Clove bud oil reduces kynurenine and inhibits pqs A gene expression in P. aeruginosa

Anti-biofilm mechanisms of action of essential oils by targeting genes involved in quorum sensing, motility, adhesion, and virulence: A review

Biofilms are a critical factor for food safety, causing important economic losses. Among the novel strategies for controlling biofilms, essential oils (EOs) can represent an environmentally friendly approach, able to act both on early and mature stages of biofilm formation. This review reports the anti-biofilm mechanisms of action of EOs against five pathogenic bacterial species known for their biofilm-forming ability. These mechanisms include disturbing the expression of genes related to quorum sensing (QS), motility, adhesion, and virulence. Biofilms and QS are interconnected processes, and EOs interfere with the communication system (e.g. regulating the expression of agrBDCA, luxR, luxS, and pqsA genes), thus influencing biofilm formation. In addition, QS is an important mechanism that regulates gene expression related to bacterial survival, virulence, and pathogenicity. Similarly, EOs also influence the expression of many virulence genes. Moreover, EOs exert their effects modulating the genes associated with bacterial adhesion and motility, for example those involved in curli (csg), fimbriae (fim, lpf), and flagella (fla, fli, flh, and mot) production, as well as the ica genes responsible for synthetizing polysaccharide intercellular adhesin. This review provides a comprehensive framework on the topic for a better understanding of EOs biofilm mechanisms of action.

Inhibitory effect of natural compounds on quorum sensing system in Pseudomonas aeruginosa: a helpful promise for managing biofilm community

Pseudomonas aeruginosa biofilm is a community of bacteria that adhere to live or non-living surfaces and are encapsulated by an extracellular polymeric substance. Unlike individual planktonic cells, biofilms possess a notable inherent resistance to sanitizers and antibiotics. Overcoming this resistance is a substantial barrier in the medical and food industries. Hence, while antibiotics are ineffective in eradicating P. aeruginosa biofilm, scientists have explored alternate strategies, including the utilization of natural compounds as a novel treatment option. To this end, curcumin, carvacrol, thymol, eugenol, cinnamaldehyde, coumarin, catechin, terpinene-4-ol, linalool, pinene, linoleic acid, saponin, and geraniol are the major natural compounds extensively utilized for the management of the P. aeruginosa biofilm community. Noteworthy, the exact interaction of natural compounds and the biofilm of this bacterium is not elucidated yet; however, the interference with the quorum sensing system and the inhibition of autoinducer production in P. aeruginosa are the main possible mechanisms. Noteworthy, the use of different drug platforms can overcome some drawbacks of natural compounds, such as insolubility in water, limited oral bioavailability, fast metabolism, and degradation. Additionally, drug platforms can deliver different antibiofilm agents simultaneously, which enhances the antibiofilm potential of natural compounds. This article explores many facets of utilizing natural compounds to inhibit and eradicate P. aeruginosa biofilms. It also examines the techniques and protocols employed to enhance the effectiveness of these compounds.

From Answers to Insights: Unveiling the Strengths and Limitations of ChatGPT and Biomedical Knowledge Graphs

Purpose

Large Language Models (LLMs) have shown exceptional performance in various natural language processing tasks, benefiting from their language generation capabilities and ability to acquire knowledge from unstructured text. However, in the biomedical domain, LLMs face limitations that lead to inaccurate and inconsistent answers. Knowledge Graphs (KGs) have emerged as valuable resources for organizing structured information. Biomedical Knowledge Graphs (BKGs) have gained significant attention for managing diverse and large-scale biomedical knowledge. The objective of this study is to assess and compare the capabilities of ChatGPT and existing BKGs in question-answering, biomedical knowledge discovery, and reasoning tasks within the biomedical domain.

