Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms

Stresses in the food chain and their impact on antibiotic resistance of foodborne pathogens: A review

Antibiotic resistance in foodborne pathogens represents a major public health concern. The farm-to-fork continuum is recognized as a critical pathway for the development and spread of this resistance. Throughout the food chain, foodborne pathogens are exposed to diverse environmental stresses, including temperature extremes, osmotic pressure, food additives, and disinfectants, and others. These stress factors can influence antibiotic resistance, with effects varying based on the type and intensity of stress, the pathogen species and strain, and the specific antibiotic involved. Stress conditions can trigger bacterial adaptive responses, such as general stress response systems, the SOS response, and genetic mutations, which can confer cross-protection and enhance antibiotic resistance. Conversely, stress-induced injury or metabolic suppression may increase bacterial susceptibility to certain antibiotics. Understanding these complex interactions is crucial, as suboptimal food processing can inadvertently select for resistant strains. Investigating the molecular mechanisms underlying stress adaptation is essential for developing effective strategies to mitigate antibiotic resistance. Optimizing food processing protocols and implementing robust monitoring systems throughout the food chain are essential steps to reduce these risks. A comprehensive understanding of stress-induced antibiotic resistance will provide a scientific basis for improving food safety and safeguarding global public health.

Metagenomic deciphers the mobility and bacterial hosts of antibiotic resistance genes under antibiotics and heavy metals co-selection pressures in constructed wetlands

Both antibiotics and heavy metals exert significant selection pressures on antibiotic-resistance genes (ARGs). This study aimed to investigate the co-selection effects of doxycycline (DC) and cadmium (Cd) on ARGs in constructed wetlands (CWs). The results demonstrated that under antibiotic and heavy metal co-selection pressures, single high concentration DC/Cd or double high, relative abundances of metagenomics assembled genomes all reached 55.1%; meanwhile, the average ratio of ARG-containing contigs located on chromosomes was 61.8% (ranging from 50.4% to 70.6%) suggesting a more stable inheritance of ARGs. Antibiotic and heavy metal co-selection in single high concentration DC/Cd or double high groups stimulate the enrichment of ARG host bacteria, which exhibited complex multiple-resistant patterns accompanied by a host-specific pattern. Additionally, the potential transfer abilities of ARGs mediated by plasmids and integrative and conjugative elements (ICEs) were enhanced under single high-concentration DC/Cd or double high stresses. Together, antibiotic and heavy metal co-selection pressures increased occurrence frequencies of ARGs, MGEs, and their combinations and altered structural communities of ARG host bacteria, increasing the risk of the spread of ARGs. This study was helpful in understanding the dissemination of ARGs and simultaneously preventing the spread of heavy metal-resistant bacteria and ARGs under antibiotic and heavy metal co-selection in small- and micro-wetlands.

Ion-conducting polymer thin films via chemical vapor deposition polymerization

Ion-conducting polymers (ICPs), benefiting from the movement of ions instead of electrons, have attracted significant interest in various scientific and technological fields, including drug delivery, water purification, and electrochemical devices. This review aims to highlight recent advances in the synthesis of ICP thin films, with a particular focus on chemical vapor deposition (CVD) technologies. Traditional solution-based methods for ICP thin film deposition face challenges, including non-uniformity, low-throughput manufacturing, and the generation of hazardous wastes. In comparison, CVD eliminates the drawbacks associated with solution-based processes. They offer precise control film properties, including high purity, conformal coating, delicate control over thickness, etc. This review organizes the latest developments in CVD-based ICP synthesis, based on material properties and the synthesis strategy, into direct deposition and post-polymerization modification, ionogels, hydrogels, and ultrathin siloxane or silazane-based polymer films. By providing an up-to-date review of the materials and synthesis, we aim to position CVD polymerization as an effective strategy for future materials development/production and device fabrication in energy, sustainability, and healthcare where ion conductivity is desired.

