Biofilms: an emergent form of bacterial life

Yielding behaviour of chemically treated Pseudomonas fluorescens biofilms

The mechanics of biofilms are intrinsically shaped by their physicochemical environment. By understanding the influence of the extracellular matrix composition, pH and elevated levels of cationic species on the biofilm rheology, novel living materials with tuned properties can be formulated. In this study, we examine the role of a chaotropic agent (urea), two divalent cations and distilled deionized water on the nonlinear viscoelasticity of a model biofilm Pseudomonas fluorescens. The structural breakdown of each biofilm is quantified using tools of non-linear rheology. Our findings reveal that urea induced a softening response, and displayed strain overshoots comparable to distilled deionized water, without altering the microstructural packing fraction and macroscale morphology. The absorption of divalent ferrous and calcium cations into the biofilm matrix resulted in stiffening and a reduction in normalized elastic energy dissipation, accompanied by macroscale morphological wrinkling and moderate increases in the packing fraction. Notably, ferrous ions induced a predominance of rate dependent yielding, whereas the calcium ions resulted in equal contribution from both rate and strain dependent yielding and structural breakdown of the biofilms. Together, these results indicate that strain rate increasingly becomes an important factor controlling biofilm fluidity with cation-induced biofilm stiffening. The finding can help inform effective biofilm removal protocols and in development of bio-inks for additive manufacturing of biofilm derived materials.

Deciphering and designing microbial communities by genome-scale metabolic modelling

Microbial communities are shaped by the complex interactions among organisms and the environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the complexity and ecological properties of various microbial communities, revealing their intricate interactions. Many researchers have modified GEMs for the microbial communities based on specific needs. Thus, GEMs need to be comprehensively summarized to better understand the trends in their development. In this review, we summarized the key developments in deciphering and designing microbial communities using different GEMs. A timeline of selected highlights in GEMs indicated that this area is evolving from the single-strain level to the microbial community level. Then, we outlined a framework for constructing GEMs of microbial communities. We also summarized the models and resources of static and dynamic community-level GEMs. We focused on the role of external environmental and intracellular resources in shaping the assembly of microbial communities. Finally, we discussed the key challenges and future directions of GEMs, focusing on the integration of GEMs with quorum sensing mechanisms, microbial ecology interactions, machine learning algorithms, and automatic modeling, all of which contribute to consortia-based applications in different fields.

Intrinsic antimicrobial resistance: Molecular biomaterials to combat microbial biofilms and bacterial persisters

The escalating rise in antimicrobial resistance (AMR) coupled with a declining arsenal of new antibiotics is imposing serious threats to global public health. A pervasive aspect of many acquired AMR infections is that the pathogenic microorganisms exist as biofilms, which are equipped with superior survival strategies. In addition, persistent and recalcitrant infections are seeded with bacterial persister cells at infection sites. Together, conventional antibiotic therapeutics often fail in the complete treatment of infections associated with bacterial persisters and biofilms. Novel therapeutics have been attempted to tackle AMR, biofilms, and persister-associated complex infections. This review focuses on the progress in designing molecular biomaterials and therapeutics to address acquired and intrinsic AMR, and the fundamental microbiology behind biofilms and persisters. Starting with a brief introduction of AMR basics and approaches to tackling acquired AMR, the emphasis is placed on various biomaterial approaches to combating intrinsic AMR, including (1) semi-synthetic antibiotics; (2) macromolecular or polymeric biomaterials mimicking antimicrobial peptides; (3) adjuvant effects in synergy; (4) nano-therapeutics; (5) nitric oxide-releasing antimicrobials; (6) antimicrobial hydrogels; (7) antimicrobial coatings. Particularly, the structure-activity relationship is elucidated in each category of these biomaterials. Finally, illuminating perspectives are provided for the future design of molecular biomaterials to bypass AMR and cure chronic multi-drug resistant (MDR) infections.

The impact of methylparaben and chlorine on the architecture of Stenotrophomonas maltophilia biofilms

The biofilm architecture is significantly influenced by external environmental conditions. Biofilms grown on drinking water distribution systems (DWDS) are exposed to environmental contaminants, including parabens, and disinfection strategies, such as chlorine. Although changes in biofilm density and culturability from chemical exposure are widely reported, little is known about the effects of parabens and chlorine on biofilm morphology and architecture. This is the first study evaluating architectural changes in Stenotrophomonas maltophilia colony biofilms (representatives of bacterial communities presented in DWDS) induced by the exposure to methylparaben (MP) at environmental (15 μg/L) and in-use (15 mg/L) concentrations, and chlorine at 5 mg/L, using widefield epi-fluorescence mesoscopy with Mesolens. The GFP fluorescence of colony biofilms allowed the visualization of internal structures and Nile Red fluorescence permitted the inspection of the distribution of lipids. Our data show that exposure to MP triggers physiological and morphological adaptation in mature colony biofilms by increasing the complexity of internal structures, which may confer protection to embedded cells from external chemical molecules. These architectural modifications include changes in lipid distribution as an adaptive response to MP exposure. Although chlorine exposure affected colony biofilm diameter and architecture, the colony roundness was completely affected by the simultaneous presence of MP and chlorine. This work is pioneer in using Mesolens to highlight the risks of exposure to emerging environmental contaminants (MP), by affecting the architecture of biofilms formed by drinking water (DW) bacteria, even when combined with routine disinfection strategies.

Genetically engineered bacterial biofilm materials enhances portable whole cell sensing

In recent years, whole-cell biosensors (WCBs) have emerged as a potent approach for environmental monitoring and on-site analyte detection. These biosensors harness the biological apparatus of microorganisms to identify specific analytes, offering advantages in sensitivity, specificity, and real-time monitoring capabilities. A critical hurdle in biosensor development lies in ensuring the robust attachment of cells to surfaces, a crucial step for practical utility. In this study, we present a comprehensive approach to tackle this challenge via engineering Escherichia coli cells for immobilization on paper through the Curli biofilm pathway. Furthermore, incorporating a cellulose-binding peptide domain to the CsgA biofilm protein enhances cell adhesion to paper surfaces, consequently boosting biosensor efficacy. To demonstrate the versatility of this platform, we developed a WCB for copper, optimized to exhibit a discernible response, even with the naked eye. To confirm its suitability for practical field use, we characterized our copper sensor under various environmental conditions-temperature, salinity, and pH-to mimic real-world scenarios. The biosensor-equipped paper discs can be freeze-dried for deployment in on-site applications, providing a practical method for long-term storage without loss of sensitivity paper discs demonstrate sustained functionality and viability even after months of storage with 5 μM limit of detection for copper with visible-to-naked-eye signal levels. Biofilm-mediated surface attachment and analyte sensing can be independently engineered, allowing for flexible utilization of this platform as required. With the implementation of copper sensing as a proof-of-concept study, we underscore the potential of WCBs as a promising avenue for the on-site detection of a multitude of analytes.

