Transcriptional profiling and metabolomic analysis of Staphylococcus aureus grown on autoclaved chicken breast

Transcriptome analysis reveals the inhibitory mechanism of phloretin on virulence expression of Staphylococcus aureus and its application in cooked chicken

Staphylococcus aureus (S. aureus) enterotoxins have aroused great concern to food safety owing to its increased risk of food poisoning. The current research aimed to investigate the anti-virulence mechanisms of phloretin against S. aureus in terms of toxin activity and gene expression. The results indicated that phloretin could effectively inhibit the production of hemolysins and enterotoxins, and its anti-virulence effect was exerted in a concentration-dependent manner. Transcriptome results indicated that phloretin could downregulate the transcription level of majority virulence factors related genes (68 %) of S. aureus, including the quorum sensing-related genes (agrB, agrC, agrA, sspA, splF, splD and others) and bacterial secretion system-related genes (secDF, secY2, and yidC). In addition, it was speculated that phloretin was most likely to bind to the AgrA DNA binding domain, thereby affecting the expression of downstream virulence genes (hla, seb, spa, rot, geh, etc) based on molecular docking. Finally, the application in cooked chicken indicated that phloretin could effectively decrease the content of enterotoxins and improve the storage quality of cooked chicken. These findings not only evidenced the feasible anti-virulence activity of phloretin, but also provided a new strategy to prevent S. aureus food poisoning in cooked meat preservation.

Genomic and in-vitro characteristics of a novel strain Lacticaseibacillus chiayiensis AACE3 isolated from fermented blueberry

Numerous different species of LAB are used in different fields due to their unique characteristics. However, Lacticaseibacillus chiayiensis, a newly established species in 2018, has limited microorganism resources, and lacks comprehensive evaluations of its properties. In this study, L. chiayiensis AACE3, isolated from fermented blueberry, was evaluated by genomic analysis and in vitro assays of the properties. The genome identified genes associated with biofilm formation (luxS, ccpA, brpA), resistance to oxidative stress (tpx, trxA, trxB, hslO), tolerance to acidic conditions (dltA, dltC), resistance to unfavorable osmotic pressure (opuBB, gbuA, gbuB, gbuC), and adhesion (luxS, dltA, dltC). The AACE3 showed 112 unique genes, relative to the other three L. chiayiensis strains. Among them, the presence of genes such as clpP, pepO, and feoA suggests a possible advantage of AACE3 over other L. chiayiensis in terms of environmental adaptation. In vitro evaluation of the properties revealed that AACE3 had robust antibacterial activity against eight common pathogens: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis, Salmonella choleraesuis, Shigella flexneri, Pseudomonas aeruginosa, and Klebsiella pneumoniae. In addition, AACE3 showed more than 80% survival rate in all tests simulating gastrointestinal fluid, and it exhibited high antioxidant capacity. Interestingly, the cell culture supernatant was superior to intact organisms and ultrasonically crushed bacterial extracts in all tests of antioxidant capacity. These results suggested that the antioxidant capacity may originate from certain metabolites and extracellular enzymes produced by AACE3. Moreover, AACE3 was a moderate biofilm producer due to the self-agglomeration effect. Taken together, L. chiayiensis AACE3 appears to be a candidate strain for combating the growing incidence of pathogen infections and antioxidant production.

Transcriptome analysis reveals the molecular mechanism of cinnamaldehyde against Bacillus cereus spores in ready-to-eat beef

The purpose of this study was to investigate the antibacterial effect and mechanism of cinnamaldehyde on Bacillus cereus spores in ready-to-eat beef. The colour difference and texture of the ready-to-eat beef supplemented with cinnamaldehyde did not differ greatly from the colour and texture of the blank beef. However, cinnamaldehyde has an effective antibacterial effect on the total number of bacterial colonies and B. cereus spores in ready-to-eat beef. Transmission electron microscopy (TEM) analysis revealed that the cell membrane of B. cereus was disrupted by cinnamaldehyde, leading to leakage of intracellular components. Transcriptome sequencing (RNA-seq) indicated that the B. cereus spore resistance regulation system (sigB, sigW, rsbW, rsbV, yfkM and yflT) and phosphoenolpyruvate phosphotransferase system (PTS) (ptsH, ptsI and ptsG) respond positively to cinnamaldehyde in an adverse environment. Intracellular disorders due to damage to the cell membrane involve some transporters (copA, opuBA and opuD) and some oxidative stress systems (ywrO, scdA and katE) in the regulation of the body. However, downregulation of K⁺ transport channels (kdpD and kdpB), osmotic pressure regulation (opuE) and some oxidative stress (norR and srrA)-related genes may accelerate spore apoptosis. In addition, cinnamaldehyde also effectively inhibits the spore germination-related genes (smc, mreB and gerE). This study provides new insights into the molecular mechanism of the antibacterial effect of cinnamaldehyde on B. cereus spores in ready-to-eat beef.

