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

1H-NMR metabolomics analysis identifies hypoxanthine as a novel metastasis-associated metabolite in breast cancer

Breast cancer is one of the leading causes of death in females, mainly because of metastasis. Oncometabolites, produced via metabolic reprogramming, can influence metastatic signaling cascades. Accordingly, and based on our previous results, we propose that metabolites from highly metastatic breast cancer cells behave differently from less-metastatic cells and may play a significant role in metastasis. For instance, we aim to identify these metabolites and their role in breast cancer metastasis. Less metastatic cells (MCF-7) were treated with metabolites secreted from highly metastatic cells (MDA-MB-231) and the gene expression of three epithelial-to-mesenchymal transition (EMT) markers including E-cadherin, N-cadherin and vimentin were examined. Some metabolites secreted from MDA-MB-231 cells significantly induced EMT activity. Specifically, hypoxanthine demonstrated a significant EMT effect and increased the migration and invasion effects of MCF-7 cells through a hypoxia-associated mechanism. Hypoxanthine exhibited pro-angiogenic effects via increasing the VEGF and PDGF gene expression and affected lipid metabolism by increasing the gene expression of PCSK-9. Notably, knockdown of purine nucleoside phosphorylase, a gene encoding for an important enzyme in the biosynthesis of hypoxanthine, and inhibition of hypoxanthine uptake caused a significant decrease in hypoxanthine-associated EMT effects. Collectively for the first time, hypoxanthine was identified as a novel metastasis-associated metabolite in breast cancer cells and represents a promising target for diagnosis and therapy.

Yeast polysaccharide supplementation: impact on lactation, growth, immunity, and gut microbiota in Dezhou donkeys

Introduction

The Dezhou donkey, a prominent Chinese breed, is known for its remarkable size, rapid growth, and resilience to tough feeding conditions, and disease resistance. These traits are crucial in meeting the growing demand for Ejiao and donkey meat. Yeast polysaccharide (YPS), a functional polysaccharide complex known for its immune-enhancing and growth-promoting properties in livestock and poultry, remains relatively understudied in donkeys.

Objectives

This study aimed to investigate the impact of YPS supplementation on lactating and growing Dezhou donkey jennies and foals.

Materials and methods

Twelve 45-day-old Dezhou donkey foals and their jennies, matched for body weight and age, were randomly allocated to two dietary groups: a control group receiving a basal diet and an experimental group receiving the basal diet supplemented with 10 g/pen of YPS. The experiment was conducted over a 23-day period, during which donkey foals and lactating jennies were co-housed.

Results and discussion

The findings revealed that YPS supplementation had no adverse effects on milk production or composition in Dezhou donkey jennies but significantly increased feed intake. Additionally, YPS was associated with increased plasma glucose and creatinine concentrations in foals, while tending to decrease alkaline phosphatase, white blood cell count, red blood cell count, and hemoglobin levels (p < 0.10). Immune indices demonstrated that YPS supplementation elevated the levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) in jennies (p < 0.05) and increased complement component C4 concentrations in foals (p < 0.05). Moreover, YPS positively influenced the fecal microbiome, promoting the abundance of beneficial microorganisms such as Lactobacillus and Prevotella in donkey foals and Terriporobacter and Cellulosilyticum in jennies, all of which contribute to enhanced feed digestion. Additionally, YPS induced alterations in the plasma metabolome for both jennies and foals, with a predominant presence of lipids and lipid-like molecules. Notably, YPS increased the concentrations of specific lipid metabolites, including 13,14-Dihydro PGF2a, 2-Isopropylmalic acid, 2,3-Dinor-TXB2, Triterpenoids, Taurocholic acid, and 3b-Allotetrahydrocortisol, all of which are associated with improved animal growth.

Conclusion

In conclusion, this study suggests that dietary supplementation of YPS enhances feed intake, boosts immunity by increasing immunoglobulin levels, stimulates the growth-promoting gut microbiota (Lactobacillus and Prevotella), and exerts no adverse effects on the metabolism of both Dezhou donkey jennies and foals.

