Quorum quenching enzymes and their effects on virulence, biofilm, and microbiomes: a review of recent advances

From Dormancy to Eradication: Strategies for Controlling Bacterial Persisters in Food Settings

Bacterial persistence, a dormant state that enables microorganisms to survive harsh conditions, is a significant concern in food-industry settings, where traditional antimicrobial treatments often fail to eliminate these resilient cells. This article goes beyond conventional review by compiling critical information aimed at providing practical solutions to combat bacterial persisters in food production environments. This review explores the primary mechanisms behind persister cell formation, including toxin-antitoxin systems, the alarmone guanosine tetraphosphate (ppGpp), stochastic processes (in which persistence occurs as a random event), and the SOS response. Given the serious implications for food safety and quality, the authors also report a range of physical, chemical, and biological methods for targeting and eradicating persister cells. The strategies discussed, whether applied individually or in combination, offer varying levels of availability and applicability within the industry and can serve as a guide for implementing microbial contamination control plans. While significant progress has been achieved, further research is crucial to fully understand the complex mechanisms underlying bacterial persistence in food and to develop effective and targeted strategies for its eradication in food-industry settings. Overall, the translation of these insights into practical applications aims to support the food industry in overcoming this persistent challenge, ensuring safer, more sustainable food production.

Diffusible Signal Factors and Xylella fastidiosa: A Crucial Mechanism Yet to Be Revealed

Xylella fastidiosa (Xf) is a xylem-limited Gram-negative phytopathogen responsible for severe plant diseases globally. Colonization and dissemination on host plants are regulated primarily by diffusible signal factors (DSFs) and quorum sensing (QS) molecules regulating biofilm formation, motility, and virulence factor synthesis. DSFs play a critical role in the transition of bacteria from adhesion to dispersal phases, influencing plant infection and transmission by vector. Because of Xf's host range (over 550 plant species), effective containment strategies are highly demanded. In this review, we discuss the molecular mechanism of DSF-mediated signalling in Xf, especially concerning its role in pathogenicity and adaptation. Moreover, we shed light on innovative approaches to manage Xf, including quorum-quenching (QQ) strategies and transgenic plants targeted to disrupt QS pathways. Improved knowledge of DSF interactions with host plants and bacterial communities could provide an entry point for novel, sustainable disease control strategies to decrease Xf's agricultural and ecological impact.

An acyl-homoserine lactone acylase found in Stenotrophomonas maltophilia exhibits both quorum quenching activity and the ability to degrade penicillin antibiotics

Stenotrophomonas maltophilia are opportunistic, multi-drug-resistant Gram-negative pathogens increasingly prevalent in clinical settings. Quorum sensing (QS) systems play a crucial role in their pathogenesis, coordinating bacterial populations and enabling interactions within polymicrobial communities. While not the primary QS mechanism in S. maltophilia, these bacteria can respond to acyl-homoserine lactone (AHL)-type autoinducers. Some isolates exhibit AHL-quorum quenching activity, though the responsible components remain unidentified. Homology searches in S. maltophilia K279a revealed a protein with the locus tag SMLT_RS07305 (old locus tag Smlt1522), annotated as a putative penicillin acylase 2 precursor. Sequence and structural analyses classify this protein within the bacterial AHL-acylase group B, characterized by a heterodimeric structure consisting of α- and β-subunits connected by a spacer polypeptide. We experimentally confirmed the dual activity of Smlt1522 as an AHL-acylase and a penicillin acylase. This protein degrades AHLs with varying acyl chains and hydrolyses penicillin antibiotics in vitro, in vivo, and as an heterologously expressed product. Its physiological role includes the modulation of beta-lactam resistance, biofilm formation and bacterial fitness under specific conditions. Evolutionary analysis suggests structural and functional conservation, pointing to its potential role in the adaptation of S. maltophilia to diverse and competitive environments.

Bioorganic compounds in quorum sensing disruption: strategies, Mechanisms, and future prospects

Recent research has shed light on the complex world of bacterial communication through quorum sensing. This sophisticated intercellular signalling mechanism, driven by auto-inducers, regulates crucial bacterial community behaviours such as biofilm formation, expression of virulence factors, and resistance mechanisms. The increasing threat of antibiotic resistance, coupled with quorum sensing mediated response, necessitates alternative strategies to combat bacterial infections. Quorum quenching has emerged as a promising approach, utilizing quorum quenching enzymes and quorum sensing inhibitors to disrupt quorum sensing signalling pathways, thus reducing virulence and biofilm formation. This review focuses on natural and synthetic bioorganic compounds that act as quorum-sensing inhibitors, providing insights into their mechanisms, structure-activity relationships, and potential as anti-virulence agents. The review also explores the communication languages of bacteria, including AHLs in gram-negative bacteria, oligopeptides in gram-positive bacteria, and LuxS, a universal microbial language. By highlighting recent advancements and prospects in bioorganic QSIs, this article underscores their crucial role in developing effective anti-virulence therapies and combating the growing threat of antimicrobial resistance.

Quorum quenching enzymes disrupt bacterial communication in a sex- and dose-dependent manner

BACKGROUND

Over the past 50 years, the incidence of obesity has gradually increased, necessitating investigation into the multifactorial contributors to this disease, including the gut microbiota. Bacteria within the human gut microbiome communicate using a density-dependent process known as quorum sensing (QS), in which autoinducer (AI) molecules (e.g., N-acyl-homoserine lactones [AHLs]) are produced to enable bacterial interactions and regulate gene expression.

METHODS

We aimed to disrupt QS using quorum quenching (QQ) lactonases GcL and SsoPox, which cleave AHL signaling molecules in a taxa-specific manner based on differing enzyme affinities for different substrates. We hypothesized that QQ hinders signals from obesity-associated pathobionts, thereby slowing or preventing obesity.

RESULTS

In a murine model of diet-induced obesity, we observed GcL and SsoPox treatments have separate sex-dependent and dose-dependent effects on intestinal community composition and diversity. Notably, male mice given 2 mg/mL SsoPox exhibited significant changes in the relative abundances of gram-negative taxa, including Porphyromonadaceae, Akkermansiaceae, Muribaculaceae, and Bacteroidales (Kruskal-Wallis p < 0.001). Additionally, we used covariance matrix network analysis to model bacterial taxa co-occurrence due to QQ enzyme administration. There were more associations among taxa in control mice, particularly among gram-negative bacteria, whereas mice receiving SsoPox had the fewest associations.

CONCLUSIONS

Overall, our study establishes proof of concept that QQ is a targetable strategy for microbial control in vivo. Further characterization and dosage optimization of QQ enzymes are necessary to harness their therapeutic capability for the treatment of chronic microbial-associated diseases.

Frontiers in superbug management: innovating approaches to combat antimicrobial resistance

Anti-microbial resistance (AMR) is a global health issue causing significant mortality and economic burden. Pharmaceutical companies' discontinuation of research hinders new agents, while MDR pathogens or "superbugs" worsen the problem. Superbugs pose a threat to common infections and medical procedures, exacerbated by limited antibiotic development and rapid antibiotic resistance. The rising tide of antimicrobial resistance threatens to undermine progress in controlling infectious diseases. This review examines the global proliferation of AMR, its underlying mechanisms, and contributing factors. The study explores various methodologies, emphasizing the significance of precise and timely identification of resistant strains. We discuss recent advancements in CRISPR/Cas9, nanoparticle technology, light-based techniques, and AI-powered antibiogram analysis for combating AMR. Traditional methods often fail to effectively combat multidrug-resistant bacteria, as CRISPR-Cas9 technology offers a more effective approach by cutting specific DNA sequences, precision targeting and genome editing. AI-based smartphone applications for antibiogram analysis in resource-limited settings face challenges like internet connectivity, device compatibility, data quality, energy consumption, and algorithmic limitations. Additionally, light-based antimicrobial techniques are increasingly being used to effectively kill antibiotic-resistant microbial species and treat localized infections. This review provides an in-depth overview of AMR covering epidemiology, evolution, mechanisms, infection prevention, control measures, antibiotic access, stewardship, surveillance, challenges and emerging non-antibiotic therapeutic approaches.