A STRUCTURAL EQUATION MODEL PREDICTS CHRONIC WOUND HEALING TIME USING PATIENT CHARACTERISTICS AND WOUND MICROBIOME COMPOSITION

Wound etiology, host characteristics, and the wound microbiome contribute to chronic wound development. Yet, there is little accounting for the relative importance of these factors to predict wound healing. Here, a structural equation model was developed to provide such an explanatory and predictive framework. Chronic wounds from 565 patients treated at a clinic practicing biofilm-based wound care were included. Patient information included DNA sequencing-based wound microbiome clinical reports corresponding to initial clinical visit. Wound microbiome data was integrated into the SEM as a latent variable using a pre-modeling parcel optimization routine presented herein for the first time (available as R library parcelR). A microbiome latent construct associated with improved healing was validated, and the final SEM included this latent construct plus three species associated with diminished healing (Anaerococcus vaginalis, Finegoldia magna, Pseudomonas aeruginosa), as well as smoking, wound volume, slough, exudate, edema, percent granulation, and wound etiology This model explained 46% of variation in healing time with the microbiome contributing the largest proportion of variance explained. Model validity was confirmed with an independent cohort (n = 79) through which ~60% of variation in healing time was predicted. This model can serve as foundation for development of a predictive tool that may have clinical utility.

Evaluation of the Synergistic Antimicrobial Activity of Essential Oils and Cecropin A Natural Peptide on Gram-Negative Bacteria

In an era dominated by the phenomenon of antibiotic resistance, it is increasingly important to look for alternatives to synthetic antibiotics. In light of these considerations, the synergistic use of essential oils and Antimicrobial Peptides (AMPs) seems a viable strategy. In this study, we assessed the Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC) and Fractional Inhibitory Concentration (FIC) of three Essential Oils (EOs): winter savory (Satureja montana), bergamot (Citrus bergamia) and cinnamon (Cinnamomum zeylanicum) and of the insect antimicrobial peptide Cecropin A (CecA), alone and in combination with EOs, against two Gram-negative ATCC bacterial strains: Escherichia coli and Salmonella enterica serovar Typhimurium. The MIC results showed that winter savory EO (SmEO) and cinnamon EO (CzEO) exhibited the strongest antibacterial activity against both bacterial strains, whereas bergamot EO (CbEO) and CecA demonstrated comparatively lower antibacterial efficacy. These results were also confirmed by the MBC values. The FIC Indices (FICI) revealed that the most effective synergies were observed with the combinations SmEO/CzEO and SmEO/CbEO against E. coli, while against S. enterica Typhimurium the best combinations were CbEO/CzEO and SmEO/CzEO. Regarding CecA, although it was not the most efficient agent either individually or in combination, it is noteworthy that, when combined, it exhibited antibacterial activity even at a 1:64 dilution.

Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome

Plant-beneficial Pseudomonas and Bacillus have been extensively studied and applied in biocontrol of plant diseases. However, there is less known about their interaction within two-strain synthetic communities (SynCom). Our study revealed that Pseudomonas protegens Pf-5 inhibits the growth of several Bacillus species, including Bacillus velezensis. We established a two-strain combination of Pf-5 and DMW1 to elucidate the interaction. In this combination, pyoluteorin conferred the competitive advantage of Pf-5. Noteworthy, pyoluteorin-deficient Pf-5 cooperated with DMW1 in biofilm formation, production of metabolites, root colonization, tomato bacterial wilt disease control, as well as in cooperation with beneficial bacteria in tomato rhizosphere, such as Bacillus spp. RNA-seq analysis and RT-qPCR also proved the pyoluteorin-deficient Pf-5 mutant improved cell motility and metabolite production. This study suggests that the cooperative effect of Bacillus-Pseudomonas consortia depends on the balance of pyoluteorin. Our finding needs to be considered in developing efficient SynCom in sustainable agriculture.

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.

