phases compared with the control cake. Eucheuma's in vitro effects on sponge cake digestion mainly reflected altered flow behaviour index. All samples showed solid-like behaviour and a decrease in viscoelastic moduli after digestion. This study forms the basis for future optimisation of food properties to control their digestive characteristics.

Antibiofilm activities of the cinnamon extract against Vibrio parahaemolyticus and Escherichia coli

Vibrio parahaemolyticus and Escherichia coli are two major foodborne pathogens. In this paper, the antibiofilm activities of the ethanol extract of cinnamon against these two bacteria were studied in detail. The antibacterial activity and the MIC of the extract were determined, and the inhibition and removing effects of the extract on the biofilms of V. parahaemolyticus and E. coli were investigated. The biofilms stained with fluorescein isothiocyanate (FITC) and concanavalin A (Con A) were also observed by confocal laser scanning microscope (CLSM). The results indicated that the extract exhibited high antibacterial activity, with the MIC against V. parahaemolyticus and E. coli was 6.25 mg/mL. The effects on V. parahaemolyticus biofilm were significant with the inhibition rate of 75.46% at MIC, and the eradication rate of 93.26% at 32MIC, respectively. As to E. coli, the inhibition rate was 48.18% at MIC, and the eradication rate was 46.16% at 8MIC. Meanwhile, the extract could notably reduce the metabolic activities and the secretion of EPS in biofilm, it inhibited 78.57% EPS formation in V. parahaemolyticus biofilm at MIC, and eliminated 61.28% EPS in mature biofilm at 4MIC. CLSM images showed that the EPS of the treated biofilm became thinner and biofilm structure was looser, when compared with the untreated control. This study elucidated that the cinnamon extract was effective to prevent biofilm formation and eradicate mature biofilms of V. parahaemolyticus and E. coli.

Recent advances in the application of metabolomics for food safety control and food quality analyses

As one of the omics fields, metabolomics has unique advantages in facilitating the understanding of physiological and pathological activities in biology, physiology, pathology, and food science. In this review, based on developments in analytical chemistry tools, cheminformatics, and bioinformatics methods, we highlight the current applications of metabolomics in food safety, food authenticity and quality, and food traceability. Additionally, the combined use of metabolomics with other omics techniques for "foodomics" is comprehensively described. Finally, the latest developments and advances, practical challenges and limitations, and requirements related to the application of metabolomics are critically discussed, providing new insight into the application of metabolomics in food analysis.

Acid Tolerance Response of Listeria monocytogenes in Various External pHs with Different Concentrations of Lactic Acid

This study evaluated the acid tolerance response (ATR) of two strains of Listeria monocytogenes (serotype 1/2a and 4b) and one strain of Listeria innocua under different mildly acid conditions. Cells were incubated in combinations of three concentrations of lactic acid medium (3, 4.75, and 15 mM) and three external pH's (pHex 5.0, 6.0, and 6.5), plus, a HCl control, and a blank control (pH 7.4). Results showed that lactic acid induced lower log reduction of all three strains when challenged in severe acid conditions (pH 3.0) after being habituated at a pHex of 5.5 or 6.0 until the log phase, compared with a pHex of 6.5 or the two controls. This indicates that when the pHex was either 5.5 or 6.0 this induced a higher ATR of the strains, which may be caused by the ability of the strains to retain intracellular pH (pHi) homeostasis with pHi maintained in the range of 7.4-7.9. It was also found that a pHex of 5.5 resulted in the highest pHi of the strains across all incubated conditions, which indicates that the pHi may play an important role in the induction of ATR when Listeria cells are habituated in lactic acid, and if the higher pHi can be maintained, the ATR would be stronger. The concentration of lactic acid per se has no significant effect on ATR, which it is proposed was due to the pHi homeostasis maintained within the cells. However, the difference in ATR among three strains was also significant, which cannot be explained by the stable pHi of all tested strains. Therefore, other underlying mechanisms to mediate ATR under different conditions need to be explored in further studies.

