Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity

Comparative Study and Transcriptomic Analysis on the Antifungal Mechanism of Ag Nanoparticles and Nanowires Against Trichosporon asahii

Background

Silver nanomaterials have been widely proven to have antifungal effects against Trichosporon asahii. However, the antifungal mechanism of silver nanomaterials with different morphologies still needs to be explored.

Methods

Herein, the antifungal effect of silver nanomaterials against fungus was comparative investigated via silver nanowires and silver nanoparticles with a similar size (30 nm).

Results

The optimal antifungal concentration of silver nanowires is 6.24 μg/mL, meanwhile the antifungal concentration of silver nanoparticles is 100 μg/mL. The silver nanowires are significantly superior to the silver nanoparticles. SEM and TEM results indicated that both silver nanoparticles and silver nanowires showed significant morphological changes in the mycelium of the strain, compared with the control. The lower MFC value of silver nanowires indicates good sterilization effect and suitability for eradication treatment, which is slower than that of silver nanoparticles. Moreover, we also investigated the toxicological effects of silver nanoparticles and silver nanowires.

Conclusion

We comparative studied and transcriptomic analyzed the antifungal mechanism of Ag nanoparticles and nanowires against Trichosporon asahii. The antifungal effects of silver nanowires were better than the silver nanoparticles, especially in the metabolic processes and oxidative phosphorylation. RNA sequencing results indicated that 15 key targets were selected for experimental verification to interpret the potential antifungal mechanism of Ag nanomaterials against fungus. This work proves that silver nanomaterials with different morphologies have potential applications in fungus therapy such as T. asahii.

Transcriptomic analyses of Vibrio parahaemolyticus under the phenyllactic acid stress

Phenyllactic acid (PLA) generally recognized as a natural organic acid shows against Vibrio parahaemolyticus activity. In this study, V. parahaemolyticus ATCC17802 (Vp17802) was cultured under the stress of 1/2MIC PLA, and then the antibacterial mechanisms were explored via transcriptomics. The minimum inhibitory concentration (MIC) of PLA against Vp17802 was 3.2 mg/mL, and the time-kill analysis resulted that Vp17802 was inhibited. PLA was able to destroy the bacterial membrane, leading to the leakage of intracellular substances and decline of ATP levels. The RNA-sequencing analysis results indicated that 1616 significantly differentially expressed genes were identified, among which 190 were up-regulated and 1426 were down-regulated. Down-regulation of the icd2 gene in the TCA cycle mediates blockage of tyrosine metabolic, arginine biosynthesis, and oxidative phosphorylation, causing insufficient energy supply of Vp17802. Moreover, PLA could cause amino acids, metal ions, and phosphate transporters to be blocked, affecting the acquisition of nutrients. The treatment by PLA altered the expression of genes encoding functions involved in quorum sensing, flagellar assembly, and cell chemotaxis pathway, which may be interfering with the biofilm formation in Vp17802, reducing cell motility. Overall, 1.6 mg/mL PLA inhibited the growth of Vp17802 by disrupting to uptake of nutrients, cell metabolism, and the formation of biofilms. The results suggested a new direction for exploring the activity of PLA against Vp17802 and provided a theoretical basis for bacterial pathogen control in the food industry. KEY POINTS: •RNA sequencing was carried out to indicate the antibacterial mechanism of Vp17802. •The icd2 gene in the TCA cycle mediates blockage of metabolic of Vp17802. •The biofilm formation has interfered with 1.6 mg/mL PLA, which could reduce cell motility and virulence.

Impact of Mt. Olympus Honeys on Virulence Factors Implicated in Pathogenesis Exerted by Pseudomonas aeruginosa

The aim of this study was to examine the impact of twenty honey samples, harvested in Mt. Olympus (Greece), on the virulence factors implicated in P. aeruginosa pathogenesis. Six key virulence factors (protease and elastase activity, pyocyanin and pyoverdine concentration, biofilm formation, and swimming motility) were selected in order to assess the effect of the tested honeys compared with Manuka honey. All tested honeys demonstrated a significant inhibition of protease and elastase activity compared with the control. Six and thirteen honeys exerted superior protease (no inhibition zone) and elastase (values lower than 55%) activity, respectively, compared with Manuka honey. Seventeen tested honeys exhibited reduced pyoverdine production compared with the control; all tested honeys, except for one, showed an inhibitory effect on pyocyanin production compared with the control. Regarding swimming motility, nine tested honeys demonstrated significantly higher inhibition compared with Manuka honey. Honey concentrations (6% v/v and 8% v/v) had the most profound impact, as they reduced biofilm formation to less than 20% compared with the control. Overall, our data demonstrate a significant inhibition of the virulence factors in the tested Mt. Olympus honeys, highlighting the strong antimicrobial activity against P. aeruginosa, an antibiotic-resistant pathogen of growing concern, which is implicated in severe nosocomial infections globally.