Biosensing of Bacterial Secretions via Topological Defects at Smectic Interfaces

Characterizing the anchoring properties of smectic liquid crystals (LCs) in contact with bacterial solutions is crucial for developing biosensing platforms. In this study, we investigate the anchoring properties of a smectic LC when exposed to Bacillus subtilis and Escherichia coli bacterial suspensions using interfaces with known anchoring properties. By monitoring the optical response of the smectic film, we successfully distinguish different types of bacteria, leveraging the distinct changes in the LC's response. Through a comprehensive analysis of the interactions between bacterial proteins and the smectic interface, we elucidate the potential underlying mechanisms responsible for these optical changes. Additionally, we introduce the utilization of topological defects, the focal conic domains (FCDs), at the smectic interface as an indicative measure of the bacterial concentration. Our findings contribute to the understanding of bacteria-LC interactions and demonstrate the significant potential of smectic LCs and their defects for biosensing applications, paving the way for advancements in pathogen detection and protein-based sensing.

Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

IMPORTANCE

There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.

In-depth characterization of food and environmental microbiomes across different meat processing plants

BACKGROUND

Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS

The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS

Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.

Phenotypic characterization for bioremediation suitability of isolates from Southern Tunisian tannery effluent

Effluents from the leather tanning industry contain diverse pollutants, including hazardous heavy metals, posing threats to public health and the surrounding environment. Indigenous bacterial isolates can represent an eco-friendly approach for tannery wastewater treatment; however, phenotypic characterization is necessary to determine whether these strains are suitable for bioremediation. In the present study, we analyzed seven new Enterococcus faecium strains and two new Bacillus subtillis strains isolated from effluents from the Southern Tunisian Tannery (ESTT). We evaluated phenotypic features beneficial for bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities. Additionally, we examined characteristics naturally occurring in environmental bacteria but less desirable in strains selected for bioremediation, such as antibiotic resistances and pathogenicity indicators. The observed phenotypes were then compared with whole-genome analysis. We observed biofilm production in two slime-producing bacteria, B. licheniformis RLT6, and E. faecium RLT8. Hydrophobicity of E. faecium strains RLT1, RLT5, RLT8, and RLT9, as well as B. licheniformis RLT6 correlated positively with increasing ESTT concentration. Exoenzyme activities were detected in E. faecium strains RLT2, RLT4, and RLT7, as well as B. licheniformis RLT6. As anticipated, all strains exhibited common resistances to antibiotics and hemolysis, which are widespread in nature and do not hinder their application for bioremediation. Importantly, none of the strains exhibited the pathogenic hypermucoviscosity phenotype. To the best of our knowledge, this is the first report consolidating all these phenotypic characteristics concurrently, providing a complete overview of strains suitability for bioremediation. IMPORTANCE: The study evaluates the bioremediation potential of seven Enterococcus faecium strains and two Bacillus subtillis strains isolated from the effluents from the Southern Tunisian tannery (ESTT), which pose threats to public health and environmental integrity. The analysis primarily examines the phenotypic traits crucial to bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities, as well as characteristics naturally occurring in environmental bacteria related to heavy metal resistance, such as antibiotic resistances. Several strains were found to have high bioremediation potential and exhibit only antibiotic resistances commonly found in nature, ensuring their application for bioremediation remains uncompromised. The results of the exhaustive phenotypic analysis are contrasted with the whole genome sequences of the nine strains, underscoring the appropriateness of these bacterial strains for eco-friendly interventions in tannery wastewater treatment.

Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities

Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified two strains that demonstrated a synergistic relationship with S. boulardii in pairwise co-cultivation. Furthermore, we computationally predicted cooperative communities with symbiotic relationships between S. boulardii and these bacteria. Experimental validation of 28 communities highlighted the role of S. boulardii as a key player in microbial communities, significantly boosting the community's cell number and production of anti-inflammatory effectors, thereby affirming its essential role in improving symbiotic dynamics. Based on our observation, one defined community significantly activated the aryl hydrocarbon receptor-a key regulator of immune response-280-fold more effectively than the community without S. boulardii. This study underscores the potential of microbial communities for the design of more effective probiotic formulations.

