Biofilms and Cyclic di-GMP (c-di-GMP) Signaling: Lessons from Pseudomonas aeruginosa and Other Bacteria

Investigations on genomic, topological and structural properties of diguanylate cyclases involved in Vibrio cholerae biofilm signalling using in silico techniques: Promising drug targets in combating cholera

During various stages of its life cycle, Vibrio cholerae initiate biofilm signalling cascade. Intercellular high level of the signalling nucleotide 3'-5' cyclic dimeric guanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclases (DGCs) from its precursor molecule GTP, is crucial for biofilm formation. Present study endeavours to in silico approaches in evaluating genomic, physicochemical, topological and functional properties of six c-di-GMP regulatory DGCs (CdgA, CdgH, CdgK, CdgL, CdgM, VpvC) of V. cholerae. Genomic investigations unveiled that codon preferences were inclined towards AU ending over GC ending codons and overall GC content ranged from 44.6 to 49.5 with codon adaptation index ranging from 0.707 to 0.783. Topological analyses deciphered the presence of transmembrane domains in all proteins. All the DGCs were acidic, hydrophilic and thermostable. Only CdgA, CdgH and VpvC were predicted to be stable during in vitro conditions. Non-polar amino acids with leucine being the most abundant amino acid among these DGCs with α-helix as the predominant secondary structure, responsible for forming the transmembrane regions by secondary structure analysis. Tertiary structures of the proteins were obtained by computation using AlphaFold and trRosetta. Predicted structures by both the servers were compared in various aspects using PROCHECK, ERRAT and Modfold8 servers. Selected 3D structures were refined using GalaxyRefine. InterPro Scan revealed presence of a conserved GGDEF domain in all DGCs and predicted the active site residues in the GGDEF domain. Molecular docking studies using CB-DOCK 2 tool revealed that among the DGCs, VpvC exhibited highest affinity for GTP (-5.6 kcal/mol), which was closely followed by CdgL (-5.5 kcal/mol). MD simulations depicted all DGC-GTP complexes to be stable due to its considerably low eigenvalues. Such studies are considered to provide maiden insights into the genomic and structural properties of V. cholerae DGCs, actively involved in biofilm signalling systems, and it is projected to be beneficial in the discovery of novel DGC inhibitors that can target and downregulate the c-di-GMP regulatory system to develop anti-biofilm strategies against the cholera pathogen.

FleQ finetunes the expression of a subset of BrlR-activated genes to enable antibiotic tolerance by Pseudomonas aeruginosa biofilms

The transcriptional regulator FleQ contributes to Pseudomonas aeruginosa biofilm formation by activating the expression and biosynthesis of matrix exopolysaccharides in a manner dependent on c-di-GMP. However, little is known about the role of FleQ in the antibiotic tolerance phenotype of P. aeruginosa biofilms. Inactivation of fleQ impaired biofilm formation and rendered biofilms susceptible to tobramycin and norfloxacin. The phenotypes were similar to biofilms inactivated in sagS encoding the orphan sensor SagS that promotes the switch from planktonic to biofilm growth via BfiSR and antibiotic tolerance via BrlR. While FleQ was found to contribute to biofilm formation independently of SagS and BfiSR, FleQ instead converged with SagS-dependent regulation at the level of BrlR. This was supported by multicopy expression of sagS failing to restore biofilm antibiotic tolerance by ΔfleQ to wild-type levels (and vice versa) and by biofilms formed by the ΔfleQΔsagS double mutant being as susceptible as ΔfleQ and ΔsagS biofilms. Increased antibiotic susceptibility was independent of BrlR abundance or BrlR DNA binding but coincided with significantly reduced transcript abundance of the BrlR-activated mexCD-oprJ and PA1874-77, encoding an ABC transporter previously shown to contribute to the tolerance of biofilms to tobramycin and norfloxacin. FleQ- dependent regulation of gene expression was indirect. Co-immunoprecipitation and BACTH assays indicated FleQ to interact with SagS via its HisKA-Rec domain, likely suggesting FleQ and SagS to likely work in concert to enable biofilm antibiotic tolerance, by finetuning the expression of BrlR activated genes.IMPORTANCEIn P. aeruginosa, FleQ inversely regulates the expression of genes encoding flagella and biofilm matrix components, including exopolysaccharide (Pel, Psl) in a manner dependent on the levels of c-di-GMP. Our findings expand on the role of FleQ from regulating the transition to the biofilm mode of growth to FleQ contributing to the antimicrobial tolerance phenotype of biofilms, by FleQ affecting the expression of PA1874-77, a downstream target of the SagS-dependent transcriptional regulator BrlR. Importantly, our findings suggest FleQ works in concert with SagS, likely via FleQ-SagS protein-protein interactions, to enable the formation of inherently tolerant P. aeruginosa biofilms.

Magnetically Tunable Hydrogel for Biofilm Control

Bacterial biofilm formation contributes to healthcare and energy challenges, and researchers are actively pursuing a range of strategies to restrict the spread of biofilms in an eco-friendly manner. Commonly used approaches in industry rely on physical removal and chemical techniques, frequently targeting mature biofilms. While effective, these methods often face implementation challenges in remote settings and can have off-target environmental impacts. As a result, an alternative strategy is to focus on controlling or limiting the biofilm formation and growth rates with remote stimuli. It has been shown that the mechanotransduction pathway intrinsic to bacteria responds to changes in the storage modulus of the growth surface, modifying the bacteria's motility and biofilm formation. We developed a material with magnetically tunable mechanical properties by intercalating magnetic nanoparticles into an agar gel matrix and investigated its ability to control Escherichia coli motility and biofilm growth. The initial storage modulus ranges from 0.5 to 2.5 kPa, depending on the material composition. Upon exposure to a 20 mT magnetic field using standard neodymium magnets, the modulus is dynamically and reversibly increased by approximately 30%. As a result of this increase, the expansion rate of the E. coli biofilm is reduced by approximately 40%. The simplicity of the manipulation of its mechanical property not only gives this biomaterial potential to further mechanosensing mechanism research but also proves to be an innovative strategy for remote and eco-conscious restriction of biofilm formation.

Throwing a spotlight on genomic dark matter: the power and potential of transposon-insertion sequencing

Linking genotype to phenotype is a central goal in biology. In the microbiological field, transposon mutagenesis is a technique that has been widely used since the 1970's to facilitate this connection. The development of modern 'omics approaches and next-generation sequencing, have allowed high-throughput association between genes and their putative function. In 2009, four different variations of modern transposon-insertion sequencing (TIS) approaches were published, being referred to as transposon-directed insertion-site sequencing (TraDIS), transposon sequencing (Tn-seq), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). These approaches exploit a similar concept to allow estimation of the essentiality or contribution to fitness of each gene in any bacterial genome. The main rationale is to perform a comparative analysis of the abundance of specific transposon mutants under one or more selective conditions. The approaches themselves only vary in the transposon used for mutagenesis, and in the methodology used for sequencing library preparation. In this review, we discuss how TIS approaches have been used to facilitate a major shift in our fundamental understanding of bacterial biology in a range of areas. We focus on several aspects including pathogenesis, biofilm development, polymicrobial interactions in various ecosystems, and antimicrobial resistance. These studies have provided new insight into bacterial physiology and revealed predicted functions for hundreds of genes previously representing genomic 'dark matter'. We also discuss how TIS approaches have been used to understand complex bacterial systems and interactions and how future developments of TIS could continue to accelerate and enrich our understanding of bacterial biology.

