New Insights Into the Response of Metabolome of Escherichia coli O157:H7 to Ohmic Heating

Analysis of heterologous expression of phaCBA promotes the acetoin stress response mechanism in Bacillus subtilis using transcriptomics and metabolomics approaches

Acetoin, a versatile platform chemical and popular food additive, poses a challenge to the biosafety strain Bacillus subtilis when produced in high concentrations due to its intrinsic toxicity. Incorporating the PHB synthesis pathway into Bacillus subtilis 168 has been shown to significantly enhance the strain's acetoin tolerance. This study aims to elucidate the molecular mechanisms underlying the response of B. subtilis 168-phaCBA to acetoin stress, employing transcriptomic and metabolomic analyses. Acetoin stress induces fatty acid degradation and disrupts amino acid synthesis. In response, B. subtilis 168-phaCBA down-regulates genes associated with flagellum assembly and bacterial chemotaxis, while up-regulating genes related to the ABC transport system encoding amino acid transport proteins. Notably, genes coding for cysteine and D-methionine transport proteins (tcyB, tcyC and metQ) and the biotin transporter protein bioY, are up-regulated, enhancing cellular tolerance. Our findings highlight that the expression of phaCBA significantly increases the ratio of long-chain unsaturated fatty acids and modulates intracellular concentrations of amino acids, including L-tryptophan, L-tyrosine, L-leucine, L-threonine, L-methionine, L-glutamic acid, L-proline, D-phenylalanine, L-arginine, and membrane fatty acids, thereby imparting acetoin tolerance. Furthermore, the supplementation with specific exogenous amino acids (L-alanine, L-proline, L-cysteine, L-arginine, L-glutamic acid, and L-isoleucine) alleviates acetoin's detrimental effects on the bacterium. Simultaneously, the introduction of phaCBA into the acetoin-producing strain BS03 addressed the issue of insufficient intracellular cofactors in the fermentation strain, resulting in the successful production of 70.14 g/L of acetoin through fed-batch fermentation. This study enhances our understanding of Bacillus's cellular response to acetoin-induced stress and provides valuable insights for the development of acetoin-resistant Bacillus strains.

Synergistic bactericidal mechanisms of RF energy simultaneously combined with cinnamon essential oil or epsilon-polylysine against Salmonella revealed at cellular and metabolic levels

Radio frequency (RF) heating and antimicrobials are considered to be effective methods for inactivating food pathogens. This study explored the bactericidal effects against Salmonella of RF heating combined with two kinds of natural antimicrobials possessing different hydrophobic properties and their synergistic bactericidal mechanisms. Results showed that RF heating caused sublethal damage to bacterial cells and enhanced the interaction of cells and antimicrobials, leading to synergistic bactericidal effects of the simultaneous combination of RF heating and antimicrobials. The combination of RF heating and ε-polylysine (ε-PL) further promoted cell morphological alteration, raised membrane permeability, intracellular adenosine triphosphate (ATP) leakage and intracellular reactive oxygen species (ROS) accumulation compared to individual treatment. The simultaneous combination of RF heating and cinnamon essential oil nanoemulsion (CEON) also further enhanced membrane permeability and ROS accumulation compared to individual treatment, but impacts were less than those in the combination of RF heating and ε-PL. The major synergistic bactericidal mechanism of RF heating and CEON was significantly inhibiting intracellular ATP synthesis. The untargeted metabolomics analysis revealed that the combined treatments enhanced disturbances to multiple intracellular metabolisms compared to individual treatment, thus leading to synergistic bactericidal effects against Salmonella. These results provide an in-depth understanding of the synergistic bactericidal mechanisms of the combination of RF heating and natural antimicrobials from cellular and metabolic levels.