The Mechanism of Transcription Factor Swi6 in Regulating Growth and Pathogenicity of Ceratocystis fimbriata: Insights from Non-Targeted Metabolomics

Ceratocystis fimbriata (C. fimbriata) is a notorious pathogenic fungus that causes sweet potato black rot disease. The APSES transcription factor Swi6 in fungi is located downstream of the cell wall integrity (CWI)-mitogen-activated protein kinase (MAPK) signaling pathway and has been identified to be involved in cell wall integrity and virulence in several filamentous pathogenic fungi. However, the specific mechanisms by which Swi6 regulates the growth and pathogenicity of plant pathogenic fungi remain elusive. In this study, the SWI6 deletion mutants and complemented strains of C. fimbriata were generated. Deletion of Swi6 in C. fimbriata resulted in aberrant growth patterns. Pathogenicity assays on sweet potato storage roots revealed a significant decrease in virulence in the mutant. Non-targeted metabolomic analysis using LC-MS identified a total of 692 potential differentially accumulated metabolites (PDAMs) in the ∆Cfswi6 mutant compared to the wild type, and the results of KEGG enrichment analysis demonstrated significant enrichment of PDAMs within various metabolic pathways, including amino acid metabolism, lipid metabolism, nucleotide metabolism, GPI-anchored protein synthesis, and ABC transporter metabolism. These metabolic pathways were believed to play a crucial role in mediating the growth and pathogenicity of C. fimbriata through the regulation of CWI. Firstly, the deletion of the SWI6 gene led to abnormal amino acid and lipid metabolism, potentially exacerbating energy storage imbalance. Secondly, significant enrichment of metabolites related to GPI-anchored protein biosynthesis implied compromised cell wall integrity. Lastly, disruption of ABC transport protein metabolism may hinder intracellular transmembrane transport. Importantly, this study represents the first investigation into the potential regulatory mechanisms of SWI6 in plant filamentous pathogenic fungi from a metabolic perspective. The findings provide novel insights into the role of SWI6 in the growth and virulence of C. fimbriata, highlighting its potential as a target for controlling this pathogen.

A multi-omics analysis strategy reveals the molecular mechanism of the inhibition of Escherichia coli O157:H7 by anthocyanins from Aronia melanocarpa and its application

Water pollution causes the propagation of pathogenic microorganisms, which poses a serious threat to human life. Escherichia coli O157:H7, as a representative organism that can directly exhibit molecular response to stress, was selected as the indicator bacteria for the study. Tandem mass tag (TMT) quantitative proteomics and non-targeted metabolomics were used to study the response of Escherichia coli O157:H7 to Aronia melanocarpa anthocyanin (AMA) treatment. The results showed that 628 proteins and 1338 metabolites changed significantly after treatment with AMAs. According to bioinformatics analysis, integrated proteomics and metabolomics analysis differentially expressed proteins (DEPs) and metabolites participate in pyruvate metabolism, glycolysis/gluconeogenesis, alanine, aspartate and glutamate metabolism and the pentose phosphate pathway. This study preliminarily proposed the inhibition mechanism of AMAs on Escherichia coli O157:H7 from the perspective of multi-omics, providing a theoretical basis for the application of natural preservatives in fresh cut vegetables.

Metabolome shifts triggered by chlorine sanitisation induce Escherichia coli on fresh produce into the viable but nonculturable state

Facing the increasing occurrence of "big six" Escherichia coli outbreaks linked to fresh produce, chlorine-based sanitisers are widely used for fresh produce decontamination in recent years. However, latest finding that chlorine may induce E. coli cells into a viable not nonculturable (VBNC) state is bringing a new challenge to the fresh produce industry. VBNC cells are undetectable by the plate count test, and yet they retain pathogenicity and are more antibiotic-resistant than culturable cells. As a result, their eradication is critical to ensure the safety of fresh produce. Understanding VBNC cells at the metabolic level may provide a breakthrough for their eradication. Therefore, this study was carried out to collect the VBNC pathogenic E. coli (O26:H11, O121:H19, and O157:H7) cells from chlorine-treated pea sprouts and characterise them using NMR-based metabolomics. From the globally increased metabolite contents detected in the VBNC E. coli cells as compared to the culturable cells, mechanisms underlying E. coli's VBNC induction were elucidated. These include rendering the energy generation scheme to become more compatible with the lowered energy needs, disaggregating protein aggregates to release amino acids for osmoprotection and later resuscitation, as well as increasing cAMP content to downregulate RpoS. These identified metabolic characteristics can inspire future development of targeted measures for VBNC E. coli cell inhibition. Our methods can also be applied to other pathogens to help lower the risk of overall foodborne diseases.

Chemomodulatory Effect of the Marine-Derived Metabolite "Terrein" on the Anticancer Properties of Gemcitabine in Colorectal Cancer Cells

BACKGROUND

Terrein (Terr) is a bioactive marine secondary metabolite that possesses antiproliferative/cytotoxic properties by interrupting various molecular pathways. Gemcitabine (GCB) is an anticancer drug used to treat several types of tumors such as colorectal cancer; however, it suffers from tumor cell resistance, and therefore, treatment failure.

METHODS

The potential anticancer properties of terrein, its antiproliferative effects, and its chemomodulatory effects on GCB were assessed against various colorectal cancer cell lines (HCT-116, HT-29, and SW620) under normoxic and hypoxic (pO₂ ≤ 1%) conditions. Further analysis via flow cytometry was carried out in addition to quantitative gene expression and ¹HNMR metabolomic analysis.

