Biofilms: an emergent form of bacterial life

Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures

Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistancetetoperon inE. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.

The effect of bovine trypsin on dental biofilm dispersion: an in vitro study

To investigate the degradation effect of bovine trypsin on multispecies biofilm of caries-related bacteria and provide an experimental foundation for the prevention of dental caries. Standard strains of S. mutans, S. sanguis, S. gordonii, and L. acidophilus were co-cultured to form 24 h, 48 h, and 72 h biofilms. The experimental groups were treated with bovine trypsin for 30 s, 1 min, and 3 min. Morphological observation and quantitative analysis of extracellular polymeric substances (EPS), live bacteria, and dead bacteria were conducted using the confocal laser scanning microscope (CLSM). The morphological changes of EPS and bacteria were also observed using a scanning electron microscope (SEM). When biofilm was treated for 1 min, the minimal inhibitory concentration (MIC) of bovine trypsin to reduce EPS was 0.5 mg/mL in 24 h and 48 h biofilms, and the MIC of bovine trypsin was 2.5 mg/mL in 72 h biofilms (P < 0.05). When biofilm was treated for 3 min, the MIC of bovine trypsin to reduce EPS was 0.25 mg/mL in 24 h and 48 h biofilms, the MIC of bovine trypsin was 1 mg/mL in 72 h biofilm (P < 0.05). The ratio of live-to-dead bacteria in the treatment group was significantly lower than blank group in 24 h, 48 h, and 72 h multispecies biofilms (P < 0.05). Bovine trypsin can destroy multispecies biofilm structure, disperse biofilm and bacteria flora, and reduce the EPS and bacterial biomass in vitro, which are positively correlated with the application time and concentration.

Multi-trait efficiency and interactivity of bacterial consortia used to enhance plant performance under water stress conditions

Water stress is a major limiting factor for agricultural production under current and projected climate change scenarios. As a sustainable strategy, plant growth-promoting bacterial consortia have been used to reduce plant water stress. However, few studies have examined the effects of stress on multi-trait efficiency and interactivity of bacterial species. In this study, we used several in-vitro experiments, plant assays and greenhouse trials to investigate the effects of stress and bacterial consortia on 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) activities, indole-3-acetic acid (IAA) production and plant growth-promoting traits (Phosphate-solubilization, starch hydrolysis, siderophores and ammonium production). We further assessed biofilm formation and the chemotactic behaviour in response to ACC. A total of fifteen ACCD rhizobacteria with multiple growth-promoting traits from the dominant plant species from the hyperseasonal Aripo Savannas were screened in this study. Five of the isolates were further analyzed based on their ACCD activities and were tested in single and dual consortium to assess their abilities in promoting growth under simulated drought stress (-0.35 MPa) and chemically induced ACC conditions (0.03 mM). Our findings showed that bacteria which produce high concentrations of IAA affected the isolates' ability to promote growth under stress, irrespective of microbial combination with ACCD activity above the minimal threshold of 20 nmol α-ketobutyrate mg-1 h-1. Biofilm production with co-culture interaction varied greatly across treatments, however, the general trend showed an increase in biofilm under stress induce conditions. The best performing co-culture, UWIGT-83 and UWIGT-120 (Burkholderia sp.) showed enhanced growth in germination assays and in greenhouse trials with Capsicum chinense (Moruga red hot peppers) under drought stress, when compared to non-inoculated treatments. The findings highlight the importance of testing interactivity of bacterial species with multiple growth promoting traits under stress conditions; and proposed the use of ACC growth media as a novel biofilm screening method for selecting potential stress plant growth-promoting bacteria. Better screening strategies for appropriate plant growth-promoting bacteria may narrow the inconsistency observed between laboratory and field trials.

Deletion of speA and aroC genes impacts the pathogenicity of Vibrio anguillarum in spotted sea bass

Vibrio anguillarum is one of the major pathogens responsible for bacterial infections in marine environments, causing significant impacts on the aquaculture industry. The misuse of antibiotics leads to bacteria developing multiple drug resistances, which is detrimental to the development of the fisheries industry. In contrast, live attenuated vaccines are gradually gaining acceptance and widespread recognition. In this study, we constructed a double-knockout attenuated strain, V. anguillarum ΔspeA-aroC, to assess its potential for preparing a live attenuated vaccine. The research results indicate a significant downregulation of virulence-related genes, including Type VI secretion system, Type II secretion system, biofilm synthesis, iron uptake system, and other related genes, in the mutant strain. Furthermore, the strain lacking the genes exhibited a 67.47% reduction in biofilm formation ability and increased sensitivity to antibiotics. The mutant strain exhibited significantly reduced capability in evading host immune system defenses and causing in vivo infections in spotted sea bass (Lateolabrax maculatus), with an LD50 that was 13.93 times higher than that of the wild-type V. anguillarum. Additionally, RT-qPCR analysis of immune-related gene expression in spotted sea bass head kidney and spleen showed a weakened immune response triggered by the knockout strain. Compared to the wild-type V. anguillarum, the mutant strain caused reduced levels of tissue damage. The results demonstrate that the deletion of speA and aroC significantly reduces the biosynthesis of biofilms in V. anguillarum, leading to a decrease in its pathogenicity. This suggests a crucial role of biofilms in the survival and invasive capabilities of V. anguillarum.

A review of experimental Assessment Processes of material resistance to marine and freshwater biofouling

Biofouling presents hazards to a variety of freshwater and marine underwater infrastructures and is one of the direct causes of species invasion. These negative impacts provide a unified goal for both industry practitioners and researchers: the development of novel antifouling materials to prevent the adhesion of biofouling. The prohibition of tributyltin (TBT) by the International Maritime Organization (IMO) in 2001 propelled the research and development of new antifouling materials. However, the evaluation process and framework for these materials remain incomplete and unsystematic. This mini-review starts with the classification and principles of new antifouling materials, discussing and summarizing the methods for assessing their biofouling resistance. The paper also compiles the relevant regulations and environmental requirements from different countries necessary for developing new antifouling materials with commercial potential. It concludes by highlighting the current challenges in antifouling material development and future outlooks. Systematic evaluation of newly developed antifouling materials can lead to the emergence of more genuinely applicable solutions, transitioning from merely laboratory products to materials that can be effectively used in real-world applications.