Fungal quorum sensing molecules as potential drugs in the treatment of chronic wounds and their delivery

INTRODUCTION

Chronic non-healing wounds have emerged as a significant global healthcare challenge. Biofilm induced wound infections has been widely acknowledged. Despite the advanced understanding of biofilm formation, the existing approaches for diagnosing biofilms in wounds remain considerably suboptimal. Chemical signals produced by fungi to sense their environment, known as quorum sensing (QS) molecules are anticipated to cause revolution in non-healing wound antisepsis.

AREAS COVERED

Biofilms render chronic wounds resistant to treatment and impede tissue repair by inducing chronic inflammation. QS is a biochemical signaling pathway that involves certain secreted molecules, namely phenylethanoids, indolyl, and sesquiterpene alcohols that can significantly minimize and obliterate bacterial biofilms if properly applied and released in wound treatments.

EXPERT OPINION

QS molecules (QSMs) possess inhibitory properties that obstruct the formation of microbial biofilms and exhibit synergism with common antimicrobials. They can disrupt biofilms formed by drug-resistant microorganisms. The understanding of the current mechanisms and advancements in the utilization of QSMs within diverse drug delivery systems, and their release dynamics will be crucial in new drug design and delivery. Exploration of co-delivery of drugs alongside QS molecules, and assessing their impact on healing of chronic wounds before moving to clinical trials remain unaddressed.

The diffusible signaling factor family in microbial signaling: a current perspective

This review discusses the chemical properties, synthesis and detection, and biological functions of a molecular group of cis-2-unsaturated fatty acids, containing fatty acid carbon chains of various lengths and cis double-bond configurations, known as the diffusible signaling factor family (DSFF). Early postulation of the conserved nature of the DSFF among Gram-negative bacteria have now been challenged by the latest evidences that unraveled their presence in a various other distinct microorganisms. Over the last decade, a significant depth and breadth of understanding has been made on the multifaceted functions of DSFFs among bacteria, and their interactions with evolutionarily divergent fungi, plants insects and small animals. While the knowledge of the chemical nature and functions of DSFF within microbial systems is still developing, DSFF molecules such as BDSF, DSF, and SDSF have been found to modulate microbial virulence, cell adhesion, biofilm formation and dispersion, cell motility, and antimicrobial tolerance. Given their capacity to influence microbial ecosystems and the rapid emergence of novel DSFF-like molecules, it is critical to identify the full spectrum of DSFF members and to better understand the functions of this complex messenger system as they offer significant potential to be exploited in the development of new therapeutic strategies to combat the rising global healthcare threat of antimicrobial resistance. This narrative review therefore provides a broad picture of the DSFF quorum sensing with a core foundation built from seminal literature while highlighting the latest developments in the field.

Biochemistry of Bacterial Biofilm: Insights into Antibiotic Resistance Mechanisms and Therapeutic Intervention

Biofilms, composed of structured communities of bacteria embedded in a self-produced extracellular matrix, pose a significant challenge due to their heightened resistance to antibiotics and immune responses. This review highlights the mechanisms underpinning antibiotic resistance within bacterial biofilms, elucidating the adaptive strategies employed by microorganisms to withstand conventional antimicrobial agents. This encompasses the role of the extracellular matrix, altered gene expression, and the formation of persister cells, contributing to the recalcitrance of biofilms to eradication. A comprehensive understanding of these resistance mechanisms provides a for exploring innovative therapeutic interventions. This study explores promising avenues for future research, emphasizing the necessity of uncovering the specific genetic and phenotypic adaptations occurring within biofilms. The identification of vulnerabilities in biofilm architecture and the elucidation of key biofilm-specific targets emerge as crucial focal points for the development of targeted therapeutic strategies. In addressing the limitations of traditional antibiotics, this review discusses innovative therapeutic approaches. Nanomaterials with inherent antimicrobial properties, quorum-sensing inhibitors disrupting bacterial communication, and bacteriophages as biofilm-specific viral agents are highlighted as potential alternatives. The exploration of combination therapies, involving antimicrobial agents, biofilm-disrupting enzymes, and immunomodulators, is emphasized to enhance the efficacy of existing treatments and overcome biofilm resilience.

Quorum sensing: the "switch" in the competitive relationship between Gram-positive bacteria based on transcriptomic analysis

Competition phenomenon is widely presented in nature, however, few reports on the competition phenomenon between bacteria based on the perspective of quorum sensing (QS), especially between Gram-positive bacteria. Here, the Gram-positive bacteria Rhodococcus sp. HD1 and Microbacterium sp. HM-2 were co-cultured, and the epiphysiological indicators, transcriptomics combined with gene engineering technique were applied to clarify the role of QS in the competition between Gram-positive bacteria. The results showed that the morphology of strain HD1 was changed into ellipsoids from long rods, the surface-to-volume ratio increased, and the competition index increased within strains HM-2 and HD1. The biomass of strain HD1(8.06×107 CFU/mL) was decreased significantly (p＜0.05) under co-culture system, compared with mono-culture (5.75×108 CFU/mL), indicating that strain HM-2 had an inhibitory effect on HD1 at 12 h. Transcriptomic analysis revealed that QS-related genes were highly expressed in strain HM-2, and the expression level of the virulence gene TM_0352 was the highest (FPKM: 1774.19). Meanwhile, the ABC transporters-related genes in strain HD1 were significantly increased. Furthermore, QS pathway-related genes in strain HM-2 and ABC transporters-related genes in strain HD1 showed a significant correlation with the gene TM_0352 expression by the Mantel test analysis (p<0.05), surmising that the TM_0352 gene played a dominant role in the co-culture system. Knockout and complementation experiments confirmed that the function of gene TM_0352. The structural equation model showed that the QS up-regulation of strain HM-2 significantly promoted the expression of virulence genes, while strain HD1 promoted ABC transporters to cope with the up-regulation of TM_0352. The up-regulation of TM_0352 promoted the biomass of strain HM-2 and inhibited the biomass of HD1.The above results displayed that the competition phenomenon appeared by QS driving the up-regulation of TM_0352 gene in strain HM-2, which led to the up-regulation of ABC transporters in strain HD1. And these findings provided new insights into the perspective of factors related to competition inhibition between bacteria.

Microbial enzymes as powerful natural anti-biofilm candidates

Bacterial biofilms pose significant challenges, from healthcare-associated infections to biofouling in industrial systems, resulting in significant health impacts and financial losses globally. Classic antimicrobial methods often fail to eradicate sessile microbial communities within biofilms, requiring innovative approaches. This review explores the structure, formation, and role of biofilms, highlighting the critical importance of exopolysaccharides in biofilm stability and resistance mechanisms. We emphasize the potential of microbial enzymatic approaches, particularly focusing on glycosidases, proteases, and deoxyribonucleases, which can disrupt biofilm matrices effectively. We also delve into the importance of enzymes such as cellobiose dehydrogenase, which disrupts biofilms by degrading polysaccharides. This enzyme is mainly sourced from Aspergillus niger and Sclerotium rolfsii, with optimized production strategies enhancing its efficacy. Additionally, we explore levan hydrolase, alginate lyase, α-amylase, protease, and lysostaphin as potent antibiofilm agents, discussing their microbial origins and production optimization strategies. These enzymes offer promising avenues for combating biofilm-related challenges in healthcare, environmental, and industrial settings. Ultimately, enzymatic strategies present environmentally friendly solutions with high potential for biofilm management and infection control.