SadB, a mediator of AmrZ proteolysis and biofilm development in Pseudomonas aeruginosa

The ability of bacteria to commit to surface colonization and biofilm formation is a highly regulated process. In this study, we characterized the activity and structure of SadB, initially identified as a key regulator in the transition from reversible to irreversible surface attachment. Our results show that SadB acts as an adaptor protein that tightly regulates the master regulator AmrZ at the post-translational level. SadB directly binds to the C-terminal domain of AmrZ, leading to its rapid degradation, primarily by the Lon protease. Structural analysis suggests that SadB does not directly interact with small molecules upon signal transduction, differing from previous findings in Pseudomonas fluorescens. Instead, the SadB structure supports its role in mediating protein-protein interactions, establishing it as a major checkpoint for biofilm commitment.

Pseudomonas aeruginosa biofilm: treatment strategies to combat infection

Pseudomonas aeruginosa is an opportunistic human pathogenic bacterium that is a common cause of both acute and chronic infections. Multidrug-resistant P. aeruginosa poses a significant challenge to antibiotics and therapeutic approaches due to its pathogenicity, virulence, and biofilm-forming ability mediated by quorum sensing. Understanding the pathogenic mechanisms is essential for developing potential drug targets. In this regard, strategies aimed at combating the targeted inhibition of virulence, quorum sensing pathways, secretion systems, biofilm-associated two-component systems, and signalling system regulators (such as c-di-GMP) associated with biofilm formation are critical. Several new antimicrobial agents have been developed using these strategies, including antimicrobial peptides, bacteriophages, nanoantibiotics, photodynamics, and natural products, which are considered promising therapeutic tools. In this review, we address the concept of biofilms, their regulation, and recent treatment strategies to target P. aeruginosa, a clinically significant pathogen known for biofilm formation.

Decoding the effect of antibiotics on biofilm formation in biofilters

Biofilms have extensive applications and important roles in biological processes. This study aimed to investigate the effect and mechanism of low-concentration sulfamethoxazole (SMX) on biofilm development in biofilters. The effects of various SMX concentrations (0, 100 ng/L, 1000 ng/L) on microbial development were compared. Compared with the control group without SMX, the start-up period of R2 and R3 filters with SMX added was decreased by 9 % and 21 %, respectively. Under antibiotic stimulation, reactive oxygen species (ROS) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) concentrations increased, aligning with changes in extracellular polymer content and biofilm formation. Microbial community results showed that the presence of SMX promoted the growth of some manganese-oxidizing bacteria (MnOB), such as Massilia, Pedomicrobium, Sphingopyxis, Pseudomonas, and Bacillus. Functional gene analysis further revealed higher expression levels of genes related to c-di-GMP transformation in the presence of SMX. These findings suggest that microbial communities can adapt to their environment by accelerating biofilm formation at lower antibiotic concentrations. The results of this study provide new insights into the impact of low-concentration antibiotics on biofilm development and offer a crucial reference for biofilter design and optimization.

Biofilm formation of Pseudomonas fluorescens induced by a novel diguanylate cyclase modulated c-di-GMP promotes spoilage of large yellow croaker (Larimichthys crocea)

Pseudomonas as major agents cause the microbial spoilage in aerobically stored seafoods due to the strong biofilm forming ability, resulting in significant economic losses. C-di-GMP regulates the transition to biofilm states in numerous bacteria, however, its function in biofilm and spoilage of Pseudomonas fluorescens has still been scarce. Here, in a fish spoiler P. fluorescens PF07 strain, 26 proteins of diguanylate cyclase (DGC) containing a GGDEF domain were characterized, and both intracellular c-di-GMP and biofilm formation consistently decreased in the constructed 12 deletion mutants of DGC domain. Compared to wild type (WT) strain, both swimming and swarming in these mutants remarkably enhanced, while the secretion of siderophore, protease activity, and the production of total volatile basic nitrogen (TVB-N) were decreased in several mutants, indicating the different modulating effects among these DGC mutants. Furthermore, correlation analysis of these six phenotypes, PF07_04309 exhibited the most significant alteration, which was identified a novel functional DGC enzyme. Moreover, the GGAAA mutation of PF07_04309 induced the down-regulation of Psl and Alg operons and increased flagellar related gene, resulting in forming the sparser and thinner biofilms. Two mutants of 04309 induced by low c-di-GMP significantly declined the accumulation of TVB-N, thiobarbituric acid, extracellular protease activity and spoilage flavor compounds, especially methylamine and carbon disulfide, in the fillets of large yellow croaker stored at 4 °C. Thus, our results indicated that a novel DGC 04309 modulated the polysaccharide secretion, flagellar, and iron carrier by synthesis of c-di-GMP, positively regulating the spoilage potential of P. fluorescens, which expanded the original insights of DGC and c-di-GMP function on microbial food spoilage.

Inhibitors of Cyclic Dinucleotide Phosphodiesterases and Cyclic Oligonucleotide Ring Nucleases as Potential Drugs for Various Diseases

The phosphodiester linkage is found in DNA, RNA and many signaling molecules, such as cyclic mononucleotide, cyclic dinucleotides (CDNs) and cyclic oligonucleotides (cONs). Enzymes that cleave the phosphodiester linkage (nucleases and phosphodiesterases) play important roles in cell persistence and fitness and have therefore become targets for various diseased states. While various inhibitors have been developed for nucleases and cyclic mononucleotide phosphodiesterases, and some have become clinical successes, there is a paucity of inhibitors of the recently discovered phosphodiesterases or ring nucleases that cleave CDNs and cONs. Inhibitors of bacterial c-di-GMP or c-di-AMP phosphodiesterases have the potential to be used as anti-virulence compounds, while compounds that inhibit the degradation of 3',3'-cGAMP, cA3, cA4, cA6 could serve as antibiotic adjuvants as the accumulation of these second messengers leads to bacterial abortive infection. In humans, 2'3'-cGAMP plays critical roles in antiviral and antitumor responses. ENPP1 (the 2'3'-cGAMP phosphodiesterase) or virally encoded cyclic dinucleotide phosphodiesterases, such as poxin, however, blunt this response. Inhibitors of ENPP1 or poxin-like enzymes have the potential to be used as anticancer and antiviral agents, respectively. This review summarizes efforts made towards the discovery and development of compounds that inhibit CDN phosphodiesterases and cON ring nucleases.

PelD is required downstream of c-di-GMP for host specialization of Pseudomonas lurida

BACKGROUND

The bacterial second messenger c-di-GMP is known to influence the formation of biofilms and thereby persistence of pathogenic and beneficial bacteria in hosts. A previous evolution experiment with Pseudomonas lurida MYb11, occasional symbiont of the nematode Caenorhabditis elegans, led to the emergence of host-specialized variants with elevated intracellular c-di-GMP. Thus far, the molecular underpinnings of c-di-GMP-mediated host specialization were unknown in this symbiosis. Therefore, the current study aimed at identifying candidate molecular processes by combining transcriptomic and functional genetic analyses.

RESULTS

We found that MYb11 host specialists differentially expressed genes related to attachment, motility and biofilm production, including pelD from the pel gene cluster. pelD deletion resulted in reduced intra-host competitive fitness, lower bacterial numbers in C. elegans and loss of biofilm biomass.