Contemporary strategies and approaches for characterizing composition and enhancing biofilm penetration targeting bacterial extracellular polymeric substances

Extracellular polymeric substances (EPS) constitutes crucial elements within bacterial biofilms, facilitating accelerated antimicrobial resistance and conferring defense against the host's immune cells. Developing precise and effective antibiofilm approaches and strategies, tailored to the specific characteristics of EPS composition, can offer valuable insights for the creation of novel antimicrobial drugs. This, in turn, holds the potential to mitigate the alarming issue of bacterial drug resistance. Current analysis of EPS compositions relies heavily on colorimetric approaches with a significant bias, which is likely due to the selection of a standard compound and the cross-interference of various EPS compounds. Considering the pivotal role of EPS in biofilm functionality, it is imperative for EPS research to delve deeper into the analysis of intricate compositions, moving beyond the current focus on polymeric materials. This necessitates a shift from heavy reliance on colorimetric analytic methods to more comprehensive and nuanced analytical approaches. In this study, we have provided a comprehensive summary of existing analytical methods utilized in the characterization of EPS compositions. Additionally, novel strategies aimed at targeting EPS to enhance biofilm penetration were explored, with a specific focus on highlighting the limitations associated with colorimetric methods. Furthermore, we have outlined the challenges faced in identifying additional components of EPS and propose a prospective research plan to address these challenges. This review has the potential to guide future researchers in the search for novel compounds capable of suppressing EPS, thereby inhibiting biofilm formation. This insight opens up a new avenue for exploration within this research domain.

Fermentative optimization and characterization of exopolysaccharides from Enterococcus faecium F58 isolated from traditional fresh goat cheese

This study focused on optimizing the fermentation-based production of Exopolysaccharides (EPS) from Enterococcus faecium F58 initially isolated from traditional Moroccan Jben, a fresh goat cheese. Using the central composite design, yeast extract, MnSO4, and time affect EPS concentration. The highest experimental and predicted EPS production yields were 2.46 g/L ± 0.38 and 2.86 g/L, respectively. Optimal concentrations of yeast extract (4.46 g/L) and MnSO4 (0.011 g/L) were identified after 26 h at 30 °C. Characterization of EPS was conducted using SEM with EDX, XRD, and FTIR analyses. These tests revealed a specific morphology and an amorphous structure. Additionally, thermogravimetric analysis indicated adequate EPS stability up to 200 °C with anti-adhesion properties against different pathogens. This study offers valuable insights into the optimized production of EPS from Enterococcus faecium F58, which exhibits significant structural and functional properties for various applications in the food and biotechnology industries.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01424-9.

Volatile methyl jasmonate from roots triggers host-beneficial soil microbiome biofilms

The rhizosphere is a niche surrounding plant roots, where soluble and volatile molecules mediate signaling between plants and the associated microbiota. The preferred lifestyle of soil microorganisms is in the form of biofilms. However, less is known about whether root volatile organic compounds (rVOCs) can influence soil biofilms beyond the 2-10 mm rhizosphere zone influenced by root exudates. We report that rVOCs shift the microbiome composition and growth dynamics of complex soil biofilms. This signaling is evolutionarily conserved from ferns to higher plants. Methyl jasmonate (MeJA) is a bioactive signal of rVOCs that rapidly triggers both biofilm and microbiome changes. In contrast to the planktonic community, the resulting biofilm community provides ecological benefits to the host from a distance via growth enhancement. Thus, a volatile host defense signal, MeJA, is co-opted for assembling host-beneficial biofilms in the soil microbiota and extending the sphere of host influence in the rhizosphere.

AgBiS2@CQDs/Ti nanocomposite coatings for combating implant-associated infections by photodynamic /photothermal therapy

Biofilm-mediated implant-associated infections are one of the most serious complications of implantation surgery, posing a grave threat to patient well-being. Effectively addressing bacterial infections is crucial for the success of implantation procedures. In this study, we prepared a bismuth sulfide silver@carbon quantum dot composite coating (AgBiS2@CQDs/Ti) on a medical titanium surface by surface engineering design to treat implant-associated infections. The photocatalytic/photothermal activity test results confirmed the excellent photogenerated ROS and photothermal properties of AgBiS2@CQDs/Ti under near-infrared laser irradiation. In vitro antibacterial and in vivo anti-infection experiments showed that the coating combined with photodynamic and photothermal therapies to eradicate bacteria and disrupt mature biofilms under 1064 nm laser irradiation. Consequently, AgBiS2@CQDs/Ti shows promise as an implant coating for treating implant-associated infections post-surgery, thereby enhancing the success rate of implantation procedures. This study also provides a new idea for combating implant-associated infections.

Microenvironment-Driven Fenton Nanoreactor Enabled by Metal-Phenolic Encapsulation of Calcium Peroxide for Effective Control of Dental Caries

Caries are one of the most common oral diseases caused by pathogenic bacterial infections, which are widespread and persistently harmful to human health. Using nanoparticles to invade biofilms and produce reactive oxygen species (ROS) in situ is a promising strategy for killing bacteria and disrupting the structure of biofilms. In this work, a biofilm-targeting Fenton nanoreactor is reported that can generate ROS responsive to the cariogenic microenvironment. The nanoreactor is constructed by metal-phenolic encapsulation of calcium peroxide (CaO2) followed by modification with a biofilm targeting ligand dextran. Within the cariogenic biofilm, the Fenton nanoreactor is activated by an acidic microenvironment to be decomposed into H2O2 and iron ions, triggering a Fenton-like reaction to generate ROS that can eliminate the biofilm by breaking down extracellular polymeric substances (EPS) and killing cariogenic bacteria. Meanwhile, the depletion of excess protons in biofilm leads to a reversal of the cariogenic microenvironment. The Fenton nanoreactor can effectively inhibit the biofilm formation of Streptococcus mutans on ex vivo human teeth and is effective in preventing caries meanwhile maintaining the oral microbial diversity in rat caries infection model. This work provides a novel and efficient modality for acid microenvironment-driven ROS therapy.