RESULTS

In normoxia, the effect of the combination treatment (GCB + Terr) was synergistic in HCT-116 and SW620 cell lines. In HT-29, the effect was antagonistic when the cells were treated with (GCB + Terr) under both normoxic and hypoxic conditions. The combination treatment was found to induce apoptosis in HCT-116 and SW620. Metabolomic analysis revealed that the change in oxygen levels significantly affected extracellular amino acid metabolite profiling.

CONCLUSIONS

Terrein influenced GCB's anti-colorectal cancer properties which are reflected in different aspects such as cytotoxicity, cell cycle progression, apoptosis, autophagy, and intra-tumoral metabolism under normoxic and hypoxic conditions.

Increased heat tolerance and transcriptome analysis of Salmonella enterica Enteritidis PT 30 heat-shocked at 42 ℃

In this study, we compared the heat tolerance parameter (D_65℃) values of Salmonella enterica serovar Enteritidis PT 30 (S. Enteritidis ) heat adapted at different degrees (at 42 ℃ for 20-180 min) and cultivated using two methods. The treated group with the highest D_65℃ value (LP-42 ℃-60 min) and the untreated groups (Control-TSB and Control-TSA) were subjected to transcriptome analysis. Heat-adaptation increased the D_65℃ values of S. Enteritidis by 24.5-60.8%. The D_65℃ values of the LP-42 ℃-60 min group (1.85 ± 0.13 min, 7.7% higher) was comparable to that of the Control-TSA. A total of 483 up- and 443 downregulated genes of S. enteritidis were identified in the LP-42 ℃-60 min group (log₂fold change > 1, adjusted p-value < 0.05). Among these genes, 5 co-expressed and 15 differentially expressed genes in the LP-42 ℃-60 min and Control-TSA grops possibly contributed to the high D_65℃ values of S. Enteritidis . The Rpo regulon was involved in the heat adaptation of S. Enteritidis , as evidenced by the significant upregulation of rpoS, rpoN, and rpoE. KEGG enrichment pathways, such as biosynthesis of secondary metabolites, tricarboxylic acid, and ribosomes were identified and mapped to reveal the molecular mechanisms of S. enteritidis during heat adaptation. This study quantified the enhanced heat tolerance of S. Enteritidis heat adapted at different degrees of heat-adaptation. The results of this study may serve as a basis for elucidating the molecular mechanisms underlying the enhanced heat tolerance at the transcriptome level.

Advances in Microbial NMR Metabolomics

Confidently, nuclear magnetic resonance (NMR) is the most informative technique in analytical chemistry and its use as an analytical platform in metabolomics is well proven. This chapter aims to present NMR as a viable tool for microbial metabolomics discussing its fundamental aspects and applications in metabolomics using some chosen examples.

Sample Preparation in Microbial Metabolomics: Advances and Challenges

Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Dual-Species Biofilms Formed by Escherichia coli and Salmonella Enhance Chlorine Tolerance

Outbreaks of Escherichia coli and Salmonella in food might be associated with the cross-contamination of biofilms on food-contact surfaces. The knowledge of the sanitization of mono-species biofilm on the food-contact surface is well established, while mixed-species biofilm occurs more naturally, which could profoundly affect the efficacy of sanitizer.

Impact of Weissella cibaria BYL4.2 and its supernatants on Penicillium chrysogenum metabolism

Lactic acid bacteria (LAB) can produce a vast spectrum of antifungal metabolites to inhibit fungal growth. The purpose of this study was to elucidate the antifungal effect of isolated Weissella cibaria BYL4.2 on Penicillium chrysogenum, the antifungal activity of W. cibaria BYL4.2 against P. chrysogenum was evaluated by the superposition method, results showed that it had obviously antifungal activity against P. chrysogenum. Studying the probiotic properties of BYL4.2 and determining it as beneficial bacteria. Furtherly, different treatments were carried out to characterize the antifungal activity of cell-free supernatant (CFS) produced by W. cibaria BYL4.2, and it was shown that the CFS was pH-dependent, partly heat-sensitive, and was not influenced by proteinaceous treatment. The CFS of W. cibaria BYL4.2 was analyzed by high-performance liquid chromatography (HPLC) and found the highest content of lactic acid. Screening of metabolic markers by a non-targeted metabolomics approach based liquid chromatography-mass spectrometry (LC-MS). The results speculated that organic acid especially detected D-tartaric acid was the main antifungal substance of CFS, which could cause the down-regulation of metabolites in the ABC transporters pathway, thereby inhibiting the growth of P. chrysogenum. Therefore, this study may provide important information for the inhibitory mechanism of W. cibaria BYL4.2 on P. chrysogenum, and provide a basis for further research on the antifungal effect of Weissella.

