Biofilms: an emergent form of bacterial life

Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies

Clinical symptoms of Clostridioides difficile infection (CDI) range from diarrhea to pseudomembranous colitis. A major challenge in managing CDI is the high rate of relapse. Several studies correlate the production of CDT binary toxin by clinical strains of C. difficile with higher relapse rates. Although the mechanism of action of CDT on host cells is known, its exact contribution to CDI is still unclear. To understand the physiological role of CDT during CDI, we established two hypoxic relevant intestinal models, Transwell and Microfluidic Intestine-on-Chip systems. Both were challenged with the epidemic strain UK1 CDT+ and its isogenic CDT- mutant. We report that CDT induces mucin-associated microcolonies that increase C. difficile colonization and display biofilm-like properties by enhancing C. difficile resistance to vancomycin. Importantly, biofilm-like microcolonies were also observed in the cecum and colon of infected mice. Hence, our study shows that CDT induces biofilm-like microcolonies, increasing C. difficile persistence and risk of relapse.

A remotely controlled nanotherapeutic with immunomodulatory property for MRSA-induced bone infection

Osteomyelitis is a deep bone tissue infection caused by pathogenic microorganisms, with the primary pathogen being methicillin-resistant Staphylococcus aureus (MRSA). Due to the tendency of the infection site to form biofilms that shield drugs and immune cells to kill bacteria, combined with the severe local inflammatory response causing bone tissue destruction, the treatment of osteomyelitis poses a significant challenge. Herein, we developed a remotely controlled nanotherapeutic (TLBA) with immunomodulatory to treat MRSA-induced osteomyelitis. TLBA, combined with baicalin and gold nanorods, is positively charged to actively target and penetrate biofilms. Near-infrared light (808 nm) triggers spatiotemporal, controllable drug release, while bacteria are eliminated through synergistic interaction of non-antibiotic drugs and photothermal therapy, enhancing bactericidal efficiency and minimizing drug resistance. TLBA eliminated nearly 100 % of planktonic bacteria and dispersed 90 % of biofilms under NIR light stimulation. In MRSA-induced osteomyelitis rat models, laser irradiation raised the infection site temperature to 50 °C, effectively eradicating bacteria, promoting M2 macrophage transformation, inhibiting bone inflammation, curbing bone destruction, and fostering bone tissue repair. In summary, TLBA proposes a more comprehensive treatment strategy for the two characteristic pathological changes of bacterial infection and bone tissue damage in osteomyelitis.

Smart bandages for wound monitoring and treatment

Wound management plays a crucial role in nursing care as it facilitates effective wound healing and prevents infections. To overcome limitations associated with traditional treatment methods, various smart bandages have been developed. The monitoring of wound parameters and the implementation of targeted treatments are crucial aspects of smart bandage development. Smart bandages, as cutting-edge flexible wearable medical devices, integrate various sensing technologies, providing new insights for dynamic monitoring and personalized treatment of chronic wounds. This paper systematically summarizes the applications and developments of smart bandages in monitoring wound environmental parameters, focusing on two major detection methods: colorimetric sensing and electrochemical sensing. Colorimetric sensors typically rely on color changes induced by physiological parameters, which can not only be identified by the naked eye but also combined with image recognition algorithms for physiological parameter detection. Electrochemical sensors, on the other hand, modify electrodes with specific enzymes and detect physiological parameters through the electrical signals generated by redox reactions. In addition to sensing, this paper further explores the integrated application of three smart therapeutic strategies in smart bandages, including promoting cell proliferation and angiogenesis through electrical stimulation, achieving controlled drug release via responsive materials, and utilizing photothermal materials for efficient antibacterial treatment of wounds. Finally, the paper delves into the challenges these bandages face in system integration and clinical translation, and discusses their potential in personalized wound care.

Vacancies-rich Z-scheme VdW heterojunction as H2S-sensitized synergistic therapeutic nanoplatform against refractory biofilm infections

Encapsulated in a self-produced negatively charged extracellular polymeric substance (EPS) matrix, the wound infected bacterial biofilms exhibit formidable resistance to conventional positively charged antibiotics and host's immune responses, which can undoubtedly lead to persistent infections and lethal complications. Nevertheless, developing efficacious strategies to root out stubborn biofilm and promote tissue regeneration still remains a challenge. To resolve this dilemma, a versatile vacancies-rich Z-scheme MoSSe Van der Waals heterojunction (MoSSe VdW HJ) is rationally fabricated as nanoplatform for hydrogen sulfide (H2S)-sensitized synergistic therapy of wound bacterial biofilm infection. The rich anion vacancies and Z-scheme heterostructure make the fabricated MoSSe VdW HJ can effectively augment H2S, localized hyperthermia, and reactive oxygen species production under the stimulation of biofilm microenvironments (BME) and irradiation of 808 nm near-infrared (NIR) light. Therefore, MoSSe VdW HJ is capable to integrate H2S gas, chemodynamic, photothermal, and photodynamic therapies to effectively destroy eDNA and polysaccharides in the EPS matrix, thereby breaching the biofilm barrier to eradicate bacteria and facilitate wound healing. The synergistic strategy exhibits superior anti-biofilm and wound repair effects both in vivo and in vitro, thus providing guideline for the development of BME and NIR light activated synergistic therapeutics to fight against refractory biofilm infections.

Exploring the correlation of linker structure and antimicrobial activities of pyridinium-based cationic biocides: Aromatic versus aliphatic architectures

Cationic biocides, particularly quaternary ammonium compounds (QACs), play a vital role in controlling microbial infections across various industries, healthcare facilities and households. As their widespread use increased drastically in the last few years due to COVID-19, there is growing concern about the development of resistance among microorganisms exposed to cationic biocides. It is crucial to recognize this threat in advance and respond by modifying and replacing the old generation of commercial biocides. Reported here is the pyridinium-based bis-QACs tuning via combination of two simple synthesis approaches to achieve novel biocide's architectures with mixed linkers. The obtained compounds were subjected to a broad bioactivity assay against a panel of 26 microbial pathogens, including multi-resistant bacterial ESKAPEE strains, fungi and biofilms. Novel hit-compounds showed improved antibacterial and antibiofilm action, rapid bacterial eradication within 15-30 min of exposure and 4.5-fold lower hemotoxicity, as well as lower potential for the development of bacterial resistance compared to commercial lead antiseptic octenidine. Highlighted findings and insights will serve as a good basis for further studies of bis-QACs as highly effective biocides.

Stable isotope probing and oligotyping reveal the impact of organophosphorus pesticides on the carbon fixation related bacterioplankton lineage

Freshwater bacterioplankton communities play a pivotal role in global carbon fixation and energy exchange. However, establishing direct linkages between environmental stressors like organophosphorus pesticides (OPPs) and the ecological functions, such as carbon-fixing related microorganisms (CFMs), remains challenging. This study investigated the effects of four OPPs - two phosphates (dichlorvos, monocrotophos) and two phosphorothioates (omethoate, parathion) - on bacterioplankton communities using stable isotope probing, high-throughput sequencing and oligotyping analysis. Seven CFMs were identified. All OPPs significantly reduced total biomass (from 7.87 ×104 to 2.30-4.11 ×104 cells/mL) but stimulated CFMs proliferation. Notably, phosphorothioates induced a greater increase in CFMs abundance (36.84 %-57.18 %, up from 21.1 %) compared to phosphates (23.85 %-37.10 %; p < 0.05). Principal coordinate analysis (PCoA) revealed that phosphorothioates exerted stronger effects on microbial community and CFMs oligotypes structure compared to phosphates (p < 0.05). Variance partitioning analysis (VPA) identified pesticide type as the dominant driver of community structure. PICRUSt2 prediction demonstrated that OPPs suppressed oxidoreductase pathways linked to energy metabolism while activating transferase pathways associated with microbial stress resistance. Phosphorothioates depleted 64 pathways and enhanced 208 pathways, far exceeding phosphate impacts (2 depleted, 22 enhanced), indicating the phosphorothioates played a more important role on bacterioplankton communities than phosphate. Additionally, OPPs exposure reduced functional redundancy and destabilized community stability in bacterioplankton, potentially granting CFMs a long-term competitive advantage and elevating algal bloom risks. These findings provide insights into active CFMs in aquatic systems and their responses to diverse OPPs, offering new perspectives for managing organophosphorus pesticide contamination.

Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis

Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m-3 h-1 with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.

Natural small-molecule compounds targeting Helicobacter pylori virulence factors: A promising strategy for overcoming antibiotic resistance

Helicobacter pylori (H. pylori) infection is an important causal factor of gastritis, peptic ulcer, and gastric cancer. High infection rates and the increasing challenge of antibiotic resistance worldwide have prompted an urgent need to develop novel therapeutic options and antimicrobial agents. This review focuses on the potential of natural small-molecule compounds as novel anti-H. pylori agents-a promising approach that mitigates the risk of resistance development and maintains the microbiome's ecological balance. We detail how H. pylori virulence factors, including urease, CagA, VacA, and biofilm, contribute to pathogenicity and underline the reassuring fact that naturally derived compounds sourced from plants and microorganisms have shown remarkable efficacy in inhibiting these virulence factors. Some compounds also exhibit synergistic effects with conventional antibiotics, potentially overcoming challenges associated with resistant strains. Furthermore, we discuss recent advancements in identifying novel drug targets within the H. pylori virulence spectrum, offering insights into future directions for research and development in H. pylori therapy.

From adhesion to biofilms formation and resilience: Exploring the impact of silver nanoparticles-based biomaterials on Pseudomonas aeruginosa

Colonization of medical devices by microorganisms, often progressing to the formation of resilient biofilms, presents a common clinical issue. To address this challenge, there is growing interest in developing novel biomaterials with antimicrobial/antibiofilm properties as a promising preventive measure. This study explores nanocomposite biomaterials based on silver nanoparticles (AgNPs) deposited on thin silica (SiO2) layers for their potential effect on the adhesion, detachment, viability and biofilm formation of the opportunistic Pseudomonas aeruginosa. The AgNPs-based biointerface effect on biofilm development is investigated on the PAO1-Tn7-gfp strain by combining experiments under static and dynamic conditions. For the latter, a shear-stress flow chamber is used to mimic conditions encountered around certain medical devices. The findings reveal a rapid bactericidal effect of the AgNPs, noticeable within 30 min of exposure. Moreover, a delay in surface colonization is observed with a thin and unstructured biofilm, even after 72h of dynamic culture. A considerable fragility and sensitivity to hydrodynamic stresses is noticed for this loosely attached bacterial monolayer when compared with the thick and resilient biofilm formed on SiO2 surface. This study underlines the potential of AgNPs-based biomaterials in the conception of novel antimicrobial/antibiofilm surfaces with controlled release of the biocidal agent.

Stratified biofilm structure of MABR enabling efficient ammonia removal from aquaculture medicated bath wastewater

The presence of high concentrations of residual antibiotics in aquaculture medicated bath wastewater poses challenges to conventional biological nitrogen removal processes. Membrane aerated biofilm reactor (MABR), known for its energy efficiency and stratified biofilm structure that supports diverse ecological niches, was therefore introduced. Experimental results revealed that MABR achieved an exceptional NH4+-N removal efficiency of 98.2 ± 1.8 % even under high oxytetracycline exposure, attributed to the protective effects of the biofilm on functional bacteria colonized in the inner layer (e.g., ammonia- and nitrite-oxidizing bacteria). Genes mediating the nitrification process, such as amoA/B and nxrA, showed an overall upward trend, with the activation of efflux pumps synergistically constituting the microbial response. Conversely, total nitrogen removal efficiency decreased from 95.3 ± 2.5 % to 76.0 ± 8.8 %, despite enrichment of Denitratisoma oestradiolicum (14.5 %) and denitrifying bacterium clone NOA-1-C (41.7 %), likely due to limited expression of the narG gene. After ceasing oxytetracycline dosing and adjusting operational parameters, total nitrogen removal improved to 87.4 ± 5.8 %. The results of this study underscore the significance and resilience of MABR technology in the treatment of aquaculture medicated bath wastewater.

Strain-dependent emergence of aminoglycoside resistance in Escherichia coli biofilms

In most Earth environments, bacteria predominantly exist within surface-associated communities known as biofilms, where they are embedded in an extracellular matrix. These collective structures play a critical role in bacterial physiology and significantly shape their evolutionary trajectories, contributing to the development of antimicrobial resistance and enhancing bacterial resilience to treatments, with profound implications for public health. This study assessed the impact of the biofilm lifestyle on the emergence of resistance to gentamicin, an aminoglycoside antibiotic, in one laboratory reference strain and seven Escherichia coli isolates from food-processing environments. Throughout a one-month evolution experiment, we observed that certain strains showed a markedly higher emergence of gentamicin-resistant variants in biofilms than in planktonic states, with the emergence of stable variants being closely linked to biofilm maturation. Genomic and phenotypic analyses of gentamicin-resistant (GenR) variants uncovered varied adaptive strategies among the strains. GenR variants from two food-processing isolates (Ec709 and Ec478) displayed point mutations in genes associated with central carbon metabolism (aceE, ygfZ, …) and cell respiration (atpG, cydA, …), while retaining relative growth and colonization capacities. Conversely, GenR variants from the reference strain (Ec1655) adapted preferentially through large genomic deletions, including consistent loss of the peptide transporter gene sbmA, significantly altering cellular fitness. These findings highlight the complexity of adaptive evolution in biofilms and underscore the importance of investigating diverse strains to grasp the full spectrum of adaptation in natural bacterial populations.

Investigations into the growth and formation of biofilm by Leptospira biflexa at temperatures encountered during infection

The genus Leptospira comprises unique atypical spirochete bacteria that includes the etiological agent of leptospirosis, a globally important zoonosis. Biofilms are microecosystems composed of microorganisms embedded in a self-produced matrix that offers protection against hostile factors. Leptospires form biofilms in vitro, in situ in rice fields and unsanitary urban areas, and in vivo while colonizing rodent kidneys. The complex three-dimensional biofilm matrix includes secreted polymeric substances such as proteins, extracellular DNA (eDNA), and saccharides. The genus Leptospira comprises pathogenic and saprophytic species with the saprophytic L. biflexa being commonly used as a model organism for the genus. In this study, the growth and formation of biofilms by L. biflexa was investigated not just at 29 °C, but at 37 °C/5 % CO2, a temperature similar to that encountered during host infection. Planktonic free-living L. biflexa grow in HAN media at both 29 °C and 37 °C/5 % CO2, but cells grown at 37 °C/5 % CO2 are longer (18.52 μm ± 3.39) compared to those at 29 °C (13.93 μm ± 2.84). Biofilms formed at 37 °C/5 % CO2 had more biomass compared to 29 °C, as determined by crystal violet staining. Confocal microscopy determined that the protein content within the biofilm matrix was more prominent than double-stranded DNA, and featured a distinct layer attached to the solid substrate. Additionally, the model enabled effective protein extraction for proteomic comparison across different biofilm phenotypes. Results highlight an important role for proteins in biofilm matrix structure by leptospires and the identification of their specific protein components holds promise for strategies to mitigate biofilm formation.

A novel MIR imaging approach for precise detection of S. epidermidis biofilms in seconds

The impact of microbial biofilm growth poses a threat to both human health and the performance of industrial systems, manifesting as a global crisis with noteworthy economic implications for modern society. Exploring new methods and alternative approaches for the detection of biofilm signatures are imperative for developing optimized and cost-effective strategies that can help to identify early-stage biofilm formation. Clinical diagnostic technologies are constantly looking for more affordable, practical and faster methods of prevention and detection of chronic infections in periprosthetic joint infections (PJIs), which are often characterized by biofilm formation on implant surfaces. Staphylococcus epidermidis (SE) is especially known for its strong biofilm production and is considered a leading cause of biomaterial-associated infections, including PJIs. Implant-associated infections are severe and difficult to treat, therefore it is crucial to continue identifying bacterial biomarkers that contribute to its structural stability and attachment to implant surfaces. This study presents a pioneering approach for fast spectral detection of biofilm formation with a novel mid-infrared (MIR) scanning system. To highlight the advantages of our MIR system, we performed a comparative analysis with measurements from a commercially available Fourier-transform infrared (FTIR) scanner. We have assessed SE biofilms grown for 3 days comparing the processing times between a commercially available infrared (IR) scanning system (∼8 h/cm2), and our innovative scanning approach with rapid self-built MIR detection, achieving a reduction in scanning time to seconds. K-means clustering analysis identified pronounced differences in distribution of clusters, representing a significant variation between biofilm producing (RP62A) and non-biofilm producing (ATCC 12228) bacterial strains. The distribution serves as a critical tool for identifying biofilm phenotypes, particularly where poly-N-acetylglucosamine (PNAG), a key constituent of extracellular polymeric substances (EPS) in S. epidermidis, represents the dominant mass fraction in the samples analyzed by our infrared (IR) scanning systems. In addition to faster processing times, our novel MIR system demonstrated significantly higher sensitivity compared to FTIR, enabling clear differentiation between the chemical signatures of biofilm and planktonic strains. The corresponding novel approach integrates advanced data analytics with a newly designed rapid MIR prototype, enabling optimized and swift detection of biofilm signatures. These signatures, now recognized as critical targets in diagnosing complex infections, provide an alternative to traditional microbial detection methods in clinical diagnostics.