Prevention and Management of Wound Infections in Burn Patients

The leading cause of morbidity in burn patients is infection with pneumonia, urinary tract infection, cellulitis, and wound infection being the most common cause. High mortality is due to the immunocompromised status of patients and abundance of multidrug-resistant organisms in burn units. Despite the criteria set forth by American Association of Burn, the diagnosis and treatment of burn infections are not always straightforward. Topical antimicrobials, isolation, hygiene, and personal protective equipment are common preventive measures. Additionally medical and nutritional optimization of the patients is crucial to reverse the immunocompromised status triggered by burn injury.

TiO2 Nanocomposite Coatings and Inactivation of Carbapenemase-Producing Klebsiella Pneumoniae Biofilm-Opportunities and Challenges

The worldwide increase of multidrug-resistant Gram-negative bacteria is a global threat. The emergence and global spread of Klebsiella pneumoniae carbapenemase- (KPC-) producing Klebsiella pneumoniae represent a particular concern. This pathogen has increased resistance and abilities to persist in human reservoirs, in hospital environments, on medical devices, and to generate biofilms. Mortality related to this microorganism is high among immunosuppressed oncological patients and those with multiple hospitalizations and an extended stay in intensive care. There is a severe threat posed by the ability of biofilms to grow and resist antibiotics. Various nanotechnology-based strategies have been studied and developed to prevent and combat serious health problems caused by biofilm infections. The aim of this review was to evaluate the implications of nanotechnology in eradicating biofilms with KPC-producing Klebsiella pneumoniae, one of the bacteria most frequently associated with nosocomial infections in intensive care units, including in our department, and to highlight studies presenting the potential applicability of TiO2 nanocomposite materials in hospital practice. We also described the frequency of the presence of bacterial biofilms on medical surfaces, devices, and equipment. TiO2 nanocomposite coatings are one of the best long-term options for antimicrobial efficacy due to their biocompatibility, stability, corrosion resistance, and low cost; they find their applicability in hospital practice due to their critical antimicrobial role for surfaces and orthopedic and dental implants. The International Agency for Research on Cancer has recently classified titanium dioxide nanoparticles (TiO2 NPs) as possibly carcinogenic. Currently, there is an interest in the ecological, non-toxic synthesis of TiO2 nanoparticles via biological methods. Biogenic, non-toxic nanoparticles have remarkable properties due to their biocompatibility, stability, and size. Few studies have mentioned the use of nanoparticle-coated surfaces as antibiofilm agents. A literature review was performed to identify publications related to KPC-producing Klebsiella pneumoniae biofilms and antimicrobial TiO2 photocatalytic nanocomposite coatings. There are few reviews on the antibacterial and antibiofilm applications of TiO2 photocatalytic nanocomposite coatings. TiO2 nanoparticles demonstrated marked antibiofilm activity, but being nano in size, these nanoparticles can penetrate cell membranes and may initiate cellular toxicity and genotoxicity. Biogenic TiO2 nanoparticles obtained via green, ecological technology have less applicability but are actively investigated.

Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.

Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis

The discovery of plant-derived compounds that are able to combat antibiotic-resistant pathogens is an urgent demand. Over years, Centaurea hyalolepis attracted considerable attention because of its beneficial medical properties. Phytochemical analyses revealed that Centaurea plant species contain several metabolites, such as sesquiterpene lactones (STLs), essential oils, flavonoids, alkaloids, and lignans.The organic extract of C. hyalolepis plant, collected in Palestine, showed significant antimicrobial properties towards a panel of Gram-negative and Gram-positive bacterial strains when the Minimal Inhibitory Concentration (MIC) values were evaluated by broth microdilution assays. A bio-guided fractionation of the active extract via multiple steps of column and thin layer chromatography allowed us to obtain three main compounds. The isolated metabolites were identified as the STLs cnicin, 11β,13-dihydrosalonitenolide and salonitenolide by spectroscopic and spectrometric analyses. Cnicin conferred the strongest antimicrobial activity among the identified compounds. Moreover, the evaluation of its antibiofilm activity by biomass assays through crystal violet staining revealed almost 30% inhibition of biofilm formation in the case of A. baumannii ATCC 17878 strain. Furthermore, the quantification of carbohydrates and proteins present in the extracellular polymeric substance (EPS) revealed the ability of cnicin to significantly perturb biofilm structure. Based on these promising results, further investigations might open interesting perspectives to its applicability in biomedical field to counteract multidrug resistant infections.

Bi-functional quercetin/copper nanoparticles integrating bactericidal and anti-quorum sensing properties for preventing the formation of biofilms

Biofilms formed by pathogenic bacteria present a persistent risk to human health. While the eradication of matured biofilms remains a formidable challenge, delaying or preventing their formation, which is coordinately regulated by quorum sensing (QS), presents a simpler and more advantageous strategy. Quercetin, a naturally occurring compound with anti-QS properties, has the potential to act as an antibiofilm agent. However, it is plagued by certain inherent drawbacks, including poor water solubility and limited bioavailability. Furthermore, solely blocking QS is not enough to prevent biofilm formation because it lacks bactericidal properties. To address these difficulties, we fabricated bi-functional nanoparticles through the co-assembly of quercetin and copper ions in a facile manner. The resulting quercetin/copper nanoparticles (QC NPs) demonstrated minimal cytotoxicity and hemolysis in vitro. In response to the low pH of microenvironments that were populated by bacterial colonies, the QC NPs underwent disassembly to release copper ions and quercetin. The former exterminated bacteria by disrupting the integrity of the cell membrane, while the latter disrupted the processes involved in QS that are responsible for the biofilm by downregulating the expression of specific genes, effectively preventing the formation of biofilms by both Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus. In addition, the QC NPs were integrated into a bacterial cellulose membrane. The composite membrane proved to be highly effective at inhibiting biofilm formation in vitro and demonstrated the ability to reduce inflammatory responses and accelerate the healing of bacteria-infected wounds in vivo. Overall, the bi-functional QC NPs hold great potential for use in addressing the challenges associated with the management of bacterial biofilms.