Enzymatic Regulation of the Gut Microbiota: Mechanisms and Implications for Host Health

The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical reactions that have an impact on the gut microbial community, affecting both the microorganisms and the gut environment. Enzymes play an important role in the regulation of the intestinal microbiota, but the interactions between enzymes and microbial communities, as well as the precise mechanisms of enzymes, remain a challenge in scientific research. Enzymes serve both traditional nutritional functions, such as the breakdown of complex substrates into absorbable small molecules, and non-nutritional roles, which encompass antibacterial function, immunomodulation, intestinal health maintenance, and stress reduction, among others. This study categorizes enzymes according to their source and explores the mechanistic principles by which enzymes drive gut microbial activity, including the promotion of microbial proliferation, the direct elimination of harmful microbes, the modulation of bacterial interaction networks, and the reduction in immune stress. A systematic understanding of enzymes in regulating the gut microbiota and the study of their associated molecular mechanisms will facilitate the application of enzymes to precisely regulate the gut microbiota in the future and suggest new therapeutic strategies and dietary recommendations. In conclusion, this review provides a comprehensive overview of the role of enzymes in modulating the gut microbiota. It explores the underlying molecular and cellular mechanisms and discusses the potential applications of enzyme-mediated microbiota regulation for host gut health.

Targeting quorum sensing for manipulation of commensal microbiota

Bacteria communicate through the accumulation of autoinducer (AI) molecules that regulate gene expression at critical densities in a process called quorum sensing (QS). Extensive work using simple systems and single strains of bacteria have revealed a role for QS in the regulation of virulence factors and biofilm formation; however, less is known about QS dynamics among communities, especially in vivo. In this review, we summarize the diversity of QS signals as well as their ability to influence "non-target" behaviors among species that have receptors but not synthases for those signals. We highlight host-microbe interactions facilitated by QS and describe cross-talk between QS and the mammalian endocrine and immune systems, as well as host surveillance of QS. Further, we describe emerging evidence for the role of QS in non-infectious, chronic, microbially associated diseases including inflammatory bowel diseases and cancers. Finally, we describe potential therapeutic approaches that involve leveraging QS signals as well as quorum quenching approaches to block signaling in vivo to mitigate deleterious consequences to the host. Ultimately, QS offers a previously underexplored target that may be leveraged for precision modification of the microbiota without deleterious bactericidal consequences.

Unraveling the role of UilS, a urea-induced acyl-homoserine lactonase that enhances Serratia marcescens fitness, interbacterial competition, and urinary tract infection

Serratia marcescens, a member of the Enterobacteriaceae family, is an opportunistic human pathogen and a frequent cause of urinary tract infections. Clinical isolates often exhibit resistance to multiple antibiotics, posing challenges for successful treatment. Understanding its pathogenic mechanisms is crucial for elucidating new potential targets to develop effective therapeutic interventions and manage S. marcescens infections. This work identifies urea-induced lactonase of Serratia (UilS), a lactonase encoded in the S. marcescens RM66262 strain isolated from a patient with a urinary tract infection. The study explores the bacterium's response to urea, a major component of urine, and its impact on uilS expression. We found that UilS degrades acyl-homoserine lactones (AHL) autoinducers traditionally associated with quorum sensing mechanisms. Surprisingly, UilS is able to degrade self and non-self AHL, exhibiting quorum-quenching activity toward Pseudomonas aeruginosa. We found that LuxR regulates uilS expression that is enhanced in the presence of AHL. In addition, urea-dependent induction of UilS expression is controlled by the transcriptional response regulator CpxR. UilS confers fitness advantage to S. marcescens, especially in the presence of urea, emphasizing the adaptive plasticity of strains to modulate gene expression based on environmental signals and population density. We also discovered a novel bacterial killing capacity of S. marcescens that involves UilS, indicating its importance in the interspecies interaction of Serratia. Finally, we found that a uilS mutant strain displays attenuated colonization in a mouse model of catheter-associated urinary tract infection. uilS is present in clinical but absent in environmental isolates, suggesting an evolutionary adaptation to host-specific selective pressures.

IMPORTANCE

This work reveals the acyl-homoserine lactonase urea-induced lactonase of Serratia as a novel virulence factor of Serratia marcescens, unraveling a potential target to develop antimicrobial strategies and shedding light on the complex regulatory network governing pathogenicity and adaptation to host environments.

Insights into Women's health: Exploring the vaginal microbiome, quorum sensing dynamics, and therapeutic potential of quorum sensing quenchers

The vaginal microbiome is an important aspect of women's health that changes dynamically with various stages of the woman's life. Just like the gut microbiome, the vaginal microbiome can also be affected by pathologies that dramatically change the typical composition of native vaginal microorganisms. However, the mechanism as to how both vaginal endemic and gut endemic opportunistic microbes can express pathogenicity in vaginal polymicrobial biofilms is poorly understood. Quorum sensing is the cellular density-dependent bacterial and fungal communication process in which chemical signaling molecules, known as autoinducers, activate expression for genes responsible for virulence and pathogenicity, such as biofilm formation and virulence factor production. Quorum sensing inhibition, or quorum quenching, has been explored as a potential therapeutic route for both bacterial and fungal infections. By applying these quorum quenchers, one can reduce biofilm formation of opportunistic vaginal microbes and combine them with antibiotics for a synergistic effect. This review aims to display the relationship between the vaginal and gut microbiome, the role of quorum sensing in polymicrobial biofilm formation which cause pathology in the vaginal microbiome, and how quorum quenchers can be utilized to attenuate the severity of bacterial and fungal infections.

Molecular characterization of Klebsiella pneumoniae in clinical bovine mastitis in 14 provinces in China

The mastitis caused by Klebsiella pneumoniae (K. pneumoniae) is increasing in the dairy cows. To investigate the epidemic of K. pneumoniae of China, 131 strains were isolated from 495 clinical mastitis milk samples (26.5%) from 14 provinces in China. Among the isolates, K57 was the dominant serotype (45.0%) and 19 (14.5%) isolates were identified as hypervirulent K. pneumoniae (hvKP). The mrkA, entB, wabG and fimH genes were prevalent virulence genes while rmpA, magA, and ycf were not found in K. pneumoniae. Furthermore, K. pneumoniae had serious antibiotic resistance and multiple β-lactamase genes, including blaTEM, blaSHV, blaNDM, blaCTX-M, blaDHA, and blaKPC. Biofilm was an important factor in bacterial resistance and persistent infection, and 77.1% isolates could form biofilm. Although acylated homoserine lactone (AHL, a Gram-negative bacterial quorum sensing signal molecule) was not confirmed among the K. pneumoniae isolates, exogenous AHLs could reduce the biofilm formation ability of the K. pneumoniae strains. Three new ST types (ST6781, ST6782, and ST6783) were first identified in this study. The MLST phylogenetic tree showed the distribution of mastitis associated K. pneumoniae strains had no regular pattern, which confirmed high genomic diversity of mastitis associated K. pneumoniae. In conclusion, the high rate of isolation and serious antibiotic resistance of K. pneumonia were found in this study and indicated a potential threat to public health from the food chain.

Strategies for quorum sensing inhibition as a tool for controlling Pseudomonas aeruginosa infections

Antibiotic resistance is one of the most important concerns in global health today. A growing number of infections are becoming harder to treat with conventional drugs and fewer new antibiotics are being developed. In this context, strategies based on blocking or attenuating virulence pathways that do not focus on eradication of bacteria are potential therapeutic approaches that should reduce the selective pressure exerted on the pathogen. This virulence depletion can be achieved by inhibiting the conserved quorum sensing (QS) system, a mechanism that enables bacteria to communicate with one another in a density-dependent manner. QS regulates gene expression, leading to the activation of important processes such as virulence and biofilm formation. This review highlights the approaches reported so far for disrupting different steps of the QS system of the multiresistant pathogen Pseudomonas aeruginosa. The authors describe different types of molecules (including enzymes, natural and synthetic small molecules, and antibodies) already identified as P. aeruginosa quorum quenchers (QQs) or QS inhibitors (QSIs), grouped according to the QS circuit that they block (Las, Rhl, Pqs and some examples from the controversial pathway Iqs). The discovery of new QQs and QSIs is expected to help reduce antibiotic doses, or at least to provide options that act as adjuvants to enhance the effect of antibiotic treatment. Moreover, this article outlines the advantages and possible drawbacks of each strategy and provides perspectives on the potential developments in this field in the future.