Biodegradation of organosulfur with extra carbon source: Insights into biofilm formation and bacterial metabolic processes

Organosulfur compounds are prevalent in wastewater, presenting challenges for biodegradation, particularly in low-carbon environments. Supplementing additional carbon sources not only provides essential nutrients for microbial growth but also serves as regulators, influencing adaptive changes in biofilm and enhancing the survival of microorganisms in organosulfur-induced stress bioreactors. This study aims to elucidate the biodegradation of organosulfur under varying carbon source levels, placing specific emphasis on functional bacteria and metabolic processes. It has been observed that higher levels of carbon supplementation led to significantly improved total sulfur (TS) removal efficiencies, exceeding 83 %, and achieve a high organosulfur CH3SH removal efficiency of ~100 %. However, in the reactor with no external carbon source added, the oxidation end-product SO42- accumulated significantly, surpassing 120 mEq/m2-day. Furthermore, the TB-EPS concentration consistently increasedwith the ascending glucose concentration. The analysis of bacterial community reveals the enrichment of functional bacteria involved in sulfur metabolism and biofilm formation (e.g. Ferruginibacter, Rhodopeudomonas, Gordonia, and Thiobacillus). Correspondingly, the gene expressions related to the pathway of organosulfur to SO42- were notably enhanced (e.g. MTO increased by 27.7 %). In contrast, extra carbon source facilitated the transfer of organosulfur into amino acids in sulfur metabolism and promoted assimilation. These metabolic insights, coupled with kinetic transformation results, further validate distinct sulfur pathways under different carbon source conditions. The intricate interplay between bacteria growth regulation, pollutant biodegradation, and microbial metabolites underscores a complex network relationship that significantly contributes to efficient operation of bioreactors.

Restoration-mediated protein substances preferentially drive underlying bauxite residue macroaggregate formation during the simulated ecological reconstruction process

Constructing a restoration strategy from bauxite residue to Technosols is a cost-effective and sustainable strategy for addressing the ecological and environmental issues caused by high alkalinity, salinity, and fine-grained bauxite residues. However, the quantitative contribution of restoration strategies on the upper bauxite residue-derived Technosols to the underlying untreated bauxite residue in the short term remains poorly understood. This study investigated the mediating mechanisms of vegetation and microbial metabolic effects on the alkalinity, nutrient content, and structure of the underlying bauxite residue (20-50 cm) through a simulated ecological reconstruction of the bauxite residue stockpile. Results indicated that implementing plant restoration strategies resulted in the content of polyphenolic compounds, lipids, tannins, and carbohydrates in bauxite residue dissolved organic matter (DOM) increased significantly from 52.5, 8.2, 3.3, and 2.0 % to 54.4, 10.4, 5.6, and 2.8 %, respectively, while the content of condensed aromatics, unsaturated hydrocarbons, and proteins/amino sugars decreased significantly from 15.5, 12.0, and 6.5 % to 12.1, 9.7, and 5.1 %, respectively. The newly produced molecules were concentrated in regions with low O/C and high H/C ratios, suggesting that short-term vegetation restoration strategies facilitate the transformation of substrate DOM towards easily decomposable and highly bioavailable substances. This led to the migration of the newly produced molecules to the underlying bauxite residue, and as a result, the protein and soluble microbial products of the underlying bauxite residue increased significantly, as well as the pH, exchangeable Na, and < 0.054 mm particles decreased from 10.2, 44.2 cmol kg-1, and 28.1 % to 9.7, 27.1 cmol kg-1, and 19.4 %, respectively, available nitrogen, urease, and 1-2 mm particles increased from 7.3 mg kg-1, 0.2 U mg-1, and 14.5 % to 7.6 mg kg-1, 0.3 U kg-1, and 21.7 %, respectively. Results of the structural equation model further confirmed that plant biomass, proteins/amino sugars, and condensed aromatics in the upper Technosol were the main factors controlling the aggregate formation of the underlying bauxite residue by mediating the protein-dominated biogenic organic matter produced by microbial metabolism.

Microbial biofilms as a platform for diverse biocatalytic applications

Microbial biofilms have gained significant traction in commercial wastewater treatment due to their inherent resilience, well-organized structure, and potential for collaborative metabolic processes. As our understanding of their physiology deepens, these living catalysts are finding exciting applications beyond wastewater treatment, including the production of bulk and fine chemicals, bioelectricity generation, and enzyme immobilization. While the biological applications of biofilms in different biocatalytic systems have been extensively summarized, the applications of artificially engineered biofilms were rarely discussed. This review aims to bridge this gap by highlighting the untapped potential of engineered microbial biofilms in diverse biocatalytic applications, with a focus on strategies for biofilms engineering. Strategies for engineering biofilm-based systems will be explored, including genetic modification, synthetic biology approaches, and targeted manipulation of biofilm formation processes. Finally, the review will address key challenges and future directions in developing robust biofilm-based biocatalytic platforms for large-scale production of chemicals, pharmaceuticals, and biofuels.

Migration of natural organic matter and Pseudomonas fluorescens-associated polystyrene on natural substrates in aquatic environments

This study investigated the migration behavior of microplastics (MPs) covered with natural organic matter (NOM) and biofilm on three substrates (silica, Pseudomonas fluorescent and Pseudomonas aeruginosa biofilms) in various ionic strengths, focusing on the alterations in surface properties based on surface energy theory that affected their deposition and release processes. Peptone and Pseudomonas fluorescens were employed to generate NOM-attached and biofilm-coated polystyrene (PS) (NOM-PS and Bio-PS). NOM-PS and Bio-PS both exhibited different surface properties, as increased roughness and particle sizes, more hydrophilic surfaces and altered zeta potentials which increased with ionic strength. Although the deposition of NOM-PS on biofilms were enhanced by higher ionic strengths and the addition of Ca2+, while Bio-PS deposited less on biofilms and more on the silica surface. Both types exhibited diffusion-driven adsorption on the silica surface, with Bio-PS also engaging in synergistic and competitive interactions on biofilm surfaces. Release tests revealed that NOM-PS and Bio-PS were prone to release from silica than from biofilms. The Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory furtherly demonstrated that mid-range electrostatic (EL) repulsion had significantly impacts on NOM-PS deposition, and structural properties of extracellular polymeric substances (EPS) and substrate could affect Bio-PS migration.

Earthworm gut digestion drives the transfer behavior of antibiotic resistance genes in layers of extracellular polymeric substances during vermicomposting of dewatered sludge

Gut digestion by earthworms (GDE) is a crucial step in vermicomposting, affecting the fate of antibiotic resistance genes (ARGs) in vermicompost sludge. The extracellular polymeric substance (EPS) matrix of sludge is an important space for ARG transfer. However, the effect of GDE on EPS-associated ARGs remains unclear. Therefore, this study explored the role of GDE in driving the transfer of ARGs within different EPS layers in sludge. For this, the changes in intracellular ARGs and EPS-associated ARGs in sludge were analyzed after 5 days of the GDE process. The results showed that after the GDE process, both nitrate and dissolved organic carbon significantly increased in all EPS layers of sludge, while the proteins and polysaccharides only enhanced in soluble and loosely bound EPS of sludge. In addition, a 7.0% decrease in bacterial diversity was recorded after the GDE process, with a functional bacterial community structure emerging. Moreover, the absolute abundance of total ARGs and mobile genetic elements decreased by 90.71% and 61.83%, respectively, after the GDE process. Intracellular ARGs decreased by 92.1%, while EPS-associated ARGs increased by 4.9%, indicative of intracellular ARG translocation into the EPS during the GDE process. Notably, the ARGs exhibited significant enrichment in both the soluble and loosely bound EPS, whereas they were reduced in the tightly bound EPS. The structural equation modeling revealed that the GDE process effectively mitigated the ARG dissemination risk by modulating both the EPS structure and microenvironment, with the organic structure representing a primary factor influencing ARGs in the EPS.

Inhibition of zinc ions in sulfur-driven autotrophic denitrification process: What is the behavior of extracellular polymeric substances?