Methods

We conducted a series of experiments to assess the performance of ChatGPT and the BKGs in various aspects of querying existing biomedical knowledge, knowledge discovery, and knowledge reasoning. Firstly, we tasked ChatGPT with answering questions sourced from the "Alternative Medicine" sub-category of Yahoo! Answers and recorded the responses. Additionally, we queried BKG to retrieve the relevant knowledge records corresponding to the questions and assessed them manually. In another experiment, we formulated a prediction scenario to assess ChatGPT's ability to suggest potential drug/dietary supplement repurposing candidates. Simultaneously, we utilized BKG to perform link prediction for the same task. The outcomes of ChatGPT and BKG were compared and analyzed. Furthermore, we evaluated ChatGPT and BKG's capabilities in establishing associations between pairs of proposed entities. This evaluation aimed to assess their reasoning abilities and the extent to which they can infer connections within the knowledge domain.

Results

The results indicate that ChatGPT with GPT-4.0 outperforms both GPT-3.5 and BKGs in providing existing information. However, BKGs demonstrate higher reliability in terms of information accuracy. ChatGPT exhibits limitations in performing novel discoveries and reasoning, particularly in establishing structured links between entities compared to BKGs.

Conclusions

To address the limitations observed, future research should focus on integrating LLMs and BKGs to leverage the strengths of both approaches. Such integration would optimize task performance and mitigate potential risks, leading to advancements in knowledge within the biomedical field and contributing to the overall well-being of individuals.

Modulation of immune cell function, IDO expression and kynurenine production by the quorum sensor 2-heptyl-3-hydroxy-4-quinolone (PQS)

Many invasive micro-organisms produce 'quorum sensor' molecules which regulate colony expansion and may modulate host immune responses. We have examined the ability of Pseudomonas Quorum Sensor (PQS) to influence cytokine expression under conditions of inflammatory stress. The administration of PQS in vivo to mice with collagen-induced arthritis (CIA) increased the severity of disease. Blood and inflamed paws from treated mice had fewer regulatory T cells (Tregs) but normal numbers of Th17 cells. However, PQS (1μM) treatment of antigen-stimulated lymph node cells from collagen-immunised mice in vitro inhibited the differentiation of CD4+IFNγ+ cells, with less effect on CD4+IL-17+ cells and no change in CD4+FoxP3+Tregs. PQS also inhibited T cell activation by anti-CD3/anti-CD28 antibodies. PQS reduced murine macrophage polarisation and inhibited expression of IL1B and IL6 genes in murine macrophages and human THP-1 cells. In human monocyte-derived macrophages, IDO1 gene, protein and enzyme activity were all inhibited by exposure to PQS. TNF gene expression was inhibited in THP-1 cells but not murine macrophages, while LPS-induced TNF protein release was increased by high PQS concentrations. PQS is known to have iron scavenging activity and its suppression of cytokine release was abrogated by iron supplementation. Unexpectedly, PQS decreased the expression of indoleamine-2, 3-dioxygenase genes (IDO1 and IDO2), IDO1 protein expression and enzyme activity in mouse and human macrophages. This is consistent with evidence that IDO1 inhibition or deletion exacerbates arthritis, while kynurenine reduces its severity. It is suggested that the inhibition of IDO1 and cytokine expression may contribute to the quorum sensor and invasive actions of PQS.

Recent advances in nutritional composition, phytochemistry, bioactive, and potential applications of Syzygium aromaticum L. (Myrtaceae)

Syzygium aromaticum is an aromatic plant native to Indonesia, and introduced to tropical regions worldwide. As an ingredient in perfumes, lotions, and food preservation, it is widely used in the food and cosmetic industries. Also, it is used to treat toothache, ulcers, type 2 diabetes, etc. A variety of nutrients such as amino acids, proteins, fatty acids, and vitamins are found in S. aromaticum. In addition to eugenol, isoeugenol, eugenol acetate, β-caryophyllene and α-humulene are the main chemical constituents. The chemical constituents of S. aromaticum exhibit a wide range of bioactivities, such as antioxidant, antitumor, hypoglycemic, immunomodulatory, analgesic, neuroprotective, anti-obesity, antiulcer, etc. This review aims to comprehend the information on its taxonomy and botany, nutritional composition, chemical composition, bioactivities and their mechanisms, toxicity, and potential applications. This review will be a comprehensive scientific resource for those interested in pursuing further research to explore its value in food.

