Bacterially speaking

Synergistic effect of the combination of phenolic compounds and tobramycin on the inhibition of Pseudomonas aeruginosa biofilm

Bacteria coordinate gene expression in a cell density-dependent manner using a communication process called quorum sensing (QS). The expression of virulence factors, biofilm formation and enzyme production are examples of QS-regulated phenotypes that can interfere with food quality and safety. Due to the importance of these phenotypes, the inhibition of bacterial communication as an anti-virulence strategy is of great interest. This work aimed to evaluate the effect of phenolic compounds on the inhibition of biofilm formation by Pseudomonas aeruginosa PAO1, using concentrations that do not interfere in bacterial growth. The synergistic effect of rosmarinic acid, baicalein, curcumin and resveratrol with tobramycin and between the phenolics themselves was evaluated. The tested combinations proved to be a good strategy for reducing the dose of antibiotics used in treatments and obtaining satisfactory results against P. aeruginosa biofilms. The combination of the four compounds at the highest concentration (500 μM) completely inhibited biofilm formation. The obtained results contribute to understanding the effect of phenolic compounds on QS inhibition, which may help to define the mechanism of inhibition, in addition to expanding the biotechnological potential of these compounds for future applications in the food, pharmaceutical and medical fields.

Identification of new SdiA regulon members of Escherichia coli, Enterobacter cloacae, and Salmonella enterica serovars Typhimurium and Typhi

Bacteria can coordinate behavior in response to population density through the production, release, and detection of small molecules, a phenomenon known as quorum sensing. Salmonella enterica is among a group of Enterobacteriaceae that can detect signaling molecules of the N-acyl homoserine lactone (AHL) type but lack the ability to produce them. The AHLs are detected by the LuxR-type transcription factor, SdiA. This enables a behavior known as eavesdropping, where organisms can sense the signaling molecules of other species of bacteria. The role of SdiA remains largely unknown. Here, we use RNA-seq to more completely identify the sdiA regulons of two clinically significant serovars of Salmonella enterica: Typhimurium and Typhi. We find that their sdiA regulons are largely conserved despite the significant differences in pathogenic strategy and host range of these two serovars. Previous studies identified sdiA-regulated genes in Escherichia coli and Enterobacter cloacae, but there is surprisingly no overlap in regulon membership between the different species. This led us to individually test orthologs of each regulon member in the other species and determine that there is indeed some overlap. Unfortunately, the functions of most sdiA-regulated genes are unknown, with the overall function of eavesdropping in these organisms remaining unclear.

IMPORTANCE

Many bacterial species detect their own population density through the production, release, and detection of small molecules (quorum sensing). Salmonella and other Enterobacteriaceae have a modified system that detects the N-acyl-homoserine lactones of other bacteria through the solo quorum sensing receptor SdiA, a behavior known as eavesdropping. The roles of sdiA-dependent eavesdropping in the lifecycles of these bacteria are unknown. In this study, we identify sdiA-dependent transcriptional responses in two clinically relevant serovars of Salmonella, Typhimurium and Typhi, and note that their responses are partially conserved. We also demonstrate for the first time that sdiA-dependent regulation of genes is partially conserved in Enterobacter cloacae and Escherichia coli as well, indicating a degree of commonality in eavesdropping among the Enterobacteriaceae.

Short-range C-signaling restricts cheating behavior during Myxococcus xanthus development

Myxococcus xanthus uses short-range C-signaling to coordinate multicellular mound formation with sporulation during fruiting body development. A csgA mutant deficient in C-signaling can cheat on wild type (WT) in mixtures and form spores disproportionately, but our understanding of cheating behavior is incomplete. We subjected mixtures of WT and csgA cells at different ratios to co-development and used confocal microscopy and image analysis to quantify the arrangement and morphology of cells. At a ratio of one WT to four csgA cells (1:4), mounds failed to form. At 1:2, only a few mounds and spores formed. At 1:1, mounds formed with a similar number and arrangement of WT and csgA rods early in development, but later the number of csgA spores near the bottom of these nascent fruiting bodies (NFBs) exceeded that of WT. This cheating after mound formation involved csgA forming spores at a greater rate, while WT disappeared at a greater rate, either lysing or exiting NFBs. At 2:1 and 4:1, csgA rods were more abundant than expected throughout the biofilm both before and during mound formation, and cheating continued after mound formation. We conclude that C-signaling restricts cheating behavior by requiring sufficient WT cells in mixtures. Excess cheaters may interfere with positive feedback loops that depend on the cellular arrangement to enhance C-signaling during mound building. Since long-range signaling could not likewise communicate the cellular arrangement, we propose that C-signaling was favored evolutionarily and that other short-range signaling mechanisms provided selective advantages in bacterial biofilm and multicellular animal development.

IMPORTANCE

Bacteria communicate using both long- and short-range signals. Signaling affects community composition, structure, and function. Adherent communities called biofilms impact medicine, agriculture, industry, and the environment. To facilitate the manipulation of biofilms for societal benefits, a better understanding of short-range signaling is necessary. We investigated the susceptibility of short-range C-signaling to cheating during Myxococcus xanthus biofilm development. A mutant deficient in C-signaling fails to form mounds containing spores (i.e., fruiting bodies) but cheats on C-signaling by wild type in starved cell mixtures and forms spores disproportionately. We found that cheating requires sufficient wild-type cells in the initial mix and can occur both before mound formation and later during the sporulation stage of development. By restricting cheating behavior, short-range C-signaling may have been favored evolutionarily rather than long-range diffusible signaling. Cheating restrictions imposed by short-range signaling may have likewise driven the evolution of multicellularity broadly.