Sulfur-driven autotrophic denitrification (SAD) process is a cost-effective and sustainable method for nitrogen removal from wastewater. However, a higher concentration of zinc ions (Zn(II)) flowing into wastewater treatment plants poses a potential threat to the SAD process. This study examined that a half maximal inhibitory concentration (IC50) of Zn(II) was 7 mg·L-1 in the SAD process. Additionally, the addition of 20 mg·L-1 Zn(II) resulted in a severe accumulation of nitrite to 150.20 ± 6.00 mg·L-1 when the initial concentration of nitrate was 500 mg·L-1. Moreover, the activities of nitrate reductase, nitrite reductase, dehydrogenase and electron transport system were significantly inhibited under Zn(II) stress. The addition of Zn(II) inhibited EPS secretion and worsened electrochemical properties. The result was attributed to the spontaneous binding between EPS and Zn(II), with a ΔG of -17.50 KJ·mol-1 and a binding constant of 1.77 × 104 M-1, respectively. Meanwhile, the protein, fulvic acid, and humic-like substances occurred static quenching after Zn(II) addition, with -OH and -C=O groups providing binding sites. The binding sequence was fulvic acid→protein→humic acid and -OH → -C=O. Zn(II) also reduced the content of α-helix, which was unfavorable for electron transfer. Additionally, the Zn(II) loosened protein structure, resulting in a 50 % decrease in α-helix/(β-sheet+random coil). This study reveals the effect of Zn(II) on the SAD process and enhances our understanding of EPS behavior under metal ions stress.

Osmoregulation by choline-based deep eutectic solvent induces electroactivity in Bacillus subtilis biofilms

Gram-positive Bacillus subtilis is a model organism for the biotechnology industry and has recently been characterized as weakly electroactive in both planktonic cultures and biofilms. Increasing the extracellular electron transfer (EET) rate in B. subtilis biofilms will help to develop an efficient microbial electrochemical technology (MET) and improve the bioproduction of high-value metabolites under electrofermentative conditions. In our previous work, we have shown that the addition of compatible solute precursors such as choline chloride (ChCl) to the growth medium formulation increases current output and biofilm formation in B. subtilis. In this work, we utilized a low-carbon tryptone yeast extract medium with added salts to further expose B. subtilis to salt stress and observe the osmoregulatory and/or nutritional effects of a D-sorbitol/choline chloride (ChCl) (1:1 mol mol-1) deep eutectic solvents (DESs) on the electroactivity of the formed biofilm. The results show that ChCl and D-sorbitol alleviate the osmotic stress induced by the addition of NaH2PO4 and KH2PO4 salts and boost biofilm production. This is probably due to the osmoprotective effect of ChCl, a precursor of the osmoprotectant glycine betaine, and the induction of electroactive exopolymeric substances within the B. subtilis biofilm. Since high ionic strength media are commonly used in microbial biotechnology, the combination of ChCl-containing DESs and salt stress could enhance biofilm-based electrofermentation processes that bring significant benefits for biotechnological applications.

Effect of siaD on Ag-8 to improve resistance to crown gall in grapes and related mechanisms

Crown gall caused by Agrobacterium vitis (A. vitis) is one of the crucial issues restricting the to grape industry. In this study, Agrobacterium tumefaciens (Ag-8) was separated from the soil that could prevent the occurrence of grape crown gall. By the mutagenesis of Ag-8 transposon, the siaD gene deletion strain (ΔsiaD) showed significantly lower efficacy in grape and tomato plants for controlling grape crown gall, but the relevant mechanism was not clear. The biofilm formation and motility of ΔsiaD were significantly decreased, and the colonization ability of ΔsiaD in tomato roots was significantly reduced. RNA-seq analysis showed that the expression of nemR significantly reduced in the ΔsiaD and that the expression of nemR showed a high correlation with biofilm and motility. Further studies showed that the nemR gene deletion strain of Ag-8 (ΔnemR) showed significantly reduced motility, biofilm formation and control of grape crown gall compared to Ag-8, and the nemR gene complementary strain of Ag-8 (ΔnemR-comp) recovered to Ag-8 wild-type levels. The inoculation experiments of preventive, curative or simultaneous treatment further showed that the preferential inoculation with Ag-8 reduced the incidence of grape crown gall on tomato plants, and studies showed that the mutation of siaD affected the site competition between Ag-8 and A. vitis, and that the mutation of nemR was consistent with the previous results. This study provides a new strategy for the prevention and control of grape crown gall, which is of great significance to the grape industry to increase production and income.

Synergistic effects of arginine and fluoride on human dental biofilm control

OBJECTIVES

The aim of this study was to quantitatively and comprehensively investigate the combined effects of arginine and fluoride on the suppression of pathogenicity using an in situ biofilm model and next-generation sequencing (NGS).

METHODS

Using the in situ model, dental biofilms were formed and the viable bacterial counts and arginine activity in the arginine- and fluoride-containing dentifrice and control groups were measured. We also compared their effects on the bacterial microbiota and predictive functional factors in the control, arginine (arg), and arginine + fluoride (argF) groups using NGS analysis.

RESULTS

Compared to the control treatment, the use of 8 % arginine and 1450 ppm fluoride toothpaste resulted in significantly high oral NH4+ concentrations without affecting the number of viable bacteria (P < 0.05). NGS analysis revealed that the oral microbiota of the control, arg, and argF groups were significantly different. Heat map analysis of the predicted functional factors revealed that the arg group had different properties from the other groups and activated specific substrate metabolic pathways; contrastingly, argF treatment inhibited the activity of these pathways and prevented an increase in the abundance of bacterial genera that utilize substrates such as sucrose, suggesting the synergistic effect of arginine and fluoride.

CONCLUSIONS

This study indicates that the combination of arginine and fluoride has a synergistic effect on the bacterial microbiota and pathogenicity of dental biofilms compared with arginine alone.

CLINICAL SIGNIFICANCE

Our findings suggest that the combination of arginine and fluoride could be used as an effective prebiotic and may inhibit the growth of bacteria associated with dental diseases.

Control of Staphylococcus epidermidis biofilm by surfactins of an endophytic bacterium Bacillus sp. 15 F

The present paper deals with the preparation and annotation of a surfactin(s) derived from a culture of the endophytic bacterium Bacillus 15 F. The LC-MS analysis of the acetonitrile fraction confirmed the presence of surfactins Leu/Ile7 C15, Leu/Ile7 C14 and Leu/Ile7 C13 with [M+H]+ at m/z 1036.6895, 1022.6741 and 1008.6581, respectively. Various concentrations of the surfactin(s) (hereafter referred to as surfactin-15 F) were used to reduce the adhesion of Staphylococcus epidermidis S61, which served as a model for studying antibiofilm activity on polystyrene surfaces. Incubation of Staphylococcus epidermidis S61 with 62.5 µg/ml of surfactin-15 F resulted in almost complete inhibition of biofilm formation (90.3 ± 3.33 %), and a significant reduction of cell viability (resazurin-based fluorescence was more than 200 times lower). The antiadhesive effect of surfactin-15 F was confirmed by scanning electron microscopy. Surfactin-15 F demonstrated an eradication effect against preformed biofilm, causing severe disruption of Staphylococcus epidermidis S61 biofilm structure and reducing viability. The results suggest that surfactins produced by endophytic bacteria could be an alternative to synthetic products. Surfactin-15 F, used in wound dressings, demonstrated an efficient treatment of the preformed Staphylococcus epidermidis S61 biofilm, and thus having a great potential in medical applications.