Restraining Staphylococcus aureus Virulence Factors and Quorum Sensing through Lactic Acid Bacteria Supernatant Extracts

The escalating prevalence of antibiotic-resistant bacteria poses a grave threat to human health, necessitating the exploration of novel alternatives to conventional antibiotics. This study investigated the impact of extracts derived from the supernatant of four lactic acid bacteria strains on factors contributing to the pathogenicity of three Staphylococcus aureus strains. The study evaluated the influence of lactic acid bacteria supernatant extracts on the growth, biofilm biomass formation, biofilm metabolic activity, and biofilm integrity of the S. aureus strains. Additionally, the impact on virulence factors (hemolysin and coagulase) was examined. Gas chromatography coupled with mass spectrometry was used to identify the bioactive compounds in the extracts, while molecular docking analyses explored potential interactions. Predominantly, the extracts contain eight 2,5-diketopiperazines, which are cyclic forms of peptides. The extracts demonstrated inhibitory effects on biofilm formation, the ability to disrupt mature biofilms, and reduce the biofilm cell metabolic activity of the S. aureus strains. Furthermore, they exhibited the ability to inhibit α-hemolysin production and reduce coagulase activity. An in silico docking analysis reveals promising interactions between 2,5-diketopiperazines and key proteins (SarA and AgrA) in S. aureus, confirming their antivirulence and antibiofilm activities. These findings suggest that 2,5-diketopiperazines could serve as a promising lead compound in the fight against antibiotic-resistant S. aureus.

Anti-Biofilm Strategies: A Focused Review on Innovative Approaches

Biofilm (BF) can give rise to systemic infections, prolonged hospitalization times, and, in the worst case, death. This review aims to provide an overview of recent strategies for the prevention and destruction of pathogenic BFs. First, the main phases of the life cycle of BF and maturation will be described to identify potential targets for anti-BF approaches. Then, an approach acting on bacterial adhesion, quorum sensing (QS), and the extracellular polymeric substance (EPS) matrix will be introduced and discussed. Finally, bacteriophage-mediated strategies will be presented as innovative approaches against BF inhibition/destruction.

Robust Electrochemical Biosensors Based on Antifouling Peptide Nanoparticles for Protein Quantification in Complex Biofluids

Peptides with distinct physiochemical properties and biocompatibility hold significant promise across diverse domains including antifouling biosensors. However, the stability of natural antifouling peptides in physiological conditions poses significant challenges to their viability for sustained practical applications. Herein, a unique antifouling peptide FFFGGGEKEKEKEK was designed and self-assembled to form peptide nanoparticles (PNPs), which possessed enhanced stability against enzymatic hydrolysis in biological fluids. The PNP-coated interfaces exhibited superior stability and antifouling properties in preventing adsorption of nonspecific materials, such as proteins and cells in biological samples. Moreover, a highly sensitive and ultralow fouling electrochemical biosensor was developed through the immobilization of the PNPs and specific aptamers onto the polyaniline nanowire-modified electrode, achieving the biomarker carcinoembryonic antigen detection in complex biofluids with reliable accuracy. This research not only addresses the challenge of the poor proteolytic resistance observed in natural peptides but also introduces a universal strategy for constructing ultralow fouling sensing devices.

Flip the switch: the role of FleQ in modulating the transition between the free-living and sessile mode of growth in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen causing chronic infections that are associated with the sessile/biofilm mode of growth rather than the free-living/planktonic mode of growth. The transcriptional regulator FleQ contributes to both modes of growth by functioning both as an activator and repressor and inversely regulating flagella genes associated with the planktonic mode of growth and genes contributing to the biofilm mode of growth. Here, we review findings that enhance our understanding of the molecular mechanism by which FleQ enables the transition between the two modes of growth. We also explore recent advances in the mechanism of action of FleQ to both activate and repress gene expression from a single promoter. Emphasis will be on the role of sigma factors, cyclic di-GMP, and the transcriptional regulator AmrZ in inversely regulating flagella and biofilm-associated genes and converting FleQ from a repressor to an activator.

Degradation of Listeria monocytogenes biofilm by phages belonging to the genus Pecentumvirus

Listeria monocytogenes is a pathogenic foodborne bacterium that is a significant cause of mortality associated with foodborne illness and causes many food recalls attributed to a bacteriological cause. Their ability to form biofilms contributes to the persistence of Listeria spp. in food processing environments. When growing as biofilms, L. monocytogenes are more resistant to sanitizers used in the food industry, such as benzalkonium chloride (BAC), as well as to physical stresses like desiccation and starvation. Lytic phages of Listeria are antagonistic to a broad range of Listeria spp. and may, therefore, have utility in reducing the occurrence of Listeria-associated food recalls by preventing food contamination. We screened nine closely related Listeria phages, including the commercially available Listex P100, for host range and ability to degrade microtiter plate biofilms of L. monocytogenes ATCC 19111 (serovar 1/2a). One phage, CKA15, was selected and shown to rapidly adsorb to its host under conditions relevant to applying the phage in dairy processing environments. Under simulated dairy processing conditions (SDPC), CKA15 caused a 2-log reduction in Lm19111 biofilm bacteria. This work supports the biosanitation potential of phage CKA15 and provides a basis for further investigation of phage-bacteria interactions in biofilms grown under SDPC.

IMPORTANCE

Listeria monocytogenes is a pathogenic bacterium that is especially dangerous for children, the elderly, pregnant women, and immune-compromised people. Because of this, the food industry takes its presence in their plants seriously. Food recalls due to L. monocytogenes are common with a high associated economic cost. In food-processing plants, Listeria spp. typically reside in biofilms, which are structures produced by bacteria that shield them from environmental stressors and are often attached to surfaces. The significance of our work is that we show a bacteriophage-a virus-infecting bacteria-can reduce Listeria counts by two orders of magnitude when the bacterial biofilms were grown under simulated dairy processing conditions. This work provides insights into how phages may be tested and used to develop biosanitizers that are effective but are not harmful to the environment or human health.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

Mechanisms of Antibiotic Resistance and Developments in Therapeutic Strategies to Combat Klebsiella pneumoniae Infection

Infections with drug-resistant bacteria have become one of the greatest public health challenges, and K. pneumoniae is among the top six drug-resistant bacteria. K. pneumoniae often causes nosocomial infections, leading to illnesses such as pneumonia, liver abscesses, soft tissue infections, urinary tract infections, bacteremia, and in some cases death. As the pathogen continues to evolve and its multidrug resistance increases, K. pneumoniae poses a direct threat to humans. Drug resistance in K. pneumoniae may occur due to the formation of biofilms, efflux pumps, and the production of β-lactamases. In many cases, resistance is further enhanced by enzymatic modification and loss of porins. Drug resistance to K. pneumoniae has led to a decline in the effectiveness of conventional therapies against this pathogen. Therefore, there is an urgent need to accelerate the development of new antibiotics and explore new therapeutic approaches such as antimicrobial peptides, phages, traditional Chinese medicine, immunotherapy, Antimicrobial nanoparticle technology, antisense oligonucleotides and gene editing technologies. In this review, we discuss the mechanisms of drug resistance in K. pneumoniae and compare several new potential therapeutic strategies to overcome drug resistance in the treatment of K. pneumoniae infections.