CONCLUSION

Our results identify pelD as a previously unknown key modulator of beneficial symbiont-host associations that acts downstream of c-di-GMP.

Physical communication pathways in bacteria: an extra layer to quorum sensing

Bacterial communication is essential for survival, adaptation, and collective behavior. While chemical signaling, such as quorum sensing, has been extensively studied, physical cues play a significant role in bacterial interactions. This review explores the diverse range of physical stimuli, including mechanical forces, electromagnetic fields, temperature, acoustic vibrations, and light that bacteria may experience with their environment and within a community. By integrating these diverse communication pathways, bacteria can coordinate their activities and adapt to changing environmental conditions. Furthermore, we discuss how these physical stimuli modulate bacterial growth, lifestyle, motility, and biofilm formation. By understanding the underlying mechanisms, we can develop innovative strategies to combat bacterial infections and optimize industrial processes.

Genetic Dissection of Cyclic di-GMP Signalling in Pseudomonas aeruginosa via Systematic Diguanylate Cyclase Disruption

The second messenger bis-(3' → 5')-cyclic dimeric guanosine monophosphate (c-di-GMP) governs adaptive responses in the opportunistic pathogen Pseudomonas aeruginosa, including biofilm formation and the transition from acute to chronic infections. Understanding the intricate c-di-GMP signalling network remains challenging due to the overlapping activities of numerous diguanylate cyclases (DGCs). In this study, we employed a CRISPR-based multiplex genome-editing tool to disrupt all 32 GGDEF domain-containing proteins (GCPs) implicated in c-di-GMP signalling in P. aeruginosa PA14. Phenotypic and physiological analyses revealed that the resulting mutant was unable to form biofilms and had attenuated virulence. Residual c-di-GMP levels were still detected despite the extensive GCP disruption, underscoring the robustness of this regulatory network. Taken together, these findings provide insights into the complex c-di-GMP metabolism and showcase the importance of functional overlapping in bacterial signalling. Moreover, our approach overcomes the native redundancy in c-di-GMP synthesis, providing a framework to dissect individual DGC functions and paving the way for targeted strategies to address bacterial adaptation and pathogenesis.

A small periplasmic protein governs broad physiological adaptations in Vibrio cholerae via regulation of the DbfRS two-component system

Two-component signaling pathways allow bacteria to sense and respond to environmental changes, yet the sensory mechanisms of many remain poorly understood. In the pathogen Vibrio cholerae, the DbfRS two-component system controls the biofilm lifecycle, a critical process for environmental persistence and host colonization. Here, we identified DbfQ, a small periplasmic protein encoded adjacent to dbfRS, as a direct modulator of pathway activity. DbfQ directly binds the sensory domain of the histidine kinase DbfS, shifting it toward phosphatase activity and promoting biofilm dispersal. In contrast, outer membrane perturbations, caused by mutations in lipopolysaccharide biosynthesis genes or membrane-damaging antimicrobials, activate phosphorylation of the response regulator DbfR. Transcriptomic analyses reveal that DbfR phosphorylation leads to broad transcriptional changes spanning genes involved in biofilm formation, central metabolism, peptidoglycan synthesis, and cellular stress responses. Constitutive DbfR phosphorylation imposes severe fitness costs in an infection model, highlighting this pathway as a potential target for anti-infective therapeutics. We find that dbfQRS-like genetic modules are widely present across bacterial phyla, underscoring their broad relevance in bacterial physiology. Collectively, these findings establish DbfQ as a new class of periplasmic regulator that influences two-component signaling and bacterial adaptation.

Biofilm detection in the food industry: Challenges in identifying biofilm eps markers and analytical techniques with insights for Listeria monocytogenes

Extracellular polymeric substances (EPS) in biofilms are promising targets for eradicating biofilms and monitoring their presence, especially in the food industry. For this understanding, the composition of the EPS matrix is crucial. Ideally, a biofilm marker is found serving both purposes, but such a compound has not yet been discovered. This review aims to identify general biofilm EPS markers distinct from planktonic cells, focusing on macromolecules in the EPS matrix. It also evaluates the feasibility of this goal across different bacterial groups and environmental conditions and discusses EPS analysis methods. This review digs deeper into the EPS matrix starting with an introduction to the EPS matrix itself and describing some of its influencing factors. Next, a brief description of cell-to-cell communication within biofilms is provided, as these interactions significantly influence the EPS matrix. The main part of this review describes the macromolecules inside the EPS matrix and attempts to find biofilm EPS markers applied to bacteria in general and specifically to Listeria monocytogenes as biofilms are a major contributor to its persistence. The last part of the review focuses on the analytical techniques available to characterize the EPS matrix. The review revealed that although multiple candidates showed great potential as biofilm markers, none were unique but ubiquitous in all bacteria tested. To achieve easy biofilm detection with current techniques, it's necessary to identify markers specific to the environmental conditions and common bacterial groups within each food category, sector, or facility, due to the lack of standardization in these techniques. This tailored approach ensures more accurate and effective biofilm monitoring. Moreover, the lack of standardized analytical techniques, including quantification techniques, complexifies studying the EPS matrix and developing monitoring and intervention strategies. Optimizing analytical techniques is crucial for this tailored approach, as it requires refined methods for detection, characterization, and quantification. This ensures the accurate identification of biofilm markers specific to environmental conditions and bacterial groups within each food sector.

c-di-GMP phosphodiesterase ProE interacts with quorum sensing protein PqsE to promote pyocyanin production in Pseudomonas aeruginosa

The universal bacterial second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays critical roles in regulating a variety of bacterial functions such as biofilm formation and virulence. The metabolism of c-di-GMP is inversely controlled by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs). Recently, increasing studies suggested that the protein-protein interactions between DGCs/PDEs and their partners appear to be a common way to achieve specific regulation. In this work, we showed that the PDE ProE can interact with PQS quorum sensing protein PqsE to regulate pyocyanin production in Pseudomonas aeruginosa. Our bacterial two-hybrid assay demonstrated that ProE directly interacts with PqsE, and isothermal titration calorimetry and surface plasmon resonance assay further confirmed that the binding affinity of ProE with PqsE is at micromolar level. Both ProE and PqsE negatively regulate intracellular c-di-GMP levels. Furthermore, our transcriptomic study showed that co-expression of ProE and PqsE significantly changes the gene expression profiles in P. aeruginosa, especially with increased expression of pyocyanin genes, and the qPCR and phenotypic results confirmed the transcriptome data. Taken together, our study suggested that the interaction between ProE and PqsE plays a critical role in regulation of pyocyanin production and highlights the importance of protein-protein interaction mediated c-di-GMP signaling in P. aeruginosa.IMPORTANCEc-di-GMP is pivotal in orchestrating various bacterial functions. In Pseudomonas aeruginosa, the nuanced balance of intracellular c-di-GMP is maintained by approximately 41 diguanylate cyclases (DGCs) and phosphodiesterases (PDEs). Emerging studies indicate that the c-di-GMP metabolic DGCs and PDEs may be involved in the signal transduction process by directly binding to the target protein, thus influencing downstream function. Despite their known importance, the precise functions of these proteins, especially their interacting partners, remain unclear. In this study, we identified that PQS quorum sensing system protein PqsE is a binding partner of c-di-GMP phosphodiesterase ProE; further analysis suggested that the ProE specifically interacts with PqsE to promote pyocyanin production. Our study extended the regulatory mechanism of the c-di-GMP signal transduction and quorum sensing in governing bacterial physiology.