Metabolomics investigation of global responses of Cronobacter sakazakii against common sanitizing in infant formula processing environments

Cronobacter sakazakii, an opportunistic bacterium, has raised a serious outbreak in powdered infant formula recent years. In this work, four sanitizing strategies used during infant formula processing, including chlorine, quaternary ammonium chloride (QAC), 60 °C heating, and malic acid (MA), were utilized against C. sakazakii among planktonic, air-dried (A), and air-dried & washed (AW) state, followed by an exploration of the metabolic responses induced by these treatments via a dual-platform metabolomics analysis with the ultra-high performance liquid chromatography-mass spectrometry and nuclear magnetic resonance. In the planktonic state, MA was the most effective in inhibiting bacterial growth, followed by chlorine, QAC, and 60 °C heating. Under A state, the efficacy of heating improved considerably, compared to that in the planktonic state, and remained unaltered under AW state. Chlorine and QAC were ineffective to control bacterial growth under A state, but their efficacy rose under AW state. Furthermore, the metabolomic analysis revealed chlorine induces amino acids catabolism, membrane lysis, and depression in carbohydrate and nucleotide metabolism in both planktonic and AW states, while the initiation of antioxidation mechanism was only found under AW state. Although the metabolic change caused by QAC in the planktonic state was similar to chlorine, the accumulation of osmoprotectant and membrane phospholipids within the AW cells reflected the effort to restore intracellular homeostasis upon QAC. Heating was characterized by considerable amino acid anabolism, along with mildly perturbed carbohydrate and nucleotide metabolism for heat shock protein preparation in both states. Lastly, MA promoted amino acid-dependent acid resistance under the planktonic state, and the regulation of antioxidation and osmoprotection under AW state. The metabolomics study elucidated the intracellular perturbation induced by common sanitizing, as well as the bacterial response, which provides insights for novel sanitization development.

Decoding the Gene Regulatory Network of Muscle Stem Cells in Mouse Duchenne Muscular Dystrophy: Revelations from Single-Nuclei RNA Sequencing Analysis

The gene dystrophin is responsible for Duchenne muscular dystrophy (DMD), a grave X-linked recessive ailment that results in respiratory and cardiac failure. As the expression of dystrophin in muscle stem cells (MuSCs) is a topic of debate, there exists a limited understanding of its influence on the gene network of MuSCs. This study was conducted with the objective of investigating the effects of dystrophin on the regulatory network of genes in MuSCs. To comprehend the function of dystrophin in MuSCs from DMD, this investigation employed single-nuclei RNA sequencing (snRNA-seq) to appraise the transcriptomic profile of MuSCs obtained from the skeletal muscles of dystrophin mutant mice (DMDmut) and wild-type control mice. The study revealed that the dystrophin mutation caused the disruption of several long non-coding RNAs (lncRNAs), leading to the inhibition of MEG3 and NEAT1 and the upregulation of GM48099, GM19951, and GM15564. The Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the dystrophin mutation activated the cell adhesion pathway in MuSCs, inhibited the circulatory system process, and affected the regulation of binding. The study also revealed that the metabolic pathway activity of MuSCs was altered. The metabolic activities of oxidative phosphorylation (OXPHOS) and glycolysis were elevated in MuSCs from DMDmut. In summary, this research offers novel insights into the disrupted gene regulatory program in MuSCs due to dystrophin mutation at the single-cell level.

Characterization and metabolomic profiling of two pigment producing fungi from infected fruits of Indian Gooseberry

Two pigment producing fungi, Talaromyces atroroseus and Penicillium choerospondiatis, were isolated and identified from infected fruits of Phyllanthus emblica L. based on amplification and sequencing of internal transcribed spacer region and beta-tubulin gene. This is the first occurrence report of these two fungi from fruits of P. emblica. Culture extract containing metabolites of T. atroroseus and P. choerospondiatis contained phenolics of 26.35 mg and 30.89 mg GAE/g dry extract respectively; whereas no significant amount of flavonoids and tannins were detected. P. choerospondiatis metabolites extract showed higher DPPH and ABTS activity with IC₅₀ values of 21.94 mg/ml and 27.03 mg/ml respectively than T. atroroseus. LC-HRMS analysis of metabolites extract of T. atroroseus revealed presence of trimethyl-isopropyl-butanamide, perlolyrine, N-hexadecanoylpyrrolidine etc. whereas P. choerospondiatis displayed presence of tangeraxanthin, ugaxanthone, daphniphylline, etc. Therefore, fungal metabolites are rich natural sources of diversified compounds that can be utilized in dyeing industries, cosmetics and novel drug development.

