Biofilms: the matrix revisited

Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein

Cyanobacterial biofilms are ubiquitous and play important roles in diverse environments, yet, understanding of the processes underlying the development of these aggregates is just emerging. Here we report cell specialization in formation of Synechococcus elongatus PCC 7942 biofilms-a hitherto unknown characteristic of cyanobacterial social behavior. We show that only a quarter of the cell population expresses at high levels the four-gene ebfG-operon that is required for biofilm formation. Almost all cells, however, are assembled in the biofilm. Detailed characterization of EbfG4 encoded by this operon revealed cell-surface localization as well as its presence in the biofilm matrix. Moreover, EbfG1-3 were shown to form amyloid structures such as fibrils and are thus likely to contribute to the matrix structure. These data suggest a beneficial 'division of labor' during biofilm formation where only some of the cells allocate resources to produce matrix proteins-'public goods' that support robust biofilm development by the majority of the cells. In addition, previous studies revealed the operation of a self-suppression mechanism that depends on an extracellular inhibitor, which supresses transcription of the ebfG-operon. Here we revealed inhibitor activity at an early growth stage and its gradual accumulation along the exponential growth phase in correlation with cell density. Data, however, do not support a threshold-like phenomenon known for quorum-sensing in heterotrophs. Together, data presented here demonstrate cell specialization and imply density-dependent regulation thereby providing deep insights into cyanobacterial communal behavior.

Profiling the composition and metabolic functions of microbial community in pellicle-forming radish paocai

Pellicle formation is an obvious indicator of spoilage and is followed by a loss of flavor in a variety of fermented vegetables. In this study, the pellicle-forming microorganisms were isolated using culture-dependent approaches, then a comparative analysis between the pellicle-forming (PF) radish paocai and normal fermented paocai in the diversity and function of microbial community was conducted by metagenome sequencing. Based on a pairwise t-test and OPLS-DA analysis, diallyl sulfide, (z)-1-allyl-2-(prop-1-en-1-yl) disulfane, and terpineol were considered to be the main components responsible for the unpleasant flavor of PF paocai. Yarrowia spp., Enterobacter spp., and Pichia spp. were the main pellicle-forming microorganisms. All 17 isolated Enterobacter strains showed pectinase-producing and cellulase-producing abilities, and 3 isolated Pichia strains showed gas-producing capacity. According to LEfSe analysis based on metagenomes, unclassified_g__Citrobacter and Yarrowia lipolytica were the uppermost biomarkers that distinguished the PF paocai from normal paocai. Unclassified_g__Lactobacillus and Lactobacillus plantarum were found to be actively engaged in starch and sucrose metabolism, cysteine and methionine metabolism, galactose metabolism, fructose and mannose metabolism, lysine biosynthesis, fatty acid biosynthesis, and arginine biosynthesis, all of which contributed to the flavor formation of paocai. Combining the results of metagenome sequencing with the data obtained based on the culture-dependent method, we could deduce that the growth of Yarrowia lipolytica first promoted the increase of pH and the formation of pellicle, which provided a suitable niche for the growth of some harmful bacteria such as Enterobacter, Citrobacter, and Serratia. These hazardous bacteria then worked in concert to induce the odorous stench and texture softening of paocai, as well as more pellicle formation.

Meat extract casein peptone agar - A novel culture medium for the enumeration of Bacillus endospores in commercial products

Here we propose a novel culture medium, Meat Extract Casein Peptone (MECP) agar, to support the enumeration of Bacillus endospores in commercial products. The formulation is the result of screening eight different veterinary, pharmaceutical, and industrial grade peptones for the ability to support the formation of small, well-defined Bacillus colonies on solid culture medium. The impact of agar purity, agar formulation rate, and metal cation additives were examined in prototype medium batches prepared from preferred peptone inputs. A customized plate counting assay based on the resultant MECP agar formulation was compared with standardized pour-plate and spread-plate assays (ISO 4833) and flow cytometry for the ability to accurately enumerate five Bacillus-based biostimulants and biofertilizers. Estimations of Bacillus endospore concentration generated by the customized spread-plate assay were significantly higher than those produced by ISO 4833 pour-plate and spread-plate assays for four out of the five tested products and were in better agreement with flow cytometry values; however, flow cytometry values were numerically higher than values returned by both plating methods. Both flow cytometry and plating assays based on MECP or similar culture media represent potential candidates for standardization and validation through organizations such as ISO and AOAC International for the enumeration of Bacillus-based products.

CsgI (YccT) Is a Novel Inhibitor of Curli Fimbriae Formation in Escherichia coli Preventing CsgA Polymerization and Curli Gene Expression

Curli fimbriae are amyloids-found in bacteria (Escherichia coli)-that are involved in solid-surface adhesion and bacterial aggregation during biofilm formation. The curli protein CsgA is coded by a csgBAC operon gene, and the transcription factor CsgD is essential to induce its curli protein expression. However, the complete mechanism underlying curli fimbriae formation requires elucidation. Herein, we noted that curli fimbriae formation was inhibited by yccT-i.e., a gene that encodes a periplasmic protein of unknown function regulated by CsgD. Furthermore, curli fimbriae formation was strongly repressed by CsgD overexpression caused by a multicopy plasmid in BW25113-the non-cellulose-producing strain. YccT deficiency prevented these CsgD effects. YccT overexpression led to intracellular YccT accumulation and reduced CsgA expression. These effects were addressed by deleting the N-terminal signal peptide of YccT. Localization, gene expression, and phenotypic analyses revealed that YccT-dependent inhibition of curli fimbriae formation and curli protein expression was mediated by the two-component regulatory system EnvZ/OmpR. Purified YccT inhibited CsgA polymerization; however, no intracytoplasmic interaction between YccT and CsgA was detected. Thus, YccT-renamed CsgI (curli synthesis inhibitor)-is a novel inhibitor of curli fimbriae formation and has a dual role as an OmpR phosphorylation modulator and CsgA polymerization inhibitor.