Harnessing Cyclic di-GMP Signaling: A Strategic Approach to Combat Bacterial Biofilm-Associated Chronic Infections

Cyclic dimeric guanosine monophosphate (c-di-GMP) plays a vital role within the nucleotide signaling network of bacteria, participating in various biological processes such as biofilm formation and toxin production, among others. Substantial evidence demonstrates its critical involvement in the progression of chronic infections. Treating chronic infections seems critical, and there is a worldwide quest for drugs that target pathogens' unique and complex virulence-associated signaling networks. c-di-GMP is a promising therapeutic target by serving as a distinct virulence factor, solving problems associated with drug resistance, biofilm dispersion, and its related septicemia complications. c-di-GMP levels act as checkpoints for several biofilm-associated molecular pathways, viz., Gac/Rsm, BrlR, and SagS signaling systems. C-di-GMP is also engaged in the Wsp chemosensory pathway responsible for rugose small colony variants observed in cystic fibrosis-related lung infections. Considering all factors, c-di-GMP serves as a pivotal hub in the intricate cascade of biofilm regulation. By overseeing QS systems, exopolysaccharide synthesis, and antibiotic resistance pathways in chronic infections, it emerges as a linchpin for effective drug development strategies against biofilm-related ailments. This underscores the significance of understanding the multifaceted signaling networks. c-di-GMP's role is highlighted in this review as a concealed virulence component in various bacterial pathogens, suggesting that medications targeting it could hold promise in treating chronic disorders associated with biofilms.

Biofilm dynamics in space and their potential for sustainable space exploration - A comprehensive review

Microbial biofilms are universal. The intricate tapestry of biofilms has remarkable implications for the environment, health, and industrial processes. The field of space microbiology is actively investigating the effects of microgravity on microbes, and discoveries are constantly being made. Recent evidence suggests that extraterrestrial environments also fuel the biofilm formation. Understanding the biofilm mechanics under microgravitational conditions is crucial at this stage and could have an astounding impact on inter-planetary missions. This review systematically examines the existing understanding of biofilm development in space and provides insight into how molecules, physiology, or environmental factors influence biofilm formation during microgravitational conditions. In addition, biocontrol strategies targeting the formation and dispersal of biofilms in space environments are explored. In particular, the article highlights the potential benefits of using microbial biofilms in space for bioremediation, life support systems, and biomass production applications.

Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution

Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.

Crosstalk between cyclic-di-guanosine monophosphate and the sensor kinase MtrB regulates MtrA-dependent genes, bacterial growth, biofilm formation and lysosomal trafficking of Mycobacterium tuberculosis

Cyclic-di-guanosine monophosphate (c-di-GMP) plays an important role in bacterial signalling networks. C-di-GMP exerts a regulatory function through binding to diverse molecules that include transcription factors, riboswitches and sensor kinases (SKs), thereby regulating diverse processes. Here, we demonstrate the crosstalk between c-di-GMP and the SK MtrB of Mycobacterium tuberculosis. MtrB phosphorylates and regulates its cognate response regulator MtrA. C-di-GMP binds directly to the cytosolic domain of MtrB to inhibit its autophosphorylation. C-di-GMP levels in M. tuberculosis were manipulated by overexpressing a c-di-GMP synthesizing enzyme ydeH and a degrading enzyme rv1357c. We demonstrate that overexpression of ydeH lowers growth of the bacterium both in vitro and in M. tuberculosis grown in macrophages. This is in conformity with lowered expression of mtrA and selected genes of the mtrA regulon involved in cell wall turnover in the ydeH-overexpressing strain compared to the parent strain. We also demonstrate that overexpression of ydeH in M. tuberculosis hinders biofilm formation, whereas overexpression of rv1357c has the opposite effect. Neither of the two genes could rescue the biofilm defective phenotype of the MtrB knock out mutant (ΔmtrB), suggesting that c-di-GMP exerts its role on biofilm formation through MtrB. Finally, we show by fluorescence microscopy that the trafficking of M. tuberculosis overexpressing ydeH is significantly higher than that of the parent strain and that this is linked to reduced expression of the MtrB-dependent genes esxG and esxH, which play a role in subversion of lysosomal trafficking of M. tuberculosis. These results provide important new insight into the crosstalk between c-di-GMP and MtrB in M. tuberculosis.

Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy

Dispersal plays a crucial role in the development and ecology of biofilms. While extensive studies focused on elucidating the molecular mechanisms governing this process, few have characterized the associated temporal changes in composition and structure. Here, we employed solid-state nuclear magnetic resonance (NMR) techniques to achieve time-resolved characterization of Bacillus subtilis biofilms over a 5-day period. The mature biofilm, established within 48 h, undergoes significant degradation in following 72 h. The steepest decline of proteins precedes that of exopolysaccharides, likely reflecting their distinct spatial distribution. Exopolysaccharide sugar units display clustered temporal patterns, suggesting the presence of distinct polysaccharide types. A sharp rise in aliphatic carbon signals on day 4 probably corresponds to a surge in biosurfactant production. Different dynamic regimes respond differently to dispersal: the mobile domain exhibits increased rigidity, while the rigid domain remains stable. These findings provide novel insights and perspectives on the complex process of biofilm dispersal.

Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis

The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.

Anti-Biofilm Agents to Overcome Pseudomonas aeruginosa Antibiotic Resistance

Pseudomonas aeruginosa is one of world's most threatening bacteria. In addition to the emerging prevalence of multi-drug resistant (MDR) strains, the bacterium also possesses a wide variety of virulence traits that worsen the course of the infections. Particularly, its ability to form biofilms that protect colonies from antimicrobial agents is a major cause of chronic and hard-to-treat infections in immune-compromised patients. This protective barrier also ensures cell growth on abiotic surfaces and thus enables bacterial survival on medical devices. Hence, as the WHO alerted to the need to develop new treatments, the use of anti-biofilm agents (ABAs) appeared as a promising approach. Given the selection pressure imposed by conventional antibiotics, a new therapeutic strategy has emerged that aims at reducing bacterial virulence without inhibiting cell growth. So-called anti-virulence agents (AVAs) would then restore the efficacy of conventional antibiotics (ATBs) or potentiate the effectiveness of the immune system. The last decade has seen the development of ABAs as AVAs against P. aeruginosa. This review aims to highlight the design strategy and critical features of these molecules to pave the way for further discoveries of highly potent compounds.

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.

Capturing the micro-communities: Insights into biogenesis and architecture of bacterial biofilms

Biofilm is an assemblage of microorganisms embedded within the extracellular matrix that provides mechanical stability, nutrient absorption, antimicrobial resistance, cell-cell interactions, and defence against host immune system. Various biomolecules such as lipids, carbohydrates, protein polymers (amyloid), and eDNA are present in the matrix playing significant role in determining the distinctive properties of biofilm. The formation of biofilms contributes to resistance against antimicrobial therapy in most of the human infections and exacerbates existing diseases. Therefore, this field requires several state-of-the-art techniques to fully understand the 3-D organization of biofilms, their cell behaviour and responses to pharmaceutical treatments. Here, we explore the assembly and regulation of biofilm biogenesis in the context of matrix components and highlight the significance of high-resolution imaging and analysing techniques for monitoring complex biofilm architecture. Our review also emphasizes the novelty and advancements in techniques to visualise biofilm structure and composition, providing valuable insights to understand biofilm-related infections.

Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells

Bacteria assume two distinct lifestyles: the planktonic and biofilm modes of growth. Additionally, dispersion has emerged as a third phenotype, accompanied by the distinct phenotypes and the unique expression of >600 genes. Here, we asked whether the distinct phenotype of dispersed cells is already apparent within minutes of egressing from the biofilm. We used RNA-seq to show that the physiology of freshly dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells, apparent by dispersed cells uniquely expressing 194 genes. Unique and differentially expressed genes relative to planktonic or biofilm cells include genes associated with type IV pili, pyoverdine, type III and type VI secretion systems, and antibiotic resistance that are downregulated in dispersed cells, whereas the transcript abundance of genes involved in swimming motility, Hxc type II secretion system and various other virulence factors, and metabolic and energy-generating pathways are increased, indicative of dispersion coinciding with an awakening and re-energizing of dispersed cells, and a switch in virulence, further apparent by freshly dispersed cells significantly subverting engulfment by macrophages. The findings suggest that dispersed cells display a distinct phenotype within minutes of egressing from the biofilm, with freshly dispersed cells already capable of efficiently evading phagocytosis.

IMPORTANCE

Dispersion is considered a transitionary phenotype, enabling bacteria to switch between the communal, biofilm lifestyle, where cells share resources and are protected from harmful conditions to the planktonic state. Here, we demonstrate that within minutes of leaving the biofilm, dispersed cells express genes and display phenotypic traits that are distinct from biofilms and planktonic cells. Our findings suggest that dispersed cells quickly adapt to a less structured and protected but more nutrient-rich environment, with this trade-off in environment coinciding with an awakening and a switch in virulence, specifically a switch from directly intoxicating host cells and potential competitors toward more broadly active virulence factors and strategies of evasion. To our knowledge, this is the first report of dispersed cells' distinct (trade-off) phenotype and their enhanced resilience so soon after egressing from the biofilm.

Harnessing the Power of Our Immune System: The Antimicrobial and Antibiofilm Properties of Nitric Oxide

Nitric oxide (NO) is a free radical of the human innate immune response to invading pathogens. NO, produced by nitric oxide synthases (NOSs), is used by the immune system to kill microorganisms encapsulated within phagosomes via protein and DNA disruption. Owing to its ability to disperse biofilm-bound microorganisms, penetrate the biofilm matrix, and act as a signal molecule, NO may also be effective as an antibiofilm agent. NO can be considered an underappreciated antimicrobial that could be levied against infected, at-risk, and hard-to-heal wounds due to the inherent lack of bacterial resistance, and tolerance by human tissues. NO produced within a wound dressing may be an effective method of disrupting biofilms and killing microorganisms in hard-to-heal wounds such as diabetic foot ulcers, venous leg ulcers, and pressure injuries. We have conducted a narrative review of the evidence underlying the key antimicrobial and antibiofilm mechanisms of action of NO for it to serve as an exogenously-produced antimicrobial agent in dressings used in the treatment of hard-to-heal wounds.

Phenotypic changes and gene expression profiles of Vibrio parahaemolyticus in response to low concentrations of ampicillin

Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis and possesses intrinsic resistance to ampicillin. While ampicillin can trigger transcriptional responses of global genes, the behavioral and molecular changes that occur in V. parahaemolyticus when exposed to ampicillin are not fully understood. In this work, we investigated the effects of low concentrations of ampicillin on the physiology and gene expression of V. parahaemolyticus by combining phenotypic assays and RNA sequencing (RNA-seq) analysis. Our results showed that the growth of V. parahaemolyticus were notably delayed, and both motility and c-di-GMP production were significantly inhibited in the response to low concentrations of ampicillin stress. In contrast, biofilm formation by V. parahaemolyticus was enhanced by exposure to low concentrations of ampicillin. However, low concentrations of ampicillin had no effect on the cytotoxicity or adherence activity of V. parahaemolyticus. The RNA-seq data revealed that a low concentration of ampicillin significantly affected the expression levels of 676 genes, including those involved in antibiotic resistance, virulence, biofilm formation, and regulation. This work contributes to our understanding of how V. parahaemolyticus alters its behavior and gene expression in response to ampicillin exposure.

The Gene Cluster Cj0423-Cj0425 Negatively Regulates Biofilm Formation in Campylobacter jejuni

Campylobacter jejuni (C. jejuni) is a zoonotic foodborne pathogen that is widely distributed worldwide. Its optimal growth environment is microaerophilic conditions (5% O2, 10% CO2), but it can spread widely in the atmospheric environment. Biofilms are thought to play an important role in this process. However, there are currently relatively few research works on the regulatory mechanisms of C. jejuni biofilm formation. In this study, a pan-genome analysis, combined with the analysis of biofilm phenotypic information, revealed that the gene cluster Cj0423-Cj0425 is associated with the negative regulation of biofilm formation in C. jejuni. Through gene knockout experiments, it was observed that the Cj0423-Cj0425 mutant strain significantly increased biofilm formation and enhanced flagella formation. Furthermore, pull-down assay revealed that Cj0424 interacts with 93 proteins involved in pathways such as fatty acid synthesis and amino acid metabolism, and it also contains the quorum sensing-related gene luxS. This suggests that Cj0423-Cj0425 affects fatty acid synthesis and amino acid metabolism, influencing quorum sensing and strain motility, ultimately inhibiting biofilm formation.

Oxidative stress response in avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) leads to significant economic losses in the poultry industry worldwide and restricts the development of the poultry industry. Oxidative stress, through the production of reactive oxygen species (ROS), damage iron‑sulfur (FeS) clusters, cysteine and methionine protein residues, and DNA, and then result in bacterial cells death. APEC has evolved a series of regulation systems to sense and quickly and appropriately respond to oxidative stress. Quorum sensing (QS), second messenger (SM), transcription factors (TFs), small regulatory RNAs (sRNAs), and two-component system (TCS) are important regulation systems ubiquitous in bacteria. It is of great significance to control APEC infection through investigating the molecular regulation mechanism on APEC adapting to oxidative stress. However, how the cross-talk among these regulation systems co-regulates transcription of oxidative stress-response genes in APEC has not been reported. This review suggests exploring connector proteins that co-regulate these regulation systems that co-activate transcription of oxidative stress-response genes to disrupt bacterial antioxidative defense mechanism in APEC, and then using these connector proteins as drug targets to control APEC infection. This review might contribute to illustrating the functional mechanism of APEC adapting to oxidative stress and exploring potential drug targets for the prevention and treatment of APEC infection.