Potential targets of phytochemical immunomodulatory therapy in periodontitis immunopathogenesis: A narrative review

Introduction

Periodontitis is one of the most prevalent diseases occurring worldwide, and is caused by an imbalance of host immunological defenses and microbiome profile which occurs in the oral cavity. This imbalance leads to irregularity and uncontrolled activities of immune cells, resulting in over-reactivity of periodontopathogens and tissue destruction. To alleviate periodontitis, exact targeting of specific events involving particular cells could be a potential application of immunomodulatory agents. Phytochemical drug development targeting specific immunopathogenesis events could be a promising complementary, alternative approach to periodontal therapy.

Objectives

This review aimed to explore various events involving a variety of cells in the immunopathogenesis of periodontitis in order to determine potential specific immunomodulation targets for future development of effective phytochemical drugs.

Results

Immunopathogenesis of periodontitis contributes significantly to the disease onset and resolution. Various events occur during the disease development, which involve a variety of immune cells and mediators. Among these, neutrophils, cytokines and lymphocytes, especially Th17 cells, were reported to be the most relevant components in the disease pathogenesis. These components affect the initial responses to periodontopathogens, inhibit oxidative stress formation, control intercellular communication to enhance inflammation, and promote effector cells' migration to induce alveolar bone resorption. Several phytochemical drugs were developed to cure periodontitis, however, the development of phytochemical immunomodulatory drugs to target specific events has not been realized.

Conclusion

This review concluded that development of phytochemical immunomodulatory drugs to target particular events generated by neutrophils, pro-inflammatory cytokines and lymphocytes has tremendous potential to regulate and modulate the immunopathogenesis of periodontitis.

The best practice for microbiome analysis using R

With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity

The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.

Biofilm-Mediated Heavy Metal Removal from Aqueous System by Multi-Metal-Resistant Bacterial Strain Bacillus sp. GH-s29

Worldwide ever-augmenting urbanization, modernization, and industrialization have contributed to the release of pernicious compounds and a variety of pollutants into the environment. The pollutants discharged due to industrialization are of global concern. Industrial waste and effluent are comprised of hazardous organic and inorganic chemicals including heavy metals which pose a significant threat to the environment and may bring about numerous diseases or abnormalities in human beings. This brings on greater urgency for remediation of these polluted soil and water using sustainable approaches and mechanisms. In the present research, a multi-metal-resistant, gram-positive, non-virulent bacterial strain Bacillus sp. GH-s29 was isolated from contaminated groundwater of Bhojpur district, Bihar, India. The strain had the potential to develop a biofilm that was able to remediate different heavy metals [arsenic, cadmium, and chromium] from individual and multi-heavy metal solutions. Maximum removal for As (V), Cd (II), and Cr (VI) from individual-metal and the multi-metal solution was observed to be 73.65%, 57.37%, 61.62%, and 48.92%, 28.7%, and 35.46%, respectively. SEM-EDX analysis revealed the sequestration of multi-heavy metals by bacterial biofilm. Further characterization by FTIR analysis ensured that the presence of negatively charged functional groups on the biofilm-EPS such as hydroxyl, phosphate, sulfate, and carboxyl helps in binding to the positively charged metal ions. Thus, Bacillus sp. GH-s29 proved to be an effective and economical alternative for different heavy metal remediation from contaminated sites.

Effect of natural antibacterial clays against single biofilm formation by Staphylococcus aureus and Salmonella Typhimurium bacteria on a stainless-steel surface