Evaluation of water-assisted UV-C light and its additive effect with peracetic acid for the inactivation of Listeria monocytogenes, Salmonella enterica and murine norovirus on whole and fresh-cut strawberries during shelf-life

BACKGROUND

The purpose of the present study was to examine the inactivation of Salmonella enterica (50 μL; 10⁹  CFU g^-1 ), Listeria monocytogenes (50 μL; 10⁹  CFU g^-1 ), and murine norovirus (MNV-1; 50 μL; 10⁷ 50% tissue culture infectious dose (TCID₅₀ ) mL^-1 ) on whole and fresh-cut strawberries after 2 min disinfection treatments (water (H₂ O), chlorine 200 mg L^-1 (NaClO), water-assisted ultraviolet-C (UV-C) (WUV), and the combination WUV and 40 mg L^-1 of PA (WUV + PA)) in a water tank (15 L) equipped with 4 UV-C lamps (17.2 W each), and after 7 days of cold storage (4 and 10 °C). For MNV-1, dry UV-C treatment (DUV) was also tested. For all UV-C treatments, an irradiation dose of 1.3 kJ m^-2 was used.

RESULTS

When strawberries were washed with WUV, L. monocytogenes and S. enterica were reduced by 2.8 and 2.2 log CFU g^-1 , respectively. The addition of 40 mg L^-1 of PA to WUV (WUV + PA) increased the reduction range of L. monocytogenes and S. enterica by 1.9 and 0.8 log, respectively. Regarding the wash water, no pathogens were recovered after the WUV + PA treatment (detection limit 50 CFU mL^-1 ). Depending on storage conditions (7 days at 4 or 10 °C), reductions observed were 0.5 to 2.0 log for S. enterica and 0.5 to 3.0 log for L. monocytogenes. The reductions in MNV-1 titer after disinfection treatments ranged from 1.3 to 1.7 log. No significant differences between storage conditions were observed for MNV-1: titers did not decline or were reduced up to 0.3 log after 7 days of cold storage.

CONCLUSION

The three-way action for disinfecting strawberries by UV-C irradiation and PA, plus the physical removal of the microorganisms by agitated water, are effective against foodborne pathogens on strawberries and water wash. During storage, WUV had a larger impact on the inactivation kinetics of S. enterica. Storage had little impact on MNV-1 inactivation. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Integrated metabolomics of "big six" Escherichia coli on pea sprouts to organic acid treatments

Naturally occurring organic acids (OAs) have demonstrated satisfactory effects in inhibiting common pathogens on fresh produce; however, their effectiveness on "big six" Escherichia coli serotypes, comprised of E. coli O26:H11, O45:H2, O103:H11, O111, O121:H19 and O145, remained unaddressed. Regarding this, using nuclear magnetic resonance (NMR) spectroscopy and ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS), the sanitising efficacy and the underlying antimicrobial mechanisms of 10-min treatments with 0.2 mol/L ascorbic acid (AA), citric acid (CA) and malic acid (MA) against the "big six" strains on pea sprouts were thoroughly investigated in this study. Despite the varying antimicrobial efficacy (AA: 0.12-0.99, CA: 0.36-1.72, MA: 0.75-3.28 log CFU/g reductions), the three OAs induced consistent metabolic changes in the E. coli strains, particularly in the metabolism of membrane lipids, nucleotide derivatives and amino acids. Comparing all strains, the most OA-resistant strain, O26 (0.36-1.12 log CFU/g reductions), had the largest total amino acids accumulated to resist osmotic stress; its ulteriorly suppressed cell activity further strengthened its endurance. In contrast, the lowest OA-resistance of O121 (0.99-3.28 log CFU/g reductions) might be explained by the depletion of putrescine, an oxidative stress regulator. Overall, the study sheds light on the effectiveness of a dual-platform metabolomics investigation in elucidating the metabolic responses of "big six" E. coli to OAs. The manifested antimicrobial effects of OAs, especially MA, together with the underlying metabolic perturbations detected in the "big six" strains, provided scientific basis for applying OA treatments to future fresh produce sanitisation.