Cyclic di-GMP incorporates the transcriptional factor FleQ03 in Pseudomonas syringae MB03 to elicit biofilm-dependent resistance in response to Caenorhabditis elegans predation

Bacteria usually form biofilms as a defense mechanism against predation by bacterivorous nematodes. In this context, the second messenger c-di-GMP from the wild-type Pseudomonas syringae MB03 actuates the transcriptional factor FleQ03 to elicit biofilm-dependent nematicidal activity against Caenorhabditis elegans N2. P. syringae MB03 cells exhibited nematicidal activity and c-di-GMP content in P. syringae MB03 cells was increased after feeding to nematodes. Expression of a diguanylate cyclase (DGC) gene in P. syringae MB03 resulted in an increased c-di-GMP content, biofilm yield and nematicidal activity, whereas converse effects were obtained when expressing a phosphodiesterase (PDE) gene. Molecular docking and isothermal titration calorimetry assays verified the affinity activity between c-di-GMP and the FleQ03 protein. The disruption of the fleQ03 gene in P. syringae MB03, while increasing c-di-GMP content, significantly diminished both biofilm formation and nematicidal activity. Interestingly, P. syringae MB03 formed a full-body biofilm around the worms against predation, probably extending from the tail to the head, whereas it was not observed in the fleQ03 gene disrupted cells. Thus, we hypothesized that c-di-GMP incorporated FleQ03 to reinforce bacterial biofilm and biofilm-dependent pathogenicity in response to C. elegans predation, providing insights into a possible means of resisting bacterivorous nematodes by bacteria in natural ecosystems.

Wastewater-based surveillance of Vibrio cholerae: Molecular insights on biofilm regulatory diguanylate cyclases, virulence factors and antibiotic resistance patterns

Vibrio cholerae is an inherent inhabitant of aquatic ecosystems. The Indian state of West Bengal, especially the Gangetic delta region is the highest cholera affected region and is considered as the hub of Asiatic cholera. V. cholerae were isolated from publicly accessible wastewater of Midnapore, West Bengal, India. Serotyping determined all isolates to be of non-O1/non-O139 serogroups. Moderate biofilm-forming abilities were noticed in most of the isolates (74.7 %) while, high biofilm formation was recorded for only 6.3 % isolates and 19 % of isolates exhibited low/non-biofilm-forming abilities. PCR-based screening of crucial diguanylate cyclases (DGCs) involved in cyclic-di-GMP-mediated biofilm signaling was performed. cdgH and cdgM were the most abundant DGCs among 93.7 % and 91.5 % of isolates, respectively. Other important DGCs, i.e., cdgK, cdgA, cdgL, and vpvC were present in 84 %, 75.5 %, 72 % and 68 % of isolates, respectively. Besides, the non-O1/non-O139 isolates were screened for the occurrence of virulence factor encoding genes. Moreover, among these non-O1/non-O139 isolates, two strains (3.17 %) harbored both ctxA and ctxB genes, which encode the cholera toxin associated with epidemic cholera. ompU was the most prevalent virulence factor, present in 24.8 % of isolates. Other virulence factors like, zot and st were found in 4.7 % and 9.5 % of isolates. Genes encoding tcp and ace were found to be PCR-negative for the isolates. Additionally, crucial virulence factor regulators, toxT, toxR and hapR were found to be PCR-positive in all the isolates. Antibiotic resistance patterns displayed further vulnerabilities with decreased sensitivity towards commonly used antibiotics with multiple antibiotic resistance index ranging between 0.37 and 0.62. The presence of cholera toxin-encoding multi-drug resistant (MDR) V. cholerae strains in environmental settings is alarming. High occurrence of DGCs are considered to encourage further investigations to use them as alternative therapeutic targets against MDR cholera pathogen due to their unique presence in bacterial systems.

Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication

Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.

Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.

Bacterial Iron Siderophore Drives Tumor Survival and Ferroptosis Resistance in a Biofilm-Tumor Spheroid Coculture Model

Interactions between tumoral cells and tumor-associated bacteria within the tumor microenvironment play a significant role in tumor survival and progression, potentially impacting cancer treatment outcomes. In lung cancer patients, the Gram-negative pathogen Pseudomonas aeruginosa raises questions about its role in tumor survival. Here, a microfluidic-based 3D-human lung tumor spheroid-P. aeruginosa model is developed to study the bacteria's impact on tumor survival. P. aeruginosa forms a tumor-associated biofilm by producing Psl exopolysaccharide and secreting iron-scavenging pyoverdine, which is critical for establishing a bacterial community in tumors. Consequently, pyoverdine promotes cancer progression by reducing susceptibility to iron-induced death (ferroptosis), enhancing cell viability, and facilitating several cancer hallmarks, including epithelial-mesenchymal transition and metastasis. A promising combinatorial therapy approach using antimicrobial tobramycin, ferroptosis-inducing thiostrepton, and anti-cancer doxorubicin could eradicate biofilms and tumors. This work unveils a novel phenomenon of cross-kingdom cooperation, where bacteria protect tumors from death, and it paves the way for future research in developing antibiofilm cancer therapies. Understanding these interactions offers potential new strategies for combatting cancer and enhancing treatment efficacy.

The surface interface and swimming motility influence surface-sensing responses in Pseudomonas aeruginosa

Bacterial biofilms have been implicated in several chronic infections. After initial attachment, a critical first step in biofilm formation is a cell inducing a surface-sensing response. In the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, two second messengers, cyclic diguanylate monophosphate (c-di-GMP) and cyclic adenosine monophosphate (cAMP), are produced by different surface-sensing mechanisms. However, given the disparate cellular behaviors regulated by these second messengers, how newly attached cells coordinate these pathways remains unclear. Some of the uncertainty relates to studies using different strains, experimental systems, and usually focusing on a single second messenger. In this study, we developed a tricolor reporter system to simultaneously gauge c-di-GMP and cAMP levels in single cells. Using PAO1, we show that c-di-GMP and cAMP are selectively activated in two commonly used experimental systems to study surface sensing. By further examining the conditions that differentiate a c-di-GMP or cAMP response, we demonstrate that an agarose-air interface activates cAMP signaling through type IV pili and the Pil-Chp system. However, a liquid-agarose interface favors the activation of c-di-GMP signaling. This response is dependent on flagellar motility and correlated with higher swimming speed. Collectively, this work indicates that c-di-GMP and cAMP signaling responses are dependent on the surface context.

Research progress on the regulatory mechanism of biofilm formation in probiotic lactic acid bacteria

Probiotic lactic acid bacteria (LAB) must undergo three key stages of testing, including food processing, storage, and gastrointestinal tract environment, their beneficial effects could exert. The biofilm formation of probiotic LAB is helpful for improving their stress resistances, survival rates, and colonization abilities under adverse environmental conditions, laying an important foundation for their probiotic effects. In this review, the formation process, the composition and function of basic components of probiotic LAB biofilm have been summarized. This review focuses on the regulatory mechanism of probiotic LAB biofilm formation. In addition, the characteristics and related mechanisms of probiotics in biofilm state have been analyzed to guide the application of probiotic LAB biofilms in the field of health and food. The biofilm formation of LAB is an extremely complex process involving multiple regulatory factors. Besides quorum sensing (QS), other regulatory factors are not yet fully understood. The probiotic LAB in biofilm state exhibit superior survival rate, adhesion performance, and immunomodulation ability, attribute to various metabolic processes, including stress response, exopolysaccharide (EPS) metabolism, amino acid and protein metabolisms, etc. The understanding about regulatory mechanism of biofilm formation of different probiotic species and strains will accelerate the development and application of probiotics products.

Dual-species proteomics and targeted intervention of animal-pathogen interactions

INTRODUCTION

Host-microbe interactions are important to human health and ecosystems globally, so elucidating the complex host-microbe interactions and associated protein expressions drives the need to develop sensitive and accurate biochemical techniques. Current proteomics techniques reveal information from the point of view of either the host or microbe, but do not provide data on the corresponding partner. Moreover, it remains challenging to simultaneously study host-microbe proteomes that reflect the direct competition between host and microbe. This raises the need to develop a dual-species proteomics method for host-microbe interactions.