Staphylococcus aureus and Salmonella Typhimurium have a propensity to develop biofilms on food contact surfaces, such as stainless-steel, that persist despite rigorous cleaning and sanitizing procedures. Since both bacterial species pose a significant public health risk within the food chain, improved anti-biofilm measures are needed. This study examined the potential of clays as antibacterial and anti-biofilm agents against these two pathogens on appropriate contact surfaces. Natural soil was processed to yield leachates and suspensions of both untreated and treated clays. Soil particle size, pH, cation-exchange capacity, and metal ions were characterized to assess their importance in bacterial killing. Initial antibacterial screening was performed on nine distinct types of natural Malaysian soil using a disk diffusion assay. Untreated leachate from Kuala Gula and Kuala Kangsar clays were found to inhibit S. aureus (7.75 ± 0.25 mm) and Salmonella Typhimurium (11.85 ± 1.63 mm), respectively. The treated Kuala Gula suspension (50.0 and 25.0 %) reduced S. aureus biofilms by 4.4 and 4.2 log at 24 and 6 h, respectively, while treated Kuala Kangsar suspension (12.5 %) by a 4.16 log reduction at 6 h. Although less effective, the treated Kuala Gula leachate (50.0 %) was effective in removing Salmonella Typhimurium biofilm with a decrease of >3 log in 24 h. In contrast to Kuala Kangsar clays, the treated Kuala Gula clays contained a much higher soluble metal content, especially Al (301.05 ± 0.45 ppm), Fe (691.83 ± 4.80 ppm) and Mg (88.44 ± 0.47 ppm). Elimination of S. aureus biofilms correlated with the presence of Fe, Cu, Pb, Ni, Mn and Zn irrespective of the pH of the leachate. Our findings demonstrate that a treated suspension is the most effective for eradication of S. aureus biofilms with a potential as a sanitizer-tolerant, natural antibacterial against biofilms for applications in the food industry.

Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity

While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are coordinated naturally.

Hidden agenda of Enterococcus faecalis lifestyle transition: planktonic to sessile state

Enterococcus faecalis, a human gastrointestinal tract commensal, is known to cause nosocomial infections. Interestingly, the pathogen's host colonization and persistent infections are possibly linked to its lifestyle changes from planktonic to sessile state. Also, the multidrug resistance and survival fitness acquired in the sessile stage of E. faecalis has challenged treatment regimes. This situation exists because of the critical role played by several root genes and their molecular branches, which are part of quorum sensing, aggregation substance, surface adhesions, stress-related response and sex pheromones in the sessile state. It is therefore imperative to decode the hidden agenda of E. faecalis and understand the significant factors influencing biofilm formation. This would, in turn, augment the development of novel strategies to tackle E. faecalis infections.

Electrochemical Control of Biofilm Formation and Approaches to Biofilm Removal

This review deals with microbial adhesion to metal-based surfaces and the subsequent biofilm formation, showing that both processes are a serious problem in the food industry, where pathogenic microorganisms released from the biofilm structure may pollute food and related material during their production. Biofilm exhibits an increased resistance toward sanitizers and disinfectants, which complicates the removal or inactivation of microorganisms in these products. In the existing traditional techniques and modern approaches for clean-in-place, electrochemical biofilm control offers promising technology, where surface properties or the reactions taking place on the surface are controlled to delay or prevent cell attachment or to remove microbial cells from the surface. In this overview, biofilm characterization, the classification of bacteria-forming biofilms, the influence of environmental conditions for bacterial attachment to material surfaces, and the evaluation of the role of biofilm morphology are described in detail. Health aspects, biofilm control methods in the food industry, and conventional approaches to biofilm removal are included as well, in order to consider the possibilities and limitations of various electrochemical approaches to biofilm control with respect to potential applications in the food industry.

A Survey of Statistical Methods for Microbiome Data Analysis

In the last decade, numerous statistical methods have been developed for analyzing microbiome data generated from high-throughput next-generation sequencing technology. Microbiome data are typically characterized by zero inflation, overdispersion, high dimensionality, and sample heterogeneity. Three popular areas of interest in microbiome research requiring statistical methods that can account for the characterizations of microbiome data include detecting differentially abundant taxa across phenotype groups, identifying associations between the microbiome and covariates, and constructing microbiome networks to characterize ecological associations of microbes. These three areas are referred to as differential abundance analysis, integrative analysis, and network analysis, respectively. In this review, we highlight available statistical methods for differential abundance analysis, integrative analysis, and network analysis that have greatly advanced microbiome research. In addition, we discuss each method's motivation, modeling framework, and application.