Gum Arabic as a potential candidate in quorum quenching and treatment of periodontal diseases

Periodontal diseases are chronic inflammatory conditions influenced by bacterial biofilm formation and host immune responses, affecting millions worldwide. Traditional treatments like mechanical debridement and systemic antibiotics often face limitations, including biofilm resilience and antibiotic resistance. Gum Arabic (GA), a natural exudate from Acacia trees, presents a promising alternative with its anti-biofilm and anti-inflammatory properties. This review highlights the role of GA in periodontal therapy, particularly its ability to interfere with quorum sensing (QS) pathways, specifically the AI-2 signaling system used by key periodontal pathogens such as Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Fusobacterium nucleatum. By disrupting QS, GA inhibits biofilm formation, reduces bacterial virulence, and promotes a balanced oral microbiome. GA's prebiotic properties also encourage the growth of beneficial bacteria, enhancing the host's immune response while preserving the systemic microbiome. Clinical studies demonstrate GA's effectiveness as an adjunct in periodontal therapy, with significant reductions in plaque accumulation, gingival inflammation, and bleeding. This highlights GA's potential as a natural therapeutic agent, offering an effective, antibiotic-sparing option in managing periodontal disease. However, further research is warranted to fully establish GA's role in comprehensive periodontal care and its long-term benefits.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N-acyl L-homoserine lactones (AHLs). They play a role in a microbial communication system known as quorum sensing, which contributes to pathogenicity and biofilm formation. Designing quorum quenching (QQ) enzymes that can interfere with this communication allows them to be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific communication signals requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of GcL, which is a highly proficient and thermostable MLL with broad substrate specificity. We show that GcL not only accepts a broad range of substrates but also hydrolyzes these substrates through at least two different mechanisms. Further, the preferred mechanism appears to depend on both the substrate structure and/or the nature of the residues lining the active site. We demonstrate that other lactonases, such as AiiA and AaL, show similar mechanistic promiscuity, suggesting that this is a shared feature among MLLs. Mechanistic promiscuity has been seen previously in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and protein engineering perspective: in addition to optimizing for specific substrates, it may be possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes but also of other mechanistically promiscuous enzymes.

Recent Development in Detection and Control of Psychrotrophic Bacteria in Dairy Production: Ensuring Milk Quality

Milk is an ideal environment for the growth of microorganisms, especially psychrotrophic bacteria, which can survive under cold conditions and produce heat-resistant enzymes. Psychrotrophic bacteria create the great problem of spoiling milk quality and safety. Several ways that milk might get contaminated by psychrotrophic bacteria include animal health, cowshed hygiene, water quality, feeding strategy, as well as milk collection, processing, etc. Maintaining the quality of raw milk is critically essential in dairy processing, and the dairy sector is still affected by the premature milk deterioration of market-processed products. This review focused on the recent detection and control strategies of psychrotrophic bacteria and emphasizes the significance of advanced sensing methods for early detection. It highlights the ongoing challenges in the dairy industry caused by these microorganisms and discusses future perspectives in enhancing milk quality through innovative rapid detection methods and stringent processing controls. This review advocates for a shift towards more sophisticated on-farm detection technologies and improved control practices to prevent spoilage and economic losses in the dairy sector.

Molecular insights into PGPR fluorescent Pseudomonads complex mediated intercellular and interkingdom signal transduction mechanisms in promoting plant's immunity

The growth-promoting and immune modulatory properties of different strains of plant growth promoting rhizobacteria (PGPR) fluorescent Pseudomonads complex (PFPC) can be explored to combat food security challenges. These PFPC prime plants through induced systemic resistance, fortify plants to overcome future pathogen-mediated vulnerability by eliciting robust systemic acquired resistance through regulation by nonexpressor of pathogenesis-related genes 1. Moreover, outer membrane vesicles released from Pseudomonas fluorescens also elicit a broad spectrum of immune responses, presenting a rapid viable alternative to whole cells. Thus, PFPC can help the host to maintain an equilibrium between growth and immunity, ultimately leads to increased crop yield.

Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa

The switch between planktonic and biofilm lifestyle correlates with intracellular concentration of the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). While bacteria possess cyclase and phosphodiesterase enzymes to catalyse formation or hydrolysis of c-di-GMP, both enzymatic domains often occur in a single protein. It is tacitly assumed that one of the two enzymatic activities is dominant, and that additional domains and protein interactions enable responses to environmental conditions and control activity. Here we report the structure of the phosphodiesterase domain of the membrane protein RbdA (regulator of biofilm dispersal) in a dimeric, activated state and show that phosphodiesterase activity is controlled by the linked cyclase. The phosphodiesterase region around helices α5/α6 forms the dimer interface, providing a rationale for activation, as this region was seen in contact with the cyclase domain in an auto-inhibited structure previously described. Kinetic analysis supports this model, as the activity of the phosphodiesterase alone is lower when linked to the cyclase. Analysis of a computed model of the RbdA periplasmatic domain reveals an all-helical architecture with a large binding pocket that could accommodate putative ligands. Unravelling the regulatory circuits in multi-domain phosphodiesterases like RbdA is important to develop strategies to manipulate or disperse bacterial biofilms.

Novel Insights into the Antimicrobial and Antibiofilm Activity of Pyrroloquinoline Quinone (PQQ); In Vitro, In Silico, and Shotgun Proteomic Studies

Microbial infections pose a significant global health threat, affecting millions of individuals and leading to substantial mortality rates. The increasing resistance of microorganisms to conventional treatments requires the development of novel antimicrobial agents. Pyrroloquinoline quinone (PQQ), a natural medicinal drug involved in various cellular processes, holds promise as a potential antimicrobial agent. In the present study, our aim was, for the first time, to explore the antimicrobial activity of PQQ against 29 pathogenic microbes, including 13 fungal strains, 8 Gram-positive bacteria, and 8 Gram-negative bacteria. Our findings revealed potent antifungal properties of PQQ, particularly against Syncephalastrum racemosum, Talaromyces marneffei, Candida lipolytica, and Trichophyton rubrum. The MIC values varied between fungal strains, and T. marneffei exhibited a lower MIC, indicating a greater susceptibility to PQQ. In addition, PQQ exhibited notable antibacterial activity against Gram-positive and -negative bacteria, with a prominent inhibition observed against Staphylococcus epidermidis, Proteus vulgaris, and MRSA strains. Remarkably, PQQ demonstrated considerable biofilm inhibition against the MRSA, S. epidermidis, and P. vulgaris strains. Transmission electron microscopy (TEM) studies revealed that PQQ caused structural damage and disrupted cell metabolism in bacterial cells, leading to aberrant morphology, compromised cell membrane integrity, and leakage of cytoplasmic contents. These findings were further affirmed by shotgun proteomic analysis, which revealed that PQQ targets several important cellular processes in bacteria, including membrane proteins, ATP metabolic processes, DNA repair processes, metal-binding proteins, and stress response. Finally, detailed molecular modeling investigations indicated that PQQ exhibits a substantial binding affinity score for key microbial targets, including the mannoprotein Mp1P, the transcriptional regulator TcaR, and the endonuclease PvuRTs1I. Taken together, our study underscores the effectiveness of PQQ as a broad-spectrum antimicrobial agent capable of combating pathogenic fungi and bacteria, while also inhibiting biofilm formation and targeting several critical biological processes, making it a promising therapeutic option for biofilm-related infections.