Antioxidant and Antibacterial Properties of a Functional Sports Beverage Formulation

Athletes often consume functional beverages in order to improve performance and reduce oxidative stress caused by high-intensity exercise. The present study aimed to evaluate the antioxidant and antibacterial properties of a functional sports beverage formulation. The beverage's antioxidant effects were assessed on human mesenchymal stem cells (MSCs) by determining thiobarbituric acid reactive substances (TBARS; TBARS levels decreased significantly by 52.67% at 2.0 mg/mL), total antioxidant capacity (TAC; TAC levels increased significantly by 80.82% at 2.0 mg/mL) and reduced glutathione (GSH; GSH levels increased significantly by 24.13% at 2.0 mg/mL) levels. Furthermore, the beverage underwent simulated digestion following the INFOGEST protocol to assess its oxidative stability. The analysis of the total phenolic content (TPC) using the Folin-Ciocalteu assay revealed that the beverage contained a TPC of 7.58 ± 0.066 mg GAE/mL, while the phenolics identified by HPLC were catechin (2.149 mg/mL), epicatechin (0.024 mg/mL), protocatechuic acid (0.012 mg/mL), luteolin 7-glucoside (0.001 mg/mL), and kaempferol-3-O-β-rutinoside (0.001 mg/mL). The beverage's TPC was strongly correlated with TAC (R² = 896). Moreover, the beverage showcased inhibitory and bacteriostatic effects against Staphylococcus aureus and Pseudomonas aeruginosa. Lastly, the sensory acceptance test demonstrated that the functional sports beverage was well accepted by the assessors.

Antibacterial activity and mechanism of flavonoids from Chimonanthus salicifolius S. Y. Hu. and its transcriptome analysis against Staphylococcus aureus

Introduction

Chimonanthus salicifolius S. Y. Hu. (FCS) possess many biological activities, but the antibacterial activity and underlying mechanisms of flavonoids from Chimonanthus salicifolius S. Y. Hu. (FCS) is still unknown.

Method

Maximum diameter of inhibition zone (DIZ), maximum diameter of inhibition zone (DIZ), the lowest minimum inhibition concentration (MIC), and the lowest minimum bactericide concentration (MBC) were used to detect the antibacterial activity. Meanwhile, related enzyme activities, the transcriptome analysis and quantitative RT-PCR were used to investigate the antibacterial activity mechanisms.

Results

The results showed that FCS (with a purity of 84.2 ± 2.0%) has potential effects on tested strains with the maximum diameter of inhibition zone (DIZ) was 15.93 ± 2.63 mm, the lowest minimum inhibition concentration (MIC) was 1.56 mg/ml and the lowest minimum bactericide concentration (MBC) was 6.25 mg/ml. In addition, the bacterial growth curve test, release of extracellular alkaline phosphatase (AKP), loss of intracellular components, DNA damage and transmission electron microscope (TEM) suggested that FCS could destroy the cell wall and membrane, cause the loss of intracellular substance, cause DNA damage and even lead to cell death. Moreover, the antibacterial mechanism of FCS against Staphylococcus aureus (S. aureus, Gram-positive bacteria) was further confirmed by the transcriptome analysis and quantitative RT-PCR at the molecular level for the first time. A total of 671 differentially expressed genes (DEGs) were identified after treated with FCS (1/2 MIC), with 338 and 333 genes showing up-regulation and down-regulation, respectively. The highlighted changes were those related to the biosynthesis of bacteria wall and membrane, DNA replication and repair, and energy metabolism.

Discussion

Overall, our research provides theoretical guidance for the application of FCS, which is expected to be potentially used as a natural antimicrobial agent in food safety.

The Effect of Selected Bee Products on Adhesion and Biofilm of Clostridioides difficile Strains Belonging to Different Ribotypes