Poly-Gamma-Glutamic Acid Secretion Protects Bacillus subtilis from Zinc and Copper Intoxication

Zinc and copper are essential micronutrients that serve as a cofactors for numerous enzymes. However, when present at elevated concentrations, zinc and copper are highly toxic to bacteria. To combat the effects of zinc and copper excess, bacteria have evolved a wide array of defense mechanisms. Here, we show that the Gram-positive soil bacterium, Bacillus subtilis, produces the extracellular polymeric substance, poly-gamma-glutamate (γ-PGA) as a protective mechanism in response to zinc and copper excess. Furthermore, we provide evidence that zinc and copper dependent γ-PGA production is independent of the DegS-DegQ two-component regulatory system and likely occurs at a posttranscriptional level through the small protein, PgsE. These data provide new insight into bacterial metal resistance mechanisms and contribute to our understanding of the regulation of bacterial γ-PGA biosynthesis. IMPORTANCE Zinc and copper are potent antimicrobial compounds. As such, bacteria have evolved a diverse range of tools to prevent metal intoxication. Here, we show that the Gram-positive model organism, Bacillus subtilis, produces poly-gamma-glutamic acid (γ-PGA) as a protective mechanism against zinc and copper intoxication and that zinc and copper dependent γ-PGA production occurs by a yet undefined mechanism independent of known γ-PGA regulation pathways.

Microbiota medicine: towards clinical revolution

The human gastrointestinal tract is inhabited by the largest microbial community within the human body consisting of trillions of microbes called gut microbiota. The normal flora is the site of many physiological functions such as enhancing the host immunity, participating in the nutrient absorption and protecting the body against pathogenic microorganisms. Numerous investigations showed a bidirectional interplay between gut microbiota and many organs within the human body such as the intestines, the lungs, the brain, and the skin. Large body of evidence demonstrated, more than a decade ago, that the gut microbial alteration is a key factor in the pathogenesis of many local and systemic disorders. In this regard, a deep understanding of the mechanisms involved in the gut microbial symbiosis/dysbiosis is crucial for the clinical and health field. We review the most recent studies on the involvement of gut microbiota in the pathogenesis of many diseases. We also elaborate the different strategies used to manipulate the gut microbiota in the prevention and treatment of disorders. The future of medicine is strongly related to the quality of our microbiota. Targeting microbiota dysbiosis will be a huge challenge.

Pyrones Identified as LuxR Signal Molecules in Photorhabdus and Their Synthetic Analogues Can Alter Multicellular Phenotypic Behavior of Bacillus atropheaus

Individual bacteria communicate by the release and interpretation of small molecules, a phenomenon known as quorum sensing (QS). We hypothesized that QS compounds extruded by Photorhabdus could be interpreted by Bacillus-a form of interspecies communication. We interrogate the structure-activity relationship within the recently discovered pyrone QS network and reveal the exquisite structural features required for targeted phenotypic behavior. The interruption of QS is an exciting, nonbiocidal approach to tackling infection, and understanding its nuances can only be achieved by studies such as this.

Wetting properties of dehydrated biofilms under different growth conditions

Biofilms are resilient to environmental conditions and often resistant even to strong disinfectants. It is crucial to investigate their interfacial properties, which can be effectively characterized by wetting analysis. Wetting phenomena on biofilm surfaces have been poorly investigated in literature, in particular a systematic study of wetting on real biofilm-coated substrates including the application of external body forces (forced wetting, i.e.: centrifugal and gravitational forces) is missing. The aim of this work is to study the role of nutrient and shear flow conditions on wetting properties of Pseudomonas fluorescens dehydrated biofilms, grown on glass substrates. An innovative device (Kerberos®), capable to study spreading/sliding behavior under the application of external body forces, is used here for a systematic analysis of wetting/de-wetting liquid droplets on horizontal substrates under the action of tangential forces. Results prove that, under different growth conditions, (i.e., nutrients and imposed flow), biofilms exhibit different wetting properties. At lower nutrient/shear flow conditions, biofilms show spreading/sliding behavior close to that of pure glass. At higher nutrient and shear flow conditions, droplets on biofilms show spreading followed by imbibition soon after deposition, which leads to peculiar droplet depinning during the rotation test. Wetting properties are derived as a function of the rotation speed from both top and side views videoframes through a dedicated image analysis technique. A detailed analysis of biofilm formation and morphology/topography is also provided here.