Screening and isolation of quorum sensing inhibitors of Pseudomonas aeruginosa from Phellodendron amurense extracts using bio-affinity chromatography

Drug-resistant bacterial infections pose a significant challenge in the field of bacterial disease treatment. Finding new antibacterial pathways and targets to combat drug-resistant bacteria is crucial. The bacterial quorum sensing (QS) system regulates the expression of bacterial virulence factors. Inhibiting bacterial QS and reducing bacterial virulence can achieve antibacterial therapeutic effects, making QS inhibition an effective strategy to control bacterial pathogenicity. This article mainly focused on the PqsA protein in the QS system of Pseudomonas aeruginosa. An affinity chromatography medium was developed using the SpyTag/SpyCatcher heteropeptide bond system. Berberine, which can interact with the PqsA target, was screened from Phellodendron amurense by affinity chromatography. We characterized its structure, verified its inhibitory activity on P. aeruginosa, and preliminarily analyzed its mechanism using molecular docking technology. This method can also be widely applied to the immobilization of various protein targets and the effective screening of active substances.

Review of quorum-quenching probiotics: A promising non-antibiotic-based strategy for sustainable aquaculture

The emergence of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquaculture underscores the urgent need for alternative veterinary strategies to combat antimicrobial resistance (AMR). These measures are vital to reduce the likelihood of entering a post-antibiotic era. Identifying environmentally friendly biotechnological solutions to prevent and treat bacterial diseases is crucial for the sustainability of aquaculture and for minimizing the use of antimicrobials, especially antibiotics. The development of probiotics with quorum-quenching (QQ) capabilities presents a promising non-antibiotic strategy for sustainable aquaculture. Recent research has demonstrated the effectiveness of QQ probiotics (QQPs) against a range of significant fish pathogens in aquaculture. QQ disrupts microbial communication (quorum sensing, QS) by inhibiting the production, replication, and detection of signalling molecules, thereby reducing bacterial virulence factors. With their targeted anti-virulence approach, QQPs have substantial promise as a potential alternative to antibiotics. The application of QQPs in aquaculture, however, is still in its early stages and requires additional research. Key challenges include determining the optimal dosage and treatment regimens, understanding the long-term effects, and integrating QQPs with other disease control methods in diverse aquaculture systems. This review scrutinizes the current literature on antibiotic usage, AMR prevalence in aquaculture, QQ mechanisms and the application of QQPs as a sustainable alternative to antibiotics.

Regulation of anti-phage defense mechanisms by using cinnamaldehyde as a quorum sensing inhibitor

Background

Multidrug-resistant bacteria and the shortage of new antibiotics constitute a serious health problem. This problem has led to increased interest in the use of bacteriophages, which have great potential as antimicrobial agents but also carry the risk of inducing resistance. The objective of the present study was to minimize the development of phage resistance in Klebsiella pneumoniae strains by inhibiting quorum sensing (QS) and thus demonstrate the role of QS in regulating defense mechanisms.

Results

Cinnamaldehyde (CAD) was added to K. pneumoniae cultures to inhibit QS and thus demonstrate the role of the signaling system in regulating the anti-phage defense mechanism. The QS inhibitory activity of CAD in K. pneumoniae was confirmed by a reduction in the quantitative expression of the lsrB gene (AI-2 pathway) and by proteomic analysis. The infection assays showed that the phage was able to infect a previously resistant K. pneumoniae strain in the cultures to which CAD was added. The results were confirmed using proteomic analysis. Thus, anti-phage defense-related proteins from different systems, such as cyclic oligonucleotide-based bacterial anti-phage signaling systems (CBASS), restriction-modification (R-M) systems, clustered regularly interspaced short palindromic repeat-Cas (CRISPR-Cas) system, and bacteriophage control infection (BCI), were present in the cultures with phage but not in the cultures with phage and CAD. When the QS and anti-phage defense systems were inhibited by the combined treatment, proteins related to phage infection and proliferation, such as the tail fiber protein, the cell division protein DamX, and the outer membrane channel protein TolC, were detected.

Conclusion

Inhibition of QS reduces phage resistance in K. pneumoniae, resulting in the infection of a previously resistant strain by phage, with a significant increase in phage proliferation and a significant reduction in bacterial growth. QS inhibitors could be considered for therapeutic application by including them in phage cocktails or in phage-antibiotic combinations to enhance synergistic effects and reduce the emergence of antimicrobial resistance.

Bacillus Strains as Effective Biocontrol Agents Against Phytopathogenic Bacteria and Promoters of Plant Growth

Modern crop production relies on the application of chemical pesticides and fertilizers causing environmental and economic challenges. In response, less environmentally impactful alternatives have emerged such as the use of beneficial microorganisms. These microorganisms, particularly plant growth-promoting bacteria (PGPB), have demonstrated their ability to enhance plant growth, protect against various stresses, and reduce the need for chemical inputs. Among the PGPB, Bacillus species have garnered attention due to their adaptability and commercial potential. Recent reports have highlighted Bacillus strains as biocontrol agents against phytopathogenic bacteria while concurrently promoting plant growth. We also examined Bacillus plant growth-promoting abilities in Arabidopsis thaliana seedlings. In this study, we assessed the potential of various Bacillus strains to control diverse phytopathogenic bacteria and inhibit quorum sensing using Chromobacterium violaceum as a model system. In conclusion, our results suggest that bacteria of the genus Bacillus hold significant potential for biotechnological applications. This includes developments aimed at reducing agrochemical use, promoting sustainable agriculture, and enhancing crop yield and protection.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.

An In-Depth Study on the Inhibition of Quorum Sensing by Bacillus velezensis D-18: Its Significant Impact on Vibrio Biofilm Formation in Aquaculture

Amid growing concerns about antibiotic resistance, innovative strategies are imperative in addressing bacterial infections in aquaculture. Quorum quenching (QQ), the enzymatic inhibition of quorum sensing (QS), has emerged as a promising solution. This study delves into the QQ capabilities of the probiotic strain Bacillus velezensis D-18 and its products, particularly in Vibrio anguillarum 507 communication and biofilm formation. Chromobacterium violaceum MK was used as a biomarker in this study, and the results confirmed that B. velezensis D-18 effectively inhibits QS. Further exploration into the QQ mechanism revealed the presence of lactonase activity by B. velezensis D-18 that degraded both long- and short-chain acyl homoserine lactones (AHLs). PCR analysis demonstrated the presence of a homologous lactonase-producing gene, ytnP, in the genome of B. velezensis D-18. The study evaluated the impact of B. velezensis D-18 on V. anguillarum 507 growth and biofilm formation. The probiotic not only controls the biofilm formation of V. anguillarum but also significantly restrains pathogen growth. Therefore, B. velezensis D-18 demonstrates substantial potential for preventing V. anguillarum diseases in aquaculture through its QQ capacity. The ability to disrupt bacterial communication and control biofilm formation positions B. velezensis D-18 as a promising eco-friendly alternative to conventional antibiotics in managing bacterial diseases in aquaculture.

AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria

Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.

Biofilm inhibition/eradication: exploring strategies and confronting challenges in combatting biofilm

Biofilms are complex communities of microorganisms enclosed in a self-produced extracellular matrix, posing a significant threat to different sectors, including healthcare and industry. This review provides an overview of the challenges faced due to biofilm formation and different novel strategies that can combat biofilm formation. Bacteria inside the biofilm exhibit increased resistance against different antimicrobial agents, including conventional antibiotics, which can lead to severe problems in livestock and animals, including humans. In addition, biofilm formation also imposes heavy economic pressure on industries. Hence it becomes necessary to explore newer alternatives to eradicate biofilms effectively without applying selection pressure on the bacteria. Excessive usage of antibiotics may also lead to an increase in the number of resistant strains as bacteria employ an advanced antimicrobial resistance mechanism. This review provides insight into multifaceted technologies like quorum sensing inhibition, enzymes, antimicrobial peptides, bacteriophage, phytocompounds, and nanotechnology to neutralize biofilms without developing antimicrobial resistance (AMR). Furthermore, it will pave the way for developing newer therapeutic agents to deal with biofilms more efficiently.