Inhibition of Cronobacter sakazakii in an infant simulator of the human intestinal microbial ecosystem using a potential synbiotic

Powdered infant formula (PIF) can be contaminated with Cronobacter sakazakii, which can cause severe illnesses in infants. Synbiotics, a combination of probiotics and prebiotics, could act as an alternative control measure for C. sakazakii contamination in PIF and within the infant gut, but synbiotics have not been well studied for their ability to inhibit C. sakazakii. Using a Simulator of the Human Intestinal Microbial Ecosystem (SHIME^®) inoculated with infant fecal matter, we demonstrated that a potential synbiotic, consisting of six lactic acid bacteria (LAB) strains and Vivinal GOS, can inhibit the growth of C. sakazakii in an infant possibly through either the production of antimicrobial metabolites like acetate, increasing species diversity within the SHIME compartments to compete for nutrients or a combination of mechanisms. Using a triple SHIME set-up, i.e., three identical SHIME compartments, the first SHIME (SHIME 1) was designated as the control SHIME in the absence of a treatment, whereas SHIME 2 and 3 were the treated SHIME over 2, 1-week treatment periods. The addition of the potential synbiotic (LAB + VGOS) resulted in a significant decrease in C. sakazakii levels within 1 week (p < 0.05), but in the absence of a treatment the significant decline took 2 weeks (p < 0.05), and the LAB treatment did not decrease C. sakazakii levels (p ≥ 0.05). The principal component analysis showed a distinction between metabolomic profiles for the control and LAB treatment, but similar profiles for the LAB + VGOS treatment. The addition of the potential synbiotic (LAB + VGOS) in the first treatment period slightly increased species diversity (p ≥ 0.05) compared to the control and LAB, which may have had an effect on the survival of C. sakazakii throughout the treatment period. Our results also revealed that the relative abundance of Bifidobacterium was negatively correlated with Cronobacter when no treatments were added (ρ = −0.96; p < 0.05). These findings suggest that C. sakazakii could be inhibited by the native gut microbiota, and inhibition can be accelerated by the potential synbiotic treatment.

Evaluation of Cronobacter sakazakii biofilm formation after sdiA knockout in different osmotic pressure conditions

This study characterizes the impact of sdiA on biofilm formation under normal or osmotic stress conditions in Cronobacter sakazakii by constructing a sdiA deletion mutant (ΔsdiA). Here, the downregulation of flagellar assembly-related genes and upregulation of capsular, cellulose and lipopolysaccharide biosynthesis-associated genes in ΔsdiA were observed when compared to the wild type strain (WT) through transcriptomic analysis. Meanwhile, reduced ability of motility, enhanced cell surface hydrophobicity and stronger biofilms with extracellular matrix were observed in WT with deletion of sdiA. Both WT and ΔsdiA formed more biofilm in low osmotic stress medium, while in hyperosmolarity conditions, formation of biofilm was dramatically reduced. Our findings supported that sdiA might suppress biofilm formation of C. sakazakii by regulating biosynthesis of flagellar and extracellular polymeric substances. This study investigates the role of sdiA on biofilm formation in C. sakazakii, and provides the basis for the inhibition of C. sakazakii in food industry and infant-feeding.

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.