Effect of chlorine sanitizer on metabolic responses of Escherichia coli biofilms "big six" during cross-contamination from abiotic surface to sponge cake

The effect of chlorine on Escherichia coli biofilm O157:H7 are well established; however, the effect on biofilm adhesion to food as well as the six emerging E. coli serotypes ("big six") have not been fully understood. Chlorine sanitization with 1-min 100 mg/L was applied against seven pathogenic E. coli (O111, O121:H19, O45:H2, O26:H11, O103:H11, O145, and O157:H7) biofilms on high-density polyethylene (HDPE) and stainless steel (SS) coupons, respectively. Using sponge cake as a food model, the adhesion behavior was evaluated by comparison of bacteria transfer rate before and after treatment. Besides, the metabolic profiles of biofilms were analyzed by nuclear magnetic resonance (NMR) spectrometer. A significant decrease in transfer rate (79% decline on SS and 33% decline on HDPE) was recorded as well as the distinctive pattern between SS and HDPE coupons was also noticed, with a low population (6-7 log CFU/coupon) attached and low survivals (0-3 log CFU/coupon) upon chlorine on SS, while high population (7-8 log CFU/coupon) attached and high survivals (5-7 log CFU/coupon) on HDPE. Moreover, O121:H19 and O26:H11 demonstrated the highest resistance to chlorine with the least metabolic status and pathways affected. O103:H11, O145, and O111 followed similar metabolic patterns on both surfaces. Distinct metabolic patterns were found in O45:H2 and O157:H7, where the former had more affected metabolic status and pathways on SS but less on HDPE, whereas the latter showed an opposite trend. Overall, a potential contamination source of STEC infection in flour products was demonstrated and metabolic changes induced by chlorine were revealed by NMR-based metabolomics, which provides insights to avoid "big six" biofilms contamination in food.

Formation and Transfer of Multi-Species Biofilms Containing E. coli O103:H2 on Food Contact Surfaces to Beef

Interactions of Shiga toxin–producing E. coli (STEC; O103:H2) with lactic acid bacteria (LAB) or spoilage bacteria (SP) multispecies biofilms on polyurethane (TPU) and stainless-steel (SS) were assessed at 10 and 25°C under wet and dry conditions after 6, 30, and 60 days of storage. One LAB T1: Carnobacterium piscicola + Lactobacillus bulgaricus, and two SP T2: Comamonas koreensis + Raoultella terrigena; T3: Pseudomonas aeruginosa + C. koreensis were assessed for their ability to form multispecies biofilms with O103:H2. O103:H2 single-species biofilms served as a control positive (T4). Coupons were stored dry (20–50% relative humidity; RH) or moist (60–90% RH) for up to 60 days, at which point O103:H2 transfer to beef and survival was evaluated. At 25°C, T3 decreased beef contamination with O103:H2 by 2.54 log₁₀ CFU/g (P < 0.001). Overall, at 25°C contamination of beef with O103:H2 decreased (P < 0.001) from 3.17 log₁₀ CFU/g on Day 6 to 0.62 log₁₀ CFU/g on Day 60. With 60 days dry biofilms on TPU, an antagonistic interaction was observed among O103:H2 and multispecies biofilm T1 and T3. E. coli O103:H2 was not recovered from T1 and T3 after 60 days but it was recovered (33%) from T2 and T4 dry biofilms. At 10°C, contamination of beef with O103:H2 decreased (P < 0.001) from 1.38 log₁₀ CFU/g after 6 days to 0.47 log₁₀ CFU/g after 60 days. At 10°C, recovery of O103:H2 from 60 days dry biofilms could only be detected after enrichment and was always higher for T2 than T4 biofilms. Regardless of temperature, the transfer of O103:H2 to beef from the biofilm on TPU was greater (P < 0.001) than SS. Moist biofilms also resulted in greater (P < 0.001) cell transfer to beef than dry biofilms at 10 and 25°C. Development of SP or LAB multispecies biofilms with O103:H2 can either increase or diminish the likelihood of beef contamination. Environmental conditions such as humidity, contact surface type, as well as biofilm aging all can influence the risk of beef being contaminated by STEC within multi-species biofilms attached to food contact surfaces.

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.

Regulation of Escherichia coli fim gene transcription by GadE and other acid tolerance gene products

Uropathogenic Escherichia coli (UPEC) cause millions of urinary tract infections each year in the United States. Type 1 pili are important for adherence of UPEC to uroepithelial cells in the human and murine urinary tracts where osmolality and pH vary. Previous work has shown that an acidic pH adversely affects the expression of type 1 pili. To determine if acid tolerance gene products may be regulating E. coli fim gene expression, a bank of K-12 strain acid tolerance gene mutants were screened using fimA-lux, fimB-lux, and fimE-lux fusions on single copy number plasmids. We have determined that a mutation in gadE increased transcription of all three fim genes, suggesting that GadE may be acting as a repressor in a low pH environment. Complementation of the gadE mutation restored fim gene transcription to wild-type levels. Moreover, mutations in gadX, gadW, crp, and cya also affected transcription of the three fim genes. To verify the role GadE plays in type 1 pilus expression, the NU149 gadE UPEC strain was tested. The gadE mutant had higher fimE gene transcript levels, a higher frequency of Phase-OFF positioning of fimS, and hemagglutination titres that were lower in strain NU149 gadE cultured in low pH medium as compared to the wild-type bacteria. The data demonstrate that UPEC fim genes are regulated directly or indirectly by the GadE protein and this could have some future bearing on the ability to prevent urinary tract infections by acidifying the urine and shutting off fim gene expression.