OBJECTIVES

We aim to establish a forward + reverse Stable Isotope Labeling with Amino acids in Cell culture (SILAC) proteomics approach to simultaneously label and quantify newly-expressed proteins of host and microbe without physical isolation, for investigating mechanisms in direct host-microbe interactions.

METHODS

Using Caenorhabditis elegans-Pseudomonas aeruginosa infection model as proof-of-concept, we employed SILAC proteomics and molecular pathway analysis to characterize the differentially-expressed microbial and host proteins. We then used molecular docking and chemical characterization to identify chemical inhibitors that intercept host-microbe interactions and eliminate microbial infection.

RESULTS

Based on our proteomics results, we studied the iron competition between pathogen iron scavenger and host iron uptake protein, where P. aeruginosa upregulated pyoverdine synthesis protein (PvdA) (fold-change of 5.2313) and secreted pyoverdine, and C. elegans expressed ferritin (FTN-2) (fold-change of 3.4057). Targeted intervention of iron competition was achieved using Galangin, a ginger-derived phytochemical that inhibited pyoverdine production and biofilm formation in P. aeruginosa. The Galangin-ciprofloxacin combinatorial therapy could eliminate P. aeruginosa biofilms in a fish wound infection model, and enabled animal survival.

CONCLUSION

Our work provides a novel SILAC-based proteomics method that can simultaneously evaluate host and microbe proteomes, with future applications in higher host organisms and other microbial species. It also provides insights into the mechanisms dictating host-microbe interactions, offering novel strategies for anti-infective therapy.

Antioxidant, antibacterial, and anti-biofilm activities of selected indigenous plant species against nosocomial bacterial pathogens

Biofilms are responsible for over 60% of nosocomial infections. The focus of this study was to investigate the antioxidant, antibacterial, antibiofilm, and anti-motility activities of Gardenia volkensii, Carissa bispinosa, Peltophorum africanum, and Senna petersiana. Antioxidant activity was evaluated using free radical (DPPH) scavenging and ferric reducing power assays. Antibacterial and antibiofilm activities were evaluated using the broth micro-dilution and the crystal violet assays, respectively. Anti-motility was evaluated using anti-swarming activities, and the brine shrimp lethality assay was used for cytotoxicity. Gardenia volkensii and C. bispinosa acetone extracts had low EC50 values of 9.59 and 9.99 μg ml-1on the free-radical scavenging activity, respectively. All the plant extracts demonstrated broad-spectrum antibacterial activity against Klebsiella pneumoniae, Pseudomonasa aeruginosa, Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus [minimum inhibitory concentration (MIC) < 0.63 mg ml-1]. The initial cell adherence stage of P. aeruginosa and E. coli was the most susceptible stage where sub-MICs resulted in inhibitions >50%. Peltophorum africanum had the least cytotoxic effects. All extracts had anti-motility activity against P. aeruginosa and E. coli. This study showed that not only do the plants have strong antibacterial activity but had noteworthy inhibition (>50%) of initial cell adherence and may be suitable candidates for the treatment of nosocomial pathogens.

Rhizosphere bacterial exopolysaccharides: composition, biosynthesis, and their potential applications

Bacterial exopolysaccharides (EPS) are biopolymers of carbohydrates, often released from cells into the extracellular environment. Due to their distinctive physicochemical properties, biocompatibility, biodegradability, and non-toxicity, EPS finds applications in various industrial sectors. However, the need for alternative EPS has grown over the past few decades as lactic acid bacteria's (LAB) low-yield EPS is unable to meet the demand. In this case, rhizosphere bacteria with the diverse communities in soil leading to variations in composition and structure, are recognized as a potential source of EPS applicable in various industries. In addition, media components and cultivation conditions have an impact on EPS production, which ultimately affects the quantity, structure, and biological functions of the EPS. Therefore, scientists are currently working on manipulating bacterial EPS by developing cultures and applying abiotic and biotic stresses, so that better production of exopolysaccharides can be attained. This review highlights the composition, biosynthesis, and effects of environmental factors on EPS production along with the potential applications in different fields of industry. Ultimately, an overview of potential future paths and tactics for improving EPS implementation and commercialization is pointed out.

RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested this hypothesis by measuring transcriptome changes in Pseudomonas aeruginosa exposed to the supernatant of its competitor Burkholderia cenocepacia. We found that P. aeruginosa exhibited significant growth-medium-dependent transcriptome changes in response to competition. In an iron-rich medium, P. aeruginosa upregulated genes encoding the type-VI secretion system and the siderophore pyoverdine, whereas genes encoding phenazine toxins and hydrogen cyanide were upregulated under iron-limited conditions. Moreover, general stress response and quorum sensing regulators were upregulated upon supernatant exposure. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when confronted with B. cenocepacia supernatant, integrating both environmental and social cues.

The role of extracellular structures in Clostridioides difficile biofilm formation

C. difficile infection (CDI) is a costly and increasing burden on the healthcare systems of many developed countries due to the high rates of nosocomial infections. Despite the availability of several antibiotics with high response rates, effective treatment is hampered by recurrent infections. One potential mechanism for recurrence is the existence of C. difficile biofilms in the gut which persist through the course of antibiotics. In this review, we describe current developments in understanding the molecular mechanisms by which C. difficile biofilms form and are stabilized through extracellular biomolecular interactions.

Intact and mutated Shigella diguanylate cyclases increase c-di-GMP

The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger cyclic di-GMP (c di-GMP) signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but five of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the four intact DGCs in a S. flexneri strain, where these four DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these four DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN, which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC pseudogenes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.

Pseudomonas aeruginosa Biofilm Lifecycle: Involvement of Mechanical Constraints and Timeline of Matrix Production

Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections, especially in immunocompromised patients. Its remarkable adaptability and resistance to various antimicrobial treatments make it difficult to eradicate. Its persistence is enabled by its ability to form a biofilm. Biofilm is a community of sessile micro-organisms in a self-produced extracellular matrix, which forms a scaffold facilitating cohesion, cell attachment, and micro- and macro-colony formation. This lifestyle provides protection against environmental stresses, the immune system, and antimicrobial treatments, and confers the capacity for colonization and long-term persistence, often characterizing chronic infections. In this review, we retrace the events of the life cycle of P. aeruginosa biofilm, from surface perception/contact to cell spreading. We focus on the importance of extracellular appendages, mechanical constraints, and the kinetics of matrix component production in each step of the biofilm life cycle.

Engineered plastic-associated bacteria for biodegradation and bioremediation

The global plastic waste crisis has triggered the development of novel methods for removal of recalcitrant polymers from the environment. Biotechnological approaches have received particular attention due to their potential for enabling sustainable, low-intensity bioprocesses which could also be interfaced with microbial upcycling pathways to support the emerging circular bioeconomy. However, low biodegradation efficiency of solid plastic materials remains a bottleneck, especially at mesophilic conditions required for one-pot degradation and upcycling. A promising strategy used in nature to address this is localisation of plastic-degrading microbes to the plastic surface via biofilm-mediated surface association. This review highlights progress and opportunities in leveraging these naturally occurring mechanisms of biofilm formation and other cell-surface adhesion biotechnologies to co-localise engineered cells to plastic surfaces. We further discuss examples of combining these approaches with extracellular expression of plastic-degrading enzymes to accelerate plastic degradation. Additionally, we review this topic in the context of nano- and microplastics bioremediation and their removal from wastewater and finally propose future research directions for this nascent field.