Machine learning modeling of the effects of media formulated with various yeast extracts on heterologous protein production in Escherichia coli

In microbial manufacturing, yeast extract is an important component of the growth media. The production of heterologous proteins often varies because of the yeast extract composition. To identify why this reduces protein production, the effects of yeast extract composition on the growth and green fluorescent protein (GFP) production of engineered Escherichia coli were investigated using a deep neural network (DNN)-mediated metabolomics approach. We observed 205 peaks from the various yeast extracts using gas chromatography-mass spectrometry. Principal component analyses of the peaks identified at least three different clusters. Using 20 different compositions of yeast extract in M9 media, the yields of cells and GFP in the yeast extract-containing media were higher than those in the control without yeast extract by approximately 3.0- to 5.0-fold and 1.5- to 2.0-fold, respectively. We compared machine learning models and found that DNN best fit the data. To estimate the importance of each variable, we performed DNN with a mean increase error calculation based on a permutation algorithm. This method identified the significant components of yeast extract. DNN learning with varying numbers of input variables provided the number of significant components. The influence of specific components on cell growth and GFP production was confirmed with a validation cultivation.

Understanding the Interactions between Staphylococcus aureus and the Raw-Meat-Processing Environment Isolate Klebsiella oxytoca in Dual-Species Biofilms via Discovering an Altered Metabolic Profile

In a raw-meat-processing environment, members of the Enterobacteriaceae family can coexist with Staphylococcus aureus to form dual-species biofilms, leading to a higher risk of food contamination. However, very little is known about the effect of inter-species interactions on dual-species biofilm formation. The aim of this study was to investigate the interactions between S. aureus and raw-meat-processing environment isolates of Klebsiella oxytoca in dual-species biofilms, by employing an untargeted metabolomics tool. Crystal violet staining assay showed that the biomass of the dual-species biofilm significantly increased and reached its maximum after incubation for 21 h, compared with that of single species grown alone. The number of K. oxytoca in the dual-species biofilm was significantly higher than that of S. aureus. Field emission scanning electron microscopy (FESEM) revealed that both species were evenly distributed, and were tightly wrapped by extracellular polymeric substances in the dual-species biofilms. Ultra-high-pressure liquid chromatography equipped with a quadrupole-time-of-flight mass spectrometer (UHPLC-Q-TOF MS) analysis exhibited a total of 8184 positive ions, and 6294 negative ions were obtained from all test samples. Multivariate data analysis further described altered metabolic profiling between mono- and dual-species biofilms. Further, 18 and 21 different metabolites in the dual-species biofilm were screened as biomarkers by comparing the mono-species biofilms of S. aureus and K. oxytoca, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were exclusively upregulated in the dual-species biofilm included ABC transporters, amino acid metabolism, and the two-component signal transduction system. Our results contribute to a better understanding of the interactive behavior of inter-species biofilm communities, by discovering altered metabolic profiling.

Comparative transcriptomic study of Escherichia coli O157:H7 in response to ohmic heating and conventional heating

In this study, the high-throughput Illumina HiSeq 2000 mRNA sequencing technique was used to investigate the transcriptome response of Escherichia coli O157:H7 exposed to ohmic heating (OH) and water bath heating (WB). Compared to untreated samples, a total of 293, 516, and 498 genes showed differential expression after HVOH (high voltage short time ohmic heating), LVOH (low voltage long time ohmic heating), and WB, respectively. Therefore, LVOH had the potential to cause comparable effects on the transcriptome of E. coli O157:H7 as compared to WB, but not HVOH. These results indicated that additional non-thermal effects were not reflected on transcriptome of E. coli O157:H7 using both HVOH and LVOH, in particular the HVOH. Most of differentially expressed genes involved in information storage and processing, and cellular processes and signaling showed up-regulation whereas most of genes related to the metabolism were down-regulated after HVOH, LVOH, and WB. In addition, more attention needs to be paid to the up-regulation of a large number of virulence genes, which might increase the ability of surviving E. coli O157:H7 to infect host cells after HVOH, LVOH, and WB. This transcriptomic study on the response of E. coli O157:H7 to OH protomes the understanding of inactivation mechanism of OH on the molecular level and opens the door to future studies for OH.