The role of antibiotics and heavy metals on the development, promotion, and dissemination of antimicrobial resistance in drinking water biofilms

Antimicrobial resistance (AMR), as well as the development of biofilms in drinking water distribution systems (DWDSs), have become an increasing concern for public health and management. As bulk water travels from source to tap, it may accumulate contaminants of emerging concern (CECs) such as antibiotics and heavy metals. When these CECs and other selective pressures, such as disinfection, pipe material, temperature, pH, and nutrient availability interact with planktonic cells and, consequently, DWDS biofilms, AMR is promoted. The purpose of this review is to highlight the mechanisms by which AMR develops and is disseminated within DWDS biofilms. First, this review will lay a foundation by describing how DWDS biofilms form, as well as their basic intrinsic and acquired resistance mechanisms. Next, the selective pressures that further induce AMR in DWDS biofilms will be elaborated. Then, the pressures by which antibiotic and heavy metal CECs accumulate in DWDS biofilms, their individual resistance mechanisms, and co-selection are described and discussed. Finally, the known human health risks and current management strategies to mitigate AMR in DWDSs will be presented. Overall, this review provides critical connections between several biotic and abiotic factors that influence and induce AMR in DWDS biofilms. Implications are made regarding the importance of monitoring and managing the development, promotion, and dissemination of AMR in DWDS biofilms.

Identification of cbiO Gene Critical for Biofilm Formation by MRSA CFSa36 Strain Isolated from Pediatric Patient with Cystic Fibrosis

The colonization of Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), has a detrimental effect on the respiratory care of pediatric patients with cystic fibrosis (CF). In addition to being resistant to multiple antibiotics, S. aureus also has the ability to form biofilms, which makes the infection more difficult to treat and eradicate. In this study, we examined the ability of S. aureus strains isolated from pediatric patients with CF to form biofilms. We screened a transposon mutant library of MRSA and identified a putative cobalt transporter ATP binding domain (cbiO) that is required for biofilm formation. We discovered that deleting cbiO creating a cbiO null mutant in CFSa36 (an MRSA strain isolated from a patient with cystic fibrosis) significantly hinders the ability of CFSa36 to form biofilm. The complementation of cbiO restored the ability of the cbiO deletion mutant to generate biofilm. Interestingly, we revealed that incorporating extra copper ions to the chemically defined medium (CDM) complemented the function of cbiO for biofilm formation in a dose-dependent manner, while the addition of extra iron ions in CDM enhanced the effect of cbiO null mutation on biofilm formation. In addition, neither the addition of certain extra amounts of copper ions nor iron ions in CDM had an impact on bacterial growth. Taken together, our findings suggest that cbiO mediates biofilm formation by affecting the transportation of copper ions in the MRSA CFSa36 strain. This study provides new insights into the molecular basis of biofilm formation by S. aureus.

Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere

Bacillus species genomes are rich in plant growth-promoting genetic elements. Bacillus subtilis and Bacillus velezensis are important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using ten Bacillus species. From the analysis, pan-genome of Bacillus subtilis and Bacillus velezensis are still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

Biofilm hydrophobicity in environmental isolates of Bacillus subtilis

Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our novel isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason for the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.