Extracellular electron transfer proteins contribute to reduction of ferric minerals by Geobacter biofilms

To investigate how the thickness and extracellular electron transfer (EET) capabilities of microbial biofilms influence the reduction of ferric iron [Fe(III)]-containing minerals, we utilized four strains of Geobacter sulfurreducens with varying biofilm thicknesses and EET capabilities. These strains were engineered by modulating intracellular levels of dinucleotide second messengers. We systematically investigated the capacity of biofilms formed by four strains to reduce different Fe(III)-containing minerals including ferrihydrite, goethite, and lepidocrocite. By growing the G. sulfurreducens biofilm on the Fe(III) mineral-coated slides, our results showed that the strains forming thin biofilms on surfaces of Fe(III) minerals exhibited faster Fe(III) reduction rates compared to those with thick biofilms. Transcriptomic analyses revealed the upregulation of the genes encoding bacterial EET-involved proteins in the thin biofilms, highlighting the significant role of these proteins in reducing Fe(III)-containing minerals by G. sulfurreducens biofilms. Furthermore, genetic characterization identified the participation of two novel c-type cytochromes (c-Cyts), GSU1996 and GSU2513, in the reduction of Fe(III)-containing minerals by G. sulfurreducens biofilms. The results from this study provide an improved understanding of mineral-microbe interaction.IMPORTANCEGeobacter is a predominant species within biofilm communities that facilitate iron reduction, a process essential for the biogeochemical cycling of iron and other elements. However, the specific properties of Geobacter biofilms crucial for iron reduction remain unclear. By manipulating intracellular levels of dinucleotide second messengers to generate strains with varying biofilm properties, this research reveals that thinner biofilms exhibit superior rates of ferric iron [Fe(III)] mineral reduction compared to thicker biofilms. This finding highlights the vital role of proteins involved in extracellular electron transfer (EET) in enhancing the reduction of Fe(III)-containing minerals. The study further identifies two novel c-type cytochromes, GSU1996 and GSU2513, as important contributors to this process. These discoveries not only advance our understanding of microbial iron reduction but also offer new perspectives on the interactions between biofilms and mineral surfaces, potentially informing future research and applications in biogeochemical cycling and bioenergy.

Stimulus-responsive nanomaterials for ocular antimicrobial therapy

Nanomaterials exhibit a promising new avenue for treating infectious keratitis, having garnered considerable interest in the ophthalmic medical community due to their unique properties including higher target specificity, enhanced bioactivity of loaded agents, reduced drug dosage, and stimulus-responsive drug release. These stimulus-responsive nanomaterial-mediated therapeutic strategies offer innovative approaches for managing ocular antimicrobial diseases. In this review, we aim to summarize current applications of stimulus-responsive nanotherapeutics for ocular antimicrobial therapy. We briefly introduce the basic ocular structure, ocular barrier, infectious keratitis classification, and its microenvironment. Following this, we summarize the nanotherapeutic antimicrobial strategies employed in treating ocular infections including endogenous stimulus-responsive ocular nanodrugs, sonodynamic therapy, and wearable device-based therapy, focusing on their design principles, developmental progress, and advantages and limitations. Finally, we critically evaluate the biosafety profiles of responsive nanomaterials, specifically addressing cytotoxicity and immune interactions. To conclude, we discuss key challenges in this research field and future opportunities with explicit emphasis on clinical translation and practical medical applications.

Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilms in vibrios enhance their survival in natural ecosystems and facilitate transmission during cholera outbreaks. Critical components of the biofilm matrix include the Vibrio polysaccharides produced by the vps-1 and vps-2 gene clusters and the biofilm matrix proteins encoded in the rbm gene cluster, together comprising the biofilm matrix cluster. However, the biofilm matrix clusters and their evolutionary patterns in other Vibrio species remain underexplored. In this study, we systematically investigated the distribution, diversity, and evolution of biofilm matrix clusters and proteins across the Vibrio genus. Our findings reveal that these gene clusters are sporadically distributed throughout the genus, even appearing in species phylogenetically distant from Vibrio cholerae. Evolutionary analysis of the major biofilm matrix proteins RbmC and Bap1 shows that they are structurally and sequentially related, having undergone structural domain and modular alterations. Additionally, a novel loop-less Bap1 variant was identified, predominantly represented in two phylogenetically distant V. cholerae subspecies clades that share specific gene groups associated with the presence or absence of the protein. Furthermore, our analysis revealed that rbmB, a gene involved in biofilm dispersal, shares a recent common ancestor with Vibriophage tail proteins, suggesting that phages may mimic host functions to evade biofilm-associated defenses. Our study offers a foundational understanding of the diversity and evolution of biofilm matrix clusters in vibrios, laying the groundwork for future biofilm engineering through genetic modification.

IMPORTANCE

Biofilms help vibrios survive in nature and spread cholera. However, the genes that control biofilm formation in vibrios other than Vibrio cholerae are not well understood. In this study, we analyzed the biofilm matrix gene clusters and proteins across diverse Vibrio species to explore their patterns and evolution. We discovered that these genes are spread across different Vibrio species, including those not closely related to V. cholerae. We also found various forms of key biofilm proteins with different structures. Additionally, we identified genes involved in biofilm dispersal that are related to vibriophage genes, highlighting the role of phages in biofilm development. This study not only provides a foundational understanding of biofilm diversity and evolution in vibrios but also leads to new strategies for engineering biofilms through genetic modification, which is crucial for managing cholera outbreaks and improving the environmental resilience of these bacteria.

Comparative genomic analysis of Flavobacterium species causing columnaris disease of freshwater fish in Thailand: insights into virulence and resistance mechanisms

BACKGROUND

Columnaris disease, a prevalent disease among farmed and wild freshwater fish, is caused by the Flavobacterium columnare group, which includes four distinct species: F. columnare, F. oreochromis, F. covae, and F. davisii. Among these, F. oreochromis, F. covae, and F. davisii are particularly prevalent in farmed freshwater fish in Thailand. In this study, a comparative genomic analysis of 22 isolates was conducted to elucidate virulence factors, antibiotic resistance genes (ARGs), genomic islands (GIs), phages, insertion elements (ISs), and clustered regularly interspaced short palindromic repeats (CRISPRs).

RESULTS

A total of 212 putative virulence genes were predicted across three species with F. oreochromis exhibiting the highest number of unique virulence genes, followed by F. davisii, and F. covae. Moreover, 195 genes were predicted as ARGs, with F. oreochromis and F. covae showing an abundance of unique genes associated with resistance to quinolone, fluoroquinolone, and tetracycline antibiotics. Antimicrobial susceptibility testing, assessed with epidemiological cut-off values (ECVs), revealed decreased susceptibility to quinolones, fluoroquinolones and tetracycline in several isolates of F. oreochromis and F. covae. F. oreochromis and F. covae exhibited notable decreased susceptibility to quinolones, with mutations observed in the quinolone resistance-determining regions (QRDRs) of gyrA, including Ser83Phe, Ser83Val, Ser83Ala, and Asp87Tyr, the latter representing a novel mutation among isolates from Thailand. As a result, these findings suggest that gyrA is major target for quinolone in F. oreochromis, F. covae, and F. davisii, while gyrB, parC, parE might be less important to the decreased phenotypic susceptibility to this class of antimicrobials. Moreover, a tetracycline resistance gene (tetA_2) was found in only one F. covae isolate, which exhibited decreased phenotypic susceptibility to this drug, marking the first report of decreased susceptibility in this species.