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

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

Spectra metrology for interaction of heavy metals with extracellular polymeric substances (EPS) of Pseudomonas aeruginosa OMCS-1 reveals static quenching and complexation dynamics of EPS with heavy metals

The adsorption behavior and interaction mechanisms of extracellular polymeric substances (EPS) of Pseudomonas aeruginosa OMCS-1 towards chromium (Cr), lead (Pb), and cadmium (Cd) were investigated. EPS-covered (EPS-C) cells exhibited significantly higher (p < 0.0001; two-way ANOVA) removal of Cr (85.58 ± 0.39%), Pb (81.98 ± 1.02%), and Cd (73.88 ± 1%) than EPS-removed (EPS-R) cells. Interactions between EPS-heavy metals were spontaneous (ΔG<0). EPS-Cr(VI) and EPS-Pb(II) binding were exothermic (ΔH<0), while EPS-Cd(II) binding was endothermic (ΔH>0) process. EPS bonded to Pb(II) via inner-sphere complexation by displacement of surrounding water molecules, while EPS-Cr(VI) and EPS-Cd(II) binding occurred through outer-sphere complexation via electrostatic interactions. Increased zeta potential of Cr (29.75%), Pb (41.46%), and Cd (46.83%) treated EPS and unchanged crystallinity (CIXRD=0.13), inferred EPS-metal binding via both electrostatic interactions and complexation mechanism. EPS-metal interaction was predominantly promoted through hydroxyl, amide, carboxyl, and phosphate groups. Metal adsorption deviated EPS protein secondary structures. Strong static quenching mechanism between tryptophan protein-like substances in EPS and heavy metals was evidenced. EPS sequestered heavy metals via complexation with C-O, C-OH, CO/O-C-O, and NH/NH2 groups and ion exchange with -COOH group. This study unveils the fate of Cr, Pb, and Cd on EPS surface and provides insight into the interactions among EPS and metal ions for metal sequestration.

Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment

Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media-such as MSgg commonly used to study Bacillus subtilis biofilms-it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how B. subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in B. subtilis biofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that B. subtilis biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.

Chestnut Honey Is Effective against Mixed Biofilms at Different Stages of Maturity

The irresponsible overuse of antibiotics has increased the occurrence of resistant bacterial strains, which represents one of the biggest patient safety risks today. Due to antibiotic resistance and biofilm formation in bacteria, it is becoming increasingly difficult to suppress the bacterial strains responsible for various chronic infections. Honey was proven to inhibit bacterial growth and biofilm development, offering an alternative solution in the treatment of resistant infections and chronic wounds. Our studies included chestnut honey, valued for its high antibacterial activity, and the bacteria Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and S. epidermidis, known to form multi-species biofilm communities. Minimum inhibitory concentrations (MIC) of chestnut honey were determined for each bacterial strain. Afterwards, the mixed bacterial biofilms were treated with chestnut honey at different stages of maturity (incubation times: 2, 4, 6, 12, 24 h). The extent of biofilm inhibition was measured with a crystal violet assay and demonstrated by scanning electron microscopy (SEM). As the incubation time increased and the biofilm became more mature, inhibition rates decreased gradually. The most sensitive biofilm was the combination MRSA-S. epidermidis, with a 93.5% inhibition rate after 2 h of incubation. Our results revealed that chestnut honey is suitable for suppressing the initial and moderately mature stages of mixed biofilms.

Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community

Flavobacterium johnsoniae is a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community, The Hitchhikers of the Rhizosphere (THOR), we determined the effects of colonization on the fitness of F. johnsoniae in the community. Insertion sequencing, a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that the deletion of colonization genes in F. johnsoniae affected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization by F. johnsoniae and form the basis for further understanding its ecology in the rhizosphere.

IMPORTANCE

Microbial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step toward unraveling these interactions, we explored the role of surface colonization in microbial community interactions using The Hitchhikers Of the Rhizosphere (THOR), a genetically tractable model community of three bacterial species, Flavobacterium johnsoniae, Pseudomonas koreensis, and Bacillus cereus. We identified F. johnsoniae genes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote the success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.

Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor

BACKGROUND

Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.

RESULTS

We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.

CONCLUSIONS

We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.

Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes

The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.

Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis

Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.

Evaluation of novel compounds as anti-bacterial or anti-virulence agents

Antimicrobial resistance is a global threat, leading to an alarming increase in the prevalence of bacterial infections that can no longer be treated with available antibiotics. The World Health Organization estimates that by 2050 up to 10 million deaths per year could be associated with antimicrobial resistance, which would equal the annual number of cancer deaths worldwide. To overcome this emerging crisis, novel anti-bacterial compounds are urgently needed. There are two possible approaches in the fight against bacterial infections: a) targeting structures within bacterial cells, similar to existing antibiotics; and/or b) targeting virulence factors rather than bacterial growth. Here, for the first time, we provide a comprehensive overview of the key steps in the evaluation of potential new anti-bacterial and/or anti-virulence compounds. The methods described in this review include: a) in silico methods for the evaluation of novel compounds; b) anti-bacterial assays (MIC, MBC, Time-kill); b) anti-virulence assays (anti-biofilm, anti-quorum sensing, anti-adhesion); and c) evaluation of safety aspects (cytotoxicity assay and Ames test). Overall, we provide a detailed description of the methods that are an essential tool for chemists, computational chemists, microbiologists, and toxicologists in the evaluation of potential novel antimicrobial compounds. These methods are cost-effective and have high predictive value. They are widely used in preclinical studies to identify new molecular candidates, for further investigation in animal and human trials.