Cinnamoyl lipids as novel signaling molecules modulate the physiological metabolism of cross-phylum microorganisms

Signaling systems of microorganisms are responsible for regulating the physiological and metabolic processes and also play vital roles in the communications of cells. Identifying signaling molecules mediating the cross-talks is challenging yet highly desirable for comprehending the microbial interactions. Here, we demonstrate that a pathogenic Gram-negative Chromobacterium violaceum exerts significant influence on the morphological differentiation and secondary metabolism of Gram-positive Streptomyces. The physiological metabolisms are directly modulated by three novel cinnamoyl lipids (CVCL1, 2, and 3) from C. violaceum CV12472, whose biosynthesis is under the control of N-acylhomoserine lactone signaling system. Furthermore, a receptor of CVCLs in Streptomyces ansochromogenes 7100 is determined to be SabR1, the cognate receptor of γ-butenolide signaling molecules. This study reveals an unprecedented mode of microbial interactions, and the quorum sensing signaling systems in these two groups of bacteria can be bridged via CVCLs, suggesting that CVCLs can modulate the physiological metabolism of cross-phylum microorganisms.

The role of AbaI quorum sensing molecule synthase in host cell inflammation induced by Acinetobacter baumannii and its effect on zebrafish infection model

Acinetobacter baumannii is currently one of the most important opportunistic pathogens causing severe nosocomial infections worldwide. Quorum Sensing (QS) system is a widespread mechanism in bacteria to coordinate group behavior by sensing the density of bacterial populations and affect eukaryotic host cell. In Acinetobacter baumannii, AbaI protein is used as QS molecule synthetase to synthesize N- acyl homoserine lactones (AHLs). Currently, QS has made great progress in the study of drug resistance, but there is still a lack of complete understanding of its damage to host cells after adhesion and invasion. Thus, in this study, we examined the effects of abaI mutant (ΔabaI) on the functions of adhesion and invasion, cell viability, inflammation, apoptosis in A. baumannii infected A549 cells, to evaluate the effects of ΔabaI in a zebrafish model. We found the group infected with ΔabaI increased cell viability, reduced adhesion and invasion, cell injury, inflammatory cytokine production and apoptosis. By RNA-Seq, we explored the possibility that abaI stimulated A549 cells inflammation by A. baumannii infection via TLR4/MAPK signaling pathway. In addition, the ΔabaI significantly reduced pathogenicity and recruitment to neutrophils in zebrafish. These observations suggest that abaI plays a major role in A. baumannii infection.

Advancing Antibiotic-Resistant Microbe Combat: Nanocarrier-Based Systems in Combination Therapy Targeting Quorum Sensing

The increase in antibiotic-resistant bacteria presents a significant risk to worldwide public health, emphasizing the necessity of novel approaches to address infections. Quorum sensing, an essential method of communication among bacteria, controls activities like the formation of biofilms, the production of virulence factors, and the synthesis of secondary metabolites according to the number of individuals in the population. Quorum quenching, which interferes with these processes, emerges as a vital approach to diminish bacterial virulence and prevent biofilm formation. Nanocarriers, characterized by their small size, high surface-area-to-volume ratio, and modifiable surface chemistry, offer a versatile platform for the disruption of bacterial communication by targeting various stages within the quorum sensing pathway. These features allow nanocarriers to infiltrate biofilms, disrupt cell membranes, and inhibit bacterial proliferation, presenting a promising alternative to traditional antibiotics. Integrating nanocarrier-based systems into combination therapies provides a multi-pronged approach to infection control, enhancing both the efficacy and specificity of treatment regimens. Nonetheless, challenges related to the stability, safety, and clinical effectiveness of nanomaterial-based antimicrobial treatments remain. Continued research and development are essential to overcoming these obstacles and fully harnessing the potential of nano-antimicrobial therapies. This review emphasizes the importance of quorum sensing in bacterial behavior and highlights the transformative potential of nanotechnology in advancing antimicrobial treatments, offering innovative solutions to combat antibiotic-resistant pathogens.

Multi-component liquid-infused systems: a new approach to functional coatings

Antifouling liquid-infused surfaces have generated interest in multiple fields due to their diverse applications in industry and medicine. In nearly all reports to date, the liquid component consists of only one chemical species. However, unlike traditional solid surfaces, the unique nature of liquid surfaces holds the potential for synergistic and even adaptive functionality simply by including additional elements in the liquid coating. In this work, we explore the concept of multi-component liquid-infused systems, in which the coating liquid consists of a primary liquid and a secondary component or components that provide additional functionality. For ease of understanding, we categorize recently reported multi-component liquid-infused surfaces according to the size of the secondary components: molecular scale, in which the secondary components are molecules; nanoscale, in which they are nanoparticles or their equivalent; and microscale, in which the additional components are micrometer size or above. We present examples at each scale, showing how introducing a secondary element into the liquid can result in synergistic effects, such as maintaining a pristine surface while actively modifying the surrounding environment, which are difficult to achieve in other surface treatments. The review highlights the diversity of fabrication methods and provides perspectives on future research directions. Introducing secondary components into the liquid matrix of liquid-infused surfaces is a promising strategy with significant potential to create a new class of multifunctional materials. Keywords: Active surfaces; Antimicrobial; Antifouling; Interfaces; Sensing surfaces.