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.

Transcriptomic and proteomic analysis of Staphylococcus aureus response to cuminaldehyde stress

The previous study indicated that cuminaldehyde (CUM) could be used as an antibacterial agent in sauced beef to reduce the propagation of Staphylococcus aureus (S. aureus). This research took sauced beef treated with 0.4 μL/mL CUM as the research object. Transcriptomic and proteomic methods were used to comprehensively analyze the changes in genes and proteins of S. aureus under CUM stress. A total of 258 differentially expressed genes (DEGs, 178 up-regulated and 80 down-regulated) and 384 differentially expressed proteins (DEPs, 61 up-regulated and 323 down-regulated) were found. It was observed that CUM destroyed the cell wall and cell membrane by inhibiting the synthesis of peptidoglycan and fatty acid. Low energy consumption strategies were formed by reducing glycolysis and ribosome de novo synthesis. The levels of genes and proteins associated with the glycine, serine, threonine, methionine, cysteine, and branched-chain amino acids were dramatically changed, which impaired protein synthesis and reduced bacterial viability. In addition, the up-regulated DEGs and DEFs involved in DNA replication, recombination and single-stranded DNA-binding contributed to DNA repair. Moreover, ATP-binding cassettes (ABC) transporters were also perturbed, such as the uptake of betaine and iron were inhibited. Thus, this study revealed the response mechanism of S. aureus under the stress of CUM, and provided a theoretical basis for the application of CUM in meat products.

The combination of thymol and cinnamaldehyde reduces the survival and virulence of Listeria monocytogenes on autoclaved chicken breast

AIMS

To reveal the antibacterial mechanism of the combination of thymol and cinnamaldehyde to Listeria monocytogenes ATCC 19115 on autoclaved chicken breast.

METHODS AND RESULTS

In this study, Listeria monocytogenes ATCC 19115 on autoclaved chicken breast was exposed to the stress of 125 μg/mL thymol and 125 μg/mL cinnamaldehyde, and transcriptome analysis was used to reveal the crucial antibacterial mechanism. According to the results, 1303 significantly differentially expressed genes (DEGs) were identified. Treated by thymol and cinnamaldehyde in combination, pyrimidine and branched-chain amino acids biosynthesis of L. monocytogenes were thwarted which impairs its nucleic acid biosynthesis and intracellular metabolism. The up-regulated DEGs involved in membrane composition and function contributed to membrane repair. Besides, pyruvate catabolism and TCA cycle were restrained which brought about the disturbance of amino acid metabolism. ABC transporters were also perturbed, for instance, the uptake of cysteine, D-methionine and betaine was activated, while the uptake of vitamin, iron and carnitine was repressed. Thus, L. monocytogenes tended to activate PTS, glycolysis, glycerol catabolism, and pentose phosphate pathways to obtain energy to adapt to the hostile condition. Noticeably, DEGs involved in virulence factors were totally down-regulated, including genes devoted to encoding flagella, chemotaxis, biofilm formation, internalin as well as virulence gene clusters.

CONCLUSIONS

The combination of thymol and cinnamaldehyde is effective to reduce the survival and potential virulence of L. monocytogenes on autoclaved chicken breast.

SIGNIFICANCE AND IMPACT OF STUDY

This work contributes to providing theoretical information for the application and optimization of thymol and cinnamaldehyde in ready-to-eat meat products to inhibit L. monocytogenes.