CONCLUSIONS

This study provides insights into the genetic and pathogenic diversity of Flavobacterium species, aiding in the development of strategies to manage columnaris disease in farmed freshwater fish in Thailand.

Analysis of gene expression within individual cells reveals spatiotemporal patterns underlying Vibrio cholerae biofilm development

Bacteria commonly exist in multicellular, surface-attached communities called biofilms. Biofilms are central to ecology, medicine, and industry. The Vibrio cholerae pathogen forms biofilms from single founder cells that, via cell division, mature into three-dimensional structures with distinct, yet reproducible, regional architectures. To define mechanisms underlying biofilm developmental transitions, we establish a single-molecule fluorescence in situ hybridization (smFISH) approach that enables accurate quantitation of spatiotemporal gene-expression patterns in biofilms at cell-scale resolution. smFISH analyses of V. cholerae biofilm regulatory and structural genes demonstrate that, as biofilms mature, overall matrix gene expression decreases, and simultaneously, a pattern emerges in which matrix gene expression becomes largely confined to peripheral biofilm cells. Both quorum sensing and c-di-GMP-signaling are required to generate the proper temporal pattern of matrix gene expression. Quorum sensing signaling is uniform across the biofilm, and thus, c-di-GMP-signaling alone sets the regional matrix gene expression pattern. The smFISH strategy provides insight into mechanisms conferring particular fates to individual biofilm cells.

Preventing Underwater Bioadhesion by Biomimetic High-entropy Metal Oxides

Exploiting adamant and biocide-free surfaces for combating the ubiquitous and obstinate bioadhesion is urgently required for underwater facilities, but substantial challenges remain due to the diversity of adhesive organisms and the complexity of their bioadhesion mechanisms. Herein, a biomimetic high entropy metal oxide Ce0.5Zr0.2Nb0.15Ta0.1Hf0.05Ox is developed for combating underwater bioadhesion. Specifically, the high-entropy oxide exhibits superior lactonase and protease-like activities in actuating the hydrolysis of (phosphorylated) proteins and quorum-sensing lactone signal molecules, and the intrinsic haloperoxidase-mimicking behavior can strengthen the hydrolysis activity. Density functional theory calculations demonstrate that the remarkable interfacial chemical effect is attributed to the proximity Ce d band center and Fermi level. When evaluated in both the laboratory setting and marine field testing, the underwater solid surfaces achieve remarkable nonfouling ability. These findings highlight the great potential of biomimetic high-entropy materials for realizing green and comprehensive underwater bioadhesion prevention.

Bio-informed synthesis of marine-sourced indole derivatives: suppressing gram-negative bacteria biofilm and virulence

Biofilms cling to surfaces to form complex architectures allowing their bacterial creators to acquire multidrug resistance and claiming countless lives worldwide. Therefore, finding novel compounds that affect virulence and biofilm-forming capacity of resistant pathogenic bacteria is imperative. Recently, we identified indole-based compounds that possess anti-biofilm properties in coral-associated bacteria. We succeeded in efficiently synthesizing two of these compounds, 1,1'-bisindole (NN) and 2,3-dihydro-2,2'-bisindole (DIV). They were found to attenuate biofilms of gram-negative bacterial pathogens, including Pseudomonas aeruginosa and Acinetobacter baumannii. Combining these compounds with the antibiotic tobramycin resulted in significant biofilm inhibition, particularly in the eradication of mature P. aeruginosa biofilms. Both of the bisindole derivatives, suppressed a number of bacterial virulence factors, reduced bacterial adhesion, and improved survival rates in infected Caenorhabditis elegans and human lung epithelial cell models. Transcriptome analyses of the bacteria treated with these compounds revealed that NN repressed or upregulated 307 genes when compared to untreated P. aeruginosa. These bacteria-derived molecules act in resistance-quenching and are potentially important candidates for inclusion in treatment protocols. The use of compounds that prevent the biofilm from accumulating the high cell densities critical to its structural and functional maintenance represents significant progress in the management of bacterial persistence. Therefore, a possible clinical implementation of these innovative compounds holds a promising future.

Cas3 of type I-Fa CRISPR-Cas system upregulates bacterial biofilm formation and virulence in Acinetobacter baumannii

Acinetobacter baumannii (A. baumannii) is an important pathogen causing various nosocomial infections. CRISPR-Cas system is the adaptive immune system of bacteria, which is also closely related to the drug resistance and virulence of bacteria. However, the effect and mechanism of cas3 (type I-Fa) in A. baumannii is still unclear. In this study, we successfully constructed a cas3 deletion mutant (19606Δcas3) and complemented strain (19606Δcas3/pcas3) to study the regulatory mechanism of type I-Fa cas3 on bacterial virulence. Our results showed that deletion of cas3(type I-Fa) significantly reduced the biofilm formation, virulence and pathogenicity to mice. The organ bacterial load of mice infected with cas3 deletion strain was significantly reduced, the lung inflammation was slightly changed, and the serum cytokine level was also decreased. All results demonstrated that cas3 enhanced the virulence and pathogenicity of A. baumannii. Mechanism analysis showed that deletion of cas3 can lead to the down-regulation of virulence factors such as biofilm formation related factors and outer membrane protein A(ompA). In addition, cas3 was also involved in the regulation of carbon metabolism and oxidative phosphorylation pathway of A. baumannii. Altogether, our study may provide cas3 as a therapeutic target in the future because of the close link to the virulence of A. baumannii.

Removal of antibiotic and disinfectant compounds from digested pig manure by an aerobic hybrid biofilm process

Using nutrient-rich manure as fertiliser on agricultural land improves crop yield, biodiversity, soil structure, water and nutrient availability. However, manure often contains high levels of antibiotics, as only 10-30 % are metabolised by the animal, thus, soil application contributes to the spread of antibiotics and antibiotic-resistant genes (ARGs). As anaerobic digestion fails to remove the antibiotics and ARGs completely, this study investigates aerobic moving bed biofilm reactors (MBBRs) as post-treatment. The dissipation of sulfadiazine, sulfamethoxazole, ofloxacin, ciprofloxacin, roxithromycin, erythromycin, tylosin, tetracycline, chlortetracycline, benzalkonium chloride C12 and -C14 (BAC-12 and -14) was observed in small laboratory batch MBBRs with digested pig manure. Proficiency testing resulted in an overall removal of 92 %. Sulfamethoxazole and erythromycin were removed by >99 % within 12 and 23 days, respectively. The digestate exhibited high concentrations of benzalkonium biocides, i.e., BAC-12 and -14 (800 μg/L and 172 μg/L, respectively), highlighting the necessity for post-treatment before application to agricultural soil. Within 23 days, the aerobic MBBRs achieved 89 % and 93 % degradation of BAC-12 and -14, respectively. The biofilms improved the total removal by 19 % and BAC degradation by 61-68 % while increasing bacterial diversity. The MBBR-operation increased the abundance of the genera Paracoccus, Parvibaculum, and Clostridium sensu stricto 1. The sulfonamide-resistance genes were the most abundant ARGs (96 % and 98 % in the sludge and carrier biofilm, respectively). The ARG-abundance increased after antibiotic spiking and declined during incubation, reducing direct ARG spread to the environment by degrading antimicrobial concentrations. We, therefore, propose to treat anaerobically digested manure by aerobic biofilm treatment for antibiotic removal.