Quorum Sensing in Emulsion Droplet Swarms Driven by a Surfactant Competition System

Quorum sensing enables unicellular organisms to probe their population density and perform behavior that exclusively occurs above a critical density. Quorum sensing is established in emulsion droplet swarms that float at a water surface and cluster above a critical density. The design involves competition between 1) a surface tension gradient that is generated upon release of a surfactant from the oil droplets, and thereby drives their mutual repulsion, and 2) the release of a surfactant precursor from the droplets, that forms a strong imine surfactant which suppresses the surface tension gradient and thereby causes droplet clustering upon capillary (Cheerios) attraction. The production of the imine-surfactant depends on the population density of the droplets releasing the precursor so that the clustering only occurs above a critical population density. The pH-dependence of the imine-surfactant formation is exploited to trigger quorum sensing upon a base stimulus: dynamic droplet swarms are generated that cluster and spread upon spatiotemporally varying acid and base conditions. Next, the clustering of two droplet subpopulations is coupled to a chemical reaction that generates a fluorescent signal. It is foreseen that quorum sensing enables control mechanisms in droplet-based systems that display collective responses in contexts of, e.g., sensing, optics, or dynamically controlled droplet-reactors.

Bacterial persisters: molecular mechanisms and therapeutic development

Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.

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.

Potential of Streptomyces avermitilis: A Review on Avermectin Production and Its Biocidal Effect

Secondary metabolites produced by the fermentation of Streptomyces avermitilis bacterium are powerful antiparasitic agents used in animal health, agriculture and human infection treatments. Avermectin is a macrocyclic lactone with four structural components (A1, A2, B1, B2), each of them containing a major and a minor subcomponent, out of which avermectin B1a is the most effective parasitic control compound. Avermectin B1a produces two homologue avermectins (B1 and B2) that have been used in agriculture as pesticides and antiparasitic agents, since 1985. It has a great affinity with the Cl-channels of the glutamate receptor, allowing the constant flow of Cl- ions into the nerve cells, causing a phenomenon of hyperpolarization causing death by flaccid paralysis. The purpose of this work was to gather information on the production of avermectins and their biocidal effects, with special emphasis on their role in the control of pests and phytopathogenic diseases. The literature showed that S. avermitilis is an important producer of macrocyclic lactones with biocidal properties. In addition, avermectin contributes to the control of ectoparasites and endoparasites in human health care, veterinary medicine and agriculture. Importantly, avermectin is a compound that is harmless to the host (no side effects), non-target organisms and the environment.

The quorum sensing SinI/R system contributes to cadmium immobilization in Ensifer adhaerens NER9 in the cadmium-contaminated solution

In this study, the cadmium (Cd)-tolerant Ensifer adhaerens strain NER9 with quorum sensing (QS) systems (responsible for N-acyl homoserine lactone (AHL) production) was characterized for QS system-mediated Cd immobilization and the underlying mechanisms involved. Whole-genome sequence analysis revealed that strain NER9 contains the QS SinI/R and TraI/R systems. Strains NER9 and the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants were constructed and compared for QS SinI/R and TraI/R system-mediated Cd immobilization in the solution and the mechanisms involved. After 24 h of incubation, strain NER9 significantly decreased the Cd concentration in the Cd-contaminated solution compared with the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants. The NER9∆sinI/R mutant had a greater impact on Cd immobilization and a lower impact on the activities of AHLs than did the NER9∆traI/R mutant. The NER9∆sinI/R mutant had significantly greater Cd concentrations and lower cell wall- and exopolysaccharide (EPS)-adsorbed Cd contents than did strain NER9. Furthermore, the NER9∆sinI/R mutant presented a decrease in the number of functional groups interacting with Cd, compared with strain NER9. These results suggested that the SinI/R system in strain NER9 contributed to Cd immobilization by mediating cell wall- and EPS-adsorption in Cd-containing solution.

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.

Plasmid-free cheater cells commonly evolve during laboratory growth

It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation.

Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation

Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.

Equations describing semi-confluent cell growth (I) Analytical approximations

A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.

tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa

The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche.

Functional antagonism and insights into the biosynthetic potential of human gut-derived microbes

The specialised small molecules encoded by commensal microbes mediate distinct functional interactions. However, there is a landscape of antagonistic interactions mediated by specialised strains and their small molecules. Herein, the antagonistic landscape within a collection of 330 human gut-derived commensal microbial strains was elucidated to evaluate antimicrobial interactions as a defensive contributor, and gain new insights into structure-related functions. The potential antagonistic gut-derived strains displayed strain-specific selective inhibition. This is in contrast to common antimicrobial drugs, which typically wipe out a broad range of species and are usually found in environmental microbes. Genome sequencing of representative gut strains revealed the presence of significant biosynthetic gene clusters (BGCs) encoding compound families that contribute to antagonistic activities, and are important in host defence and maintaining gut homeostasis. Subsets of these BGCs were abundant in metagenomic sequencing data from healthy individuals. Furthermore, the cell culture secretome of these strains revealed potential biomarkers linked to hallmark pathways. These microorganisms have biosynthetic novelty and are a source of biologically significant natural products. Such natural products are essential in the development of new antimicrobial agents to reduce the usage of broad-spectrum antibiotics and combat antimicrobial resistance.

Ecological dependencies and the illusion of cooperation in microbial communities

Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.