Metabolomic approaches for the determination of metabolites from pathogenic microorganisms: A review

Metabolomics is a high precision analytical approach to obtaining detailed information of varieties of metabolites produced in biological systems, including foods. This study reviews the use of metabolomic approaches such as liquid chromatography mass spectrometry (LCMS), gas chromatography mass spectrometry (GC-MS), matrix assisted laser desorption /ionization tandem time of flight mass spectrometry (MALDI-TOF-MS) and nuclear magnetic resonance (NMR) for investigating the presence of foodborne pathogens and their metabolites. Pathogenic fungi and their notable metabolites (mycotoxins) have been studied more extensively using metabolomics as compared to bacteria, necessitating further studies in this regard. Nevertheless, such identified fungal and bacteria metabolites could be used as biomarkers for a more rapid detection of these pathogens in food. Other important compounds detected through metabolomics could also be correlated to functionality of these pathogenic strains, determined by the composition of the foods in which they exist, thereby providing insights into their metabolism. Considering the prevalence of these food pathogens, metabolomics still has potentials in the determination of food-borne pathogenic microorganisms especially for the determination of pathogenic bacteria toxins and is expected to generate research interests for further studies and applications.

Understanding of food biofilms by the application of omics techniques

Biofilms constitute a protective barrier for foodborne pathogens to survive under stressful food processing conditions. Therefore, studies into the development and control of biofilms by novel techniques are vital for the food industry. In recent years, foodomics techniques have been developed for biofilm studies, which contributed to a better understanding of biofilm behavior, physiology, composition, as well as their response to antibiofilm methods at different molecular levels including genes, RNA, proteins and metabolic metabolites. Throughout this review, the main studies where foodomics tools used to explore the mechanisms for biofilm formation, dispersal and elimination were reviewed. The data summarized from relevant studies are important to design novel and appropriate biofilm elimination methods for enhancing food safety at any point of food processing lines.

Metabolomics profiling during biofilm development of Bacillus licheniformis isolated from milk powder

Bacillus licheniformis is a major source of microbial contamination to dairy industry, and biofilm formation by this spoilage bacterium aggravates the safety issues. Especially for milk powder manufactures, the evaporation process at temperatures between 50 °C and 70 °C before spray drying, is a critical control point against thermophilic bacteria multiplication. In our study, metabolomics analysis was performed to investigate dynamic changes of the metabolites and their roles during process of biofilm development of B. licheniformis at 55 °C for 24 h. Amino acid metabolism was quite active, with cooperation from lipid metabolism, carbohydrate metabolism and nucleotide metabolism. Amino acid biosynthesis provided significant contributions especially during early biofilm development from 8 to 12 h. Metabolites involved in specific pathways of arginine biosynthetic, galactose metabolism and sphingolipid metabolism played a crucial role in building biofilm. This work provided new insights into dynamic metabolic alternations and a comprehensive network during B. licheniformis biofilm development, which will extend the knowledge on the metabolic process of biofilm formation by B. licheniformis. The results are helpful in creating better environmental hygiene in dairy processing and new strategies for ensuring quality of dairy products.

Molecular interaction between methicillin-resistant Staphylococcus aureus (MRSA) and chicken breast reveals enhancement of pathogenesis and toxicity for food-borne outbreak

To study pathogenesis and toxicity of Staphylococcus aureus in foods, FORC_062 was isolated from a human blood sample and complete genome sequence has a type II SCCmec gene cluster and a type II toxin-antitoxin system, indicating an MRSA strain. Its mobile gene elements has many pathogenic genes involved in host infection, biofilm formation, and various enterotoxin and hemolysin genes. Clinical MRSA is often found in animal foods and ingestion of MRSA-contaminated foods causes human infection. Therefore, it is very important to understand the role of contaminated foods. To elucidate the interaction between clinical MRSA FORC_062 and raw chicken breast, transcriptome analysis was conducted, showing that gene expressions of amino acid biosynthesis and metabolism were specifically down-regulated, suggesting that the strain may import and utilize amino acids from the chicken breast, but not able to synthesize them. However, toxin gene expressions were up-regulated, suggesting that human infection of S. aureus via contaminated food may be more fatal. In addition, the contaminated foods enhance multiple-antibiotic resistance activities and virulence factors in this clinical MRSA. Consequently, MRSA-contaminated food may play a role as a nutritional reservoir as well as in enhancing factor for pathogenesis and toxicity of clinical MRSA for severe food-borne outbreaks.

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.