Self-Powered Oxygen Microbubble Generator for Decontamination of Anaerobic Biofilm-Fouled Bioimplants

Biomedical devices often feature a microgap: confined, minuscule spaces that foster bacterial infiltration and biofilm formation. For instance, peri-implantitis with prevalence rates of 4.7-45% at the patient level is a major complication driven by biofilm infections, characterized by chronic inflammation and implant failure. Anaerobic biofilm residing within the microgap serves as a major source of the peri-implantitis, but tools that remove the biofilm are lacking. Therefore, this study presents a novel preventive strategy employing self-powered microbubbler (SM) for targeted decontamination of micrographs in dental implants. SMs are assembled by doping diatoms with MnO2 nanosheets. These particles are activated to generate O2 microbubbles in H2O2 solution via catalase-mimetic activity and can penetrate the biofilm structures. The resulting oxygen bubbles induce effective mechanical disruption and oxygenation within biofilm-mimicking gelatin hydrogels and Porphyromonas gingivalis biofilms found in the peri-implantitis-affected implants. Such biofilm removal from the microgap restored mechanical stability at implant abutment-fixture connections and reduced bacterial leakage. Multispecies biofilms from patient-derived implants were similarly decontaminated with the mixture of SM-H2O2 outperforming conventional antiseptics like 0.2% chlorhexidine and 3% H2O2 alone. This innovative approach extends beyond dental implants to address biofilm-associated challenges in various biomedical devices with microgap vulnerabilities. Overall, SM-based treatments will offer an efficient and nondamaging solution to enhance the sterility and longevity of various bioimplants with intricated and confined structure.

Fe3O4/MnCO3 microbubbles for efficient elimination of bacterial biofilms by mechanical/sonodynamic effects under ultrasound irradiation and magnetic field targeting

Bacterial biofilms present significant challenges in treatment with traditional antibiotics. Ultrasound (US)-responsive antibacterial agents have emerged as promising alternatives for treating bacterial biofilm infections. However, these agents are often limited by antibiotic dependence, inadequate targeting, and low antibacterial efficacy. Herein, we develop Fe3O4/MnCO3 microbubbles (FMMB) by self-assembly of Fe3O4 nanoparticles (Fe3O4 NPs) and MnCO3 nanoparticles (MnCO3 NPs). Under the direction of the magnetic field (MF), FMMB can be directed toward the methicillin-resistant Staphylococcus aureus (MRSA) biofilm. Under US irradiation, FMMB can disrupt the structure of MRSA biofilms by cavitation-induced mechanical effects and kill bacteria with reactive oxygen species (ROS) generated by MnCO3 NPs through the sonodynamic effect. In a mouse model with catheter-associated MRSA biofilm infection, FMMB removed 58.8% of the biofilm with MF and US, and the bacterial inactivation efficiency reached as high as 4.1 log (99.992%). This work develops multifunctional microbubbles with both US-responsive mechanical and sonodynamic effects for biofilm disruption and MF-responsive properties for biofilm targeting, offering a promising strategy for designing antibiofilm agents to effectively treat bacterial biofilm infections.

Nanomedicines as disruptors or inhibitors of biofilms: Opportunities in addressing antimicrobial resistance

The problem of antimicrobial resistance (AMR) has caused global concern due to its great threat to human health. Evidences are emerging for a critical role of biofilms, one of the natural protective mechanisms developed by bacteria during growth, in resisting commonly used clinical antibiotics. Advances in nanomedicines with tunable physicochemical properties and unique anti-biofilm mechanisms provide opportunities for solving AMR risks more effectively. In this review, we summarize the five "A" stages (adhesion, amplification, alienation, aging and allocation) of biofilm formation and mechanisms through which they protect the internal bacteria. Aimed at the characteristics of biofilms, we emphasize the design "THAT" principles (targeting, hacking, adhering and transport) of nanomedicines in their interactions with biofilms and internal bacteria. Furthermore, recent progresses in multimodal antibacterial nanomedicines, including biofilms disruption and bactericidal activity, and the types of currently available antibiofilm nanomedicines contained organic and inorganic nanomedicines are outlined and highlighted their potential applications in the development of preclinical research. Last but not least, we offer a perspective for the effectiveness of nanomedicines designed to address AMR and challenges associated with their clinical translation.

WGS of a lytic phage targeting biofilm-forming carbapenem-resistant Klebsiella pneumoniae prevalent in a tertiary healthcare setup

Carbapenem-resistant Enterobacteriaceae (CRE) are listed as a priority-one critical pathogen category by the WHO because of their abysmal treatment outcomes owing to antibiotic inefficiency. Among CRE, Klebsiella pneumoniae is prevalent in acquiring resistance genes and withstanding the last-resort drugs. Additionally, its ability to form robust biofilms further exacerbates the treatment challenges. The escalating resistance and recalcitrance of biofilm-residing bacteria against standard antibiotic treatments demand an alternative to antibiotics. Phages, being nature-tailored, are a never-ending arsenal against the bacteria because of their capacity to lyse bacteria rapidly and co-evolve with bacteria. In our study, we isolated K. pneumoniae from patients at Madras Medical Mission Hospital (MMMH), India, and assessed their antibiogram profiles, presence of carbapenemase genes, and biofilm-forming abilities. 100 % of the strains were extended-spectrum beta-lactamase producing, multidrug-resistant (ESBL-MDR), with 95 % harbouring carbapenemase genes. Among the isolates, 65 % were strong biofilm formers, and the rest were moderate. Further, we isolated a bacteriophage, SAKp11, from the hospital sewage, which was able to lyse 62 out of 167 clinical isolates and successfully reduced 99.99 % viable bacterial cells of the 24-h-old biofilm of strong biofilm forming MDR K. pneumoniae strains. Whole genome analysis revealed that SAKp11, with a genome size of 59,338bp, belonged to the Casjensviridae family, one of the less explored bacteriophage families. Comprehensive characterization of SAKp11 indicated its suitability for therapeutic use. Our study highlights the severity of drug-resistant K. pneumoniae in Indian healthcare and the inadequacy of current antibiotics, underscoring the potential of phages as an alternative therapeutic option.

cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress

Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.

Angiogenesis-osteogenesis coupling and immunomodulatory CGRP@nano MOF-loaded CMCS/GelMA hydrogel for bone regeneration

The management of bone defects poses a significant challenge for clinicians, necessitating effective strategies to regulate immune inflammation, angiogenesis, and osteogenic differentiation for successful bone regeneration. In this study, we developed a novel hydrogel composed of carboxymethyl chitosan (CMCS) and gelatin methacryloyl (GelMA) designed for the sustained release of the bioactive component calcitonin gene-related peptide (CGRP) and zeolitic imidazolate framework-8 (ZIF-8). CGRP was initially encapsulated within ZIF-8 and subsequently integrated into the CMCS/GelMA hydrogel matrix. In vitro evaluations revealed that the hydrogel exhibited exceptional biocompatibility and antimicrobial properties, effectively promoting osteogenesis and angiogenesis while modulating M2 macrophage polarization. Furthermore, in vivo assessments indicated that the CGRP@MOF/CG hydrogel significantly regulated the local immune microenvironment and accelerated the healing of cranial defects in rat models. This study provides valuable references for the design and fabrication of multifunctional materials for enhancing bone regeneration.

A biomimetic nano-NET strategy for the treatment of MRSA-related implant-associated infection

Methicillin-resistant Staphylococcus aureus (MRSA) has spread across diverse global environments, and MRSA-related infection is a major threat to public health. Implant-associated infection (IAI) caused by MRSA remains a tough global clinical problem. Conventional antibiotic therapy has limited efficacy in treating MRSA-related IAI, and antibiotic abuse has resulted in the emergence of multidrug-resistant bacteria. Hence, there is a necessity to explore more effective approaches to deal with MRSA-related IAI. Herein, inspired by neutrophil extracellular traps (NETs) released by neutrophils to kill microorganisms, this study proposes a novel biomimetic nano-NET strategy using an epsilon-poly-l-lysine-coated CuO2 nanoplatform, denoted as PCPNAs. The function-adaptive nanoplatform exhibited excellent Fenton-like performance, including robust ROS generation and GSH scavenging ability. PCPNAs showed >90% cell viability in mammalian cells and reduced bacterial burden by 7.65 log10 CFU in vitro. Moreover, the positively charged PCPNAs could easily bind to negatively charged MRSA cells through charge-coupling and simultaneously exerted a trapping effect on MRSA cells. Notably, PCPNAs self-assembled into web-like structures to physically trap and kill biofilm bacteria, achieving 99.58% biofilm eradication. Furthermore, PCPNAs showed satisfactory biocompatibility in vivo and displayed ideal anti-bacterial and anti-inflammatory effects in a mouse model with implant-associated infection. With further development and optimization, the biomimetic nano-NET strategy based on PCPNAs provides a new therapeutic option for the treatment of MRSA-related implant-associated infection.