A novel thermostable YtnP lactonase from Stenotrophomonas maltophilia inhibits Pseudomonas aeruginosa virulence in vitro and in vivo

Infections caused by multidrug-resistant pathogens are one of the biggest challenges facing the healthcare system today. Quorum quenching (QQ) enzymes have the potential to be used as innovative enzyme-based antivirulence therapeutics to combat infections caused by multidrug-resistant pathogens. The main objective of this research was to describe the novel YtnP lactonase derived from the clinical isolate Stenotrophomonas maltophilia and to investigate its antivirulence potential against multidrug-resistant Pseudomonas aeruginosa MMA83. YtnP lactonase, the QQ enzyme, belongs to the family of metallo-β-lactamases. The recombinant enzyme has several advantageous biotechnological properties, such as high thermostability, activity in a wide pH range, and no cytotoxic effect. High-performance liquid chromatography analysis revealed the activity of recombinant YtnP lactonase toward a wide range of N-acyl-homoserine lactones (AHLs), quorum sensing signaling molecules, with a higher preference for long-chain AHLs. Recombinant YtnP lactonase was shown to inhibit P. aeruginosa MMA83 biofilm formation, induce biofilm decomposition, and reduce extracellular virulence factors production. Moreover, the lifespan of MMA83-infected Caenorhabditis elegans was prolonged with YtnP lactonase treatment. YtnP lactonase showed synergistic inhibitory activity in combination with gentamicin and acted additively with meropenem against MMA83. The described properties make YtnP lactonase a promising therapeutic candidate for the development of next-generation antivirulence agents.

Enzymes with Lactonase Activity against Fungal Quorum Molecules as Effective Antifungals

Since the growing number of fungi resistant to the fungicides used is becoming a serious threat to human health, animals, and crops, there is a need to find other effective approaches in the eco-friendly suppression of fungal growth. One of the main mechanisms of the development of resistance in fungi, as well as in bacteria, to antimicrobial agents is quorum sensing (QS), in which various lactone-containing compounds participate as signaling molecules. This work aimed to study the effectiveness of action of enzymes exhibiting lactonase activity against fungal signaling molecules. For this, the molecular docking method was used to estimate the interactions between these enzymes and different lactone-containing QS molecules of fungi. The catalytic characteristics of enzymes such as lactonase AiiA, metallo-β-lactamase NDM-1, and organophosphate hydrolase His6-OPH, selected for wet experiments based on the results of computational modeling, were investigated. QS lactone-containing molecules (butyrolactone I and γ-heptalactone) were involved in the experiments as substrates. Further, the antifungal activity of the enzymes was evaluated against various fungal and yeast cells using bioluminescent ATP-metry. The efficient hydrolysis of γ-heptalactone by all three enzymes and butyrolactone I by His6-OPH was demonstrated for the first time. The high antifungal efficacy of action of AiiA and NDM-1 against most of the tested fungal cells was revealed.

N-acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque

N-acyl homoserine lactones (AHLs) are small diffusible signaling molecules that mediate a cell density-dependent bacterial communication system known as quorum sensing (QS). AHL-mediated QS regulates gene expression to control many critical bacterial behaviors including biofilm formation, pathogenicity, and antimicrobial resistance. Dental plaque is a complex multispecies oral biofilm formed by successive colonization of the tooth surface by groups of commensal, symbiotic, and pathogenic bacteria, which can contribute to tooth decay and periodontal diseases. While the existence and roles of AHL-mediated QS in oral microbiota have been debated, recent evidence indicates that AHLs play significant roles in oral biofilm development and community dysbiosis. The underlying mechanisms, however, remain poorly characterized. To better understand the importance of AHL signaling in dental plaque formation, we manipulated AHL signaling by adding AHL lactonases or exogenous AHL signaling molecules. We find that AHLs can be detected in dental plaque grown under 5% CO2 conditions, but not when grown under anaerobic conditions, and yet anaerobic cultures are still responsive to AHLs. QS signal disruption using lactonases leads to changes in microbial population structures in both planktonic and biofilm states, changes that are dependent on the substrate preference of the used lactonase but mainly result in the increase in the abundance of commensal and pioneer colonizer species. Remarkably, the opposite manipulation, that is the addition of exogenous AHLs increases the abundance of late colonizer bacterial species. Hence, this work highlights the importance of AHL-mediated QS in dental plaque communities, its potential different roles in anaerobic and aerobic parts of dental plaque, and underscores the potential of QS interference in the control of periodontal diseases.

Disrupting quorum sensing as a strategy to inhibit bacterial virulence in human, animal, and plant pathogens

The development of sustainable alternatives to conventional antimicrobials is needed to address bacterial virulence while avoiding selecting resistant strains in a variety of fields, including human, animal, and plant health. Quorum sensing (QS), a bacterial communication system involved in noxious bacterial phenotypes such as virulence, motility, and biofilm formation, is of utmost interest. In this study, we harnessed the potential of the lactonase SsoPox to disrupt QS of human, fish, and plant pathogens. Lactonase treatment significantly alters phenotypes including biofilm formation, motility, and infection capacity. In plant pathogens, SsoPox decreased the production of plant cell wall degrading enzymes in Pectobacterium carotovorum and reduced the maceration of onions infected by Burkholderia glumae. In human pathogens, lactonase treatment significantly reduced biofilm formation in Acinetobacter baumannii, Burkholderia cepacia, and Pseudomonas aeruginosa, with the cytotoxicity of the latter being reduced by SsoPox treatment. In fish pathogens, lactonase treatment inhibited biofilm formation and bioluminescence in Vibrio harveyi and affected QS regulation in Aeromonas salmonicida. QS inhibition can thus be used to largely impact the virulence of bacterial pathogens and would constitute a global and sustainable approach for public, crop, and livestock health in line with the expectations of the One Health initiative.

Bacillus-based biocontrol beyond chemical control in central Africa: the challenge of turning myth into reality

Agricultural productivity in the Great Lakes Countries of Central Africa, including Burundi, Rwanda, and the Democratic Republic of Congo, is affected by a wide range of diseases and pests which are mainly controlled by chemical pesticides. However, more than 30% of the pesticides used in the region are banned in European Union due to their high toxicity. Globally available safe and eco-friendly biological alternatives to chemicals are virtually non-existent in the region. Bacillus PGPR-based biocontrol products are the most dominant in the market and have proven their efficacy in controlling major plant diseases reported in the region. With this review, we present the current situation of disease and pest management and urge the need to utilize Bacillus-based control as a possible sustainable alternative to chemical pesticides. A repertoire of strains from the Bacillus subtilis group that have shown great potential to antagonize local pathogens is provided, and efforts to promote their use, as well as the search for indigenous and more adapted Bacillus strains to local agro-ecological conditions, should be undertaken to make sustainable agriculture a reality in the region.