3-Hydroxybutyrate Derived from Poly-3-Hydroxybutyrate Mobilization Alleviates Protein Aggregation in Heat-Stressed Herbaspirillum seropedicae SmR1

Under conditions of carbon starvation or thermal, osmotic, or oxidative shock, mutants affected in the synthesis or mobilization of poly-3-hydroxybutyrate (PHB) are known to survive less well. It is still unclear if the synthesis and accumulation of PHB are sufficient to protect bacteria against stress conditions or if the stored PHB has to be mobilized. Here, we demonstrated that mobilization of PHB in Herbaspirillum seropedicae SmR1 was heat-shock activated at 45°C. In situ proton (¹H) nuclear magnetic resonance spectroscopy (i.e., ¹H-nuclear magnetic resonance) showed that heat shock increased amounts of 3-hydroxybutyrate (3HB) only in H. seropedicae strains able to synthesize and mobilize PHB. H. seropedicae SmR1 mutants unable to synthesize or mobilize PHB were more susceptible to heat shock and survived less well than the parental strain. When 100 mM 3-hydroxybutyrate was added to the medium, the ΔphaC1 strain (an H. seropedicae mutant unable to synthesize PHB) and the double mutant with deletion of both phaZ1 and phaZ2 (i.e., ΔphaZ1.2) (unable to mobilize PHB) showed partial rescue of heat adaptability (from 0% survival without 3HB to 40% of the initial viable population). Addition of 200 mM 3HB before the imposition of heat shock reduced protein aggregation to 15% in the ΔphaC1 mutant and 12% in the ΔphaZ1.2 mutant. We conclude that H. seropedicae SmR1 is naturally protected by 3HB released by PHB mobilization, while mutants unable to generate large amounts of 3HB under heat shock conditions are less able to cope with heat damage.IMPORTANCE Bacteria are subject to abrupt changes in environmental conditions affecting their growth, requiring rapid adaptation. Increasing the concentration of some metabolites can protect bacteria from hostile conditions that lead to protein denaturation and precipitation, as well as damage to plasma membranes. In this work, we demonstrated that under thermal shock, the bacterium Herbaspirillum seropedicae depolymerized its intracellular stock polymer known as poly-3-hydroxybutyrate (PHB), rapidly increasing the concentration of 3-hydroxybutyrate (3HB) and decreasing protein precipitation by thermal denaturation. Mutant H. seropedicae strains unable to produce or depolymerize PHB suffered irreparable damage during thermal shock, resulting in fast death when incubated at 45°C. Our results will contribute to the development of bacteria better adapted to high temperatures found either in natural conditions or in industrial processes. In the case of H. seropedicae and other bacteria that interact beneficially with plants, the understanding of PHB metabolism can be decisive for the development of more-competitive strains and their application as biofertilizers in agriculture.

Label free-based proteomic analysis of Escherichia coli O157:H7 subjected to ohmic heating

To investigate the inactivation mechanism of ohmic heating (OH) on Escherichia coli O157:H7 at the same inactivation levels, a label-free quantitative proteomic approach was employed in this study. Quantification of 2633 proteins was obtained with high confidence. Compared to untreated samples (CT), a total of 169, 84, and 26 proteins showed significantly differential abundance after high voltage OH (HVOH, 10 V/cm), low voltage OH (LVOH, 5 V/cm), and water bath heating (WB), respectively. Glyoxylate and dicarboxylate metabolism, ABC transporters, biosynthesis of amino acids, glycerophospholipid metabolism, and ribosome pathway were the main KEGG pathways mediated by OH, but only ribosome pathway was greatly affected by WB. The significant differences in proteome changes of E. coli O157:H7 among HVOH, LVOH, and WB treatments, especially the greater number of differential proteins in HVOH, indicated that OH might exert additional effects on proteome of E. coli O157:H7 due to the electric current, particularly in HVOH with higher electric field. This result enriched our understanding of molecular changes of E. coli O157:H7 induced by OH and provided data reference for further research into the inactivation mechanism of OH.