Bacillus subtilis biofilm formation and social interactions

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

Topography and Expansion Patterns at the Biofilm-Agar Interface in Bacillus subtilis Biofilms

Bacterial biofilms are complex microbial communities that are formed on various natural and synthetic surfaces. In contrast to bacteria in their planktonic form, biofilms are characterized by their relatively low susceptibility to anti-microbial treatments, in part due to limited diffusion throughout the biofilm and the complex distribution of bacterial cells within. The virulence of biofilms is therefore a combination of the structural properties and patterns of adhesion that anchor them to their host surface. In this paper, we analyze the topographical properties of Bacillus subtilis' biofilm-agar interface across different growth conditions. B. subtilis colonies were grown to maturity on biofilm-promoting agar-based media (LBGM), under standard and stress-inducing growth conditions. The biofilm-agar interface of the colony-type biofilms was modeled using confocal microscopy and computational analysis. Profilometry data were obtained from the macrocolonies and used for the analysis of the surface topography as it relates to the adhesion modes present at the biofilm-agar interface. Fluorescent microspheres were utilized to monitor the expansion patterns present at the interface between the macrocolonies and the solid growth medium. Contact surface analysis revealed topographical changes that could have a direct effect on the adhesion strength of the biofilm to its host surface, thus affecting its potential susceptibility to anti-microbial agents. The topographical characteristics of the biofilm-agar interface partially define the macrocolony structure and may have significant effects on bacterial survival and virulence.

Re-sensitizing Ampicillin and Kanamycin-Resistant E. coli and S. aureus Using Synergistic Metal Micronutrients-Antibiotic Combinations

Due to the recent emergence of multi-drug resistant strains, the development of novel antimicrobial agents has become a critical issue. The use of micronutrient transition metals is a promising approach to overcome this problem since these compounds exhibit significant toxicity at low concentrations in prokaryotic cells. In this work, we demonstrate that at concentrations lower than their minimal inhibitory concentrations and in combination with different antibiotics, it is possible to mitigate the barriers to employ metallic micronutrients as therapeutic agents. Here, we show that when administered as a combinatorial treatment, Cu²⁺, Zn²⁺, Co²⁺, Cd²⁺, and Ni²⁺ increase susceptibility of Escherichia coli and Staphylococcus aureus to ampicillin and kanamycin. Furthermore, ampicillin-resistant E. coli is re-sensitized to ampicillin when the ampicillin is administered in combination with Cu²⁺, Cd²⁺, or Ni². Similarly, Cu²⁺, Zn²⁺, or Cd²⁺ re-sensitize kanamycin-resistant E. coli and S. aureus to kanamycin when administered in a combinatorial treatment with those transition metals. Here, we demonstrate that for both susceptible and resistant bacteria, transition-metal micronutrients, and antibiotics interact synergistically in combinatorial treatments and exhibit increased effects when compared to the treatment with the antibiotic alone. Moreover, in vitro and in vivo assays, using a murine topical infection model, showed no toxicological effects of either treatment at the administered concentrations. Lastly, we show that combinatorial treatments can clear a murine topical infection caused by an antibiotic-resistant strain. Altogether, these results suggest that antibiotic-metallic micronutrient combinatorial treatments will play an important role in future developments of antimicrobial agents and treatments against infections caused by both susceptible and resistant strains.

Chelate chemistry governs ion-specific stiffening of Bacillus subtilis B-1 and Azotobacter vinelandii biofilms

Unwanted formation of bacterial biofilms can cause problems in both the medical sector and industrial settings. However, removing them from surfaces remains an ongoing challenge since biofilm bacteria efficiently protect themselves from external influences such as mechanical shear forces by embedding themselves into a matrix of extracellular polymeric substances. Here, we discuss microscopic principles, which are responsible for alterations in the viscoelastic properties of biofilms upon contact with metal ions. We suggest that it is a combination of mainly two parameters, that decides if biofilm stiffening occurs or not: the ion size and the detailed configuration of polyanionic macromolecules from the biofilm matrix. Our results provide new insights in the molecular mechanisms that govern the mechanical properties of biofilms. Also, they indicate that hydrogels comprising purified biopolymers can serve as suitable model systems to reproduce certain aspects of biofilm mechanics - provided that the correct biopolymer is chosen.