Single-cell encapsulation systems for probiotic delivery: Armor probiotics

Functional foods or drugs based on probiotics have gained unprecedented attention and development due to the increasingly clear relationship between probiotics and human health. Probiotics can regulate intestinal microbiota, dynamically participating in various physiological activities to directly affect human health. Some probiotic-based functional preparations have shown great potential in treating multiple refractory diseases. Currently, the survival and activity of probiotic cells in complex environments in vitro and in vivo have taken priority, and various encapsulation systems based on food-derived materials have been designed and constructed to protect and deliver probiotics. However, traditional encapsulation technology cannot achieve precise protection for a single probiotic, which makes it unable to have a significant effect after release. In this case, single-cell encapsulation systems can be assembled based on biological interfaces to protect and functionalize individual probiotic cells, maximizing their physiological activity. This review discussed the arduous challenges of probiotics in food processing, storage, human digestion, and the commonly used probiotic encapsulation system. Besides, a novel technology of probiotic encapsulation was introduced based on single-cell coating, namely, "armor probiotics". We focused on the classification, structural design, and functional characteristics of armor coatings, and emphasized the essential functional characteristics of armor probiotics in human health regulation, including regulating intestinal health and targeted bioimaging and treatment of diseased tissues. Subsequently, the benefits, limitations, potential challenges, as well as future direction of armor probiotics were put forward. We hope this review may provide new insights and ideas for developing a single-cell probiotics encapsulating system.

Microbiomes on microplastics versus natural microcarriers: Stability and transformation during aquatic travel from aquaculture ponds to adjacent stream

Microplastics (MPs) with different physical-chemical properties are considered as vectors for the propagation of microbes in aquatic environments. It remains unclear how plastic types impact on the plastisphere and whether different MPs spread microbes more rapidly than natural materials in microbes across distinct water bodies as proposed previously. We used in-situ incubation to investigate the microbes attached on MPs of polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC), versus that on two natural microcarriers (quartz sands and bamboo) during the travel from aquaculture ponds with impacted by fish farming to adjacent freshwater stream. The results showed that the microbial communities on the carriers were shaped not only by environmental conditions, which were primary determinants but also by carrier types. All the tested plastics did not carry more microbes than the natural carriers during the journey. The biofilm community composition on PVC is distinct from that on PE and PP MPs and natural carriers. The plastisphere of PE and PP kept microbial proportions as natural materials did but PVC retained less than nature materials. Bamboo carried more potential pathogens than plastic polymers and quartz. The results indicated that the communities of plastisphere is polymer-type dependent, and, compared with the natural materials, MPs did not show enhanced propagation of microbes, including pathogens, cross distinct environments.

Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics

Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm², would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.

Low concentrations of tetrabromobisphenol A promote the biofilm formation of methicillin-resistant Staphylococcus aureus

The effect and underlying mechanism of tetrabromobisphenol A (TBBPA), a plastic additive, on biofilm formation of methicillin-resistant Staphylococcus aureus (MRSA USA300) remain unknown. This study first investigated the impact of different concentrations of TBBPA on the growth and biofilm formation of USA300. The results indicated that a low concentration (0.5 mg/L) of TBBPA promoted the growth and biofilm formation of USA300, whereas high concentrations (5 mg/L and 10 mg/L) of TBBPA had inhibitory effects. Further exploration revealed that the low concentration of TBBPA enhance biofilm formation by promoting the synthesis of extracellular proteins, release of extracellular DNA (eDNA), and production of staphyloxanthin. RTqPCR analysis demonstrated that the low concentration of TBBPA upregulated genes associated with extracellular protein synthesis (sarA, fnbA, fnbB, aur) and eDNA formation (atlA) and increased the expression of genes involved in staphyloxanthin biosynthesis (crtM), suggesting a potential mechanism for enhanced resistance of USA300 to adverse conditions. These findings shed light on how low concentrations of TBBPA facilitate biofilm formation in USA300 and highlight the indirect impact of plastic additives on pathogenic bacteria in terms of human health. In the future, in-depth studies about effects of plastic additives on pathogenicity of pathogenic bacteria should be conducted. CAPSULE: The protein and eDNA contents in biofilms of methicillin-resistant Staphylococcus aureus are increased by low concentrations of TBBPA.

Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

Enzyme-responsive nanoparticles: enhancing the ability of endolysins to eradicate Staphylococcus aureus biofilm

Stimuli-responsive nanomaterials show promise in eradicating Staphylococcus aureus biofilm from implants. Peptidoglycan hydrolases (PGHs) are cationic antimicrobials that can be bioengineered to improve the targeting of persisters and drug-resistant bacteria. However, these molecules can be degraded before reaching the target and/or present limited efficacy against biofilm. Therefore, there is an urgent need to improve their potency. Herein, PGH-polyphosphate nanoparticles (PGH-PP NPs) are formed by ionotropic gelation between cationic PGHs and anionic polyphosphate, with the aim of protecting PHGs and delivering them at the target site triggered by alkaline phosphatase (AP) from S. aureus biofilm. Optimized conditions for obtaining M23-PP NPs and GH15-PP NPs are presented. Size, zeta potential, and transmission electron microscopy imaging confirm the nanoscale size. The system demonstrates outstanding performance, as evidenced by a dramatic reduction in PGHs' minimum inhibitory concentration and minimum bactericidal concentration, together with protection against proteolytic effects, storage stability, and cytotoxicity towards the Caco-2 and HeLa cell lines. Time-kill experiments show the great potential of these negatively charged delivery systems in overcoming the staphylococcal biofilm barrier. Efficacy under conditions inhibiting AP proves the enzyme-triggered delivery of PGHs. The enzyme-responsive PGH-PP NPs significantly enhance the effectiveness of PGHs against bacteria residing in biofilm, offering a promising strategy for eradicating S. aureus biofilm.

Hfq-binding small RNA PqsS regulates Pseudomonas aeruginosa pqs quorum sensing system and virulence

Pseudomonas aeruginosa is a widespread nosocomial pathogen with a significant to cause both severe planktonic acute and biofilm-related chronic infections. Small RNAs (sRNAs) are noncoding regulatory molecules that are stabilized by the RNA chaperone Hfq to trigger various virulence-related signaling pathways. Here, we identified an Hfq-binding sRNA in P. aeruginosa PAO1, PqsS, which promotes bacterial pathogenicity and pseudomonas quinolone signal quorum sensing (pqs QS) system. Specifically, PqsS enhanced acute bacterial infections by inducing host cell death and promoting rhamnolipid-regulated swarming motility. Meanwhile, PqsS reduced chronic infection traits including biofilm formation and antibiotic resistance. Moreover, PqsS repressed pqsL transcript, increasing PQS levels for pqs QS. A PQS-rich environment promoted PqsS expression, thus forming a positive feedback loop. Furthermore, we demonstrated that the PqsS interacts and destabilizes the pqsL mRNA by recruiting RNase E to drive degradation. These findings provide insights for future research on P. aeruginosa pathogenesis and targeted treatment.

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

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

Biofilms as more than the sum of their parts: lessons from developmental biology

Although our understanding of both bacterial cell physiology and the complex behaviors exhibited by bacterial biofilms is expanding rapidly, we cannot yet sum the behaviors of individual cells to understand or predict biofilm behavior. This is both because cell physiology in biofilms is different from planktonic growth and because cell behavior in biofilms is spatiotemporally patterned. We use developmental biology as a guide to examine this phenotypic patterning, discussing candidate cues that may encode spatiotemporal information and possible roles for phenotypic patterning in biofilms. We consider other questions that arise from the comparison between biofilm and eukaryotic development, including what defines normal biofilm development and the nature of biofilm cell types and fates. We conclude by discussing what biofilm development can tell us about developmental processes, emphasizing the additional challenges faced by bacteria in biofilm development compared with their eukaryotic counterparts.