Mixed Infections in the Female Lower Genital Tract: Unlocking the Current Landscape and Future Directions

Understanding mixed infections in the female lower genital tract is a critical challenge in modern infection research. The interplay of multiple pathogens complicates disease progression, often resulting in treatment failure, recurrent infections, and significant public health and economic burdens. These infections are further exacerbated by disrupted host immune responses, which hinder the recovery of the vaginal microecosystem. Additionally, microbial biofilms-a fundamental mode of pathogen coexistence-contribute to the persistence and drug resistance of these infections, complicating management strategies. This review examines the pathogenesis, diagnosis, and treatment of mixed infections in the female lower genital tract while exploring potential avenues for future research. These findings emphasize the need for greater focus on these infections and offer insights to enhance further research in this area.

Seed Endophytic Bacteria from Manilkara zapota L. and Their Influence as Rice Seed Priming Agents

In recent years, seed endophytes have gained significant attention due to their impact on the ecology, health, and productivity of host plants. Extensive research is being conducted to explore novel endophytic bacteria for sustainable crop improvement. Manilkara zapota L. P. Royen (Sapotaceae) is a highly stress-tolerant tree widely cultivated in tropical countries, yet its associated endophytes remain unexplored. In this study, nine bacterial isolates were obtained from M. zapota seeds, of which three (LA2, LA4, and NS1) were selected based on their IAA production capability which ranged from 2.3, 6.34, and 16.1 µg mL-1, respectively. Identification through 16S rRNA sequencing confirmed LA2 as Pseudomonas rhodesiae, LA4 as Bacillus cereus, and NS1 as Enterobacter cloacae. All isolates exhibited nitrogen-fixing ability, while NS1 uniquely solubilized potassium and phosphorus with KSI and PSI value as 2.9 and 2.3, respectively. Further, the efficacy of the bacterial isolates in promoting rice seedling growth was evaluated, and novel bioformulation was prepared from the consortia of LA2 + LA4, LA2 + NS1, LA4 + NS1, and LA2 + LA4 + NS1. All the isolates and bioformulations were tested as biopriming agents. Rice seedling growth experiments revealed a significant increase in germination percentage, root length, and shoot length following biopriming with individual isolates and consortia. Among treatments, the LA2 + LA4 combination exhibited the highest growth promotion, with a root length increase of 2.1-fold and shoot length increase of 2.3-fold as compared to control. Thus, our results highlighted that bioprospecting microbes from M. zapota seeds can help in nutrient management and seedling establishment.

Engineering Escherichia coli Biofilms for Curcumin Production

Biofilms are emerging platforms for the production of valuable compounds. The present study is the first to assess the capacity of Escherichia coli biofilms to produce curcumin through the expression of a biosynthetic pathway involving three genes: 4-coumarate-CoA ligase (4CL), diketide-CoA synthase (DCS), and curcumin synthase (CURS). The effects of chemical induction with isopropyl β-d-1-thiogalactopyranoside (IPTG) and ferulic acid (FA), and the incubation temperature on biofilm formation and curcumin production were evaluated. Biofilms were formed in 12-well microtiter plates over three days and then induced with 1 mM IPTG and FA at 2 or 8 mM. After induction, the samples were incubated for two days at 26 or 30 °C. Total and culturable planktonic and biofilm cells, as well as biofilm thickness and volumetric and specific curcumin production, were assessed on days 3, 4, and 5. The results demonstrated that biofilms produced up to 10-fold higher curcumin levels (0.9-2.2 fg·cell-1) than their planktonic counterparts (0.1-0.3 fg·cell-1). The highest specific curcumin production (2.2 fg·cell-1) was achieved using 8 mM FA. However, no significant differences in curcumin production were observed between the induced samples incubated at the tested temperatures. These results validated the potential of biofilm systems for expressing a complete exogenous biosynthetic pathway using metabolic engineering, particularly for curcumin production.

Competitive dynamics and balance between Streptococcus mutans and commensal streptococci in oral microecology

Dental caries, as a biofilm-related disease, is closely linked to dysbiosis in microbial ecology within dental biofilms. Beyond its impact on oral health, bacteria within the oral cavity pose systemic health risks by potentially entering the bloodstream, thereby increasing susceptibility to bacterial endocarditis, among other related diseases. Streptococcus mutans, a principal cariogenic bacterium, possesses virulence factors crucial to the pathogenesis of dental caries. Its ability to adhere to tooth surfaces, produce glucans for biofilm formation, and metabolize sugars into lactic acid contributes to enamel demineralization and the initiation of carious lesions. Its aciduricity and ability to produce bacteriocins enable a competitive advantage, allowing it to thrive in acidic environments and dominate in changing oral microenvironments. In contrast, commensal streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, act as primary colonizers and compete with S. mutans for adherence sites and nutrients during biofilm formation. This competition involves the production of alkali, peroxides, and antibacterial substances, thereby inhibiting S. mutans growth and maintaining microbial balance. This dynamic interaction influences the balance of oral microbiota, with disruptions leading to shifts in microbial composition that are marked by rapid increases in S. mutans abundance, contributing to the onset of dental caries. Thus, understanding the dynamic interactions between commensal and pathogenic bacteria in oral microecology is important for developing effective strategies to promote oral health and prevent dental caries. This review highlights the roles and competitive interactions of commensal bacteria and S. mutans in oral microecology, emphasizing the importance of maintaining oral microbial balance for health, and discusses the pathological implications of perturbations in this balance.

Selective pressures for public antibiotic resistance

The rapid increase of antibiotic-resistant pathogens is severely limiting our current treatment possibilities. An important subset of the resistance mechanisms conferring antibiotic resistance have public effects, allowing otherwise susceptible bacteria to also survive antibiotic treatment. As susceptible bacteria can survive treatment without bearing the metabolic cost of producing the resistance mechanism, there is potential to increase their relative frequency in the population and, as such, select against resistant bacteria. Multiple studies showed that this altered selection for resistance is dependent on various environmental and treatment parameters. In this review, we provide a comprehensive overview of their most important findings and describe the main factors impacting the selection for resistance. In-depth understanding of the driving forces behind selection can aid in the design and implementation of alternative treatments which limit the risk of resistance development.

Exchange-coupled bi-magnetic nanoparticles enhance magnetothermal/chemodynamic antibacterial therapy of poly-l-lactide scaffold

Bone implant-associated bacterial infection is a common cause of transplant failure. Chemodynamic therapy (CDT) has significant antibacterial efficacy by producing reactive oxygen species (ROS). However, the ROS permeability is restricted by the natural barrier of bacterial biofilms. Herein, a hard-soft magnetic biphasic nanoparticle (CF@MF) was synthesized by in-situ growth of the soft MnFe2O4 shell on the hard CoFe2O4 core. Then, the CF@MF was incorporated into poly-l-lactide powders to prepare porous scaffolds by selective laser sintering. The scaffold exhibited superior magnetothermal conversion efficiency, which was attributed to the interfacial exchange coupling of CF@MF. Importantly, the scaffold effectively dispersed biofilms by magnetothermal therapy (MTT), favoring numerous ROS pre-generated by CDT to enter the interior to kill bacteria. This study provided a synergistic MTT/CDT strategy to eradicate deep bacterial infections in biomedical application.

Dynamics of Spatial Organization of Bacterial Communities in a Tunable Flow Gut Microbiome-on-a-Chip

The human intestine, a biomechanically active organ, generates cyclic mechanical forces crucial for maintaining its health and functions. Yet, the physiological impact of these forces on gut microbiota dynamics remains largely unexplored. In this study, we investigate how cyclic intestinal motility influences the dynamics of gut microbial communities within a 3D gut-like structure (µGut). To enable the study, a tunable flow Gut Microbiome-on-a-Chip (tfGMoC) is developed that recapitulates the cyclic expansion and compression of intestinal motility while allowing high-magnification imaging of microbial communities within a 3D stratified, biomimetic gut epithelium. Using deep learning-based microbial analysis, it is found that hydrodynamic forces organize microbial communities by promoting distinct spatial exploration behaviors in microorganisms with varying motility characteristics. Empirical evidence demonstrates the impact of gut motility forces in maintaining a balanced gut microbial composition, enhancing both the diversity and stability of the community - key factors for a healthy microbiome. This study, leveraging the new tfGMoC platform, uncovers previously unknown effects of intestinal motility on modulating gut microbial behaviors and community organizations. This will be critical for a deeper understanding of host-microbiome interactions in the emerging field of microbiome therapeutics.