Potential of DPD ((S)-4,5-dihydroxy-2,3-pentanedione) Analogs in Microparticulate Formulation as Vaccine Adjuvants

The molecule (S)-4,5-dihydroxy-2,3-pentanedione (DPD) is produced by many different species of bacteria and is involved in bacterial communication. DPD is the precursor of signal molecule autoinducer-2 (AI-2) and has high potential to be used as a vaccine adjuvant. Vaccine adjuvants are compounds that enhance the stability and immunogenicity of vaccine antigens, modulate efficacy, and increase the immune response to a particular antigen. Previously, the microparticulate form of (S)-DPD was found to have an adjuvant effect with the gonorrhea vaccine. In this study, we evaluated the immunogenicity and adjuvanticity of several synthetic analogs of the (S)-DPD molecule, including ent-DPD((R)-4,5-dihydroxy-2,3-pentanedione), n-butyl-DPD ((S)-1,2-dihydroxy-3,4-octanedione), isobutyl-DPD ((S)-1,2-dihydroxy-6-methyl-3,4-heptanedione), n-hexyl-DPD ((S)-1,2-dihydroxy-3,4-decanedione), and phenyl-DPD ((S)-3,4-dihydroxy-1-phenyl-1,2-butanedione), in microparticulate formulations. The microparticulate formulations of all analogs of (S)-DPD were found to be noncytotoxic toward dendritic cells. Among these analogs, ent-DPD, n-butyl-DPD, and isobutyl-DPD were found to be immunogenic toward antigens and showed adjuvant efficacy with microparticulate gonorrhea vaccines. It was observed that n-hexyl-DPD and phenyl-DPD did not show any adjuvant effect. This study shows that synthetic analogs of (S)-DPD molecules are capable of eliciting adjuvant effects with vaccines. A future in vivo evaluation will further confirm that these analogs are promising vaccine adjuvants.

Characterization of the Human Plasma Biofilm Model (hpBIOM) to Identify Potential Therapeutic Targets for Wound Management of Chronic Infections

The treatment of chronic wounds still represents a major challenge in wound management. Recent estimates suggest that 60-80% of chronic wounds are colonized by pathogenic microorganisms, which are strongly considered to have a major inhibiting influence on the healing process. By means of an innovative biofilm model based on human plasma, the time-dependent behavior of various bacterial strains under wound-milieu-like conditions were investigated, and the growth habits of different cocci species were compared. Undescribed fusion events between colonies of MRSA as well as of Staphylococcus epidermidis were detected, which were associated with the remodeling and reorganization of the glycocalyx of the wound tissue. After reaching a maximum colony size, the spreading of individual bacteria was observed. Interestingly, the combination of different cocci species with Pseudomonas aeruginosa in the human plasma biofilm revealed partial synergistic effects in these multispecies organizations. RT-qPCR analyses gave a first impression of the relevant proteins involved in the formation and maturation of biofilms, especially the role of fibrinogen-binding proteins. Knowledge of the maturation and growth behavior of persistent biofilms investigated in a translational human biofilm model reflects a starting point for the development of novel tools for the treatment of chronic wounds.

Widespread Peptide Surfactants with Post-translational C-methylations Promote Bacterial Development

Bacteria produce a variety of peptides to mediate nutrient acquisition, microbial interactions, and other physiological processes. Of special interest are surface-active peptides that aid in growth and development. Herein, we report the structure and characterization of clavusporins, unusual and hydrophobic ribosomal peptides with multiple C-methylations at unactivated carbon centers, which help drastically reduce the surface tension of water and thereby aid in Streptomyces development. The peptides are synthesized by a previously uncharacterized protein superfamily, termed DUF5825, in conjunction with a vitamin B12-dependent radical S-adenosylmethionine metalloenzyme. The operon encoding clavusporin is wide-spread among actinomycete bacteria, suggesting a prevalent role for clavusporins as morphogens in erecting aerial hyphae and thereby advancing sporulation and proliferation.

SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway

Diatom bloom is characterized by a rapid increase of population density. Perception of population density and physiological responses can significantly influence their survival strategies, subsequently impacting bloom fate. The population density itself can serve as a signal, which is perceived through chemical signals or chlorophyll fluorescence signals triggered by high cell density, and their intracellular signaling mechanisms remain to be elucidated. In this study, we focused on the model diatom, Phaeodactylum tricornutum, and designed an orthogonal experiment involving varying cell densities and light conditions, to stimulate the release of chemical signals and light-induced chlorophyll fluorescence signals. Utilizing RNA-Seq and Weighted Gene Co-expression Network Analysis, we identified four gene clusters displaying density-dependent expression patterns. Within these, a potential hub gene, PtSLC24A, encoding a Na+/Ca2+ exchanger, was identified. Based on molecular genetics, cellular physiology, computational structural biology, and in situ oceanic data, we propose a potential intracellular signaling mechanism related to cell density in marine diatoms using Ca2+: upon sensing population density signals mediated by chemical cues, the membrane-bound PtSLC24A facilitates the efflux of Ca2+ to maintain specific intracellular calcium levels, allowing the transduction of intracellular density signals, subsequently regulating physiological responses, including cell apoptosis, ultimately affecting algal blooms fate. These findings shed light on the calcium-mediated intracellular signaling mechanism of marine diatoms to changing population densities, and enhances our understanding of diatom bloom dynamics and their ecological implications.