Integration of intestinal microbiota and metabonomics to elucidate different alleviation impacts of non-saponification and saponification astaxanthin pre-treatment on paracetamol-induced oxidative stress in rats

Intestinal microbiota and metabonomics were integrated to investigate the efficiency of non-saponification or saponification astaxanthin (N-Asta or S-Asta) derived from Penaeus sinensis by-products on alleviating paracetamol (PCM)-induced oxidative stress. Pre-treatment with N-Asta or S-Asta for 14 days restored the cellular morphology of the intestine and increased glutathione (GSH) levels under PCM overdose in rats. However, S-Asta displayed higher adsorption than that of N-Asta. PCM overdose reduced the richness and diversity of intestinal microbiota in the model group. Comparably, N-Asta or S-Asta pre-treatment increased the Actinobacteria abundance. Increased phyla Bacteroidetes and Verrucomicrobia were only found in the S-Asta-pre-treated group. At the genus level, N-Asta pre-treatment increased Lactobacillus and Parasutterella abundance, whereas S-Asta pre-treatment elevated Bacteroidales_S24-7_group_norank and Ruminococcaceae_uncultured. Compared to the control and model groups, remarkable increases of fecal short-chain fatty acids were detected in both N-Asta and S-Asta pre-treatment groups, suggesting the contribution of N-Asta and S-Asta adsorption to SCFA-producing bacteria enrichment. Furthermore, the genera of Ruminococcaceae_uncultured, Ruminiclostridium_9, Ruminococcaceae_unclassified and Ruminococcus_1 showed high correlations with propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid increases in the S-Asta pre-treated group. Seventeen plasma biomarker metabolites in more than 10 metabolic pathways were responsible for the difference between the N-Asta and S-Asta pre-treated groups. Metabolites GSH, retinol, all-trans-Retinoic acid and taurine related to antioxidant activities were significantly accumulated in the S-Asta pre-treated group, while increasing taurocholic acid levels associated with the anti-inflammatory activity was found in the N-Asta-pre-treated group. Therefore, N-Asta and S-Asta could have potential applications in counterbalancing intestinal flora and metabolite disturbances by overdose chemical induction.

Novel Millet-Based Flavored Yogurt Enriched With Superoxide Dismutase

Superoxide dismutase (SOD) is an important antioxidant enzyme with different physiological functions, which can be used as a nutritional fortifier in food. Cereal-based fermented products are becoming popular worldwide. In this study, novel millet-based flavored yogurt enriched with SOD was developed. Lactiplantibacillus plantarum subsp. plantarum was screened, which manufactured SOD activity of 2476.21 ± 1.52 U g^-1. The SOD content of millet yogurt was 19.827 ± 0.323 U mL^-1, which was 63.01, 50.11, and 146.79% higher than that of Bright Dairy Yogurt 1911, Junlebao and Nanjing Weigang, respectively. Fifty-four volatile flavor substances and 22,571 non-volatile flavor substances were found in yogurt. Compared to traditional fermented yogurt, 37 non-volatile metabolites in yogurt with millet enzymatic fermentation broth were significantly upregulated, including 2-phenyl ethanol, hesperidin, N-acetylornithine and L-methionine, which were upregulated by 3169.6, 228.36, 271.22, and 55.67 times, respectively, thereby enriching the sensory and nutritional value of yogurt. Moreover, the manufacture of unpleasant volatile flavor substances was masked, making the product more compatible with consumers' tastes.

Synergistic combination of Sapindoside A and B: A novel antibiofilm agent against Cutibacterium acnes

Sapindus saponins extracted from Sapindus mukorossi Gaertn. have been reported to exert antibacterial activity against Cutibacterium acnes (C. acnes). However, there are no reports about their potentials against its biofilm, which is a major contributor to the antibiotic resistance of C. acnes. This study aimed to investigate the synergistic antibiofilm activity and action of the combination of Sapindoside A and B (S_AB) against C. acnes. S_AB with sub-MICs significantly inhibited the early-formed and mature biofilm of C. acnes and decreased the adhesion and cell surface hydrophobicity (p < 0.05). Also, S_AB greatly reduced the production of exopolysaccharide and lipase (p < 0.05), and the binding mode of S_AB and lipase was predicted by molecular docking, via hydrogen bonds and hydrophobic interactions. Biofilm observed with electron microscopies further confirmed the high antibiofilm activity of S_AB against C. acnes. Furthermore, a significant down-regulation of biofilm biosynthesis-associated genes was observed. The combination index explained the synergistic effects of S_AB leading to the above results, and the contribution of S_A was greater than that of S_B. The current results showed that S_AB had synergistic antibiofilm activity against C. acnes, and the Sapindoside A played a major role, indicating that S_AB could be a natural antiacne additive against C. acnes biofilm-associated infections.