Modulation of Biofilm Formation and Permeability in Streptococcus mutans during Exposure To Zinc Acetate

The penetration of biofilms by antimicrobials is a potential limiting factor in biofilm control. This is relevant to oral health, as compounds that are used to control microbial growth and activities could also affect the permeability of dental plaque biofilm with secondary effects on biofilm tolerance. We investigated the effects of zinc salts on the permeability of Streptococcus mutans biofilms. Biofilms were grown with low concentrations of zinc acetate (ZA), and a transwell transportation assay was applied to test biofilm permeability in an apical-basolateral direction. Crystal violet assays and total viable counts were used to quantify the biofilm formation and viability, respectively, and short time frame diffusion rates within microcolonies were determined using spatial intensity distribution analysis (SpIDA). While the diffusion rates within biofilm microcolonies were not significantly altered, exposure to ZA significantly increased the overall permeability of S. mutans biofilms (P < 0.05) through decreased biofilm formation, particularly at concentrations above 0.3 mg/mL. Transport was significantly lower through biofilms grown in high sucrose conditions. IMPORTANCE Zinc salts are added to dentifrices to improve oral hygiene through the control of dental plaque. We describe a method for determining biofilm permeability and show a moderate inhibitory effect of zinc acetate on biofilm formation, and that this inhibitory effect is associated with increases in overall biofilm permeability.

Beyond the Risk of Biofilms: An Up-and-Coming Battleground of Bacterial Life and Potential Antibiofilm Agents

Microbial pathogens and their virulence factors like biofilms are one of the major factors which influence the disease process and its outcomes. Biofilms are a complex microbial network that is produced by bacteria on any devices and/or biotic surfaces to escape harsh environmental conditions and antimicrobial effects. Due to the natural protective nature of biofilms and the associated multidrug resistance issues, researchers evaluated several natural anti-biofilm agents, including bacteriophages and their derivatives, honey, plant extracts, and surfactants for better destruction of biofilm and planktonic cells. This review discusses some of these natural agents that are being put into practice to prevent biofilm formation. In addition, we highlight bacterial biofilm formation and the mechanism of resistance to antibiotics.

Mycobacterium biofilms

The genus Mycobacterium includes some of the deadliest pathogens of History (Mycobacterium tuberculosis, Mycobacterium leprae), but most of the species within the genus are environmental microorganisms. Because some of these nontuberculous mycobacteria (NTM) species can be human pathogens, the study of these mycobacterial biofilms has increased during the last decades, and the interest in this issue increased as well as the growing number of patients with diseases caused by NTM. Different molecular mechanisms have been described, being especially well known the importance of glycopeptidolipids. Moreover, the knowledge of the extracellular matrix has shown important differences with other microorganisms, especially because of the presence of lipidic molecules as a key component of this structure. The clinical importance of mycobacterial biofilms has been described for many chronic diseases, especially lung diseases and implant-related ones, both in vitro and in vivo, and even in patients. Moreover, the biofilm-producing capacity has been proven also in M. tuberculosis, while its importance is not well understood. Biofilm studies have also shown the increasing resistance of mycobacteria in sessile form, and the importance of this resistance in the management of the patients is beyond doubt, being surgery necessary in some cases to cure the patients. Diagnosis of mycobacterial diseases is still based on culture-based techniques designed for the detection of M. tuberculosis. Molecular biology-based methods are also broadly used but again designed for tuberculosis diagnosis. Antimicrobial susceptibility testing is also well developed for tuberculosis, but only some species of NTM have standardized techniques for this purpose. New tools or approaches are necessary to treat these patients, whose importance is increasing, as the number of potential hosts is also increasing throughout the world.

Natural Medicine a Promising Candidate in Combating Microbial Biofilm

Studies on biofilm-related infections are gaining prominence owing to their involvement in most clinical infections and seriously threatening global public health. A biofilm is a natural form of bacterial growth ubiquitous in ecological niches, considered to be a generic survival mechanism adopted by both pathogenic and non-pathogenic microorganisms and entailing heterogeneous cell development within the matrix. In the ecological niche, quorum sensing is a communication channel that is crucial to developing biofilms. Biofilm formation leads to increased resistance to unfavourable ecological effects, comprising resistance to antibiotics and antimicrobial agents. Biofilms are frequently combated with modern conventional medicines such as antibiotics, but at present, they are considered inadequate for the treatment of multi-drug resistance; therefore, it is vital to discover some new antimicrobial agents that can prevent the production and growth of biofilm, in addition to minimizing the side effects of such therapies. In the search for some alternative and safe therapies, natural plant-derived phytomedicines are gaining popularity among the research community. Phytomedicines are natural agents derived from natural plants. These plant-derived agents may include flavonoids, terpenoids, lectins, alkaloids, polypeptides, polyacetylenes, phenolics, and essential oils. Since they are natural agents, they cause minimal side effects, so could be administered with dose flexibility. It is vital to discover some new antimicrobial agents that can control the production and growth of biofilms. This review summarizes and analyzes the efficacy characteristics and corresponding mechanisms of natural-product-based antibiofilm agents, i.e., phytochemicals, biosurfactants, antimicrobial peptides, and their sources, along with their mechanism, quorum sensing signalling pathways, disrupting extracellular matrix adhesion. The review also provides some other strategies to inhibit biofilm-related illness. The prepared list of newly discovered natural antibiofilm agents could help in devising novel strategies for biofilm-associated infections.

A mechanistic understanding of microcolony morphogenesis: coexistence of mobile and sessile aggregates

Most bacteria in the natural environment self-organize into collective phases such as cell clusters, swarms, patterned colonies, or biofilms. Several intrinsic and extrinsic factors, such as growth, motion, and physicochemical interactions, govern the occurrence of different phases and their coexistence. Hence, predicting the conditions under which a collective phase emerges due to individual-level interactions is crucial. Here we develop a particle-based biophysical model of bacterial cells and self-secreted extracellular polymeric substances (EPS) to decipher the interplay of growth, motility-mediated dispersal, and mechanical interactions during microcolony morphogenesis. We show that the microcolony dynamics and architecture significantly vary depending upon the heterogeneous EPS production. In particular, microcolony shows the coexistence of both motile and sessile aggregates rendering a transition towards biofilm formation. We identified that the interplay of differential dispersion and the mechanical interactions among the components of the colony determines the fate of the colony morphology. Our results provide a significant understanding of the mechano-self-regulation during biofilm morphogenesis and open up possibilities of designing experiments to test the predictions.