Selective enrichment of virulence factor genes in the plastisphere under antibiotic and heavy metal pressures

The growing accumulation of plastic waste in the environment has created novel habitats known as the "plastisphere", where microorganisms can thrive. Concerns are rising about the potential for pathogenic microorganisms to proliferate in the plastisphere, posing risks to human health. However, our knowledge regarding the virulence and pathogenic potential of these microorganisms in the plastisphere remains limited. This study quantified the abundance of virulence factor genes (VFGs) in the plastisphere and its surrounding environments (water and soil) to better assess pathogenic risks. Our findings revealed a selective enrichment of VFGs in the plastisphere, which were attributed to the specific microbial community assembled. The presence of arsenic and ciprofloxacin in the plastisphere exerted additional co-selective pressures, intensifying the enrichment of VFGs. Notably, VFGs that encoded multiple functions or enhanced the survival of host microorganisms (e.g., encoding adherence functions) tended to accumulate in the plastisphere. These versatile and environmentally adaptable VFGs are more likely to be favored by bacteria in the environment, warranting increased attention in future investigations due to their potential for widespread dissemination. In terms of virulence and pathogenicity, this research offers new insights into evaluating pathogen-related risks in the plastisphere.

Engineered Bacillus subtilis Biofilm@Biochar living materials for in-situ sensing and bioremediation of heavy metal ions pollution

The simultaneous sensing and remediation of multiple heavy metal ions in wastewater or soil with microorganisms is currently a significant challenge. In this study, the microorganism Bacillus subtilis was used as a chassis organism to construct two genetic circuits for sensing and adsorbing heavy-metal ions. The engineered biosensor can sense three heavy metal ions (0.1-75 μM of Pb2+ and Cu2+, 0.01-3.5 μM of Hg2+) in situ real-time with high sensitivity. The engineered B. subtilis TasA-metallothionein (TasA-MT) biofilm can specifically adsorb metal ions from the environment, exhibiting remarkable removal efficiencies of 99.5% for Pb2+, 99.9% for Hg2+and 99.5% for Cu2+ in water. Furthermore, this engineered strain (as a biosensor and absorber of Pb2+, Cu2+, and Hg2+) was incubated with biochar to form a hybrid biofilm@biochar (BBC) material that could be applied in the bioremediation of heavy metal ions. The results showed that BBC material not only significantly reduced exchangeable Pb2+ in the soil but also reduced Pb2+ accumulation in maize plants. In addition, it enhanced maize growth and biomass. In conclusion, this study examined the potential applications of biosensors and hybrid living materials constructed using sensing and adsorption circuits in B. subtilis, providing rapid and cost-effective tools for sensing and remediating multiple heavy metal ions (Pb2+, Hg2+, and Cu2+).

Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms

The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.

The Biofilm Lifestyle Shapes the Evolution of β-Lactamases

The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm production. To understand how natural evolution affects this antagonistic pleiotropy, we randomly mutagenized a β-lactamase and selected for elevated biofilm formation. Our results revealed that biofilm evolution selects for β-lactamase variants able to hydrolyze β-lactams without inhibiting biofilms. Mutational analysis of evolved variants demonstrated that restoration of biofilm development was achieved either independently of enzymatic function or by actively leveraging enzymatic activity. Taken together, the biofilm lifestyle can impose a profound selective pressure on antimicrobial resistance enzymes. Shedding light on such evolutionary interplays is of importance to understand the factors driving antimicrobial resistance.

pH-responsive double-enzyme active metal-organic framework for promoting the healing of infected wounds

The abuse of antibiotics accelerates the spread and evolution of drug-resistant bacteria, which seriously threatens human health. Hydroxyl radicals (•OH) are generated by peroxidase in the presence of H2O2, which is strongly oxidizing and can effectively kill bacteria. However, high production costs and poor stability limit the clinical use of natural enzymes. "Nanozyme" is a general term for nanomaterials with catalytic activity similar to that of biological enzymes. Compared to biological enzymes, nanozymes have the advantages of low cost, facile preparation, and easy storage, making them a good choice for the development of antibacterial agents. Here, a nickel-based metal-organic framework (Ni-MOF) with dual enzymatic activity that switches depending on the pH environment was studied. In a slightly acidic environment, Ni-MOF can react with hydrogen peroxide to produce hydroxyl radicals that kill bacteria; in a neutral environment, Ni-MOF instead removes excessive reactive oxygen species (ROS) and promotes the transformation of macrophages into M2 macrophages. Compared to most nanozymes, Ni-MOF has unique electrical conductivity and better biosafety. The results of animal experiments show that Ni-MOF can not only treat infected wounds but also promote the healing of acute wounds and exhibits great clinical application potential.

Harnessing the potential of ginkgo biloba extract: Boosting denitrification performance through accelerated electron transfer

Ginkgo biloba extract (GBE) had several effects on the human body as one of the widely used phytopharmaceuticals, but it had no application in microbial enhancement in the environmental field. The study focused on the impact of GBE on denitrification specifically under neutral conditions. At the identified optimal addition ratio of 2% (v/v), the system exhibited a noteworthy increase in nitrate reduction rate (NRR) by 56.34%, elevating from 0.71 to 1.11 mg-N/(L·h). Moreover, the extraction of microbial extracellular polymeric substance (EPS) at this ratio revealed changes in the composition of EPS, the electron exchange capacity (EEC) was enhanced from 87.16 to 140.4 μmol/(g C), and the transfer impedance was reduced within the EPS. The flavin, fulvic acid (FA), and humic acid (HA) provided a π-electron conjugated structure for the denitrification system, enhancing extracellular electron transfer (EET) by stimulating carbon source metabolism. GBE also improved electron transfer system activity (ETSA) from 0.025 to 0.071 μL O2/(g·min·prot) and the content of NADH enhanced by 22.90% while significantly reducing the activation energy (Ea) by 85.6% in the denitrification process. The synergy of improving both intracellular and extracellular electron transfer, along with the reduction of Ea, notably amplified the initiation and reduction rates of the denitrification process. Additionally, GBE demonstrated suitability for denitrification across various pH levels, enhancing microbial resilience in alkaline conditions and promoting survival and proliferation. Overall, these findings open the door to potential applications of GBE as a natural additive in the environmental field to improve the efficiency of denitrification processes, which are essential for nitrogen removal in various environmental contexts.