Innovative next-generation therapies in combating multi-drug-resistant and multi-virulent Escherichia coli isolates: insights from in vitro, in vivo, and molecular docking studies

Despite notable advances in vaccine and antimicrobial therapies, treatment failure has been increasingly reported worldwide. Of note, multi-drug-resistant (MDR) Escherichia coli (E. coli) strains have a considerable share in the evolution of this crisis. So, current practice guidelines are directed towards complementary and alternative therapies. Therefore, we evaluated the antibacterial and antivirulence activities of curcumin, thymol, and eugenol essential oils (EOs) as well as EOs-EOs and EOs-antibiotics interactions on MDR and multi-virulent E. coli isolates. Unfortunately, MDR E. coli could be isolated with a prevalence rate of 95.6% (86/90). Additionally, the majority of our isolates harbored both fimH (95.6%) and ompA (91.1%) genes, and half of them (45/90) were multi-virulent. Interestingly, all the tested EOs, especially curcumin, exhibited inhibitory activities against all MDR and multi-virulent E. coli isolates. The addition of thymol enhanced the antibacterial activities of curcumin and eugenol. Moreover, the activities of piperacillin/tazobactam and imipenem were increased by adding any one of the tested EOs. Regarding the antivirulence activities of the tested EOs, the cell surfaces of treated E. coli isolates under transmission electron microscope (TEM) were uneven. The cells appeared damaged and lost their appendages. Furthermore, EOs strongly reduced the transcription of ompA and fimH genes. The antibacterial and antivirulence activities of the used EOs were confirmed by in silico and mice protection assays. Hereby, we introduced the promising uses of curcumin, thymol, and eugenol oils as complementary and alternative therapies for combating MDR and multi-virulent E. coli isolates. KEY POINTS: • Our promising results confirmed that we were right for renewed interest of EOs. • The EOs, especially curcumin, can be used to prevent treatment failure. • We supposed a new pharmaceutical formulation of antibiotic powders dissolved in EOs.

Aspergillus niger Culture Filtrate (ACF) Mediated Biocontrol of Enteric Pathogens in Wastewater

Robust control of pathogens in sewage facilitates safe reuse of wastewater rich in valuable nutrients for potential valorization through biological means. Aspergillus niger is widely reported in bioremediation of wastewater but studies on control of enteric pathogens in sewage are very sparse. So, this study aimed at exploring the antibacterial and nematicidal activity of A. niger culture filtrate (ACF). Antibacterial activity of ACF on enteric pathogens (Klebsiella pneumoniae, Pseudomonas aeruginosa, Vibrio cholerae, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Staphylococcus aureus, Klebsiella variicola) was determined by spectrophotometric growth analysis, resazurin based viability assay and biofilm formation assay. ACF showed inhibition against all enteric pathogens except Pseudomonas aeruginosa. Nematicidal studies on Caenorhabditis elegans showed 85% egg hatch inhibition and 52% mortality of L1 larvae. Sewage treatment with ACF at 1:1 (v/v) showed 2–3 log reduction in coliforms, Klebsiella, Shigella, Salmonella, S. aureus and Vibrio except Pseudomonas, indicating significant alteration of complex microbial dynamics in wastewater. Application of ACF can potentially be used as a robust biocontrol strategy against infectious microbes in wastewater and subsequent valorization by cultivating beneficial Pseudomonas.