Fouling evolution of extracellular polymeric substances in forward osmosis based microalgae dewatering

Membrane fouling was still a challenge for the potential application of forward osmosis (FO) in algae dewatering. In this study, the fouling behaviors of Chlorella vulgaris and Scenedesmus obliquus were compared in the FO membrane filtration process, and the roles of their soluble-extracellular polymeric substances (sEPS) and bound-EPS (bEPS) in fouling performance were investigated. The results showed that fouling behaviors could be divided into two stages including a quickly dropped and later a stable process. The bEPS of both species presented the highest flux decline (about 40.0%) by comparison with their sEPS, cells and broth. This performance was consistent with the largest dissolved organic carbon losses in feed solutions, and the highest interfacial free energy analyzed by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. The chemical characterizations of algal foulants further showed that the severe fouling performance was also consistent with a proper ratio of carbohydrates and proteins contents in the cake layer, as well as the higher low molecular weight (LMW) components. Compared with the bEPS, the sEPS was crucial for the membrane fouling of S. obliquus, and an evolution of the membrane fouling structure was found in both species at the later filtration stage. This work clearly revealed the fundamental mechanism of FO membrane fouling caused by real microalgal suspension, and it will improve our understanding of the evolutionary fouling performances of algal EPS.

The Cell Wall Deacetylases Spy1094 and Spy1370 Contribute to Streptococcus pyogenes Virulence

Streptococcus pyogenes, or Group A Streptococcus (GAS), is a strictly human pathogen that causes a wide range of diseases, including skin and soft tissue infections, toxic shock syndrome and acute rheumatic fever. We have recently reported that Spy1094 and Spy1370 of S. pyogenes serotype M1 are N-acetylglucosamine (GlcNAc) deacetylases. We have generated spy1094 and spy1370 gene deletion mutants in S. pyogenes and gain-of-function mutants in Lactococcus lactis. Similar to other cell wall deacetylases, our results show that Spy1094 and Spy1370 confer lysozyme-resistance. Furthermore, deletion of the genes decreased S. pyogenes virulence in a human whole blood killing assay and a Galleria mellonella (Greater wax moth) larvae infection model. Expression of the two genes in L. lactis resulted in increased lysozyme resistance and survival in whole human blood, and reduced survival of infected G. mellonella larvae. Deletion of the spy1370, but not the spy1094 gene, decreased resistance to the cationic antimicrobial peptide cecropin B, whereas both enzymes increased biofilm formation, probably resulting from the increase in positive charges due to deacetylation of the cell wall. In conclusion, Spy1094 and Spy1370 are important S. pyogenes virulence factors and might represent attractive targets for the development of antibacterial agents.

In Vivo Role of Two-Component Regulatory Systems in Models of Urinary Tract Infections

Two-component signaling systems (TCSs) are finely regulated mechanisms by which bacteria adapt to environmental conditions by modifying the expression of target genes. In bacterial pathogenesis, TCSs play important roles in modulating adhesion to mucosal surfaces, resistance to antibiotics, and metabolic adaptation. In the context of urinary tract infections (UTI), one of the most common types infections causing significant health problems worldwide, uropathogens use TCSs for adaptation, survival, and establishment of pathogenicity. For example, uropathogens can exploit TCSs to survive inside bladder epithelial cells, sense osmolar variations in urine, promote their ascension along the urinary tract or even produce lytic enzymes resulting in exfoliation of the urothelium. Despite the usefulness of studying the function of TCSs in in vitro experimental models, it is of primary necessity to study bacterial gene regulation also in the context of host niches, each displaying its own biological, chemical, and physical features. In light of this, the aim of this review is to provide a concise description of several bacterial TCSs, whose activity has been described in mouse models of UTI.

Evaluation of Antibacterial and Antibiofilm Properties of Kojic Acid against Aeromonas sobria and Staphylococcus saprophyticus

Biofilms composed of microbes and extracellular polymeric substances (EPSs) pose a significant risk to human health and lead to economic loss in the food industry. In this study, the antimicrobial and antibiofilm properties of kojic acid (KA) against Aeromonas sobria (A. sobria) and Staphylococcus saprophyticus (S. saprophyticus) were investigated by determining the leakage of DNA and protein, cell morphology, biofilm formation, the metabolic activity of biofilms, excretion of EPS, and biofilm architecture. The results indicated that the values of minimum inhibitory concentration (MIC) of A. sobria and S. saprophyticus after KA treatment were 0.4 mg/mL and 1.6 mg/mL, respectively. 1 × MIC KA showed unignorable antimicrobial activity against the two bacteria, leading to alterations in the bacterial physicochemical characteristics and cell death. Sub-MICs of KA can inhibit biofilm formation and decrease the metabolic activity and excretion of EPS, and these inhibition effects were in a dose-dependent manner. These results were further confirmed by the visual images obtained from scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Moreover, S. saprophyticus is more susceptible to KA in inhibiting biofilm formation, and for A. sobria, changes in the cell structure and the permeability of the cell membrane were more obvious. This research highlighted the antibacterial and antibiofilm activity of KA against A. sobria and S. saprophyticus.

The Polysaccharidic Nature of the Skeleton of Marennine as Determined by NMR Spectroscopy

The water-soluble blue-green pigment marennine, produced and partly excreted by the diatom Haslea ostrearia, and known for a long time for its role in the greening of oysters, was isolated from the culture medium, purified, and analyzed by Nuclear Magnetic Resonance (NMR) in order to gain insight into its chemical structure. The spectra show mainly carbohydrates of a complex composition, apparently highly branched, and with a mass in the order of 10 kDa. There are, in addition, some signals of aliphatic and, much weaker, aromatic groups that present aglycons. The latter might be responsible for the color. These carbohydrates are always associated with the blue-green color and cannot be separated from it by most treatments; they are interpreted as constituting the frame of the pigment. NMR after hydrolysis identifies the most abundant monosaccharides in marennine as galactose, xylose, mannose, rhamnose, and fucose.