Structure and Dynamics of Water in Polysaccharide (Alginate) Solutions and Gels Explained by the Core-Shell Model

In both biological and engineered systems, polysaccharides offer a means of establishing structural stiffness without altering the availability of water. Notable examples include the extracellular matrix of prokaryotes and eukaryotes, artificial skin grafts, drug delivery materials, and gels for water harvesting. Proper design and modeling of these systems require detailed understanding of the behavior of water confined in pores narrower than about 1 nm. We use molecular dynamics simulations to investigate the properties of water in solutions and gels of the polysaccharide alginate as a function of the water content and polymer cross-linking. We find that a detailed understanding of the nanoscale dynamics of water in alginate solutions and gels requires consideration of the discrete nature of water. However, we also find that the trends in tortuosity, permeability, dielectric constant, and shear viscosity can be adequately represented using the "core-shell" conceptual model that considers the confined fluid as a continuum.

Calcium Peroxide-Based Hydrogels Enable Biphasic Release of Hydrogen Peroxide for Infected Wound Healing

Wound infection is a major factor affecting the speed and quality of wound healing. While hydrogen peroxide (H2O2) is recognized for its antibacterial capacity and facilitation of wound healing, its administration requires careful dosage differentiation. Inappropriately matched dosages can protract the healing of infected wounds. Herein, a calcium peroxide-based hydrogel (CPO-Alg hydrogel) is fabricated to enable a biphasic tapered release of H2O2, ensuring robust initial antimicrobial activity followed by sustained promotion of cellular proliferation of wound healing. The design of the hydrogel allowed for the calcium peroxide nanoparticles (CPO NPs) being in two spatial niches within the gel framework. When applied to infectious wounds, CPO NPs with weak constraints are promptly released out of the gel, penetrating into infected regions to serve as antibacterial agents that eliminate bacteria and biofilms at high concentrations. Conversely, the entrapped CPO NPs structurally integrated into the gel remain confined, thus gradually degrading and allowing a mild release of H2O2 through hydrolysis in a moist environment that contributes to the cell growth in the later stage. The CPO-Alg hydrogel represents an innovative and practical solution for the antimicrobial protection of chronic wounds, offering promising prospects for advancing wound healing.

Influence of carbonyl cyanide m-chlorophenyl hydrazone on biofilm dynamics, protease, and siderophore production by Burkholderia pseudomallei

Efflux pump inhibitors are a potential therapeutic strategy for managing antimicrobial resistance and biofilm formation. This article evaluated the effect of carbonyl cyanide m-chlorophenyl hydrazone (CCCP) on the biofilm growth dynamics and the production of virulence factors by Burkholderia pseudomallei. The effects of CCCP on planktonic, growing, and mature biofilm, interaction with antibacterial drugs, and protease and siderophore production were assessed. CCCP MICs ranged between 128 and 256 µM. The CCCP (128 µM) had a synergic effect with all the antibiotics tested against biofilms. Additionally, CCCP reduced (p < .05) the biomass of biofilm growth and mature biofilms at 128 and 512 µM, respectively. CCCP also decreased (p < .05) protease production by growing (128 µM) and induced (p < .05) siderophore release by planktonic cells (128 µM) growing biofilms (12.8 and 128 µM) and mature biofilms (512 µM). CCCP demonstrates potential as a therapeutic adjuvant for disassembling B. pseudomallei biofilms and enhancing drug penetration.

Mangosteen extracts: Effects on intestinal bacteria, and application to functional fermented milk products

Mangosteen (Garcinia mangostana L.) is a tasty, polyphenol-rich tropical fruit. The edible part is highly appreciated by its aroma, taste and texture. The non-edible part, rich in polyphenols, has been traditionally used in Thai medicine. In this work, flavonoids and phenolic acid/derivatives were identified in mangosteen extracts (ME) from edible and non-edible portions. We first studied the effects of MEs on the growth, metabolism, antioxidant capacity, biofilm formation and antimicrobial capacity of eight bifidobacteria and lactobacilli strains from intestinal origin and two commercial probiotic strains (BB536 and GG). ME concentrations higher than 10-20 % were inhibitory for all strains. However, ME concentrations of 5 % significantly (P < 0.01) increased all strains antioxidant capacity, reduced biofilm-formation, and enhanced inhibition against Gram-positive pathogens. To apply these knowledge, bifunctional fermented milk products were elaborated with 5 % ME and individual strains, which were selected taking into account their growth with ME, and the widest range of values on antioxidant capacity, biofilm formation and antimicrobial activity (bifidobacteria INIA P2 and INIA P467, lactobacilli INIA P459 and INIA P708, and reference strain GG). Most strains survived well manufacture, refrigerated storage and an in vitro simulation of major conditions encountered in the gastrointestinal tract. As expected, products supplemented with ME showed higher polyphenol content and antioxidant capacity levels than control. After sensory evaluation, products containing strains INIA P2, INIA P708 and GG outstood as best.

Fabrication of photo-induced molecular superoxide radical generator for highly efficient therapy against bacterial wound infection

The pressing need for highly efficient antibacterial strategies arises from the prevalence of microbial biofilm infections and the emergence of rapidly evolving antibiotic-resistant strains of pathogenic bacteria. Photodynamic therapy represents a highly efficient and compelling antibacterial approach, offering promising prospects for effective control of the development of bacterial resistance. However, the effectiveness of many photosensitizers is limited due to the reduced generation of reactive oxygen species (ROS) in hypoxic microenvironment, which commonly occur in pathological conditions such as inflammatory and bacteria-infected wounds. Herein, we designed and prepared two phenothiazine-derived photosensitizers (NB-1 and NB-2), which can effectively generate superoxide anion radicals (O2●-) through the type I process. Both photosensitizers demonstrate significant efficacy in vitro for the eradication of broad-spectrum bacteria. Moreover, NB-2 possesses distinct advantages including strong membrane binding and strong generation of O2●-, rendering it an exceptionally efficient antibacterial agent against mature biofilms. In addition, laser activated NB-2 could be applied to treat MRSA-infected wound in vivo, which offers new opportunities for potential practical applications.

Material-based treatment strategies against intraosseous implant biofilm infection

Implant-associated infections present a significant clinical obstacle for orthopedic practitioners, with bacterial biofilm formation serving as a pivotal factor in the initiation, progression, and management of such infections. Conventional approaches have proven inadequate in fully eradicating biofilm-related infections. Consequently, novel material-based therapeutic strategies have been developed, encompassing the utilization of antimicrobial agents, delivery vehicles, and synergistic antibacterial systems. In this review, we provide a succinct overview of recent advancements in anti-biofilm strategies, with the aim of offering insights that may aid in the treatment of intraosseous implant infections.