Light-based juxtacrine signaling between synthetic cells

Cell signaling through direct physical cell-cell contacts plays vital roles in biology during development, angiogenesis, and immune response. Intercellular communication mechanisms between synthetic cells constructed from the bottom up are majorly reliant on diffusible chemical signals, thus limiting the range of responses in receiver cells. Engineering contact-dependent signaling between synthetic cells promises to unlock more complicated signaling schemes with different types of responses. Here, we design and demonstrate a light-activated contact-dependent communication tool for synthetic cells. We utilize a split bioluminescent protein to limit signal generation exclusively to contact interfaces of synthetic cells, driving the recruitment of a photoswitchable protein in receiver cells, akin to juxtacrine signaling in living cells. Our modular design not only demonstrates contact-dependent communication between synthetic cells but also provides a platform for engineering orthogonal contact-dependent signaling mechanisms.

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

Constructions of quorum sensing signaling network for activated sludge microbial community

In wastewater treatment systems, the interactions among various microbes based on chemical signals, namely quorum sensing (QS), play critical roles in influencing microbial structure and function. However, it is challenging to understand the QS-controlled behaviors and the underlying mechanisms in complex microbial communities. In this study, we constructed a QS signaling network, providing insights into the intra- and interspecies interactions of activated sludge microbial communities based on diverse QS signal molecules. Our research underscores the role of diffusible signal factors in both intra- and interspecies communication among activated sludge microorganisms, and signal molecules commonly considered to mediate intraspecies communication may also participate in interspecies communication. QS signaling molecules play an important role as communal resources among the entire microbial group. The communication network within the microbial community is highly redundant, significantly contributing to the stability of natural microbial systems. This work contributes to the establishment of QS signaling network for activated sludge microbial communities, which may complement metabolic exchanges in explaining activated sludge microbial community structure and may help with a variety of future applications, such as making the dynamics and resilience of highly complex ecosystems more predictable.

Structural basis of peptide secretion for Quorum sensing by ComA

Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as Streptococcus pneumoniae, ComA is a conserved efflux pump responsible for the maturation and secretion of peptide signals, including the competence-stimulating peptide (CSP), yet its structure and function remain unclear. Here, we functionally characterize ComA as an ABC transporter with high ATP affinity and determined its cryo-EM structures in the presence or absence of CSP or nucleotides. Our findings reveal a network of strong electrostatic interactions unique to ComA at the intracellular gate, a putative binding pocket for two CSP molecules, and negatively charged residues facilitating CSP translocation. Mutations of these residues affect ComA's peptidase activity in-vitro and prevent CSP export in-vivo. We demonstrate that ATP-Mg2+ triggers the outward-facing conformation of ComA for CSP release, rather than ATP alone. Our study provides molecular insights into the QS signal peptide secretion, highlighting potential targets for QS-targeting drugs.

The importance of the PapR7 C-terminus and amide protons in mediating quorum sensing in Bacilluscereus

The opportunistic human pathogen Bacillus cereus controls the expression of key infection-promoting phenotypes using bacterial quorum sensing (QS). QS signal transduction within the species is controlled by an autoinducing peptide, PapR7, and its cognate receptor, PlcR, indicating that the PlcR:PapR interface is a prime target for QS inhibitor development. The C-terminal region of the peptide (PapR7; ADLPFEF) has been successfully employed as a scaffold to develop potent QS modulators. Despite the noted importance of the C-terminal carboxylate and amide protons in crystallographic data, their role in QS activity has yet to be explored. In this study, an N-methyl scan of PapR7 was conducted in conjunction with a C-terminal modification of previously identified B. cereus QS inhibitors. The results indicate that the amide proton at Glu6 and the C-terminal carboxylate are important for effective QS inhibition of the PlcR regulon. Through β-galactosidase and hemolysis assays, a series of QS inhibitors were discovered, including several capable of inhibiting QS with nanomolar potency. These inhibitors, along with the structure-activity data reported, will serve as valuable tools for disrupting the B. cereus QS pathway towards developing novel anti-infective strategies.

TetR and OmpR family regulators in natural product biosynthesis and resistance

This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.

The regulatory functions of oxylipins in fungi: A review

Quorum sensing (QS) is a communication mechanism between microorganisms originally found in bacteria. In recent years, an important QS mechanism has been discovered in the field of fungi, namely, the lipoxygenase compound oxylipin of arachidonic acid acts as a QS molecule in life cycle control, particularly in the sexual and asexual development of fungi. However, the role of oxylipins in mediating eukaryotic communication has not been previously described. In this paper, we review the regulatory role of oxylipins and the underlying mechanisms and discuss the potential for application in major fungi. The role of oxylipin as a fungal quorum-sensing molecule is the main focus of the review. Besides, the quorum regulation of fungal morphological transformation, biofilm formation, virulence factors, secondary metabolism, infection, symbiosis, and other physiological behaviors are discussed. Moreover, future prospectives and applications are elaborated as well.

Engineered biosensors for the quorum sensing molecule 3,5-dimethyl-pyrazine-2-ol (DPO) reveal its presence in humans, animals, and bacterial species beyond Vibrio cholerae

A biosensor was engineered to enable the study of the novel quorum sensing molecule (QSM), 3,5-dimethylpyrazin-2-ol (DPO), employed by Vibrio cholerae to regulate biofilm formation and virulence factor production. Investigations into bacterial quorum sensing (QS), a form of communication based on the production and detection of QSMs to coordinate gene expression in a population dependent manner, offer a unique window to study the molecular underpinnings of microbial behavior and host interactions. Herein, we report the construction of an engineered microbial whole-cell bioluminescent biosensing system that incorporates the recognition of the VqmA regulatory protein of Vibrio cholerae with the bioluminescent reporting signal of luciferase for the selective, sensitive, stable, and reproducible detection of DPO in a variety of samples. Importantly, using our newly developed biosensor our studies demonstrate the detection of DPO in rodent and human samples. Employing our developed biosensor should help enable elucidation of microbial behavior at the molecular level and its impact in health and disease.

Evolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung

Chronic infection with the bacterial pathogen Pseudomonas aeruginosa often leads to coexistence of heterogeneous populations carrying diverse mutations. In particular, loss-of-function mutations affecting the quorum-sensing regulator LasR are often found in bacteria isolated from patients with lung chronic infection and cystic fibrosis. Here, we study the evolutionary dynamics of polymorphic P. aeruginosa populations using isolates longitudinally collected from patients with chronic obstructive pulmonary disease (COPD). We find that isolates deficient in production of different sharable extracellular products are sequentially selected in COPD airways, and lasR mutants appear to be selected first due to their quorum-sensing defects. Polymorphic populations including lasR mutants display survival advantages in animal models of infection and modulate immune responses. Our study sheds light on the multistage evolution of P. aeruginosa populations during their adaptation to host lungs.

Phenotypic assay for cytotoxicity assessment of Balamuthia mandrillaris against human neurospheroids

Introduction

The phenotypic screening of drugs against Balamuthia mandrillaris, a neuropathogenic amoeba, involves two simultaneous phases: an initial step to test amoebicidal activity followed by an assay for cytotoxicity to host cells. The emergence of three-dimensional (3D) cell cultures has provided a more physiologically relevant model than traditional 2D cell culture for studying the pathogenicity of B. mandrillaris. However, the measurement of ATP, a critical indicator of cell viability, is complicated by the overgrowth of B. mandrillaris in coculture with host cells during drug screening, making it challenging to differentiate between amoebicidal activity and drug toxicity to human cells.

Methods

To address this limitation, we introduce a novel assay that utilizes three-dimensional hanging spheroid plates (3DHSPs) to evaluate both activities simultaneously on a single platform.

Results and discussion

Our study showed that the incubation of neurospheroids with clinically isolated B. mandrillaris trophozoites resulted in a loss of neurospheroid integrity, while the ATP levels in the neurospheroids decreased over time, indicating decreased host cell viability. Conversely, ATP levels in isolated trophozoites increased, indicating active parasite metabolism. Our findings suggest that the 3DHSP-based assay can serve as an endpoint for the phenotypic screening of drugs against B. mandrillaris, providing a more efficient and accurate approach for evaluating both parasite cytotoxicity and viability.

Discovering functional small molecules in the gut microbiome

The human microbiome has emerged as a source of bacterially produced, functional small molecules that help regulate health and disease, and their discovery and annotation has become a popular research topic. Identifying these molecules provides an essential step in unraveling the molecular mechanisms underlying biological outcomes. The relevance of specific bacterial members of the microbiome has been demonstrated in a variety of correlative studies, and there are many possible paths from these correlations to the responsible metabolites. Herein, we summarize two studies that have recently identified gut microbiome metabolites that modulate immune responses or promote physical activity. Aside from the deep insights gained, these studies provide blueprints for successfully uncovering the molecules and mechanisms that control important physiological pathways.

Quorum sensing interference by phenolic compounds - A matter of bacterial misunderstanding

Over the past decade, numerous publications have emerged in the literature focusing on the inhibition of quorum sensing (QS) by plant extracts and phenolic compounds. However, there is still a scarcity of studies that delve into the specific mechanisms by which these compounds inhibit QS. Thus, our question is whether phenolic compounds can inhibit QS in a specific or indirect manner and to elucidate the underlying mechanisms involved. This study is focused on the most studied QS system, namely, autoinducer type 1 (AI-1), represented by N-acyl-homoserine lactone (AHL) signals and the AHL-mediated QS responses. Here, we analyzed the recent literature in order to understand how phenolic compounds act at the cellular level, at sub-inhibitory concentrations, and evaluated by which QS inhibition mechanisms they may act. The biotechnological application of QS inhibitors holds promising prospects for the pharmaceutical and food industries, serving as adjunct therapies and in the prevention of biofilms on various surfaces.

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses

Antibiotic resistance poses mounting risks to human health, as current antibiotics are losing efficacy against increasingly resistant pathogenic bacteria. Of particular concern is the emergence of multidrug-resistant strains, which has been rapid among Gram-negative bacteria such as Escherichia coli. A large body of work has established that antibiotic resistance mechanisms depend on phenotypic heterogeneity, which may be mediated by stochastic expression of antibiotic resistance genes. The link between such molecular-level expression and the population levels that result is complex and multi-scale. Therefore, to better understand antibiotic resistance, what is needed are new mechanistic models that reflect single-cell phenotypic dynamics together with population-level heterogeneity, as an integrated whole. In this work, we sought to bridge single-cell and population-scale modeling by building upon our previous experience in "whole-cell" modeling, an approach which integrates mathematical and mechanistic descriptions of biological processes to recapitulate the experimentally observed behaviors of entire cells. To extend whole-cell modeling to the "whole-colony" scale, we embedded multiple instances of a whole-cell E. coli model within a model of a dynamic spatial environment, allowing us to run large, parallelized simulations on the cloud that contained all the molecular detail of the previous whole-cell model and many interactive effects of a colony growing in a shared environment. The resulting simulations were used to explore the response of E. coli to two antibiotics with different mechanisms of action, tetracycline and ampicillin, enabling us to identify sub-generationally-expressed genes, such as the beta-lactamase ampC, which contributed greatly to dramatic cellular differences in steady-state periplasmic ampicillin and was a significant factor in determining cell survival.