Elucidating antimicrobial mechanism of nisin and grape seed extract against Listeria monocytogenes in broth and on shrimp through NMR-based metabolomics approach

Nisin and grape seed extract (GSE) have been widely used as food preservatives; however, the mechanism against pathogens at molecular level has not been well elucidated. This work aimed to investigate their antimicrobial effect against Listeria monocytogenes and to elucidate the mechanism by NMR-based metabolomics. Nisin exhibited enhanced in vitro antilisterial effect when combined with GSE (4.49 log CFU/mL reduction). Marked change in cell membrane permeability was observed in the combination group using confocal laser scanning microscopy; this was verified by increased leakage of protein and nucleic acid. The underlying antimicrobial mechanism was revealed by NMR coupled with multivariate analysis. Significant decreases in threonine, cysteine, ATP, NADP, adenine were observed, whereas a few of metabolites such as lactic acid and γ-aminobutyric acid (GABA) increased after nisin-GSE treatment (P < 0.05). Pathway analysis further manifested that the nisin-GSE inhibited the survival of L. monocytogenes by blocking the TCA cycle, amino acid biosynthesis and energy-producing pathway. Lastly, nisin and GSE were applied to shrimp and binary combination showed remarkably antilisterial activity (1.79 log CFU/g reduction). GABA shunt and protein degradation from shrimp compensated the unbalanced glycolysis and amino acid metabolism by providing energy and carbon source for L. monocytogenes inoculated on shrimp. Thus, they were more tolerant to nisin and GSE stresses as compared to the broth-grown culture.

Metabolic characterisation of eight Escherichia coli strains including "Big Six" and acidic responses of selected strains revealed by NMR spectroscopy

The metabolic diversity of Escherichia coli strains (non-pathogenic E. coli ATCC 25922, and pathogenic E. coli O157:H7, O26:H11, O45:H2, O103:H11, O111, O121:H19, and O145) was tested using nuclear magnetic resonance. Based on two representative two-dimensional ¹H-¹³C spectra, 38 metabolites were identified in E. coli intracellular samples. Principal component analysis indicated that metabolites including lysine, arginine, α-ketoglutaric acid, adenosine, and fumaric acid were responsible for the separation of E. coli ATCC 25922. Relatively large metabolic differences between ATCC 25922 and the pathogenic strains were recoded. The most varied pairwise group (ATCC 25922 vs. O26:H11) was further analysed. The screened metabolites and enrichment pathway tests revealed different amino acid metabolism and higher requirement for energy production in the pathogenic strains. The acidic responses of the selected strains were further tested. The in vitro and in vivo inactivation kinetics, morphological changes, and protein leakage showed higher acid tolerance of E. coli O26:H11. Metabolic analysis of the two strains under acidic stress revealed alternative metabolites and pathways in the two groups. Pathogenic O26:H11 was characterised by higher energy production and amino acid metabolism (lysine and glutamic acid). Real-time PCR tests confirmed that glutamic acid dependent decarboxylase/antiporter system was the major acid resistance mechanism.

Revealing the 1H NMR metabolome of mirasol chili peppers (Capsicum annuum) infected by Candidatus Phytoplasma trifolii

The infection of Capsicum annuum cv. mirasol by Candidatus Phytoplasma trifolii (16SrVI) causes devastating crop losses in northern Mexico. This study addresses the metabolomics profiling of mirasol chili peppers (Capsicum annuum cv. mirasol) infected by Candidatus Phytoplasma trifolii. For this study, 25 diseased fruits and 25 healthy fruits were used. Principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) revealed dramatic changes in the content of 42 metabolites which were identified in diseased and healthy mirasol chili peppers. The endogenous levels of fructose, glucose and formic acid were substantially decreased in the diseased chili peppers. In the same group of samples, high concentrations of alanine, asparagine, fumaric acid, sucrose and threonine were observed. The content of Choline didńt present a significant difference. This evidence supports the fact that Candidatus Phytoplasma trifolii infection reduces de CO₂ fixation into carbohydrates, decreases invertase activity, and inhibits glycolysis in the diseased plant tissues. The levels of ascorbic acid, capsaicin and dihydrocapsaicinin in diseased fruits were dramatically decreased, suggesting that Candidatus Phytoplasma trifolii can reduce the pungency and the nutraceutical value of mirasol chili peppers.