There is an ongoing search for alternative treatments for Clostridioides difficile infections. The aim of the study was to investigate the antibacterial and antibiotic activity of bee products against C. difficile strains with different polymerase chain reaction ribotypes (RTs). The minimum inhibitory concentration (MICs) of Manuka honey 550+, goldenrod honey, pine honey, and bee bread were determined by the broth dilution method. C. difficile adhesion to HT-29, HT-29 MTX, and CCD 841 CoN cell lines was assessed. Biofilm was cultured in titration plates and visualized by confocal microscopy. The MICs of Manuka honey for C. difficile 630 and ATCC 9689 strains and control strain, M 120, were 6.25%, 6.25%, and 1.56% (v/v), respectively; of goldenrod honey, 50%, 50%, and 12.5%, respectively; of pine honey, 25%, 25%, and 25%, respectively; and of bee bread, 100 mg/L, 50 mg/L, and 100 mg/L, respectively. Manuka honey (1%) increased adhesion of C. difficile RT176 strains, and one strain of RT023, to the CCD 841 cell line. Pine honey (1%) increased RT027 adhesion to the HT-29 cell line. Manuka honey, pine honey, and bee bread at subinhibitory concentrations increased the adhesion of C. difficile. Our research proved that bee products are active against the tested strains of C. difficile.

Synergistic Antibacterial Mechanism of Mannosylerythritol Lipid-A and Lactic Acid on Listeria monocytogenes Based on Transcriptomic Analysis

Mannosylerythritol lipids-A (MEL-A) is a novel biosurfactant with multiple biological effects. The synergistic antibacterial activity and mechanism of MEL-A and lactic acid (LA) against Listeria monocytogenes were investigated. The synergistic effect resulted in a significant increase in the antibacterial rate compared to LA treatment alone. Genome-wide transcriptomic analysis was applied to deeply investigate the synergistic antibacterial mechanism. Gene Ontology (GO) enrichment analysis showed that the synergy between MEL-A and LA affected many potential cellular responses, including the sugar phosphotransferase system, carbohydrate transport, and ribosomes. KEGG enrichment analysis showed that the PTS system and ribosome-related pathways were significantly enriched. In addition, synergistic treatment affected locomotion and membrane-related cellular responses in GO enrichment analysis and carbohydrate metabolism and amino acid metabolism pathways in KEGG enrichment analysis compared to LA treatment alone. The accuracy of the transcriptome analysis results was verified by qPCR (R² = 0.9903). This study will provide new insights for the prevention and control of L. monocytogenes.

Transcriptional Response and Plant Growth Promoting Activity of Pseudomonas fluorescens DR397 under Drought Stress Conditions

Drought is one of the most vulnerable factors that affect crop productivity. Little is known about plant-associated microbiomes and their functional roles in assisting plant growth under drought. We investigated the genetic and transcriptomic characteristics of opportunistic beneficial microorganisms that selectively alleviate stress through plant-bacteria interactions under drought. Pseudomonas fluorescens DR397 was isolated from the drought-prone rhizospheric soil of soybean and showed high metabolic activity at -1.25 Mpa. The genome of DR397 possesses several genes related to the synthesis of compatible solutes (choline and glycine-betaine), exopolysaccharides (alginate and cellulose), and secretion systems (type II, III, IV, and VI), as well as genes related to plant growth promotion (indole-3-acetic acid, transketolase, and thiamine phosphate synthesis). The expression of these genes was significantly upregulated (8- to 263-fold change) only under drought conditions with plant root exudate treatment, whereas subtle transcriptomic changes were observed under solely root exudate treatment. When DR397 was placed on both legume cultivars (Pisum sativum and Phaseolus vulgaris), growth was hardly affected under well-watered conditions, but the shoot and root growths were increased by up from 62.0% to 149.1% compared with the control group under drought conditions. These results provide fundamental insight on the plant-bacterial interactions that alleviate plant stress as an important ecological strategy for improving drought tolerance. IMPORTANCE Drought is a serious abiotic stress on plants as wells as the microbes that coexist with plants, which significantly lowers their fitness. The plant-bacterial interaction is an important strategy to enhance their fitness under drought. However, many knowledge gaps still exist in our understanding of transcriptomic features of bacteria interacting with plant under drought. Here, by investigating the transcriptomic profiles and pot cultivation with legume, we show that the interactions of Pseudomonas fluorescens DR397 with plants change with drought. We, therefore, provide a fundamental evidence of a hidden hero in the soil that promote plant fitness from external stress.

A Review of Commonly Used Methodologies for Assessing the Antibacterial Activity of Honey and Honey Products