Transcriptome Reveals Regulation of Quorum Sensing of Hafnia alvei H4 on the Coculture System of Hafnia alvei H4 and Pseudomonas fluorescens ATCC13525

In the food industry, foodborne spoilage bacteria often live in mixed species and attach to each other, leading to changes in spoilage characteristics. Quorum sensing (QS) has been reported to be a regulating mechanism for food spoiling by certain kinds of bacteria. Here, the contents of biofilm, extracellular polysaccharides, and biogenic amines in the coculture system of Hafnia alvei H4 and Pseudomonas fluorescens ATCC13525 were significantly reduced when the QS element of H. alvei H4 was deleted, confirming that QS of H. alvei H4 is involved in the dual-species interactions. Then, transcriptomics was used to explore the regulatory mechanism at the mRNA molecular level. The deletion of the QS element decreased the transcript levels of genes related to chemotaxis, flagellar assembly, and the two-component system pathway of H. alvei H4 in the coculture system. Furthermore, a total of 732 DEGs of P. fluorescens ATCC13525 were regulated in the dual species, which were primarily concerned with biofilm formation, ATP-binding cassette transporters, and amino acid metabolism. Taken together, the absence of the QS element of H. alvei H4 weakened the mutual cooperation of the two bacteria in the coculture system, making it a good target for managing infection with H. alvei and P. fluorescens.

Emerging trends in the inhibition of bacterial molecular communication: An overview

Quorum sensing (QS) is a molecular cell-cell communication utilized by several bacteria and some fungi. It involves cell density dependent gene expression that includes extra polymeric substance production, sporulation, antibiotic production, motility, competence, symbiosis and conjugation. These expressions were carried out by different signaling molecules like acyl homo-serine lactone (AHL) and auto-inducing peptides (AIPs) which was effluxed by gram negative and gram positive bacteria. Pathogenic bacteria and biofilms often exhibit high resistance to antibiotics, attributed to the presence of antibiotic efflux pumps, reduced membrane permeability, and enzymes that deactivate quorum sensing (QS) inhibitors. To counteract virulence and multi-drug resistance (MDR), novel strategies such as employing quorum sensing (QS) inhibitors and quorum quenchers are employed. It targets signaling molecules with synthesis and prevents the signal from binding to receptors. In this present review, the mechanisms of QS along with inhibitors from different sources are described. These strategies potentially interfere with QS and it can be applied in different fields, mainly in hospitals and marine environments where the pathogenic infections and biofilm formation are highly involved.

Methyl gallate from Camellia nitidissima Chi flowers reduces quorum sensing related virulence and biofilm formation against Aeromonas hydrophila

Aeromonas hydrophila, a Gram-negative zoonotic bacterium, causes high mortality in fish farming and immunocompromised patients. This study aimed to extract methyl gallate (MG) from the flowers of Camellia nitidissima Chi and evaluate its potential as a quorum sensing inhibitor (QSI) against Aeromonas hydrophila SHAe 115. MG reduced QS-associated virulence factors, including hemolysis, protease, and lipase, while impairing swimming motility and biofilm formation. Additionally, MG down-regulated positive regulatory genes (ahyR, fleQ) and up-regulated negative regulators (litR, fleN). This highlights MG's promise as a potent QSI for A. hydrophila SHAe 115, advancing strategies against infections in aquaculture and human health.

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.

Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 biocontrol Dickeya soft rot diseases by quenching virulence factor modulating quorum sensing signal

Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading enzymes (PCWDEs) and virulence of Dickeya. High polarity and trace of VFM signal increase the difficulty of signal separation and structure identification, and thus limit the development of quorum quenching strategy to biocontrol bacterial soft rot diseases caused by Dickeya. In order to high-throughput screen VFM quenching bacteria, a vfmE-gfp biosensor VR2 (VFM Reporter) sensitive to VFM signal was first constructed. Subsequently, two bacterial strains with high quenching efficiency were screened out by fluorescence intensity measurement and identified as Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 using multilocus sequence analysis (MLSA). L5 and L95 supernatants reduced the expression of vfm genes, and both strains also decreased the production of PCWDEs of D. zeae MS2 and significantly reduced the virulence of D. oryzae EC1 on rice seedlings, D. zeae MS2 on banana seedlings, D. dadantii 3937 on potato and D. fangzhongdai CL3 on taro. Findings in this study provide a method to high-throughput screen VFM quenching bacteria and characterize novel functions of P. chlororaphis and E. asburiae in biocontrolling plant diseases through quenching VFM QS signal.

Quorum quenching by a type IVA secretion system effector

Proteobacteria primarily utilize acyl-homoserine lactones (AHLs) as quorum-sensing signals for intra-/interspecies communication to control pathogen infections. Enzymatic degradation of AHL represents the major quorum-quenching mechanism that has been developed as a promising approach to prevent bacterial infections. Here we identified a novel quorum-quenching mechanism revealed by an effector of the type IVA secretion system (T4ASS) in bacterial interspecies competition. We found that the soil antifungal bacterium Lysobacter enzymogenes OH11 (OH11) could use T4ASS to deliver the effector protein Le1288 into the cytoplasm of another soil microbiome bacterium Pseudomonas fluorescens 2P24 (2P24). Le1288 did not degrade AHL, whereas its delivery to strain 2P24 significantly impaired AHL production through binding to the AHL synthase PcoI. Therefore, we defined Le1288 as LqqE1 (Lysobacter quorum-quenching effector 1). Formation of the LqqE1-PcoI complex enabled LqqE1 to block the ability of PcoI to recognize/bind S-adenosy-L-methionine, a substrate required for AHL synthesis. This LqqE1-triggered interspecies quorum-quenching in bacteria seemed to be of key ecological significance, as it conferred strain OH11 a better competitive advantage in killing strain 2P24 via cell-to-cell contact. This novel quorum-quenching also appeared to be adopted by other T4ASS-production bacteria. Our findings suggest a novel quorum-quenching that occurred naturally in bacterial interspecies interactions within the soil microbiome by effector translocation. Finally, we presented two case studies showing the application potential of LqqE1 to block AHL signaling in the human pathogen Pseudomonas aeruginosa and the plant pathogen Ralstonia solanacearum.

Comparison of the efficacy of physical and chemical strategies for the inactivation of biofilm cells of foodborne pathogens

Biofilm formation is a strategy in which microorganisms generate a matrix of extracellular polymeric substances to increase survival under harsh conditions. The efficacy of sanitization processes is lowered when biofilms form, in particular on industrial devices. While various traditional and emerging technologies have been explored for the eradication of biofilms, cell resistance under a range of environmental conditions renders evaluation of the efficacy of control challenging. This review aimed to: (1) classify biofilm control measures into chemical, physical, and combination methods, (2) discuss mechanisms underlying inactivation by each method, and (3) summarize the reduction of biofilm cells after each treatment. The review is expected to be useful for future experimental studies and help to guide the establishment of biofilm control strategies in the food industry.

Eugenol works synergistically with colistin against colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae isolates by enhancing membrane permeability

Colistin is a potent antibiotic for the treatment of carbapenem-resistant Gram-negative bacteria and is considered a last-resort drug. Unfortunately, the incidence of colistin-resistant bacteria isolated from patients is continuously growing due to clinical reuse of colistin. In this study, we found that the combination of colistin and eugenol has a significant synergistic antibacterial effect and reverses the sensitivity of colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae against colistin, as confirmed by checkerboard and time-kill assays. Crystal violet staining and scanning electron microscopy revealed colistin and eugenol's synergistic antibiofilm action. Concerning the synergy mechanism, the results revealed that the combination of eugenol and colistin increases membrane permeability and causes considerable membrane damage, further inhibiting bacteria synergistically. Meanwhile, up to 500 µg/mL of eugenol is non-toxic to RAW 264.7 cells, and the colistin/eugenol combination is also efficacious in vivo, as demonstrated by the Galleria mellonella infection model. Our findings indicate that the colistin/eugenol combination is a viable treatment option for colistin-resistant P. aeruginosa and K. pneumoniae clinical infections. IMPORTANCE Colistin is used as a last resort for severe infections caused by multidrug-resistant Gram-negative bacteria, however, colistin resistance is increasing. As a result, we investigated the synergistic effect of eugenol/colistin combination, and the results revealed significant antibacterial and antibiofilm action. Eugenol may help clinical colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae recover their susceptibility. These findings suggest that combining eugenol and colistin may be a viable treatment option for colistin-resistant pathogen clinical infections.