Current and future methods of probiotic therapy for necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a complex intestinal disease that primarily affects premature neonates. Given its significant mortality and morbidity, there is an urgent need to develop improved prophylactic measures against the disease. One potential preventative strategy for NEC is the use of probiotics. Although there has been significant interest for decades in probiotics in neonatal care, no clear guidelines exist regarding which probiotic to use or for which patients, and no FDA-approved products exist on the market for NEC. In addition, there is lack of agreement regarding the benefits of probiotics in neonates, as well as some concerns about the safety and efficacy of available products. We discuss currently available probiotics as well as next-generation probiotics and novel delivery strategies which may offer an avenue to capitalize on the benefits of probiotics, while minimizing the risks. Thus, probiotics may still prove to be an effective prevention strategy for NEC, although further product development and research is needed to support use in the preterm population.

Biofilm formation of pathogenic bacteria isolated from aquatic animals

Bacterial biofilm formation is one of the dynamic processes, which facilitates bacteria cells to attach to a surface and accumulate as a colony. With the help of biofilm formation, pathogenic bacteria can survive by adapting to their external environment. These bacterial colonies have several resistance properties with a higher survival rate in the environment. Especially, pathogenic bacteria can grow as biofilms and can be protected from antimicrobial compounds and other substances. In aquaculture, biofilm formation by pathogenic bacteria has emerged with an increased infection rate in aquatic animals. Studies show that Vibrio anguillarum, V. parahaemolyticus, V. alginolyticus, V. harveyi, V. campbellii, V. fischeri, Aeromonas hydrophila, A. salmonicida, Yersinia ruckeri, Flavobacterium columnare, F. psychrophilum, Piscirickettsia salmonis, Edwardsiella tarda, E. ictaluri, E. piscicida, Streptococcus parauberis, and S. iniae can survive in the environment by transforming their planktonic form to biofilm form. Therefore, the present review was intended to highlight the principles behind biofilm formation, major biofilm-forming pathogenic bacteria found in aquaculture systems, gene expression of those bacterial biofilms and possible controlling methods. In addition, the possibility of these pathogenic bacteria can be a serious threat to aquaculture systems.

Lipid-Like Biofilm from a Clinical Brain Isolate of Aspergillus terreus: Quantification, Structural Characterization and Stages of the Formation Cycle

Invasive infections caused by filamentous fungi have increased considerably due to the alteration of the host's immune response. Aspergillus terreus is considered an emerging pathogen and has shown resistance to amphotericin B treatment, resulting in high mortality. The development of fungal biofilm is a virulence factor, and it has been described in some cases of invasive aspergillosis. In addition, although the general composition of fungal biofilms is known, findings related to biofilms of a lipid nature are rarely reported. In this study, we present the identification of a clinical strain of A. terreus by microbiological and molecular tools, also its in vitro biofilm development capacity: (i) Biofilm formation was quantified by Crystal Violet and reduction of tetrazolium salts assays, and simultaneously the stages of biofilm development were described by Scanning Electron Microscopy in High Resolution (SEM-HR). (ii) Characterization of the organizational structure of the biofilm was performed by SEM-HR. The hyphal networks developed on the surface, the abundant air channels created between the ECM (extracellular matrix) and the hyphae fused in anastomosis were described. Also, the presence of microhyphae is reported. (iii) The chemical composition of the ECM was analyzed by SEM-HR and CLSM (Confocal Laser Scanning Microscopy). Proteins, carbohydrates, nucleic acids and a relevant presence of lipid components were identified. Some structures of apparent waxy appearance were highlighted by SEM-HR and backscatter-electron diffraction, for which CLSM was previously performed. To our knowledge, this work is the first description of a lipid-type biofilm in filamentous fungi, specifically of the species A. terreus from a clinical isolate.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

Antibiotic Resistance, Biofilm Formation and Sub-Inhibitory Hydrogen Peroxide Stimulation in Uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is the most prevalent cause of urinary tract infections (UTIs). Biofilm formation and antibiotic resistance could be high among the causative agent. The purpose of this study was to determine antibiotic resistance, biofilm production, and biofilm-associated genes, bcsA and csgD, and sub-inhibitory hydrogen peroxide (H2O2) stimulation in UPEC for biofilm formation. A total of 71 UPEC were collected from a tertiary care hospital in Kathmandu and subjected to identify antibiotic susceptibility using Kirby-Bauer disk diffusion. The biofilm formation was assessed using microtiter culture plate method while pellicle formation was tested by a tube method. In representative 15 isolates based on biofilm-forming ability, bcsA and csgD were screened by conventional polymerase chain reaction, and treated with sub-lethal H2O2. The UPEC were found the most susceptible to meropenem (90.2%), and the least to ampicillin (11.3%) in vitro and 90.1% of them were multi-drug resistant (MDR). Most UPEC harbored biofilm-producing ability (97.2%), and could form pellicle at 37°C. Among representative 15 isolates, csgD was detected only among 10 isolates (66.67%) while bcsA gene was present in 13 isolates (86.67%). This study revealed that level of biofilm production elevated after sub-lethal H2O2 treatment (P = .041). These findings suggested that the pathogens are emerging as MDR. The biofilm production is high and the majority of selected strains contained bcsA and csgD genes. Pellicle formation test was suggestive to be an alternative qualitative method to screen biofilm production in UPEC. The sub-inhibitory concentration of H2O2 may contribute in increasing biofilm formation in UPEC.

Novel quorum sensing inhibitor Echinatin as an antibacterial synergist against Escherichia coli

A new antibacterial strategy based on inhibiting bacterial quorum sensing (QS) has emerged as a promising method of attenuating bacterial pathogenicity and preventing bacterial resistance to antibiotics. In this study, we screened Echinatin (Ech) with high-efficiency anti-QS from 13 flavonoids through the AI-2 bioluminescence assay. Additionally, crystal violet (CV) staining combined with confocal laser scanning microscopy (CLSM) was used to evaluate the effect of anti-biofilm against Escherichia coli (E. coli). Further, the antibacterial synergistic effect of Ech and marketed antibiotics were measured by broth dilution and Alamar Blue Assay. It was found that Ech interfered with the phenotype of QS, including biofilm formation, exopolysaccharide (EPS) production, and motility, without affecting bacterial growth and metabolic activity. Moreover, qRT-PCR exhibited that Ech significantly reduced the expression of QS-regulated genes (luxS, pfs, lsrB, lsrK, lsrR, flhC, flhD, fliC, csgD, and stx2). More important, Ech with currently marketed colistin antibiotics (including colistin B and colistin E) showed significantly synergistically increased antibacterial activity in overcoming antibiotic resistance of E. coli. In summary, these results suggested the potent anti-QS and novel antibacterial synergist candidate of Ech for treating E. coli infections.