Azalomycin F4a targets peptidoglycan synthesis of Gram-positive bacteria revealed by high-throughput CRISPRi-seq analysis

Azalomycin F4a is a promising 36-membered polyhydroxy macrolide that shows antibacterial activity against drug-resistant Gram-positive bacteria, but its exact working mechanism remains to be elusive. Here, we isolated the azalomycin F4a product from a Streptomyces solisilvae and demonstrated its antibacterial activity against Gram-positive pathogens including Streptococcus pneumoniae, Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). We further showed that combination of azalomycin F4a with methicillin has an additive antimicrobial effect on MRSA, where the minimal inhibitory concentrations (MIC) of methicillin to MRSA was decreased by 1000-fold in the presence of sublethal concentration of azalomycin F4a. A CRISPRi-seq based whole genome screen was employed to identify the potential targets of azalomycin F4a, which revealed that peptidoglycan synthesis (PGS) was inhibited by azalomycin F4a. Furthermore, azalomycin F4a treatment could significantly impair S. aureus biofilm formation. Our research highlights that cell wall synthesis is an additional target for novel classes of macrolide besides ribosome.

Life at the borderlands: microbiomes of interfaces critical to One Health

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

Synergistic D-Amino Acids Based Antimicrobial Cocktails Formulated via High-Throughput Screening and Machine Learning

Antimicrobial resistance (AMR) from pathogenic bacterial biofilms has become a global health issue while developing novel antimicrobials is inefficient and costly. Combining existing multiple drugs with enhanced efficacy and/or reduced toxicity may be a promising approach to treat AMR. D-amino acids mixtures coupled with antibiotics can provide new therapies for drug-resistance infection with reduced toxicity by lower drug dosage requirements. However, iterative trial-and-error experiments are not tenable to prioritize credible drug formulations, owing to the extremely large number of possible combinations. Herein, a new avenue is provide to accelerate the exploration of desirable antimicrobial formulations via high-throughput screening and machine learning optimization. Such an intelligent method can navigate the large search space and rapidly identify the D-amino acid mixtures with the highest anti-biofilm efficiency and also the synergisms between D-amino acid mixtures and antibiotics. The optimized drug cocktails exhibit high antimicrobial efficacy while remaining non-toxic, which is demonstrated not only from in vitro assessments but also the first in vivo study using a lung infection mouse model.

Strategies to Promote the Journey of Nanoparticles Against Biofilm-Associated Infections

Biofilm-associated infections are one of the most challenging healthcare threats for humans, accounting for 80% of bacterial infections, leading to persistent and chronic infections. The conventional antibiotics still face their dilemma of poor therapeutic effects due to the high tolerance and resistance led by bacterial biofilm barriers. Nanotechnology-based antimicrobials, nanoparticles (NPs), are paid attention extensively and considered as promising alternative. This review focuses on the whole journey of NPs against biofilm-associated infections, and to clarify it clearly, the journey is divided into four processes in sequence as 1) Targeting biofilms, 2) Penetrating biofilm barrier, 3) Attaching to bacterial cells, and 4) Translocating through bacterial cell envelope. Through outlining the compositions and properties of biofilms and bacteria cells, recent advances and present the strategies of each process are comprehensively discussed to combat biofilm-associated infections, as well as the combined strategies against these infections with drug resistance, aiming to guide the rational design and facilitate wide application of NPs in biofilm-associated infections.

The role of sialidases in the pathogenesis of bacterial vaginosis and their use as a promising pharmacological target in bacterial vaginosis

Bacterial vaginosis (BV) is an infection of the genital tract characterized by disturbance of the normally Lactobacilli-dominated vaginal flora due to the overgrowth of Gardnerella and other anaerobic bacteria. Gardnerella vaginalis, an anaerobic pathogen and the major pathogen of BV, produces sialidases that cleave terminal sialic acid residues off of human glycans. By desialylation, sialidases not only alter the function of sialic acid-containing glycoconjugates but also play a vital role in the attachment, colonization and spread of many other vaginal pathogens. With known pathogenic effects, excellent performance of sialidase-based diagnostic tests, and promising therapeutic potentials of sialidase inhibitors, sialidases could be used as a biomarker of BV. This review explores the sources of sialidases and their role in vaginal dysbiosis, in aims to better understand their participation in the pathogenesis of BV and their value in the diagnosis and treatment of BV.

Rethinking the control of Streptococcus suis infection: Biofilm formation

Streptococcus suis is an emerging zoonotic pathogen that is widespread in swine populations. The control of S. suis infection and its associated diseases is a daunting challenge worldwide. Biofilm formation appears to be the main reason for the persistence of S. suis. In this review we gather existing knowledge on S. suis biofilm, describing the role of biofilm formation in S. suis virulence and drug resistance, the regulatory factors of S. suis biofilm formation, and the research progress of inhibiting S. suis biofilm formation, with the aim of providing guidance for future studies related to the field of S. suis biofilms.

Enhancing methane production and interspecies electron transfer of anaerobic granular sludge by the immobilization of magnetic biochar

Supplementation of conductive materials has been proved to be a promising approach for enhancing microbial interspecies electron transfer (IET) in anaerobic digestion systems. In this study, magnetic bamboo-based biochar was prepared at temperatures of 400-800 °C via a ball milling/carbonization method, and it immobilized in mature anaerobic granular sludge (AGS) aimed to enhance methane production by improving the IET process between syntrophic microbial communities in the AGS. Results showed that the AGS with magnetic biochar immobilization demonstrated increased glucotrophic and acetotrophic methane production by 69.54-77.56 % and 39.96-54.92 %, respectively. Magnetic biochar prepared at 800 °C with a relatively higher Fe content (0.37 g/g magnetic biochar) displayed a stronger electron charge/discharge capacity (36.66 F/g), and its immobilization into AGS promoted methane production most. The conductivity of AGS increased by 52.13-87.32 % after incorporating magnetic biochar. Furthermore, the extracellular polymeric substance (EPS) of AGS showed an increased capacitance and decreased electron transfer resistance possibly due to the binding of magnetic biochar and more riboflavin secretion in EPS, which could contribute to the accelerated IET process in the inner AGS. In addition, the immobilization of magnetic biochar could promote the production of volatile fatty acids by 15.36-22.50 %. All these improvements may jointly lead to the enhanced methane production capacity of AGS. This study provided a fundamental understanding of the role of incorporated magnetic biochar in AGS in promoting anaerobic digestion performance.