Honey, a naturally sweet and viscous substance is mainly produced by honeybees (Apis mellifera) from flower nectar. Honey exerts a plethora of biological and pharmacological activities, namely, antioxidant, antimicrobial and anti-inflammatory activity, because of the presence of an extensive variety of bioactive compounds. The antibacterial activity is one of the most reported biological properties, with many studies demonstrating that honey is active against clinically important pathogens. As a result, beside honey’s widespread utilization as a common food and flavouring agent, honey is an attractive natural antimicrobial agent. However, the use of neat honey for therapeutic purposes poses some problems, for instance, its stickiness may hamper its appeal to consumers and health care professionals, and the maintenance of an adequate therapeutic concentration over a sufficient timeframe may be challenging due to honey liquidity and leakage. It has motivated researchers to integrate honey into diverse formulations, for example, hydrogels, dressings, ointments, pastes and lozenges. The antibacterial activity of these formulations should be scientifically determined to underscore claims of effectiveness. Some researchers have made efforts to adapt the disc carrier and suspension test to assess the antimicrobial activity of topical products (e.g., silver-based wound dressings). However, there is currently no established and validated method for determining the in vitro antimicrobial potential of natural product-based formulations, including those containing honey as the active principle. Against the backdrop of a brief discussion of the parameters that contribute to its antibacterial activity, this review provides an outline of the methods currently used for investigating the antibacterial activity of neat honey and discusses their limitations for application to honey-based formulations.

Multi-Target Antibacterial Mechanism of Moringin From Moringa oleifera Seeds Against Listeria monocytogenes

Moringin [4-(α-L-rhamnosyloxy) benzyl isothiocyanate] is an isothiocyanate from Moringa oleifera seeds. It is the bioactivated form of the glucosinolate precursor glucomoringin with various health benefits. However, few studies have examined the antibacterial activity of moringin. This study aimed to investigate the antimicrobial activity and mechanism of moringin against Listeria monocytogenes. The minimum inhibitory concentration (MIC), and growth curves were used to evaluate the bacteriostatic effect of moringin against L. monocytogenes. Transcriptome analysis by RNA sequencing was performed to elucidate the underlying mechanism of moringin against L. monocytogenes. The transcriptome results were validated. The results showed that moringin inhibited the growth of L. monocytogenes with a MIC of 400 μM. RNA sequencing results showed that the differences in the expression of genes related to the cell wall and membrane biosynthesis, phosphotransferase system (PTS), oxidative stress, energy metabolism, and DNA binding were significantly affected. As with the transcriptome results, the results of the mechanism verification found that moringin damaged the integrity of the cell wall and cell membrane, stimulated oxidative stress, interfered with energy metabolism and DNA replication, and finally led to the death of L. monocytogenes. The present study provides evidence that moringin exhibits strong antimicrobial activity against L. monocytogenes and insight into its potential mechanism.

Transcriptomic Profile Analysis of Streptococcus mutans Response to Acmella paniculata Flower Extracts

Background

Acmella paniculata has been used as a traditional medicine to treat oral health diseases such as dental caries and periodontitis. Streptococcus mutans is a common bacterium that initiates dental caries at an early stage.

Aim

The aim of this study was to determine the mode of action of A. paniculata (extracts) against S. mutans growth.

Methods

Time-kill assay has been done to investigate the rate of kill and effectiveness of Acmella paniculata (AP) extracts against S. mutans growth. Phytochemical analysis was done to identify major compounds in AP extracts using gas chromatography mass spectrometry (GCMS). Scanning and transmission electron microscopy (SEM and TEM) have been done to observe the morphological changes of treated bacteria. Transcriptomic profile analysis has been done using Next Gene Sequencing.

Results

AP flower n-hexane (APFH) and AP flower dichloromethane (APFD) extracts acted as bactericidal agents after killing >3 log10 cfu/mL of S. mutans after 24 hours. Oleic and hexadecenoic acids were found to be the major compounds in APFD and APFH extracts, respectively. Photomicrographs from SEM and TEM of treated S. mutans show that the bacterial cell wall has been lysed and the cytoplasm content was decreased. Pathway analysis revealed that the APFD extract significantly affected biosynthesis peptidoglycan, gene expression, RNA processing, and macromolecule metabolism processes in S. mutans.

Conclusion

Data analysis revealed that multiple mechanisms of action were involved in antibacterial activity of A. paniculata extracts toward S. mutans.

Foodomics: Current and Future Perspectives in Food Analysis

Climate change, an increase in population, and the recent pandemic crisis triggered by SARS-CoV-2 have all contributed to a period of global problems [...].