Mixed-charge hyperbranched polymer nanoparticles with selective antibacterial action for fighting antimicrobial resistance

The escalating menace of antimicrobial resistance (AMR) presents a profound global threat to life and assets. However, the incapacity of metal ions/reactive oxygen species (ROS) or the indiscriminate intrinsic interaction of cationic groups to distinguish between bacteria and mammalian cells undermines the essential selectivity required in these nanomaterials for an ideal antimicrobial agent. Hence, we devised and synthesized a range of biocompatible mixed-charge hyperbranched polymer nanoparticles (MCHPNs) incorporating cationic, anionic, and neutral alkyl groups to effectively combat multidrug-resistant bacteria and mitigate AMR. This outcome stemmed from the structural, antibacterial activity, and biocompatibility analysis of seven MCHPNs, among which MCHPN7, with a ratio of cationic groups, anionic groups, and long alkyl chains at 27:59:14, emerged as the lead candidate. Importantly, owing to inherent differences in membrane potential among diverse species, alongside its nano-size (6 - 15 nm) and high hydrophilicity (Kow = 0.04), MCHPN7 exhibited exceptional selective bactericidal effects over mammalian cells (selectivity index > 564) in vitro and in vivo. By inducing physical membrane disruption, MCHPN7 effectively eradicated antibiotic-resistant bacteria and significantly delayed the emergence of bacterial resistance. Utilized as a coating, MCHPN7 endowed initially inert surfaces with the ability to impede biofilm formation and mitigate infection-related immune responses in mouse models. This research heralds the advent of biocompatible polymer nanoparticles and harbors significant implications in our ongoing combat against AMR. STATEMENT OF SIGNIFICANCE: The escalating prevalence of antimicrobial resistance (AMR) has been acknowledged as one of the most significant threats to global health. Therefore, a series of mixed-charge hyperbranched polymer nanoparticles (MCHPNs) with selective antibacterial action were designed and synthesized. Owing to inherent differences in membrane potential among diverse species and high hydrophilicity (Kow = 0.04), the optimal nanoparticles exhibited exceptional selective bactericidal effects over mammalian cells (selectivity index >564) and significantly delayed the emergence of bacterial resistance. Importantly, they endowed surfaces with the ability to impede biofilm formation and mitigate infection-related immune responses. Furthermore, the above findings focus on addressing the problem of AMR in Post-Pandemic, which will for sure attract attention from both academic and industry research.

Antibiotic-free ocular sterilization while suppressing immune response to protect corneal transparency in infectious keratitis treatment

Clinical guidelines for infectious keratitis treatment require that anti-inflammatory drugs can only be used after infection elimination, which causes irreversible inflammatory damage to the cornea. In this work, photodynamic metal organic frameworks (PCN-224) were used as drug carrier to load Pt NPs with catalase-like activity and anti-inflammatory drug (Dexamethasone, DXMS) for endogenous oxygen generation and reduced corneal damage, respectively. The photodynamic therapy (PDT) effect was greatly enhanced in bacteria elimination and bacterial biofilms removal through catalysis of overexpressed hydrogen peroxide (H2O2, ∼8.0 and 31.0 μM in bacterial solution and biofilms, respectively) into oxygen by Pt NPs. More importantly, the cationic liposome modified PCN-224@Pt@DXMS@Liposomes (PPDL NPs) greatly enhanced the adhesion to negatively charged ocular surface and penetration into corneal barrier and bacterial biofilms. Both in vitro cell viability test and in vivo eye irritation tests proved good biocompatibility of PPDL NPs under 660 nm laser irradiation. Furthermore, PDT of PPDL NPs in rapid bacteria killing was verified through infectious keratitis animal model. The superior bactericidal effect of antibacterial materials could largely replace the bactericidal effect of the immune system. It is worth mentioning that this simultaneous sterilization and anti-inflammation treatment mode is a new exploration against the clinical treatment guidelines.

Cellular uptake of multi-walled carbon nanotubes is associated to genotoxic and teratogenic effects towards the freshwater diatom Nitzschia linearis

The increase in industrial production of multi-walled carbon nanotubes (MWCNTs) raises concerns about their potential adverse effects associated to environmental releases, especially in aquatic environments where they are likely to accumulate. This study focuses on the environmental impact of MWCNTs, specifically on a benthic freshwater diatom (Nitzschia linearis), which plays a major role in the primary production of water bodies. The obtained results indicate that exposure to MWCNTs in the presence of natural organic matter (NOM) inhibits diatom's growth in a dose-dependent manner after 72 h of exposure. Interestingly, the photosystem II quantum yield (PSIIQY) in diatoms remains unaffected even after exposure to MWCNTs at 10 mg/L. After 48 h of exposure, MWCNTs are found to bind preferentially to extracellular polymeric substances (EPS) produced by diatoms, which could decrease their toxicity by limiting their interaction with this organism. However, measurement of genotoxicity and teratogenicity in diatoms exposed to MWCNTs revealed that the exposure to MWCNTs increased the occurrence of cells with micronuclei and abnormal frustules. Microscopy analyses including two-photon excitation microscopy (TPEM) revealed the internalization of MWCNTs. Investigations of the diatom's frustule structure using Scanning electron microscopy (SEM) indicated that the presence of pore structures constitutes a pathway allowing MWCNTs uptake. The presence in the diatom's cytoplasm of MWCNTs might possibly induce disturbances of the cellular components, leading to the observed genotoxic and teratogenic effects. In view of previous studies, this work underscores the need for further studies on the interaction between nanomaterials and different diatom species, given the species-specific nature of the interactions.

Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species

Biofilms are three-dimensional structures containing one or more bacterial species embedded in extracellular polymeric substances. Although most biofilms are stationary, Flavobacterium johnsoniae forms a motile spherical biofilm called a zorb, which is propelled by its base cells and contains a polysaccharide core. Here, we report formation of spatially organized, motile, multispecies biofilms, designated "co-zorbs," that are distinguished by a core-shell structure. F. johnsoniae forms zorbs whose cells collect other bacterial species and transport them to the zorb core, forming a co-zorb. Live imaging revealed that co-zorbs also form in zebrafish, thereby demonstrating a new type of bacterial movement in vivo. This discovery opens new avenues for understanding community behaviors, the role of biofilms in bulk bacterial transport, and collective strategies for microbial success in various environments.

Significance Statement

This paper reports the discovery of co-zorbs, which are spherical aggregates of bacteria that move and transport other bacteria. Zorbs move toward other bacteria and collect them in a manner reminiscent of phagocytes. Once inside the zorb, the new species form a striking, organized core. The discovery of co-zorbs introduces an entirely new type of bacterial movement and transport involving cooperation among bacterial species. Co-zorbs have potential for engineering microbial systems for biotechnology applications and for managing spread of bacterial pathogens in their hosts.

Low-cost and scalable projected light-sheet microscopy for the high-resolution imaging of cleared tissue and living samples

Light-sheet fluorescence microscopy (LSFM) is a widely used technique for imaging cleared tissue and living samples. However, high-performance LSFM systems are typically expensive and not easily scalable. Here we introduce a low-cost, scalable and versatile LSFM framework, which we named 'projected light-sheet microscopy' (pLSM), with high imaging performance and small device and computational footprints. We characterized the capabilities of pLSM, which repurposes readily available consumer-grade components, optimized optics, over-network control architecture and software-driven light-sheet modulation, by performing high-resolution mapping of cleared mouse brains and of post-mortem pathological human brain samples, and via the molecular phenotyping of brain and blood-vessel organoids derived from human induced pluripotent stem cells. We also report a method that leverages pLSM for the live imaging of the dynamics of sparsely labelled multi-layered bacterial pellicle biofilms at an air-liquid interface. pLSM can make high-resolution LSFM for biomedical applications more accessible, affordable and scalable.

High-resolution 3D spatial distribution of complex microbial colonies revealed by mass spectrometry imaging

INTRODUCTION

Bacterial living states and the distribution of microbial colony signaling molecules are widely studied using mass spectrometry imaging (MSI). However, current approaches often treat 3D colonies as flat 2D disks, inadvertently omitting valuable details. The challenge of achieving 3D MSI in biofilms persists due to the unique properties of microbial samples.

OBJECTIVES

The study aimed to develop a new biofilm sample preparation method that can realize high-resolution 3D MSI of bacterial colonies to reveal the spatial organization of bacterial colonies.