Biofilm formation by selected microbial strains isolated from wastewater and their consortia: mercury resistance and removal potential

Wastewater often contains an increased amount of mercury and, at the same time, resistant microorganisms. During wastewater treatment, a biofilm of indigenous microorganisms is often unavoidable. Therefore, the objective of this research is to isolate and identify microorganisms from wastewater and investigate their ability to form biofilms for possible application in mercury removal processes. The resistance of planktonic cells and their biofilms to the effects of mercury was investigated using Minimum Biofilm Eradication Concentration-High Throughput Plates. The formation of biofilms and the degree of resistance to mercury were confirmed in polystyrene microtiter plates with 96 wells. Biofilm on AMB Media carriers (Assisting Moving Bad Media) was quantified using the Bradford protein assay. The removal of mercury ions by biofilms formed on AMB Media carriers of selected isolates and their consortia was determined by a removal test in Erlenmeyer flasks simulating MBBR. All isolates in planktonic form showed some degree of resistance to mercury. The most resistant microorganisms (Enterobacter cloacae, Klebsiella oxytoca, Serratia odorifera, and Saccharomyces cerevisiae) were tested for their ability to form biofilms in the presence and absence of mercury, both in polystyrene plates and on ABM carriers. The results showed that among planktonic forms, K. oxytoca was the most resistant. A biofilm of the same microorganisms was more than 10-fold resistant. Most consortia biofilms had MBEC values > 100,000 μg/mL. Among individual biofilms, E. cloacae showed the highest mercury removal efficiency (97.81% for 10 days). Biofilm consortia composed of three species showed the best ability to remove mercury (96.64%-99.03% for 10 days). This study points to the importance of consortia of different types of wastewater microorganisms in the form of biofilms and suggests that they can be used to remove mercury in wastewater treatment bioreactors.

Electrofermentation increases concentration of poly γ-glutamic acid in Bacillus subtilis biofilms

Fluctuations in redox conditions in bioprocesses can alter the end-products, reduce their concentration, and lengthen the process time. Electrofermentation enables rapid metabolic modulation of biosynthesis and allows control of redox imbalances in biofilm-based fermentation processes. In this study, electrofermentation is used to boost the production of the bacterial biopolymer poly-γ-glutamic acid (γ-PGA) from Bacillus subtilis ATCC 6051. When compared to control experiments (3.3 ± 0.99 g L-1 ), the application of an electrode potential E = 0.4 V versus Ag/AgCl results in a more than two-fold increase in the production of γ-PGA (9.13 ± 1.4 g L-1 ). Using an engineered B. subtilis strain, in which γ-PGA production is driven by isopropyl β-d-1-thiogalactopyranoside, electrofermentation improves polymer concentrations from 15.4 ± 1.5 to 23.1 ± 1.6 versus g L-1 . These results confirm that electrofermentation conditions can be adopted to increase the concentration of γ-PGA and perhaps other extracellular biopolymers in industrial strains.

The Story of Ferumoxytol: Synthesis Production, Current Clinical Applications, and Therapeutic Potential

Ferumoxytol, approved by the U.S. Food and Drug Administration in 2009, is one of the intravenous iron oxide nanoparticles authorized for the treatment of iron deficiency in chronic kidney disease and end-stage renal disease. With its exceptional magnetic properties, catalytic activity, and immune activity, as well as good biocompatibility and safety, ferumoxytol has gained significant recognition in various biomedical diagnoses and treatments. Unlike most existing reviews on this topic, this review primarily focuses on the recent clinical and preclinical advances of ferumoxytol in disease treatment, spanning anemia, cancer, infectious inflammatory diseases, regenerative medicine application, magnetic stimulation for neural modulation, etc. Additionally, the newly discovered mechanisms associated with the biological effects of ferumoxytol are discussed, including its magnetic, catalytic, and immunomodulatory properties. Finally, the summary and future prospects concerning the treatment and application of ferumoxytol-based nanotherapeutics are presented.

Impact of Mycobacteroides abscessus colony morphology on biofilm formation and antimicrobial resistance

Mycobacteroides abscessus is one of the most resistant bacteria so far known and causes severe and hard to treat lung infections in predisposed patients such as those with Cystic Fibrosis (CF). Further, it causes nosocomial infections by forming biofilms on medical devices or water reservoirs. An eye-catching feature of M. abscessus is the growth in two colony morphotypes. Depending on the presence or absence of glycopeptidolipids on the cell surface, it forms smooth or rough colonies. In this study, a porous glass bead biofilm model was used to compare biofilm formation, biofilm organization and biofilm matrix composition in addition to the antimicrobial susceptibility of M. abscessus biofilms versus suspensions of isogenic (smooth and rough) patient isolates. Both morphotypes reached the same cell densities in biofilms. The biofilm architecture, however, was dramatically different with evenly distributed oligo-layered biofilms in smooth isolates, compared to tightly packed, voluminous biofilm clusters in rough morphotypes. Biofilms of both morphotypes contained more total biomass of the matrix components protein, lipid plus DNA than was seen in corresponding suspensions. The biofilm mode of growth of M. abscessus substantially increased resistance to the antibiotics amikacin and tigecycline. Tolerance to the disinfectant peracetic acid of both morphotypes was increased when grown as biofilm, while tolerance to glutaraldehyde was significantly increased in biofilm of smooth isolates only. Overall, smooth colony morphotypes had more pronounced antimicrobial resistance benefit when growing as biofilm than M. abscessus showing rough colony morphotypes.

Hedscandines A-C, three undescribed indole alkaloids from Hedyotis scandens with their anti-MRSA activity

Hedscandines A-C (1-3), three undescribed indole alkaloids were isolated from Hedyotis scandens Roxb, a traditional Chinese medicine widely used in the treatment of respiratory ailments. Their structures were elucidated by extensive spectroscopic data and electronic circular dichroism calculation. Hedscandine A (1), possessed a unique carbon skeleton with a 1,4-oxazonin-2(3H)-one core system and displayed a rapid bactericidal activity against MRSA with a MIC value of 16 μg/mL. Mechanistic studies showed that compound 1 could disrupt the integrity of bacterial cell membranes and thus lead to bacterial death.