Attenuation of Aeromonas hydrophila Infection in Carassius auratus by YtnP, a N-acyl Homoserine Lactonase from Bacillus licheniformis T-1

In this experiment, the quorum quenching gene ytnP of Bacillus licheniformis T-1 was cloned and expressed, and the effect against infection of Aeromonas hydrophila ATCC 7966 was evaluated in vitro and vivo. The BLAST results revealed a 99% sequence identity between the ytnP gene of T-1 and its homolog in B.subtilis sub sp. BSP1, and the dendroGram showed that the similarity in the YtnP protein in T-1 was 100% in comparison with B.subtilis 3610, which was categorized as the Aidc cluster of the MBL family. The AHL lactonase activity of the purified YtnP was detected as 1.097 ± 0.7 U/mL with C6-HSL as the substrate. Otherwise, purified YtnP protein could significantly inhibit the biofilm formation of A.hydrophila ATCC 7966 with an inhibition rate of 68%. The MIC of thiamphenicol and doxycycline hydrochloride against A. hydrophila reduced from 4 μg/mL and 0.5 μg/mL to 1 μg/mL and 0.125 μg/mL, respectively, in the presence of YtnP. In addition, YtnP significantly inhibited the expression of five virulence factors hem, ahyB, ast, ep, aerA of A. hydrophila ATCC 7966 as well (p < 0.05). The results of inhibition on virulence showed a time-dependence tendency, while the strongest anti-virulence effects were within 4–24 h. In vivo, when the YtnP protein was co-injected intraperitoneally with A. hydrophila ATCC 7966, it attenuated the pathogenicity of A. hydrophila and the accumulated mortality was 27 ± 4.14% at 96 h, which was significantly lower than the average mortality of 78 ± 2.57% of the Carassius auratus injected with 10⁸ CFU/mL of A. hydrophila ATCC 7966 only (p < 0.001). In conclusion, the AHL lactonase in B. licheniformis T-1 was proven to be YtnP protein and could be developed into an agent against infection of A. hydrophila in aquaculture.

Antivirulence properties and related mechanisms of spice essential oils: A comprehensive review

In recent decades, reduced antimicrobial effectiveness, increased bacterial infection, and newly emerged microbial resistance have become global public issues, leading to an urgent need to find effective strategies to counteract these problems. Strategies targeting bacterial virulence factors rather than bacterial survival have attracted increasing interest, since the modulation of virulence factors may prevent the development of drug resistance in bacteria. Spices are promising natural sources of antivirulence compounds owing to their wide availability, diverse antivirulence phytochemical constituents, and generally favorable safety profiles. Essential oils are the predominant and most important antivirulence components of spices. This review addresses the recent efforts of using spice essential oils to inhibit main bacterial virulence traits, including the quorum sensing system, biofilm formation, motility, and toxin production, with an intensive discussion of related mechanisms. We hope that this review can provide a better understanding of the antivirulence properties of spice essential oils, which have the potential to be used as antibiotic alternatives by targeting bacterial virulence.

Natural quorum sensing inhibitors effectively downregulate gene expression of Pseudomonas aeruginosa virulence factors

At present, anti-virulence drugs are being considered as potential therapeutic alternatives and/or adjuvants to currently failing antibiotics. These drugs do not kill bacteria but inhibit virulence factors essential for establishing infection and pathogenesis through targeting non-essential metabolic pathways reducing the selective pressure to develop resistance. We investigated the effect of naturally isolated plant compounds on the repression of the quorum sensing (QS) system which is linked to virulence/pathogenicity in Pseudomonas aeruginosa. Our results show that trans-cinnamaldehyde (CA) and salicylic acid (SA) significantly inhibit expression of QS regulatory and virulence genes in P. aeruginosa PAO1 at sub-inhibitory levels without any bactericidal effect. CA effectively downregulated both the las and rhl QS systems with lasI and lasR levels inhibited by 13- and 7-fold respectively compared to 3- and 2-fold reductions with SA treatment, during the stationary growth phase. The QS inhibitors (QSI) also reduced the production of extracellular virulence factors with CA reducing protease, elastase and pyocyanin by 65%, 22% and 32%, respectively. The QSIs significantly reduced biofilm formation and concomitantly with repressed rhamnolipid gene expression, only trace amount of extracellular rhamnolipids were detected. The QSIs did not completely inhibit virulence factor expression and production but their administration significantly lowered the virulence phenotypes at both the transcriptional and extracellular levels. This study shows the significant inhibitory effect of natural plant-derived compounds on the repression of QS systems in P. aeruginosa.