Perturbation of Quorum Sensing after the Acquisition of Bacteriophage Resistance Could Contribute to Novel Traits in Vibrio alginolyticus

Bacteria employ a wide range of molecular mechanisms to confer resistance to bacteriophages, and these mechanisms are continuously being discovered and characterized. However, there are instances where certain bacterial species, despite lacking these known mechanisms, can still develop bacteriophage resistance through intricate metabolic adaptation strategies, potentially involving mutations in transcriptional regulators or phage receptors. Vibrio species have been particularly useful for studying the orchestrated metabolic responses of Gram-negative marine bacteria in various challenges. In a previous study, we demonstrated that Vibrio alginolyticus downregulates the expression of specific receptors and transporters in its membrane, which may enable the bacterium to evade infection by lytic bacteriophages. In our current study, our objective was to explore how the development of bacteriophage resistance in Vibrio species disrupts the quorum-sensing cascade, subsequently affecting bacterial physiology and metabolic capacity. Using a real-time quantitative PCR (rt-QPCR) platform, we examined the expression pattern of quorum-sensing genes, auto-inducer biosynthesis genes, and cell density regulatory proteins in phage-resistant strains. Our results revealed that bacteriophage-resistant bacteria downregulate the expression of quorum-sensing regulatory proteins, such as LuxM, LuxN, and LuxP. This downregulation attenuates the normal perception of quorum-sensing peptides and subsequently diminishes the expression of cell density regulatory proteins, including LuxU, aphA, and LuxR. These findings align with the diverse phenotypic traits observed in the phage-resistant strains, such as altered biofilm formation, reduced planktonic growth, and reduced virulence. Moreover, the transcriptional depletion of aphA, the master regulator associated with low cell density, was linked to the downregulation of genes related to virulence. This phenomenon appears to be phage-specific, suggesting a finely tuned metabolic adaptation driven by phage-host interaction. These findings contribute to our understanding of the role of Vibrio species in microbial marine ecology and highlight the complex interplay between phage resistance, quorum sensing, and bacterial physiology.

N-acyl homoserine lactonase attenuates the virulence of Salmonella typhimurium and its induction of intestinal damages in broilers

This study aimed to investigate the potential mitigating effects of N-acyl homoserine lactonase (AHLase) on the virulence of Salmonella typhimurium and its induction of intestinal damages in broilers. In vitro study was firstly conducted to examine if AHLase treatment could attenuate the virulence of S. typhimurium. Then, an in vivo experiment was performed by allocating 240 broiler chicks at 1 d old into 3 groups (8 replicates per group): negative control (NC), positive control (PC), and PC supplemented with 10,000 U/kg AHLase. All chicks except those in NC were orally challenged by S. typhimurium from 8 to 10 d of age. Parameters were measured on d 11 and 21. The results showed that treatment with 1 U/mL AHLase suppressed the biofilm-forming ability (including biofilm biomass, extracellular DNA secretion and biofilm formation-related gene expression), together with swarming motility and adhesive capacity of S. typhimurium. Supplemental 10,000 U/kg AHLase counteracted S. typhimurium-induced impairments (P < 0.05) in broiler growth performance (including final body weight, average daily gain and average daily feed intake) during either 1-11 d or 12-21 d, and increases (P < 0.05) in the indexes of liver, spleen and bursa of Fabricius on d 11, together with reductions (P < 0.05) in ileal villus height and its ratio to crypt depth on both d 11 and 21. AHLase addition also normalized the increased (P < 0.05) mRNA expression of ileal occludin on both d 11 and 21 in S. typhimurium-challenged broilers. However, neither S. typhimurium challenge nor AHLase addition altered (P > 0.05) serum diamine oxidase activity of broilers. Noticeably, S. typhimurium challenge caused little change in the mRNA expression of ileal inflammatory cytokines except for an increase (P < 0.05) in interleukin-8 expression on d 11, whereas AHLase addition normalized (P < 0.05) this change. In conclusion, AHLase treatment could attenuate the virulence and pathogenicity of S. typhimurium, thus contributing to alleviate S. typhimurium-induced growth retardation and intestinal damages in broilers.

Biofouling in Membrane Bioreactors-Mitigation and Current Status: a Review

Biological fouling as termed biofouling is caused by varied living organisms and is difficult to eliminate from the environment thus becoming a major issue during membrane bioreactors. Biofouling in membrane bioreactors (MBRs) is a crucial problem in increasing liquid pressure due to reduced pore diameter, clogging of the membrane pores, and alteration of the chemical composition of the water which greatly limits the growth of MBRs. Thus, membrane biofouling and/or microbial biofilms is a hot research topic to improve the market competitiveness of the MBR technology. Though several antibiofouling strategies (addition of bioflocculant or sponge into MBRs) came to light, biological approaches are sustainable and more practicable. Among the biological approaches, quorum sensing-based biofouling control (so-called quorum quenching) is an interesting and promising tool in combating biofouling issues in the MBRs. Several review articles have been published in the area of membrane biofouling and mitigation approaches. However, there is no single source of information about biofouling and/or biofilm formation in different environmental settings and respective problems, antibiofilm strategies and current status, quorum quenching, and its futurity. Thus, the objectives of the present review were to provide latest insights on mechanism of membrane biofouling, quorum sensing molecules, biofilm-associated problems in different environmental setting and antibiofilm strategies, special emphasis on quorum quenching, and its futurity in the biofilm/biofouling control. We believe that these insights greatly help in the better understanding of biofouling and aid in the development of sustainable antibiofouling strategies.

Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts

Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.

Anti-Biofilm Enzymes-Assisted Antibiotic Therapy against Burn Wound Infection by Pseudomonas aeruginosa

Pseudomonas aeruginosa can form biofilms at the site of burn wound, leading to infection and the failure of treatment regimens. The previous in vitro study demonstrated that a combination of the quorum-quenching enzyme AidHA147G and the extracellular matrix hydrolase PslG was effective in inhibiting biofilm and promoting antibiotic synergy. The aim of the present study was to evaluate the efficacy of this combination of enzymes in conjunction with tobramycin in treating burn wound infected with P. aeruginosa. The results showed that this treatment was effective in quorum-quenching and biofilm inhibition on infected wounds. Compared with the tobramycin treatment only, simultaneous treatment with the enzymes and antibiotics significantly reduced the severity of tissue damage, decreased the bacterial load, and reduced the expression of the inflammatory indicators myeloperoxidase (MPO) and malondialdehyde (MDA). Topical application of the enzymes also reduced the bacterial load and inflammation to some extent. These results indicate that the combined-enzyme approach is a potentially effective treatment for P. aeruginosa biofilm infections of burn wounds.

Quorum Sensing in Oral Biofilms: Influence on Host Cells

Quorum sensing molecules (QSMs) in the oral cavity regulate biofilm formation, the acquisition of iron, stress responses, and the expression of virulence factors. However, knowledge of the direct QSM-host interactions in the oral environment is limited, although their understanding could provide greater insight into the cross-kingdom communication occurring during oral disease development. This review aims to explore the literature on oral QSM-host interactions and to highlight areas of advancement in this field. The studies included in this review encompass an array of cell types and oral QSMs, with particular emphasis on immune cells and their relationship to periodontal diseases. It can be inferred from the current literature that QSMs are utilised by host cells to detect bacterial presence and, in the majority of cases, elicit an immune response towards the environmental QSMs. This may provide a base to target QSMs as a novel treatment of oral diseases. However, N-acyl homoserine lactone (AHL) detection methods remain an area for development, through which a greater understanding of the influence of oral QSMs on host cells could be achieved.