Physicochemical Characterization and Biological Properties of Pine Honey Produced across Greece

Pine honey is a honeydew honey produced in the East Mediterranean region (Greece and Turkey) from the secretions of the plant sucking insect Marchalina hellenica (Gennadius) (Coccoidea: Marchalini-dae) feeding on living parts of Pinus species. Nowadays, honeydew honey has attracted great attention due to its biological activities. The aim of this study was to study unifloral pine honey samples produced in Greece regarding their physicochemical parameters and antioxidant and antibacterial activity against five nosocomial and foodborne pathogens. These honeys showed physicochemical and microscopic characteristics within the legal limits, except for diastase activity, a parameter known to be highly variable, depending on various factors. Substantially higher levels of H2O2 were estimated compared to other types of honeydew honey, whereas protein content was similar. The total phenolic content was 451.38 ± 120.38 mg GAE/kg and antiradical activity ranged from 42.43 to 79.33%, while FRAP values (1.87 to 9.43 mmol Fe+2/kg) were in general higher than those reported in the literature. Various correlations could be identified among these parameters. This is the first attempt to investigate in depth the antibacterial activity of pine honey from Greece and correlate it with honey quality parameters. All tested honeys exerted variable but significant antibacterial activity, expressed as MIC and MBC values, comparable or even superior to manuka honey for some tested samples. Although honey antibacterial activity is mainly attributed to hydrogen peroxide and proteins in some cases (demonstrated by elevated MICs after catalase and Proteinase K treatment, respectively), no strong correlation between the antibacterial activity and hydrogen peroxide concentration or total protein content was demonstrated in this study. However, there was a statistically significant correlation of moisture, antioxidant and antibacterial activity against Klebsiella pneuomoniae, as well as antioxidant and antibacterial activity against Salmonella ser. Typhimurium. Interestingly, a statistically significant negative correlation has been observed between diastase activity and Staphylococcus aureus antibacterial activity. Overall, our data indicate multiple mechanisms of antibacterial activity exerted by pine honey.

Combined Inhibitory Effect of Fir (Abies alba Mill.) Honeydew Honey and Probiotic Bacteria Lactiplantibacillus plantarum on the Growth of Salmonella enterica Serotype Typhimurium

Honey is a natural food consisting mainly of sugars, enzymes, amino acids, organic acids, vitamins, minerals and aromatic substances. In addition to specific organoleptic properties, honey also has other components that contribute to its nutritional and health value. Proteins, vitamins, minerals, organic acids and phenolic compounds, the most variable components of honey, are predominantly responsible for its strong bioactive effect. Honeydew honey is a less known type of honey with outstanding antimicrobial and antioxidant properties that also demonstrates prebiotic effects and can promote the growth of probiotic bacteria. Foodborne illnesses can be prevented by using probiotic strains in combination with prebiotics. The aim of this study was for the first time to determine potential synergistic antimicrobial effect of fir (Abies alba Mill.) honeydew honey (HS) and probiotic bacteria Lactiplantibacillus plantarum on Salmonella enterica serotype Typhimurium, a primary cause of foodborne illnesses. The effect of three different samples of fir honeydew honey on the growth of L. plantarum in de Man, Rogosa and Sharpe (MRS) medium and the potential synergistic effect of HSs and L. plantarum on the growth of S. Typhimurium in the Brain Heart Infusion (BHI) medium were examined. The results indicate that concentrations of 1 and 5% of all three HS samples stimulate the growth and metabolic activity of L. plantarum, while a concentration of 10% inhibits the growth of L. plantarum. The concentration of 5% of all three HS and L. plantarum combined inhibits the growth of S. Typhimurium in BHI broth. Fir honeydew honey showed potential prebiotic properties and antimicrobial activity, both of which can synergistically enhance the probiotic efficacy of L. plantarum against S. Typhimurium To conclude, the combination of fir honeydew honey and L. plantarum represents a successful combination against S. Typhimurium and additional experiments are necessary regarding the mechanisms of their combined effect.

In Vitro Antibacterial and Antibiofilm Activity of Hungarian Honeys against Respiratory Tract Bacteria

Honey is a rich source of carbohydrates, while minor compounds such as amino acids and polyphenols contribute to its health-promoting effects. Honey is one of the oldest traditional remedies applied for microbial infections, due to its antibacterial, anti-inflammatory, and antioxidant properties. The aim of this study was to investigate the antibacterial and antibiofilm effects of Hungarian black locust, linden, and sunflower honeys against the most common biofilm-forming respiratory tract pathogens Haemophilus spp., Pseudomonas aeruginosa, and Streptococcus pneumoniae. The unifloral character of all three honey types was confirmed by melissopalynological analysis. The antibacterial activity of each honey sample against each bacterium strain was proven with agar well diffusion assay and thin layer chromatography—direct bioautography. Kinetics and mechanisms of antibacterial action were clarified with time-kill assay and membrane degradation study. The anti-biofilm activity was evidenced using crystal violet assay. In each assay, linden honey was the most effective, followed by sunflower and black locust honey. In addition, each honey sample had greater potential to suppress respiratory tract bacteria, compared to major sugar components. In conclusion, honey in general and linden honey in particular, can have a role in the treatment of respiratory tract infections caused by biofilm-forming bacteria.