Quorum sensing inhibitors as antipathogens: biotechnological applications

The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.

Progress on the Antimicrobial Activity Research of Clove Oil and Eugenol in the Food Antisepsis Field

As potential and valuable antiseptics in the food industry, clove oil and its main effective composition eugenol show beneficial advantages on antibacterial and antifungal activity, aromaticity, and safety. Researches find that both clove oil and eugenol express significantly inhibitory effects on numerous kinds of food source microorganisms, and the mechanisms are associated with reducing the migratory and adhesion and inhibiting the synthesis of biofilm and various virulence factors of these microorganisms. Clove oil and eugenol are generally regarded as safe in vivo experiments. However, they may express certain cytotoxicity on fibroblasts and other cells in vitro. Studies on the quality and additive standard of clove oil and eugenol should be strengthened to promote the antiseptic effects of them in the food antiseptic field.

Clove Bud Oil Modulates Pathogenicity Phenotypes of the Opportunistic Human Pathogen Pseudomonas aeruginosa

Earlier studies from our laboratory have demonstrated that clove bud oil (CBO) attenuates expression of certain virulence factors of Pseudomonas aeruginosa PAO1. Here, we probe more deeply into the effect of CBO on four pseudomonal proteases - elastase A, elastase B, protease IV and alkaline protease - each known to play key roles in disease pathogenesis. CBO inhibited the activity of these proteases present in the bacterial culture supernatant. Zymography studies indicated that these proteases can activate host matrix metalloproteases (MMPs) to establish infection, through conversion of pro-MMP-2 to active MMP-2. PAO1 is a predominant pathogen in burn wound infections and we show the modulatory effect of CBO on MMPs in an in vitro model of burn injury. Furthermore, CBO induced dose-dependent neutrophil extracellular trap formation in human neutrophils. CBO also increased the survival of C. elegans infected with PAO1, establishing an anti-infective role in a whole animal model of pathogenesis. LC-MS/MS analysis indicated that CBO treatment elicited a significant reduction of signalling molecules (Acyl-Homoserine-Lactone) involved in quorum sensing regulation. Our observations demonstrate that CBO attenuates key virulence mechanisms of this important human pathogen, while concomitantly enhancing host innate immunomodulatory functions, with potential implications for topical therapy against antibiotic-resistant infections.

New Perspectives on the Use of Phytochemicals as an Emergent Strategy to Control Bacterial Infections Including Biofilms

The majority of current infectious diseases are almost untreatable by conventional antibiotic therapy given the advent of multidrug-resistant bacteria. The degree of severity and the persistence of infections are worsened when microorganisms form biofilms. Therefore, efforts are being applied to develop new drugs not as vulnerable as the current ones to bacterial resistance mechanisms, and also able to target bacteria in biofilms. Natural products, especially those obtained from plants, have proven to be outstanding compounds with unique properties, making them perfect candidates for these much-needed therapeutics. This review presents the current knowledge on the potentialities of plant products as antibiotic adjuvants to restore the therapeutic activity of drugs. Further, the difficulties associated with the use of the existing antibiotics in the treatment of biofilm-related infections are described. To counteract the biofilm resistance problems, innovative strategies are suggested based on literature data. Among the proposed strategies, the use of phytochemicals to inhibit or eradicate biofilms is highlighted. An overview on the use of phytochemicals to interfere with bacterial quorum sensing (QS) signaling pathways and underlying phenotypes is provided. The use of phytochemicals as chelating agents and efflux pump inhibitors is also reviewed.