High-throughput sequencing-based metagenomic and transcriptomic analysis of intestine in piglets infected with salmonella

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

An avirulent Ralstonia solanacearum strain FJAT1458 outcompetes with virulent strain and induces tomato plant resistance against bacterial wilt

BACKGROUND

Bacterial wilt (BW) caused by Ralstonia solanacearum (RS) is considered as one of the most destructive plant diseases. An avirulent strain of RS, FJAT1458, is a potential biocontrol agent of BW. In this study, the mechanism of FJAT1458 against BW was evaluated.

RESULTS

FJAT1458 was tagged with the red fluorescent protein gene, and the resulting strain was named as FJAT1458-RFP. When FJAT1458-RFP and FJAT91-GFP (a virulent strain of RS labelled with the green fluorescent protein gene), were co-inoculated in potted tomato plants, the colonization of FJAT91-GFP reached an almost undetectable level at 7 days post-inoculation (dpi) in the roots and at 9 dpi in rhizosphere soil. When they were co-inoculated in a hydroponic tomato growing system, numbers of the two strains were similar at 3 dpi in the root tissues; however, FJAT91-GFP was not detected at 9 dpi while FJAT1458-RFP maintained 1.77 × 10⁵  CFU g^-1 . The inoculation of FJAT1458-RFP alone or combination with FJAT91-GFP significantly increased tomato root activity. Moreover, expression levels of the defense-related genes PR-1a, GLUA, and CHI3 in tomato roots were significantly up-regulated by FJAT1458-RFP and co-inoculation of FJAT1458-RFP and FJAT91-GFP at 5 dpi, compared to the control (water, CK) treatment. Noteworthy, expression levels of GLUA in the treatments of FJAT1458-RFP and FJAT1458-RFP + FJAT91-GFP were 12.22- and 12.05-fold higher than that in the CK at 5 dpi, respectively.

CONCLUSIONS

The results suggested that the avirulent strain FJAT1458-RFP could suppress colonization of the virulent strain in tomato roots, and induce tomato plant resistance against BW. © 2022 Society of Chemical Industry.

Potential functions and applications of diverse microbial exopolysaccharides in marine environments

Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in applications including medications, nutraceuticals and functional foods, cosmetics, and insecticides. Several microbes can synthesize and excrete EPSs with chemical properties and structures that make them suitable for several important applications. Microbes secrete EPSs outside their cell walls, as slime or as a "jelly" into the extracellular medium. These EPS-producing microbes are ubiquitous and can be isolated from aquatic and terrestrial environments, such as freshwater, marine water, wastewater, and soils. They have also been isolated from extreme niches like hot springs, cold waters, halophilic environments, and salt marshes. Recently, microbial EPSs have attracted interest for their applications such as environmental bio-flocculants because they are degradable and nontoxic. However, further efforts are required for the cost-effective and industrial-scale commercial production of microbial EPSs. This review focuses on the exopolysaccharides obtained from several extremophilic microorganisms, their synthesis, and manufacturing optimization for better cost and productivity. We also explored their role and applications in interactions between several organisms.

Effects of Sub-Minimum Inhibitory Concentrations of Imipenem and Colistin on Expression of Biofilm-Specific Antibiotic Resistance and Virulence Genes in Acinetobacter baumannii Sequence Type 1894

Antibiotics at suboptimal doses promote biofilm formation and the development of antibiotic resistance. The underlying molecular mechanisms, however, were not investigated. Here, we report the effects of sub-minimum inhibitory concentrations (sub-MICs) of imipenem and colistin on genes associated with biofilm formation and biofilm-specific antibiotic resistance in a multidrug-tolerant clinical strain of Acinetobacter baumannii Sequence Type (ST) 1894. Comparative transcriptome analysis was performed in untreated biofilm and biofilm treated with sub-MIC doses of imipenem and colistin. RNA sequencing data showed that 78 and 285 genes were differentially expressed in imipenem and colistin-treated biofilm cells, respectively. Among the differentially expressed genes (DEGs), 48 and 197 genes were upregulated exclusively in imipenem and colistin-treated biofilm cells, respectively. The upregulated genes included those encoding matrix synthesis (pgaB), multidrug efflux pump (novel00738), fimbrial proteins, and homoserine lactone synthase (AbaI). Upregulation of biofilm-associated genes might enhance biofilm formation when treated with sub-MICs of antibiotics. The downregulated genes include those encoding DNA gyrase (novel00171), 30S ribosomal protein S20 (novel00584), and ribosome releasing factor (RRF) were downregulated when the biofilm cells were treated with imipenem and colistin. Downregulation of these genes affects protein synthesis, which in turn slows down cell metabolism and makes biofilm cells more tolerant to antibiotics. In this investigation, we also found that 5 of 138 small RNAs (sRNAs) were differentially expressed in biofilm regardless of antibiotic treatment or not. Of these, sRNA00203 showed the highest expression levels in biofilm. sRNAs regulate gene expression and are associated with biofilm formation, which may in turn affect the expression of biofilm-specific antibiotic resistance. In summary, when biofilm cells were exposed to sub-MIC doses of colistin and imipenem, coordinated gene responses result in increased biofilm production, multidrug efflux pump expression, and the slowdown of metabolism, which leads to drug tolerance in biofilm. Targeting antibiotic-induced or repressed biofilm-specific genes represents a new strategy for the development of innovative and effective treatments for biofilm-associated infections caused by A. baumannii.