Comparison of bacteria disintegration methods and their influence on data analysis in metabolomics

Metabolomic experiments usually contain many different steps, each of which can strongly influence the obtained results. In this work, metabolic analyses of six bacterial strains were performed in light of three different bacterial cell disintegration methods. Three strains were gram-negative (Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae), and three were gram-positive (Corynebacterium glutamicum, Bacillus cereus, and Enterococcus faecalis). For extraction, the methanol–water extraction method (1:1) was chosen. To compare the efficiency of different cell disintegration methods, sonication, sand mill, and tissue lyser were used. For bacterial extract metabolite analysis, ¹H NMR together with univariate and multivariate analyses were applied. The obtained results showed that metabolite concentrations are strongly dependent on the cell lysing methodology used and are different for various bacterial strains. The results clearly show that one of the disruption methods gives the highest concentration for most identified compounds (e. g. sand mill for E. faecalis and tissue lyser for B. cereus). This study indicated that the comparison of samples prepared by different procedures can lead to false or imprecise results, leaving an imprint of the disintegration method. Furthermore, the presented results showed that NMR might be a useful bacterial strain identification and differentiation method. In addition to disintegration method comparison, the metabolic profiles of each elaborated strain were analyzed, and each exhibited its metabolic profile. Some metabolites were identified by the ¹H NMR method in only one strain. The results of multivariate data analyses (PCA) show that regardless of the disintegration method used, the strain group can be identified. Presented results can be significant for all types of microbial studies containing the metabolomic targeted and non-targeted analysis.

Dietary Beta-Hydroxy-Beta-Methyl Butyrate Supplementation Affects Growth, Carcass Characteristics, Meat Quality, and Serum Metabolomics Profile in Broiler Chickens

This study aimed to explore the effects of beta-hydroxy-beta-methyl butyrate (HMB) on serum metabolic profiles and meat quality of muscles in Wenshi broiler chickens. Birds were fed a basal diet with an additional 0, 0.05, 0.10, or 0.15% HMB, respectively. Results showed that dietary HMB quadratically increased the average daily gain (P = 0.058) and decreased feed:gain (P < 0.05) mainly in the starter phase. At 51 days of age, birds receiving 0.10% HMB diet exhibited less abdominal fat and more breast yield than the control (P < 0.05). Moreover, dietary HMB quadratically decreased the L^∗ value and drip loss in selected muscles (P < 0.05) and increased the a^∗ value in breast muscle (P < 0.05). Serum metabolome profiling showed that the most differentially abundant metabolites are lipids and lipid-like molecules, including phosphatidylcholines. It was concluded that HMB improved growth performance and meat quality of muscle in broilers.

Quantitative proteomic analysis reveals the mechanisms of polymyxin B toxicity to Escherichia coli

Polymyxin B is increasingly employed all over the world to treat patients who affected by multidrug-resistant Gram-negative bacteria. Although the mechanism of resistance to polymyxin B is well known, the metabolic role of bacteria in stress response to polymyxin B remains an important task and may help to better understand polymyxin B-related stress response. In this study, the proteome changes of Escherichia coli (E. coli) continuously induced in concentrations of 1.0 mg/L and 10.0 mg/L polymyxin B were revealed. Compared to E. coli (PMB₀), E. coli exposed to polymyxin B at 1.0 mg/L (PMB₁) and 10.0 mg/L (PMB₁₀) resulted in 89 and 314 differentially expressed proteins (DEPs), respectively. Such differences related to fatty acid degradation, quorum sensing and two-component regulatory system pathways. Based on absolute quantitative (iTRAQ) proteomics analysis, this study comprehensively studied the changes of E. coli proteome in culture with concentrations of 1.0 mg/L and 10.0 mg/L polymyxin B through confocal laser scanning microscopy observation, cell viability detection and reactive oxygen species analysis. The results showed that E. coli cultured at concentration of 10.0 mg/L polymyxin B increased the expression levels of multidrug-resistant efflux transporters and efflux pump membrane transporters, which might further improve the pathogens of polymyxin B-resistant bacteria lastingness and evolution. It has emerged globally to resist polymyxin B. The reuse of polymyxin B should be aroused public attention to avoid causing more serious environmental pollution. These findings could provide new insights into polymyxin B-related stress.