METHODS

This article introduces the moisture-assisted cryo-section (MACS) method, enabling embedding-free sectioning parallel to the growth plane. The MACS method secures intact sections by controlling ambient humidity and slice thickness, preventing molecular delocalization.

RESULTS

Combined with matrix-assisted laser desorption ionization mass spectrometry (MALDI)-MSI, the MACS method provides high-resolution insights into endogenic and exogenous molecule distributions in Pseudomonas aeruginosa (P. aeruginosa) biofilms, including isomeric pairs. Moreover, analyzed colonies are revived into 3D models, vividly depicting molecular distribution from inner to outer layers. Additionally, we investigated metabolite spatiotemporal dynamics in multiple colonies, observing changes over time and distinct patterns in single versus merged colonies. These findings shed light on the repel-merge process for multi-colony formation. Furthermore, our study monitored chemical responses inside biofilms after antibiotic treatment, showing increased antibiotic levels in the outer biofilm layer over time while maintaining low levels in the inner region. Moreover, the MACS method demonstrated its universality and applicability to other bacterial strains.

CONCLUSION

These results unveil complex cell activities within biofilm colonies, offering insights into microbe communities. The MACS method is universally applicable to loosely packed microorganism colonies, overcoming the limitations of previously reported MSI methods. It has great potential for studying bacterial-infected cancer tissues and artificial organs, making it a valuable tool in microbiological research.

Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth

Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.

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

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

Interspecies synergistic interactions mediated by cofactor exchange enhance stress tolerance by inducing biofilm formation

Metabolic exchange plays a crucial role in shaping microbial community interactions and functions, including the exchange of small molecules such as cofactors. Cofactors are fundamental to enzyme catalytic activities; however, the role of cofactors in microbial stress tolerance is unclear. Here, we constructed a synergistic consortium containing two strains that could efficiently mineralize di-(2-ethylhexyl) phthalate under hyperosmotic stress. Integration of transcriptomic analysis, metabolic profiling, and a genome-scale metabolic model (GEM) facilitated the discovery of the potential mechanism of microbial interactions. Multi-omics analysis revealed that the vitamin B12-dependent methionine-folate cycle could be a key pathway for enhancing the hyperosmotic stress tolerance of synergistic consortium. Further GEM simulations revealed interspecies exchange of S-adenosyl-L-methionine and riboflavin, cofactors needed for vitamin B12 biosynthesis, which was confirmed by in vitro experiments. Overall, we proposed a new mechanism of bacterial hyperosmotic stress tolerance: bacteria might promote the production of vitamin B12 to enhance biofilm formation, and the species collaborate with each other by exchanging cofactors to improve consortium hyperosmotic stress tolerance. These findings offer new insights into the role of cofactors in microbial interactions and stress tolerance and are potentially exploitable for environmental remediation.

IMPORTANCE

Metabolic interactions (also known as cross-feeding) are thought to be ubiquitous in microbial communities. Cross-feeding is the basis for many positive interactions (e.g., mutualism) and is a primary driver of microbial community assembly. In this study, a combination of multi-omics analysis and metabolic modeling simulation was used to reveal the metabolic interactions of a synthetic consortium under hyperosmotic stress. Interspecies cofactor exchange was found to promote biofilm formation under hyperosmotic stress. This provides a new perspective for understanding the role of metabolic interactions in microbial communities to enhance environmental adaptation, which is significant for improving the efficiency of production activities and environmental bioremediation.

A self-supplied hydrogen peroxide and nitric oxide-generating nanoplatform enhances the efficacy of chemodynamic therapy for biofilm eradication

Bacterial biofilms present a profound challenge to global public health, often resulting in persistent and recurrent infections that resist treatment. Chemodynamic therapy (CDT), leveraging the conversion of hydrogen peroxide (H2O2) to highly reactive hydroxyl radicals (•OH), has shown potential as an antibacterial approach. Nonetheless, CDT struggles to eliminate biofilms due to limited endogenous H2O2 and the protective extracellular polymeric substances (EPS) within biofilms. This study introduces a multifunctional nanoplatform designed to self-supply H2O2 and generate nitric oxide (NO) to overcome these hurdles. The nanoplatform comprises calcium peroxide (CaO2) for sustained H2O2 production, a copper-based metal-organic framework (HKUST-1) encapsulating CaO2, and l-arginine (l-Arg) as a natural NO donor. When exposed to the acidic microenvironment within biofilms, the HKUST-1 layer decomposes, releasing Cu2+ ions and l-Arg, and exposing the CaO2 core to initiate a cascade of reactions producing reactive species such as H2O2, •OH, and superoxide anions (•O2-). Subsequently, H2O2 catalyzes l-Arg to produce NO, which disperses the biofilm and reacts with •O2- to form peroxynitrite, synergistically eradicating bacteria with •OH. In vitro assays demonstrated the nanoplatform's remarkable antibiofilm efficacy against both Gram-positive Methicillin-resistant Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa, significantly reducing bacterial viability and EPS content. In vivo mouse model experiments validated the nanoplatform's effectiveness in eliminating biofilms and promoting infected wound healing without adverse effects. This study represents a breakthrough in overcoming traditional CDT limitations by integrating self-supplied H2O2 with NO's biofilm-disrupting capabilities, offering a promising therapeutic strategy for biofilm-associated infection.

Enhancing Root Canal Therapy with NIR-II Semiconducting Polymer AIEgen and Low-Concentration Sodium Hypochlorite Synergy

Despite significant efforts to eliminate bacterial biofilm within root canals, achieving effective disinfection remains challenging due to the complex anatomy and limitations of disinfectants. In this study, a second near-infrared (NIR-II) semiconducting polymer with aggregation-induced emission (AIE) properties, named PIDT-TBT, is deliberately designed and synthesized. This proposes an AIE luminogen-based sterilization strategy in synergy with a low concentration of sodium hypochlorite (NaClO). Water-dispersible PIDT-TBT nanoparticles (NPs) are prepared, demonstrating good biocompatibility, as well as photothermal and photodynamic properties. Subsequent antibacterial tests show that PIDT-TBT NPs exhibit excellent bactericidal effects against three bacterial strains: Staphylococcus aureus, Streptococcus mutans, and Enterococcus faecalis, upon 808 nm laser irradiation. In synergy with a low concentration of NaClO (0.5%) solution, PIDT-TBT NPs significantly improves the outcome of root canal treatment under 808 nm laser irradiation in a human extracted tooth root canal infection model. Additionally, it is found that PIDT-TBT NPs combine with a low concentration of NaClO solution could safely dissolve dentin debris and further increase the efficiency of root canal preparation by altering the elemental composition of the inner root canal wall.

An integrated preventive and therapeutic magnetic nanoparticle loaded with rhamnolipid and vancomycin for combating subgingival biofilms

OBJECTIVES

Mechanical debridement supplemented with antibacterial agents effectively eradicates subgingival biofilms formed in the periodontal pockets of severe periodontitis patients. However, the available antimicrobial agents have limited penetrating ability to kill the bacteria encased in the deep layers of biofilms. This study aimed to fabricate a novel magnetic nanoparticle (MNP) loaded with rhamnolipid (RL) and vancomycin (Vanc, Vanc/RL-Ag@Fe3O4) to combat subgingival biofilms.

METHODS

The multispecies subgingival biofilm was formed by periodontal pathogens, including Streptococcus oralis (S. oralis), Streptococcus sanguinis (S. sanguinis), Actinomyces naeslundii (A. naeslundii), Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum). Scanning electron microscope (SEM), confocal laser scanning microscopy (CLSM), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to determine the anti-biofilm efficacy of Vanc/RL-Ag@Fe3O4 with or without a magnetic field on multispecies subgingival biofilms.