Matrix-producing cells formed 'Van Gogh bundles' facilitate Bacillus subtilis biofilm self-healing

Biofilms grow and expand through cell differentiation into various phenotypes, which have different functions and cooperate with each other. In our experiments, we find that biofilms can heal after damaged, and we also find there is a special structure near the cut, which is called the 'Van Gogh bundles' by Jordi et al. because of its resemblance to Van Gogh's famous painting 'The Starry Night'. Here, we study the 'Van Gogh bundles' structure evolution near the cut area, and how 'Van Gogh bundles' structure facilitates the cut healing by observing microscopic images of bacterial colonies growing from wild-type and mutant strains. We find that the amount of matrix-producing cells contributes to the 'Van Gogh bundles' structure, such as curvature. Through the comparison of curvatures of 'Van Gogh bundles' and the rate of the cut healing, we find that the smaller the curvature, the faster healing rate. To better explain the above experiment observations, we establish an individual-based model and simulate the formation and growth of 'Van Gogh bundles' along the cut by giving rules for an individual cell like cell growth, division and turning rules, and also 'Van Gogh bundles' fold division rule.

Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1

Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures are manifested through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene were repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE's primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identified the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses showed that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community. IMPORTANCE In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces; however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE's paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.

Glucosyltransferase modulated Streptococcus mutans adhesion to different surfaces involved in biofilm formation by atomic force microscope

Biofilm on dental restorative materials is an important determinant in the aetiology of secondary caries development. Formation of biofilm involving adhesion of bacteria onto substrate, bacterial cell and biofilm surfaces. Glucosyltransferase B and C (GtfB and GtfC) are essential factors for regulation of Streptococcus mutans biofilm formation, but the mechanisms involving different kind of bacterial adhesion still lack detailed description. In this study, nanoscale adhesion force measurement was performed using atomic force microscopy (AFM). Bacteria-coated cantilevers were used to probe S. mutans adhesion to substrates, bacterial cells and early biofilms. Two representative dental materials, Glass ionomer cement (GIC) and composite resin, served as substrates. It was found that deletion of gtfB and gtfC genes both reduced adhesion forces of S. mutans towards substrate and bacterial cell surfaces (P<0.05). Notably, reduction of gtfB gene remarkably decreased bacterial adhesion to biofilm surfaces(P<0.05), while gtfC showed no obvious effect during this stage. Biofilms cultured on GIG further decreased cell-biofilm adhesion, compared with that on resin (P<0.05). Confocal fluorescence images and scanning electron microscopy images showed that deletion of gtfB lead to reduced microcolony formation and less production of exopolysaccharides (EPS) in the biofilm, and after bacteria culturing on GIC, the EPS content was further decreased. Our findings suggest that EPS mainly mediate bacterial adhesion to early biofilm surface. Deletion of gtfB and co-culture with GIC could significantly reduce the cell-biofilm adhesion, which is probably through decreasing of EPS production. gtfB exerts a critical role in the bacterial adhesion for the whole process of biofilm development, while gtfC possibly works only in the early stages. This article is protected by copyright. All rights reserved.

A Pan-Global Study of Bacterial Leaf Spot of Chilli Caused by Xanthomonas spp

Bacterial Leaf Spot (BLS) is a serious bacterial disease of chilli (Capsicum spp.) caused by at least four different Xanthomonas biotypes: X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, X. hortorum pv. gardneri, and X. vesicatoria. Symptoms include black lesions and yellow halos on the leaves and fruits, resulting in reports of up to 66% losses due to unsalable and damaged fruits. BLS pathogens are widely distributed in tropical and subtropical regions. Xanthomonas is able to survive in seeds and crop residues for short periods, leading to the infections in subsequent crops. The pathogen can be detected using several techniques, but largely via a combination of traditional and molecular approaches. Conventional detection is based on microscopic and culture observations, while a suite of Polymerase Chain Reaction (PCR) and Loop-Mediated Isothermal Amplification (LAMP) assays are available. Management of BLS is challenging due to the broad genetic diversity of the pathogens, a lack of resilient host resistance, and poor efficacy of chemical control. Some biological control agents have been reported, including bacteriophage deployment. Incorporating stable host resistance is a critical component in ongoing integrated management for BLS. This paper reviews the current status of BLS of chilli, including its distribution, pathogen profiles, diagnostic options, disease management, and the pursuit of plant resistance.

Antioxidant and anti-inflammatory properties of an aminoglycan-rich exopolysaccharide from the submerged fermentation of Bacillus thuringiensis

Proteins from Bacillus thuringiensis are widely used as biopesticides but little is known about its exopolysaccharides. The exopolysaccharide BPS-2 was extracted from B. thuringiensis IX-01 after high-cell-density fermentation. BPS-2 is a heteropolysaccharide (molecular weight 29.36 kDa) composed of D-galactosamine, arabinose, glucosamine, glucose, and mannose in molar ratios 5.53: 1.77:4.74:3.24:1. In vitro upper gastrointestinal simulations showed that BPS-2 has strong anti-digestive capacity, with scavenging of DPPH, hydroxyl, ABTS, and superoxide anions radicals of 31.34 ± 1.67 %, 32.43 ± 3.01 %, 34.31 ± 2.12 %, and 48.53 ± 3.55 %, respectively, after BPS-2 entered the colon. It significantly inhibited production of lipopolysaccharide-induced nitric oxide and multiple pro-inflammatory cytokines and had proliferative effects on RAW 264.7 cells. BPS-2 inhibited malondialdehyde secretion and elevated activities of glutathione peroxidase, superoxide dismutase, and total antioxidants, significantly improving the antioxidant status of inflammation model cells. This first report of the in vitro anti-inflammation and antioxidant properties of BPS-2 from B. thuringiensis provides a basis for biopharmaceutical applications.

Control Measurements of Escherichia coli Biofilm: A Review

Escherichia coli (E. coli) is a common pathogen that causes diarrhea in humans and animals. In particular, E. coli can easily form biofilm on the surface of living or non-living carriers, which can lead to the cross-contamination of food. This review mainly summarizes the formation process of E. coli biofilm, the prevalence of biofilm in the food industry, and inhibition methods of E. coli biofilm, including chemical and physical methods, and inhibition by bioactive extracts from plants and animals. This review aims to provide a basis for the prevention and control of E. coli biofilm in the food industry.