The exometabolome as a hidden driver of bacterial virulence and pathogenesis

The traditional view of metabolism as merely supplying energy and biosynthetic precursors is undergoing a paradigm shift. Metabolic dynamics not only regulates gene expression but also orchestrates cellular processes with remarkable precision. Most bacterial pathogens exhibit exceptional metabolic plasticity, enabling them to adapt to diverse environments, including hostile conditions within a host. While the role of intracellular bacterial metabolism in pathogen-host interactions has been extensively studied, the contributions of the extracellularly released or secreted bacterial metabolites (referred to here as the bacterial 'exometabolome') to metabolic adaptations and disease pathogenesis remain largely unexplored. In this review, we highlight the significant and intriguing roles of bacterial exometabolomes in drug tolerance, immune suppression, and disease pathogenesis, opening a new frontier in our understanding of bacterial-host interactions.

Trends of biomolecule-conjugated nanoparticles as antibiofilm

Biofilm is a powerful barrier that significantly enhances the pathogenicity of bacteria and the development of multidrug resistance. Nanoparticles (NPs) coupled with biomolecules provide a novel approach to addressing this issue. This review briefly discusses the current trends in Biomolecule-Conjugated NPs combined with enzymes, antibiotics, biosurfactants, and natural bioactive compounds as antibiofilm agents emphasizing their superior antibiofilm activity. This conjugation enhances bioavailability, lowers toxicity, requires smaller dosage, and reduces complications caused by infections associated with biofilms. These conjugated systems offer an avenue for industrial, ecological, and medical applications. By increasing the variety of these conjugation techniques, innovative approaches to biofilm-related problems will become possible, with significant advantages for healthcare and other fields.

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Zinc Oxide@Tetracycline Spiky Microparticles Design for Persistent Antibacterial Therapy

Antibiotics have revolutionized medical treatment by effectively combating bacterial infections, particularly those associated with chronic wounds and implant complications. Nevertheless, the persistent use of these drugs has resulted in an increase in antibiotic-resistant bacteria and biofilm infections, highlighting the urgent need for alternative therapies. This study presents an approach for combating persistent bacterial and biofilm infections through the integration of biomimetic design and advanced nanotechnology. Inspired by the natural defense mechanisms of pollen grains and lotus leaves, we engineered zinc oxide spiky microparticles combined with tetracycline-loaded beads mimicking the structure of lotus leaf papillae. This biomimetic design exhibits a multifaceted antimicrobial strategy, leveraging hierarchical micro/nanostructures and the inherent antibacterial properties of their natural counterparts. ZnO microparticles, which mimic the morphology of pollen grains, provide topological cues to rupture adhered bacteria, whereas tetracycline beads, inspired by lotus leaf papillae, deliver a controlled release of antibiotics to target persistent bacteria. Using a synergistic multimodal approach, our biomimetic materials demonstrated exceptional efficacy in eradicating persistent methicillin-resistant Staphylococcus aureus and Escherichia coli infections, offering promising prospects for the development of advanced antibacterial therapies. This study not only underscores the importance of biomimicry in material design but also highlights the potential of integrating nature-inspired strategies with nanotechnology for biomedical applications.

Chitosan-based xerogel film incorporating Nystatin: Synthesis, structural Analysis, and biological evaluation

Wound infections are challenging to manage, requiring innovative wound dressing systems with prescribed properties. Active wound dressings should provide a moist environment, protect from secondary infections, and remove wound exudate to accelerate tissue regeneration. Hydrogels are encouraging matrices for bioactive compound encapsulation in pharmaceutical applications. The aim of the present study is to design chitosan/gelatin /polyvinyl alcohol-based xerogel film containing nystatin for wound dressing applications with antifungal properties. The xerogel film is developed using a film-casting method and evaluated for its chemical and physical characteristics using FTIR, SEM, AFM, and tensile analysis. Water barrier properties of the film, such as the moisture content (17.84 ± 3.62 %), water solubility (44.50 ± 5.55 %), gel fraction (55.50 ± 5.55 %), and water vapour transmission rate (1912.25 ± 248.12 g m-2 per day), suggest a humid microenvironment suitable for wound. The xerogel film, characterized by its robust mechanical strength, substantial swelling capacity (∼120-400 %) across various pH levels, and acceptable bio-adhesive properties, reveals as a potential antifungal wound dressing material. In vitro toxicity assessments confirm its biocompatibility towards both RBCs and NIH-3 T3 fibroblast cells. The findings confirm that the film formulation has strong antifungal properties, with a minimum inhibitory concentration of 2-8 μL/mL against Candida species, as well as outstanding antibiofilm effectiveness (∼85 %) and a significant reduction of the fungal colony count (∼100 %). Moreover, its controlled drug release capabilities, along with antifungal properties, offer it as an appealing dressing for the localized treatment of superficial fungal infections. As a result, this xerogel film can be used as a versatile platform for advanced wound care and therapeutic applications.

Biofilm formation and analysis of EPS architecture comprising polysaccharides and lipids by Pseudomonas aeruginosa and Escherichia coli on food processing surfaces

Biofilms are silent but formidable threats in seafood processing, where Pseudomonas aeruginosa and Escherichia coli can quickly transform contact surfaces into reservoirs of contamination. This study explores the dynamic biofilm formation on aluminum, silicone rubber, stainless steel, and polyethylene terephthalate over 24 and 72 h. Quantitative assays including Colony Forming Unit (CFU), Crystal Violet (CV), 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) revealed a significant increase in biofilm density, particularly on aluminum and silicone rubber. Fourier-Transform Infrared Spectroscopy (FTIR) and 1H Nuclear Magnetic Resonance (NMR) analyses showed that biofilm EPS exhibits an evolving amphiphilic nature, with stable polysaccharides and increasing lipid content enhancing resilience. Confocal Laser Scanning Microscopy (CLSM), and Field Emission Scanning Electron Microscopy (FE-SEM) captured the shift from early attachment to mature, dense biofilms. These findings underscore the crucial impact of surface material on biofilm growth and the pressing need for tailored cleaning protocols to curb contamination risks in food processing environments.

Structures of α-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases

Endo-galactosaminidases are an underexplored family of enzymes involved in the degradation of galactosaminogalactan (GAG) and other galactosamine-containing cationic exopolysaccharides produced by fungi and bacteria. These exopolysaccharides are part of the cell wall and extracellular matrix of microbial communities. Currently, these galactosaminidases are found in three distinct CAZy families: GH114, GH135 and GH166. Despite the widespread occurrence of these enzymes in nearly all bacterial and fungal clades, only limited biochemical and structural data are available for these three groups. To expand our knowledge of endo-galactosaminidases, we selected several sequences predicted to encode endo-galactosaminidases and produced them recombinantly for structural and functional studies. Only very few predicted proteins could be produced in soluble form, and activity against bacterial Pel (pellicle) polysaccharide could only be confirmed for one enzyme. Here, we report the structures of two bacterial and one fungal enzyme. Whereas the fungal enzyme belongs to family GH114, the two bacterial enzymes do not lie in the current GH families but instead define a new family, GH191. During structure solution we realized that crystals of all three enzymes had various defects including twinning and partial disorder, which in the case of a more severe pathology in one of the structures required the design of a specialized refinement/model-building protocol. Comparison of the structures revealed several features that might be responsible for the described activity pattern and substrate specificity compared with other GAG-degrading enzymes.