RESULTS

The minimal inhibitory concentration (MIC) values of Vanc/RL-Ag@Fe3O4 on S. oralis, S. sanguinis, A. naeslundii, P. gingivalis, and F. nucleatum were 25, 50, 100, 50, and 25 μg/mL, respectively. Vanc/RL-Ag@Fe3O4 (200 μg/mL) reduced the 7-d biofilm thickness from 22 to 13 µm by degrading extracellular polymeric substance (EPS) and killing most bacteria except for tolerant F. nucleatum. A magnetic field enhanced the anti-biofilm effect of Vanc/RL-Ag@Fe3O4 by facilitating its penetration into the bottom layers of biofilms and killing tolerant F. nucleatum.

SIGNIFICANCE

Vanc/RL-Ag@Fe3O4 MNPs can release RL, Vanc, and Ag and eradicate subgingival biofilms by disrupting EPS and killing bacteria. Vanc/RL-Ag@Fe3O4 combined with a magnetic force is a promising approach for combating periodontal infection.

Sludge-derived alginate-like extracellular polymers (ALE) for preparation of Fe-ALE and FeCaMg-ALE: Application to the adsorption of phosphate

Excess phosphorus (P) in wastewater has potential risk of causing harmful algal bloom and eutrophication in receiving wastewater. In this study, alginate-like extracellular polymers (ALE) derived from conventional activated sludge were modified with ionic cross-linking agents (Fe3+, Ca2+, and Mg2+) to develop Fe-ALE and FeCaMg-ALE for the adsorption of phosphate from wastewater. The adsorption process of phosphate by Fe-ALE and FeCaMg-ALE can be well described by pseudo-second-order kinetics and Freundlich isotherm model with a high level of accuracy, indicating that the adsorption processes were chemical, multi-layer adsorption process. The maximum adsorption capacity of dry Fe-ALE and FeCaMg-ALE concerning phosphate were 15.06 and 20.10 mg/g, respectively at 298 K. The adsorption capacity remained relatively consistent across a pH range of 2.0-11.0. FT-IR, XRD, SEM coupled with XPS analysis demonstrated the ALE had been successfully compounded with Fe3+ or Fe3+/Ca2+/Mg2+. Based on the experimental results and characteristic analysis, the main mechanism of phosphate by Fe-ALE and FeCaMg-ALE are physical filling, electrostatic attraction, ligand exchange and precipitation reaction. This work provides a new perspective for preparing ALE-based adsorbent using conventional activated sludge as raw material, realizing the treatment of waste with waste and effectively recovering phosphate from wastewater.

Anti-biofilm mechanisms of action of essential oils by targeting genes involved in quorum sensing, motility, adhesion, and virulence: A review

Biofilms are a critical factor for food safety, causing important economic losses. Among the novel strategies for controlling biofilms, essential oils (EOs) can represent an environmentally friendly approach, able to act both on early and mature stages of biofilm formation. This review reports the anti-biofilm mechanisms of action of EOs against five pathogenic bacterial species known for their biofilm-forming ability. These mechanisms include disturbing the expression of genes related to quorum sensing (QS), motility, adhesion, and virulence. Biofilms and QS are interconnected processes, and EOs interfere with the communication system (e.g. regulating the expression of agrBDCA, luxR, luxS, and pqsA genes), thus influencing biofilm formation. In addition, QS is an important mechanism that regulates gene expression related to bacterial survival, virulence, and pathogenicity. Similarly, EOs also influence the expression of many virulence genes. Moreover, EOs exert their effects modulating the genes associated with bacterial adhesion and motility, for example those involved in curli (csg), fimbriae (fim, lpf), and flagella (fla, fli, flh, and mot) production, as well as the ica genes responsible for synthetizing polysaccharide intercellular adhesin. This review provides a comprehensive framework on the topic for a better understanding of EOs biofilm mechanisms of action.

Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore in vivo colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.

IMPORTANCE

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

Interfacial Stresses within Droplets and Channels Influence Bacterial Physiology: A Perspective

Bacterial cells frequently experience fluid motion in their natural environments, like water bodies, aerosols, fomites, human capillaries, etc., a phenomenon that researchers have largely overlooked. Nevertheless, some reports have suggested that the interfacial stresses caused by fluid motion inside evaporating droplets or shear flows within capillaries may trigger physiological and morphological changes in the bacterial cells. Remarkably, the virulence of bacterial cells exhibits significant alterations in response to fluctuations in stress levels and external environmental factors. The dynamics of bacterial systems are analogous to colloidal systems but with the distinction that bacterial systems exhibit responsiveness, necessitating thorough exploration in dynamic environments. In this perspective, we discuss the important issue pertaining to bacterial survival, virulence, and disease transmission. Furthermore, we delineate a pathway and underscore emerging opportunities that demand exploration to unveil new avenues in the domains of bacterial pathogenicity, drug development, and strategies for disease mitigation.

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.

Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms

The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.

Multiple biological characteristics and functions of intestinal biofilm extracellular polymers: friend or foe?

The gut microbiota is vital to human health, and their biofilms significantly impact intestinal immunity and the maintenance of microbial balance. Certain pathogens, however, can employ biofilms to elude identification by the immune system and medical therapy, resulting in intestinal diseases. The biofilm is formed by extracellular polymorphic substances (EPS), which shield microbial pathogens from the host immune system and enhance its antimicrobial resistance. Therefore, investigating the impact of extracellular polysaccharides released by pathogens that form biofilms on virulence and defence mechanisms is crucial. In this review, we provide a comprehensive overview of current pathogenic biofilm research, deal with the role of extracellular polymers in the formation and maintenance of pathogenic biofilm, and elaborate different prevention and treatment strategies to provide an innovative approach to the treatment of intestinal pathogen-based diseases.

Mixed species biofilm: Structure, challenge and its intricate involvement in hospital associated infections

Hospital associated infections or healthcare associated infections (HAIs) are a major threat to healthcare and medical management, mostly because of their recalcitrant nature. The primary cause of these HAIs is bacterial associations, especially the interspecies interactions. In interspecies interactions, more than one species co-exists in a common platform of extracellular polymeric substances (EPS), establishing a strong interspecies crosstalk and thereby lead to the formation of mixed species biofilms. In this process, the internal microenvironment and the surrounding EPS matrix of the biofilms ensure the protection of the microorganisms and allow them to survive under antagonistic conditions. The communications between the biofilm members as well as the interactions between the bacterial cells and the matrix polymers, also aid in the rigidity of the biofilm structure and allow the microorganisms to evade both the host immune response and a wide range of anti-microbials. Therefore, to design a treatment protocol for HAIs is difficult and it has become a growing point of concern. This review therefore first aims to discuss the role of microenvironment, molecular structure, cell-cell communication, and metabolism of mixed species biofilms in manifestation of HAIs. In addition, we discuss the electrochemical properties of mixed-species biofilms and their mechanism in developing drug resistance. Then we focus on the most dreaded bacterial HAI including oral and gut multi-species infections, catheter-associated urinary tract infections, surgical site infections, and ventilator-associated pneumonia. Further, we highlight the challenges to eradication of the mixed species biofilms and the current and prospective future strategies for the treatment of mixed species-associated HAI. Together, the review presents a comprehensive understanding of mixed species biofilm-mediated infections in clinical scenario, and summarizes the current challenge and prospect of therapeutic strategies against HAI.