Precisely controlled and deeply penetrated micro-nano hybrid multifunctional motors with enhanced antibacterial activity against refractory biofilm infections

The biofilm resistance of microorganisms has severe economic and environmental implications, especially the contamination of facilities associated with human life, including medical implants, air-conditioning systems, water supply systems, and food-processing equipment, resulting in the prevalence of infectious diseases. Once bacteria form biofilms, their antibiotic resistance can increase by 10-1,000-fold, posing a great challenge to the treatment of related diseases. In order to overcome the contamination of bacterial biofilm, destroying the biofilm's matrix so as to solve the penetration depth dilemma of antibacterial agents is the most effective way. Here, a magnetically controlled multifunctional micromotor was developed by using H₂O₂ as the fuel and MnO₂ as the catalyst to treat bacterial biofilm infection. In the presence of H₂O₂, the as-prepared motors could be self-propelled by the generated oxygen microbubbles. Thereby, the remotely controlled motors could drill into the EPS of biofilm and disrupt them completely with the help of bubbles. Finally, the generated highly toxic •OH could efficiently kill the unprotected bacteria. This strategy combined the mechanical damage, highly toxic •OH, and precise magnetic guidance in one system, which could effectively eliminate biologically infectious fouling in microchannels within 10 min, possessing a wide range of practical application prospects especially in large scale and complex infection sites.

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot

Simple Summary

Bacterial soft rot, attributed to Pectobacterium brasiliense infection, has caused destructive impacts and colossal economic losses to China’s agricultural industry. Chemical control, which was ubiquitously used, cannot manage this disease as expected, so biocontrol has been followed with interest to date. In this study, we found a Paenibacillus peoriae strain ZF390 that had a potent control efficiency over cucumber plants against Pectobacterium brasiliense, and the comparative genomic analysis revealed biocontrol mechanisms might be involved in the strain ZF390.

Abstract

Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation.

Isolation, Partial Characterization and Application of Bacteriophages in Eradicating Biofilm Formation by Bacillus cereus on Stainless Steel Surfaces in Food Processing Facilities

The Bacillus cereus (B. cereus) group is a widespread foodborne pathogen with a persistent ability to form biofilm, and with inherent resistance to traditional treatment in the food industry. Bacteriophages are a promising biocontrol agent that could be applied to prevent or eliminate biofilms formation. We have described, in this study, the isolation from sewage samples and preliminary characterization of bacteriophages that are active against the B. cereus group. The effectiveness of phage treatment for reducing B. cereus attachment and biofilms on stainless steel surfaces has been also assessed using three incubation periods at different titrations of each phage. Out of 62 phages isolated, seven showed broad-spectrum lytic action against 174 B. cereus isolates. All selected phages appeared to be of the Siphoviridae family. SDS-PAGE proved that two phages have a similar profile, while the remainder are distinct. All isolated phages have the same restriction pattern, with an estimated genome size of around 37 kb. The isolated bacteriophages have been shown to be effective in preventing biofilm formation. Reductions of up to 1.5 log10 UFC/cm2 have been achieved, compared to the untreated biofilms. Curative treatment reduced the bacterial density by 0.5 log10 UFC/cm2. These results support the prospect of using these phages as a potential alternative strategy for controlling biofilms in food systems.

The Antimicrobial and Antibiofilm Activity of Oregano Essential Oil against Enterococcus faecalis and Its Application in Chicken Breast

Oregano essential oil (OEO) possesses anti-inflammatory, antioxidant, and cancer-suppressive properties. Enterococcus faecalis is a foodborne opportunistic pathogen that can be found in nature and the food processing industry. The goal of this investigation was to explore the antimicrobial action and mechanism of OEO against E. faecalis, inactivation action of OEO on E. faecalis in mature biofilms, and its application in chicken breast. The minimum inhibitory concentration (MIC) of OEO against E. faecalis strains (ATCC 29212 and nine isolates) ranged from 0.25 to 0.50 μL/mL. OEO therapy reduced intracellular adenosine triphosphate (ATP) levels, caused cell membrane hyperpolarization, increased the intracellular reactive oxygen species (ROS), and elevated extracellular malondialdehyde (MDA) concentrations. Furthermore, OEO treatment diminished cell membrane integrity and caused morphological alterations in the cells. In biofilms on stainless-steel, OEO showed effective inactivation activity against E. faecalis. OEO reduced the number of viable cells, cell viability and exopolysaccharides in the biofilm, as well as destroying its structure. Application of OEO on chicken breast results in a considerable reduction in E. faecalis counts and pH values, in comparison to control samples. These findings suggest that OEO could be utilized as a natural antibacterial preservative and could effectively control E. faecalis in food manufacturing.

Microbiomics for enhancing electron transfer in an electrochemical system

In microbial electrochemical systems, microorganisms catalyze chemical reactions converting chemical energy present in organic and inorganic molecules into electrical energy. The concept of microbial electrochemistry has been gaining tremendous attention for the past two decades, mainly due to its numerous applications. This technology offers a wide range of applications in areas such as the environment, industries, and sensors. The biocatalysts governing the reactions could be cell secretion, cell component, or a whole cell. The electroactive bacteria can interact with insoluble materials such as electrodes for exchanging electrons through colonization and biofilm formation. Though biofilm formation is one of the major modes for extracellular electron transfer with the electrode, there are other few mechanisms through which the process can occur. Apart from biofilm formation electron exchange can take place through flavins, cytochromes, cell surface appendages, and other metabolites. The present article targets the various mechanisms of electron exchange for microbiome-induced electron transfer activity, proteins, and secretory molecules involved in the electron transfer. This review also focuses on various proteomics and genetics strategies implemented and developed to enhance the exo-electron transfer process in electroactive bacteria. Recent progress and reports on synthetic biology and genetic engineering in exploring the direct and indirect electron transfer phenomenon have also been emphasized.

RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths

Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.