Comparative Transcriptomics of Shiga Toxin-Producing and Commensal Escherichia coli and Cytokine Responses in Colonic Epithelial Cell Culture Infections

Ingestion of Shiga toxin-producing Escherichia coli (STEC) can result in a range of illness severity from asymptomatic to hemorrhagic colitis and death; thus risk assessment of STEC strains for human pathogenicity is important in the area of food safety. Illness severity depends in part on the combination of virulence genes carried in the genome, which can vary between strains even of identical serotype. To better understand how core genes are regulated differently among strains and to identify possible novel STEC virulence gene candidates that could be added to the risk assessment repertoire, we used comparative transcriptomics to investigate global gene expression differences between two STEC strains associated with severe illness and a commensal E. coli strain during in vitro intestinal epithelial cell (IEC) infections. Additionally, we compared a wide array of concomitant cytokine levels produced by the IECs. The cytokine expression levels were examined for a pattern representing STEC pathogenicity; however, while one STEC strain appeared to elicit a proinflammatory response, infection by the other strain produced a pattern comparable to the commensal E. coli. This result may be explained by the significant differences in gene content and expression observed between the STEC strains. RNA-Seq analysis revealed considerable disparity in expression of genes in the arginine and tryptophan biosynthesis/import pathways between the STEC strains and the commensal E. coli strain, highlighting the important role some amino acids play in STEC colonization and survival. Contrasting differential expression patterns were observed for genes involved in respiration among the three strains suggesting that metabolic diversity is a strategy utilized to compete with resident microflora for successful colonization. Similar temporal expression results for known and putative virulence genes were observed in the STEC strains, revealing strategies used for survival prior to and after initial adherence to IECs. Additionally, three genes encoding hypothetical proteins located in mobile genetic elements were, after interrogation of a large set of E. coli genomes, determined to likely represent novel STEC virulence factors.

Chronic Exposure to Low Concentration of Graphene Oxide Increases Bacterial Pathogenicity via the Envelope Stress Response

Graphene oxide (GO), which has diverse antimicrobial mechanisms, is a promising material to address antibiotic resistance. Considering the emergence of antibiotic tolerance/resistance due to prolonged exposure to sublethal antibiotics, it is imperative to assess the microbiological effects and related adaptive mechanisms under chronic exposure to sublethal levels of GO, which have rarely been explored. After repetitive exposure to 5 mg/L GO for 200 subcultures (400 days), evolved Escherichia coli (E. coli) cells (E_GO) differed significantly from their ancestor cells according to transcriptomic and metabolomic analyses. Contact with GO surfaces transformed E. coli by activating the Cpx envelope stress response (ESR), resulting in more than twofold greater extracellular protease release and biofilm formation. The ESR also modulated the envelope structure and function via increases in membrane fluidity, permeation, and lipopolysaccharide content to fulfill growth requirements and combat envelope stress. As a consequence of metabolic adjustment, E_GO cells showed advantages of surviving in an acidic and oxidative environment, which resembles the cytosol of host cells. With these adaptive features, E_GO cells exhibited higher pathogenicity than ancestor E. coli cells as evidenced by increased bacterial invasion and intracellular survival and a more severe inflammatory response in macrophage cells. To conclude, we seek to raise awareness of the possible occurrence of microbial adaptation to antimicrobial nanomaterials, which may be implicated in cross-adaptation to harsh environments and eventually the prevalence of virulence.

Understanding How Microorganisms Respond to Acid pH Is Central to Their Control and Successful Exploitation

Microbes from the three domains of life, Bacteria, Archaea, and Eukarya, share the need to sense and respond to changes in the external and internal concentrations of protons. When the proton concentration is high, acidic conditions prevail and cells must respond appropriately to ensure that macromolecules and metabolic processes are sufficiently protected to sustain life. While, we have learned much in recent decades about the mechanisms that microbes use to cope with acid, including the unique challenges presented by organic acids, there is still much to be gained from developing a deeper understanding of the effects and responses to acid in microbes. In this perspective article, we survey the key molecular mechanisms known to be important for microbial survival during acid stress and discuss how this knowledge might be relevant to microbe-based applications and processes that are consequential for humans. We discuss the research approaches that have been taken to investigate the problem and highlight promising new avenues. We discuss the influence of acid on pathogens during the course of infections and highlight the potential of using organic acids in treatments for some types of infection. We explore the influence of acid stress on photosynthetic microbes, and on biotechnological and industrial processes, including those needed to produce organic acids. We highlight the importance of understanding acid stress in controlling spoilage and pathogenic microbes in the food chain. Finally, we invite colleagues with an interest in microbial responses to low pH to participate in the EU-funded COST Action network called EuroMicropH and contribute to a comprehensive database of literature on this topic that we are making publicly available.