Efflux pumps and microbial biofilm formation

Biofilm-related infections are resistant forms of pathogens that are regarded as a medical problem, particularly due to the spread of multiple drug resistance. One of the factors associated with biofilm drug resistance is the presence of various types of efflux pumps in bacteria. Efflux pumps also play a role in biofilm formation by influencing Physical-chemical interactions, mobility, gene regulation, quorum sensing (QS), extracellular polymeric substances (EPS), and toxic compound extrusion. According to the findings of studies based on efflux pump expression analysis, their role in the anatomical position within the biofilm will differ depending on the biofilm formation stage, encoding gene expression level, the type and concentration of substrate. In some cases, the function of the efflux pumps can overlap with each other, so it seems necessary to accurate identify the efflux pumps of biofilm-forming bacteria along with their function in this process. Such studies will help to choose treatment strategy, at least in combination with antibiotics. Furthermore, if the goal of treatment is an efflux pump manipulation, we should not limit it to inhibition.

A Geneticist Transcribing the Chemical Language of Bacteria

The study of quorum sensing, bacterial cell-to-cell communication mediated by the production and detection of small molecule signals, has skyrocketed since its discovery in the last third of the 20th century. Building from early investigations of bacterial bioluminescence, the process has been characterized to control a numerous and growing number of group behaviors, including virulence and biofilm formation. Bonnie Bassler has made key contributions to the understanding of quorum sensing, leading interdisciplinary efforts to characterize key signaling pathway components and their respective signaling molecules across a range of gram-negative bacteria. This review highlights her work in the field, with a particular emphasis on the chemical contributions of her work.

Plasmid-free cheater cells commonly evolve during laboratory growth

It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, secretion of beta-lactamase from resistant cells, and subsequent degradation of nearby penicillin and related antibiotics, allows neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss still occurred. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.

Plant-Derived Quorum Sensing Inhibitors (Quercetin, Vanillin and Umbelliferon) Modulate Cecal Microbiome, Reduces Inflammation and Affect Production Efficiency in Broiler Chickens

Quorum sensing inhibitors (QSIs) are an attractive alternative to antibiotic growth promoters in farmed animal nutrition. The goal of the study was the diet supplementation of Arbor Acres chickens with quercetin (QC), vanillin (VN), and umbelliferon (UF), which are plant-derived QSIs preliminarily showing cumulative bioactivity. Chick cecal microbiomes were analyzed by 16s rRNA sequencing, inflammation status was assessed by blood sample analyses, and zootechnical data were summarized in the European Production Efficiency Factor (EPEF). When compared to the basal diet control group, a significant increase in the Bacillota:Bacteroidota ratio in the cecal microbiome was found in all experimental subgroups, with the highest expression > 10 at VN + UV supplementation. Bacterial community structure in all experimental subgroups was enriched with Lactobacillaceae genera and also changed in the abundance of some clostridial genera. Indices of richness, alpha diversity, and evenness of the chick microbiomes tended to increase after dietary supplementation. The peripheral blood leukocyte content decreased by 27.9-45.1% in all experimental subgroups, likely due to inflammatory response reduction following beneficial changes in the cecal microbiome. The EPEF calculation showed increased values in VN, QC + UF, and, especially, VN + UF subgroups because of effective feed conversion, low mortality, and broiler weight daily gain.

Biofilm formation in Gram-positives as an answer to combined salt and metal stress

Biofilm formation can lead to tolerance against stressors like antibiotics, toxic metals, salts, and other environmental contaminants. Halo- and metal-tolerant bacilli and actinomycete strains isolated from a former uranium mining and milling site in Germany were shown to form biofilm in response to salt and metal treatment; specifically, Cs and Sr exposition led to biofilm formation. Since the strains were obtained from soil samples, a more structured environment was tested using expanded clay to provide porous structures resembling the natural environment. There, accumulation of Cs could be shown for Bacillus sp. SB53B, and high Sr accumulation ranging from 75% to 90% was seen with all isolates tested. We could, therefore, show that biofilms in a structured environment like soil will contribute to the water purification obtained by the passage of water through the critical zone of soil, providing an ecosystem benefit that can hardly be overestimated.

Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria

Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.

In silico and biological activity evaluation of quercetin-boron hybrid compounds, anti-quorum sensing effect as alternative potential against microbial resistance

Boronic acid compounds and the natural flavonoid compound quercetin were handled to synthesize two novel ligands encoded as B1(2,2'-(1,4-phenylenebis (benzo [1,3,2] dioxaborole-2,5-diyl)) bis (3,5,7-trihydroxy-4H- chromen-4-one) and B2(3.3.6. 3,5,7-trihydroxy-2-(2-(6-methoxypyridin-3-yl)benzo[d][1,3,2]dioxaborol-5-yl)- 4 H-chromene-4). Antioxidant activities of ligands were investigated by DPPH, ABTS and CUPRAC methods. Cholinesterase inhibition effects of ligands were determined by acetylcholinesterase and butyrylcholinesterase enzyme inhibition methods, cytotoxic effects of ligands were applied to healthy breast and colon cancer cell lines by MTT method, and urease and tyrosinase enzyme activities were determined. Antimicrobial properties of the compounds were analyzed by detecting their anti-QS potentials on Chromobacterium violaceum biosensor strain. Both compounds were found to have significant antioxidant effects compared to controls. It was determined that the compound B1 at 1-10 µg/mL was more active than the reference compounds (α-TOC and BHT). Moreover, the enzyme activity studies on ligands demonstrated that acetylchoinesterase and butyrylcholinesterase enzyme inhibitions were higher than the reference compounds. As expected, boron derivatives exhibited respectable activity against the biofilms of Escherichia coli (E. coli) and P. aeruginosa (P. aeruginosa). These results demonstrate the potential applicability of boron derivatives in the treatment of biofilm-associated infections and provide a practical strategy for the design of new boron-based antimicrobial materials. In silico molecular docking studies were performed on ligands to identify newly synthesized compounds. The binding parameter values and binding sites of the compounds were also determined. In conclusion, our studies showed that newly synthesized hybrid compounds could be solutions for antimicrobial resistance and enzyme-related disorders.