VmsR, a LuxR-Type Regulator, Contributes to Virulence, Cell Motility, Extracellular Polysaccharide Production and Biofilm Formation in Xanthomonas oryzae pv. oryzicola

LuxR-type regulators play pivotal roles in regulating numerous bacterial processes, including bacterial motility and virulence, thereby exerting a significant influence on bacterial behavior and pathogenicity. Xanthomonas oryzae pv. oryzicola, a rice pathogen, causes bacterial leaf streak. Our research has identified VmsR, which is a response regulator of the two-component system (TCS) that belongs to the LuxR family. These findings of the experiment reveal that VmsR plays a crucial role in regulating pathogenicity, motility, biofilm formation, and the production of extracellular polysaccharides (EPSs) in Xoc GX01. Notably, our study shows that the vmsR mutant exhibits a reduced swimming motility but an enhanced swarming motility. Furthermore, this mutant displays decreased virulence while significantly increasing EPS production and biofilm formation. We have uncovered that VmsR directly interacts with the promoter regions of fliC and fliS, promoting their expression. In contrast, VmsR specifically binds to the promoter of gumB, resulting in its downregulation. These findings indicate that the knockout of vmsR has profound effects on virulence, motility, biofilm formation, and EPS production in Xoc GX01, providing insights into the intricate regulatory network of Xoc.

Metabolic pathways and antimicrobial peptide resistance in bacteria

Antimicrobial resistance is a pressing concern that poses a significant threat to global public health, necessitating the exploration of alternative strategies to combat drug-resistant microbial infections. Recently, antimicrobial peptides (AMPs) have gained substantial attention as possible replacements for conventional antibiotics. Because of their pharmacodynamics and killing mechanisms, AMPs display a lower risk of bacterial resistance evolution compared with most conventional antibiotics. However, bacteria display different mechanisms to resist AMPs, and the role of metabolic pathways in the resistance mechanism is not fully understood. This review examines the intricate relationship between metabolic genes and AMP resistance, focusing on the impact of metabolic pathways on various aspects of resistance. Metabolic pathways related to guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) [collectively (p)ppGpp], the tricarboxylic acid (TCA) cycle, haem biosynthesis, purine and pyrimidine biosynthesis, and amino acid and lipid metabolism influence in different ways metabolic adjustments, biofilm formation and energy production that could be involved in AMP resistance. By targeting metabolic pathways and their associated genes, it could be possible to enhance the efficacy of existing antimicrobial therapies and overcome the challenges exhibited by phenotypic (recalcitrance) and genetic resistance toward AMPs. Further research in this area is needed to provide valuable insights into specific mechanisms, uncover novel therapeutic targets, and aid in the fight against antimicrobial resistance.

The role of rcpA gene in regulating biofilm formation and virulence in Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a common seafood-borne pathogen that can colonize the intestine of host and cause gastroenteritis. Biofilm formation by V. parahaemolyticus enhances its persistence in various environments, which poses a series of threats to food safety. This work aims to investigate the function of rcpA gene in biofilm formation and virulence of V. parahaemolyticus. Deletion of rcpA significantly reduced motility, biofilm biomass, and extracellular polymeric substances, and inhibited biofilm formation on a variety of food and food contact surfaces. In mice infection model, mice infected with ∆rcpA strain exhibited a decreased rate of pathogen colonization, a lower level of inflammatory cytokines, and less tissue damage when compared to mice infected with wild type strain. RNA-seq analysis revealed that 374 genes were differentially expressed in the rcpA deletion mutant, which include genes related to quorum sensing, flagellar system, ribosome, type VI secretion system, biotin metabolism and transcriptional regulation. In conclusion, rcpA plays a role in determining biofilm formation and virulence of V. parahaemolyticus and further research is necessitated to fully understand its function in V. parahaemolyticus.

Cultivation of phosphate-accumulating biofilm: Study of the effects of acyl-homoserine lactones (AHLs) and cyclic dimeric guanosine monophosphate (c-di-GMP) on the formation of biofilm and the enhancement of phosphate metabolism capacity

This study investigated the mechanisms of microbial growth and metabolism during biofilm cultivation in the biofilm sequencing batch reactor (BSBR) process for phosphate (P) enrichment. The results showed that the sludge discharge was key to biofilm growth, as it terminated the competition for carbon (C) source between the nascent biofilm and the activated sludge. For the tested reactor, after the sludge discharge on 18 d, P metabolism and C source utilization improved significantly, and the biofilm grew rapidly. The P concentration of the recovery liquid reached up to 157.08 mg/L, which was sufficient for further P recovery via mineralization. Meta-omics methods were used to analyze metabolic pathways and functional genes in microbial growth during biofilm cultivation. It appeared that the sludge discharge activated the key genes of P metabolism and inhibited the key genes of C metabolism, which strengthened the polyphosphate-accumulating metabolism (PAM) as a result. The sludge discharge not only changed the types of polyphosphate-accumulating organisms (PAOs) but also promoted the growth of dominant PAOs. Before the sludge discharge, the necessary metabolic abilities that were spread among different microorganisms gradually concentrated into a small number of PAOs, and after the sludge discharge, they further concentrated into Candidatus_Contendobacter (P3) and Candidatus_Accumulibacter (P17). The messenger molecule C-di-GMP, produced mostly by P3 and P17, facilitated P enrichment by regulating cellular P and C metabolism. The glycogen-accumulating organism (GAO) Candidatus_Competibacter secreted N-Acyl homoserine lactones (AHLs), which stimulated the secretion of protein in extracellular polymeric substances (EPS), thus promoting the adhesion of microorganisms to biofilm and improving P metabolism via EPS-based P adsorption. Under the combined action of the dominant GAOs and PAOs, AHLs and C-di-GMP mediated QS to promote biofilm development and P enrichment. The research provides theoretical support for the cultivation of biofilm and its wider application.

Local control: a hub-based model for the c-di-GMP network

The genome of Pseudomonas fluorescens encodes >50 proteins predicted to play a role in bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)-mediated biofilm formation. We built a network representation of protein-protein interactions and extracted key information via multidimensional scaling (i.e., principal component analysis) of node centrality measures, which measure features of proteins in a network. Proteins of different domain types (diguanylate cyclase, dual domain, phosphodiesterase, PilZ) exhibit unique network behavior and can be accurately classified by their network centrality values (i.e., roles in the network). The predictive power of protein-protein interactions in biofilm formation indicates the possibility of localized pools of c-di-GMP. A regression model showed a statistically significant impact of protein-protein interactions on the extent of biofilm formation in various environments. These results highlight the importance of a localized c-di-GMP signaling, extend our understanding of signaling by this second messenger beyond the current "Bow-tie Model," support a newly proposed "Hub Model," and suggest future avenues of investigation.

A Label-Free Approach for Relative Spatial Quantitation of c-di-GMP in Microbial Biofilms

Microbial biofilms represent an important lifestyle for bacteria and are dynamic three-dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable toward understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest from a single sample.