Evaluation of Antibacterial Activity in Some Algerian Essential Oils and Selection of Thymus vulgaris as a Potential Biofilm and Quorum Sensing Inhibitor Against Pseudomonas aeruginosa

Biofilm formation and virulence factor production by Pseudomonas aeruginosa are identified as the main mechanisms of its antibiotic resistance and pathogenicity. In this context, the study of the chemical composition of three Algerian essential oils (EOs) and the screening of their antibacterial, antibiofilm, and virulence factor inhibitory activities enabled us to select the thyme EO as the best oil to control the P. aeruginosa strain isolated from hospital environments. This EO, composed essentially of thymol (55.82%) associated with carvacrol, had an anti-adhesive activity of 69.8% at a concentration of 5 µL/mL and a biofilm eradication activity of 74.86% at a concentration of 2.5 µL/mL. In addition, this EO was able to inhibit P. aeruginosa twitching motility by 100% at a concentration of 2.5 µL/mL. Pyocyanin was inhibited by 99.33% at a thyme EO concentration of 1.25 µL/mL. Rhamnolipids were significantly inhibited by 63.33% in the presence of thyme EO at a concentration of 1.25 µL/mL after 24 h of incubation. Molecular docking showed that carvacrol and thymol can bind to the three quorum sensing receptors in P. aeruginosa, RhlR, LasR, and PqsR, with good affinities, which can inhibit or modulate biofilm formation and the production of certain virulence factors.

Structural characteristics, biotechnological production and applications of exopolysaccharides from Bacillus sp.: A comprehensive review

Exopolysaccharides (EPS) produced by Bacillus species display various biological activities and characteristics such as anti-oxidant, immunomodulatory, anti-bacterial, and bioadhesive effects. These attributes confer Bacillus species broad potential applications in diverse fields such as food, medicine, environment, and agriculture. Moreover, Bacillus-derived EPS are easier to produce and yield higher quantities than plant-derived polysaccharides. Despite these advantages, Bacillus-derived EPS still encounter numerous obstacles in industrial production and commercial applications, including elevated costs, the absence of mature fermentation tank production procedures, and the lack of systematic in vivo and in vitro activity and metabolic evaluation. Therefore, it is essential to gain insight into the current status of structure, production, and applications of Bacillus-derived EPS for facilitating their future broader application. This paper provides a comprehensive overview of the current research on the production, separation, characteristics and applications of these related biological products. Furthermore, this paper summarizes the current challenges impeding industrial production of Bacillus-derived EPS, along with potential solutions, and their prospective applications in enhancing the attributes of beneficial biofilms, laying a solid scientific foundation for the applications of Bacillus-derived EPS in industry and agriculture.

Emergent Locomotion in Self-Sustained, Mechanically Connected Soft Matter Ringsf

In nature, the interplay between individual organisms often leads to the emergence of complex belabours, of which sophistication has been refined through millions of years of evolution. Synthetic materials research has focused on mimicking the natural complexity, e.g., by harnessing non-equilibrium states to drive self-assembly processes. However, it is highly challenging to understand the interaction dynamics between non-equilibrium entities and to obtain collective behavior that can arise autonomously through interaction. In this study, thermally fueled, twisted rings exhibiting self-sustained movements are used as fundamental units and their interactive behaviors and emergent functions are investigated. The rings are fabricated from connected thermoresponsive liquid crystal elastomers (LCEs) strips that undergo zero-elastic-energy-mode, autonomous motions upon a heat gradient. Single-ring structures with various twisting numbers and nontrivial links, and connected knots where several LCE rings (N = 2,3,4,5) are studied and linked. The observations uncover that controlled locomotion of the structures can emerge when N ≥ 3. The locomotion can be programmed by controlling the handedness at the connection points between the individual rings. These findings illustrate how group activity emerges from individual responsive material components through mechanical coupling, offering a model for programming autonomous locomotion in soft matter constructs.

Inhibitory effect of plant flavonoid cyanidin on oral microbial biofilm

As primary colonizers of the tooth surface, oral streptococci play a crucial role in dental caries development. Numerous natural compounds, including flavonoids, are emerging as promising agents for inhibiting dental biofilm formation without compromising bacterial viability, underscoring their potential in non-bactericidal antibiofilm strategies. This study investigated the effects and mechanism of action of the unmodified plant flavonoid cyanidin on the growth and sucrose-dependent biofilm formation of oral streptococci, with a particular focus on the cariogenic pathogen Streptococcus mutans. At concentrations above 100 µg/mL, cyanidin significantly inhibited biofilm formation by S. mutans without impacting bacterial viability. The flavonoid reduced the biomass of surface-associated bacteria and exopolysaccharides (EPS), particularly by inhibiting water-insoluble glucan (WIG) production mediated by the glucosyltransferases GtfB and GtfC. While cyanidin did not exhibit a bactericidal effect on early colonizer streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, Streptococcus oralis, and Streptococcus mitis, it showed a significant inhibitory effect on bacterial acidogenicity and mixed-species streptococcal biofilms in the presence of S. mutans. Remarkably, cyanidin gradually reduced the proportion of S. mutans in the mixed biofilm, suggesting a selective impact that may promote a more commensal-dominant community by disrupting S. mutans glucan production and biofilm competitiveness.

IMPORTANCE

The identification of compounds with potent antibiofilm effects that do not compromise bacterial viability presents a promising strategy for oral health management. By preventing biofilm formation and keeping bacteria in a planktonic state, such agents could enhance bacterial susceptibility to targeted therapies, including probiotics or phage-based treatments. Cyanidin, which exhibits strong antibiofilm activity against oral streptococcal biofilms, reduces bacterial acidogenicity and may promote a more commensal-dominant biofilm in vitro, potentially hindering the maturation of cariogenic biofilms.

Cecropin A-Derived Peptide for the Treatment of Osteomyelitis by Inhibiting the Growth of Multidrug-Resistant Bacteria and Eliminating Inflammation

Osteomyelitis poses substantial therapeutic challenges due to the prevalence of multidrug-resistant bacterial infections and associated inflammation. Current treatment regimens often rely on a combination of corticosteroids and antibiotics, which can lead to complications and impede effective bacterial clearance. In this study, we present CADP-10, a Cecropin A-derived peptide, designed to target methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Escherichia coli (MRE), while simultaneously addressing inflammatory responses. CADP-10 self-assembles into nanobacterial net (NBacN) that selectively identify and bind to bacterial endotoxins (LPS and LTA), disrupting membrane integrity and depolarizing membrane potential, which culminates in bacterial death. Importantly, these NBacN are bound to LPS and LTA from dead bacteria, preventing their engagement with TLR receptors and effectively blocking downstream inflammatory pathways. Our assessments of CADP-10 demonstrate good biosafety in both in vitro and in vivo models. Notably, in a rabbit osteomyelitis model, CADP-10 eliminated MRSA-induced bone infections, mitigated inflammation, and promoted bone tissue regeneration. This research highlights the potential of CADP-10 as a multifunctional antimicrobial agent for the management of infectious inflammatory diseases.

Host selection and nutrient status jointly drive algal and bacterial interactions in epiphytic biofilms of submerged macrophytes: Structural and functional insights

Epiphytic biofilms play a crucial role in aquatic biogeochemical cycles but are simultaneously influenced by host selection and eutrophication. However, the compositional structure and interaction mechanisms of these factors on algal and bacterial communities remain poorly understood. In this study, we employed Confocal Laser Scanning Microscopy (CLSM), Scanning Electron Microscopy (SEM), and high-throughput sequencing to investigate the physicochemical properties, algal and bacterial diversity, and community structure of epiphytic biofilms on two submerged macrophytes - Vallisneria natans (VN) and Hydrilla verticillata (HV) - across three urban shallow lakes with varying trophic levels in the Yangtze River Basin. Our results revealed distinct algal and bacterial communities influenced by both host plants and lake nutrient conditions, with unique core species identified in VN, HV, and the surrounding water. Host-environment effects index (HEEI = 1.79) indicated that bacterial communities were predominantly shaped by host selection, exhibiting lower diversity in HV (1.66 ± 0.92) and VN (2.31 ± 1.12) biofilms compared to surrounding waters (3.80 ± 0.47). In contrast, algal communities were primarily regulated by environmental factors (HEEI = 0.43), with higher diversity in less eutrophic lakes. Algal-bacterial co-occurrence network analysis revealed greater network complexity in VN biofilms than that in HV, with predominantly synergistic interactions facilitating carbon and nitrogen cycling. Eutrophication increased biofilm thickness, nutrient content, and extracellular polymeric substance (EPS) production but reduced microbial diversity and altered community interaction patterns. This study advances our understanding of epiphytic biofilms and offers insights into optimizing host-microbe interactions for improving lake restoration strategies.