Derivatized chitosan-oil-in-water nanocapsules for trans-cinnamaldehyde delivery

trans-Cinnamaldehyde, known for its bacterial anti-quorum sensing activity when applied at sublethal concentrations, has gained traction given its potential use against multidrug resistant bacteria. In this work, trans-cinnamaldehyde-loaded oil-in-water nanocapsules coated with chitosan, N,N,N-trimethyl chitosan chloride, N-(2-(N,N,N-trimethylammoniumyl)acetyl) chitosan chloride or N-(6-(N,N,N-trimethylammoniumyl)hexanoyl)chitosan chloride were obtained. All the formulated nanocapsules showed a Z-average hydrodynamic diameter ~ 160 nm and ζ-potential higher than +40 mV. N,N,N-trimethyl chitosan-coated oil-in-water nanocapsules showed the greatest trans-cinnamaldehyde association efficiency (99.3 ± 7.6) % and total payload release (88.6 ± 22.5) %, while N-(6-(N,N,N-trimethylammoniumyl)hexanoyl)chitosan chloride chitosan-coated oil-in-water nanocapsules were the only formulations stable in phosphate buffer saline PBS (pH 7.4) upon incubation at 37 °C for 24 h. Future work should address the stability of the developed nanocapsules in culture media and their biological performance.

Application of Quorum Sensing in Metabolic Engineering

Metabolic engineering is widely utilized in the food and other fields and has the benefits of low-cost substrates, eco-friendly fermentation processes, and efficient substrate synthesis. Microbial synthesis by metabolic engineering requires maintaining the productive capacity of the microorganism. Moreover, economic reasons limit the use of inducers in the exogenous synthesis pathway. Most unicellular microorganisms can interact by emitting signaling molecules; this mechanism, known as quorum sensing (QS), is an autoinduced system of microorganisms. With the deepening research on QS systems of different microorganisms, its components are widely used to regulate the metabolic synthesis of microorganisms as a dynamic regulatory system. In this Review, we described the typical bacterial QS mechanisms. Then, we summarized various regulatory strategies for QS and their applications to metabolic engineering. Finally, we underlined the potential for QS modularity in future metabolic engineering and suggested stimulating research on fungal QS systems.

Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments

Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium (Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using ¹³C-labeled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of ¹³C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1-14.2%), labeling ratio (LR, 0.13-0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of ¹³C-labeled fungal metabolites into bacterial proteins. Distinct ¹³C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).

The Biological Production of Spacetime: A Sketch of the E-series Universe

Space and time, which should properly be taken conjointly, are both communicatively produced and created with certain contextual perspectives-they are not independent physical entities. The standpoint of production makes the relationship between space and time comprehensible. They can either be mental-subjective, physical-objective, or social-intersubjective. Social and intersubjective (or E-series) spacetime might shed new light on biological thinking. For general readers, this paper provides a clue regarding an alternative conceptualization of spacetime based on biology.

Paecilomycone Inhibits Quorum Sensing in Gram-Negative Bacteria

Pseudomonas aeruginosa is an opportunistic pathogen that causes major health care concerns due to its virulence and high intrinsic resistance to antimicrobial agents. Therefore, new treatments are greatly needed. An interesting approach is to target quorum sensing (QS). QS regulates the production of a wide variety of virulence factors and biofilm formation in P. aeruginosa. This study describes the identification of paecilomycone as an inhibitor of QS in both Chromobacterium violaceum and P. aeruginosa. Paecilomycone strongly inhibited the production of virulence factors in P. aeruginosa, including various phenazines, and biofilm formation. In search of the working mechanism, we found that paecilomycone inhibited the production of 4-hydroxy-2-heptylquinoline (HHQ) and 3,4-dihydroxy-2-heptylquinoline (PQS), but not 2'-aminoacetophenone (2-AA). Therefore, we suggest that paecilomycone affects parts of QS in P. aeruginosa by targeting the PqsBC complex and alternative targets or alters processes that influence the enzymatic activity of the PqsBC complex. The toxicity of paecilomycone toward eukaryotic cells and organisms was low, making it an interesting lead for further clinical research. IMPORTANCE Antibiotics are becoming less effective against bacterial infections due to the evolution of resistance among bacteria. Pseudomonas aeruginosa is a Gram-negative pathogen that causes major health care concerns and is difficult to treat due to its high intrinsic resistance to antimicrobial agents. Therefore, new targets are needed, and an interesting approach is to target quorum sensing (QS). QS is the communication system in bacteria that regulates multiple pathways, including the production of virulence factors and biofilm formation, which leads to high toxicity in the host and low sensitivity to antibiotics, respectively. We found a compound, named paecilomycone, that inhibited biofilm formation and the production of various virulence factors in P. aeruginosa. The toxicity of paecilomycone toward eukaryotic cells and organisms was low, making it an interesting lead for further clinical research.