Small Carbohydrate Derivatives as Potent Antibiofilm Agents

Biofilm formation by most pathogenic bacteria is considered as one of the key mechanisms associated with virulence and antibiotic resistance. Biofilm-forming bacteria adhere to the surfaces of biological or implant medical devices and create communities within their self-produced extracellular matrix that are difficult to treat by existing antibiotics. There is an urgent need to synthesize and screen structurally diverse molecules for their antibiofilm activity that can remove or minimize the bacterial biofilm. The development of carbohydrate-based small molecules as antibiofilm agents holds a great promise in addressing the problem of the eradication of biofilm-related infections. Owing to their structural diversity and specificity, the sugar scaffolds are valuable entities for developing antibiofilm agents. In this perspective, we discuss the literature pertaining to carbohydrate-based natural antibiofilm agents and provide an overview of the design, activity, and mode of action of potent synthetic carbohydrate-based molecules.

Next-Generation Probiotic Therapy to Protect the Intestines From Injury

Probiotics are live microorganisms that, when administered in adequate amounts, provide health benefits to the host. Some strains of the probiotic Lactobacillus reuteri (L. reuteri) have both antimicrobial and anti-inflammatory properties that may be exploited for the treatment and prevention of different gastrointestinal diseases, including necrotizing enterocolitis (NEC) and Clostridioides difficile (C. difficile) infection. Our laboratory has developed a new delivery system for L. reuteri in which the probiotic is incubated with biocompatible, semipermeable, porous dextranomer microspheres (DM) that can be loaded with beneficial and diffusible cargo. L. reuteri can be induced to form a biofilm by incubating the bacteria on the surface of these microspheres, which enhances the efficacy of the probiotic. Loading the DM with sucrose or maltose induces L. reuteri to produce more biofilm, further increasing the efficacy of the probiotic. Using a rat model of NEC, L. reuteri administered in its biofilm state significantly increases animal survival, reduces the incidence of NEC, preserves gut barrier function, and decreases intestinal inflammation. In a murine model of Clostridiodes difficile infection, L. reuteri administered in its biofilm state decreases colitis when administered either before or after C. difficile induction, demonstrating both prophylactic and therapeutic efficacy. There are currently no FDA-approved probiotic preparations for human use. An FDA-approved phase I clinical trial of L. reuteri in its biofilm state in healthy adults is currently underway. The results of this trial will be used to support a phase 1 clinical trial in neonates, with the goal of utilizing L. reuteri in its biofilm state to prevent NEC in premature neonates in the future.

The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms

In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.

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The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms

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A novel subpopulation—mineral-forming cells—is essential for biofilm formation

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This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate

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Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure

Characterization of the Lytic Phage Flora With a Broad Host Range Against Multidrug-Resistant Escherichia coli and Evaluation of Its Efficacy Against E. coli Biofilm Formation

Escherichia coli is a gram-negative bacterium that is distributed widely throughout the world; it is mainly found in contaminated food, the poultry industry, and animal feces. The emergence of antibiotic-resistant E. coli poses a threat to human and animal health, which has led to renewed interest in phage-based therapy. E. coli biofilm control and prevention are of great importance. In this study, the isolated phages Flora and KM18 were found to belong to the family Myoviridae; the optimal preservation buffer was pH = 6~7, and the phage genome sizes were 168,909 (Flora) and 168,903 (KM18) bp. Phage Flora had a broader lytic spectrum than KM18. Phage Flora had a better antibiofilm effect than kanamycin sulfate in high-concentration E. coli cultures. A combination of the phage Flora and kanamycin sulfate showed better antibiofilm effects than Flora or kanamycin sulfate alone in low-concentration E. coli cultures. These characteristics can serve as a guideline for the selection of effective candidates for phage therapy, in this case antibiotic-resistant E. coli control in the poultry industry.

Functional Characterisation of Two Novel Deacetylases from Streptococcus pyogenes

Streptococcus pyogenes (Group A Streptococcus, GAS) is an exclusively human pathogen that causes a wide range of diseases. We have identified two novel proteins, Spy1094 and Spy1370, which show sequence similarity with peptidoglycan deacetylases (PGDAs) from other streptococcal species like S. pneumoniae and S. iniae, that represent important virulence factors. Recombinant Spy1094 and Spy1370 were active at a wide pH range (pH 4.0–9.0) and showed metal ion-dependence, with the highest activities observed in the presence of Mn2+, Mg2+and Zn2+. The enzymes showed typical Michaelis–Menten saturation kinetics with the pseudo-substrate GlcNAc3. Binding affinities for rSpy1094 and rSpy1370 were high (Km = 2.2 ± 0.9 μM and 3.1 ± 1.1 μM, respectively), but substrate turnover was low (Kcat = 0.0075/s and 0.0089/s, respectively) suggesting that peptidoglycan might not be the preferred target for deacetylation. Both enzymes were expressed during bacterial growth.

Cell Cycle Progression Influences Biofilm Formation in Saccharomyces cerevisiae 1308

Biofilm-immobilized continuous fermentation is a novel fermentation strategy that has been utilized in ethanol fermentation. Continuous fermentation contributes to the self-proliferation of Saccharomyces cerevisiae biofilms. Previously, we successfully described the cell cycle differences between biofilm-immobilized fermentation and calcium alginate-immobilized fermentation. In the present study, we investigated the relationship between biofilm formation and the cell cycle. We knocked down CLN3, SIC1, and ACE2 and found that Δcln3 and Δsic1 exhibited a predominance of G₂/M phase cells, increased biofilm formation, and significantly increased extracellular polysaccharide formation and expression of genes in the FLO gene family during immobilisation fermentation. Δace2 exhibited a contrasting performance. These findings suggest that the increase in the proportion of cells in the G₂/M phase of the cell cycle facilitates biofilm formation and that the cell cycle influences biofilm formation by regulating cell adhesion and polysaccharide formation. This opens new avenues for basic research and may also help to provide new ideas for biofilm prevention and optimization. IMPORTANCE Immobilised fermentation can be achieved using biofilm resistance, resulting in improved fermentation efficiency and yield. The link between the cell cycle and biofilms deserves further study since reports are lacking in this area. This study showed that the ability of Saccharomyces cerevisiae to produce biofilm differed when cell cycle progression was altered. Further studies suggested that cell cycle regulatory genes influenced biofilm formation by regulating cell adhesion and polysaccharide formation. Findings related to cell cycle regulation of biofilm formation set the stage for biofilm in Saccharomyces cerevisiae and provide a theoretical basis for the development of a new method to improve biofilm-based industrial fermentation.