The LuxS Based Quorum Sensing Governs Lactose Induced Biofilm Formation by Bacillus subtilis

The promotion of biofilm dispersion: a new strategy for eliminating foodborne pathogens in the food industry

Food safety is a critical global concern due to its direct impact on human health and overall well-being. In the food processing environment, biofilm formation by foodborne pathogens poses a significant problem as it leads to persistent and high levels of food contamination, thereby compromising the quality and safety of food. Therefore, it is imperative to effectively remove biofilms from the food processing environment to ensure food safety. Unfortunately, conventional cleaning methods fall short of adequately removing biofilms, and they may even contribute to further contamination of both equipment and food. It is necessary to develop alternative approaches that can address this challenge in food industry. One promising strategy in tackling biofilm-related issues is biofilm dispersion, which represents the final step in biofilm development. Here, we discuss the biofilm dispersion mechanism of foodborne pathogens and elucidate how biofilm dispersion can be employed to control and mitigate biofilm-related problems. By shedding light on these aspects, we aim to provide valuable insights and solutions for effectively addressing biofilm contamination issues in food industry, thus enhancing food safety and ensuring the well-being of consumers.

Potentiation effect of the AI-2 signaling molecule on postharvest disease control of pear and loquat by Bacillus amyloliquefaciens and its mechanism

An autoinducer-2 (AI-2) signaling molecule from Bacillus was synthesized, and its mechanism on the biofilm formation and biocontrol ability of B. amyloliquefaciens was verified in vitro and in vivo. The 16S/ITS amplicon sequencing was used to analyze the effect of B. amyloliquefaciens B4 with or without AI-2 on the microflora of pears during storage. The results showed that B. amyloliquefaciens B4 secreted AI-2, which promoted biofilm formation. Additionally, AI-2 at a concentration of 40 μmol/L enhanced the biocontrol ability of B. amyloliquefaciens B4 on postharvest pear and loquat fruits. Finally, amplicon sequencing demonstrated that the addition of AI-2 increased the abundance of B. amyloliquefaciens B4 in fruit by stimulating the growth and biofilm formation of this bacterium.

Invited review: Current perspectives for analyzing the dairy biofilms by integrated multiomics

Biofilms formed by pathogenic or spoilage microorganisms have become serious issues in the dairy industry, as this mode of life renders such microorganisms highly resistant to cleaning-in-place (CIP) procedures, disinfectants, desiccation, and other control strategies. The advent of omics techniques, especially the integration of different omics tools, has greatly improved our understanding of the features of microbial biofilms, and provided in-depth knowledge on developing effective methods that are directly against deleterious biofilms. This review provides novel insights into the single use of each omics tool and the application of multiomics tools to unravel the mechanisms of biofilm formation, specific molecular phenotypes exhibited by biofilms, and biofilm control strategies. Challenges and future perspective on the integration of omics tools for biofilm studies are also addressed.

Multiomics reveals the mechanism of B. longum in promoting the formation of mixed-species biofilms

It has been found previously that Bifidobacterium longum, Bacteroides ovatus, Enterococcus faecalis, and Lactobacillus gasseri can form a biofilm better when co-cultured in vitro and B. longum is the core biofilm-formation-promoting strain in this community. B. longum is part of the core microbiota in the gut and is widely recognized as a probiotic. Therefore, it is necessary to explore its role in mixed-species biofilms through transcriptomics and metabolomics. Metabolomics showed that the increase in amino acid and purine content could promote biofilm formation. In transcriptomic analysis, many genes related to carbohydrate metabolism, amino acid metabolism, and environmental tolerance of B. longum were up-regulated. Combined with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis, the differentially expressed genes (DEGs) of B. longum in mixed-species biofilms were mainly correlated to "quorum sensing (QS)", "ABC transporters", "biosynthesis of amino acids", "microbial metabolism in different environments", "carbohydrate metabolism" and "two-component system". In addition, the rpl and rps gene families, which function in the metabolism of organic substances and the biosynthesis of amino acids, were the core DEGs according to the analysis of the protein-protein interaction (PPI) network. Finally, by combining metabolomics and quorum sensing mechanisms, it was found that the metabolism of autoinducer peptides (proliylglycine and glycylleucine), N-acyl homoserine lactone (N-(3-oxo hydroxy) homoserine lactone), and AI-2 can promote the formation of biofilms, both mono- and mixed-species biofilms composed of B. longum. Our research enabled us to understand the critical role of B. longum in mixed-species biofilms and the interactions between biofilm metabolism and gut health. In addition, the generated knowledge will be of great significance for us to develop biofilm products with beneficial functions in future.

Regulation of biofilm formation in Zymomonas mobilis to enhance stress tolerance by heterologous expression of pfs and luxS

Zymomonas mobilis is a potential alternative of Saccharomyces cerevisiae to produce cellulosic ethanol with strengths in cofactor balance, but its lower tolerance to inhibitors in the lignocellulosic hydrolysate restricts the application. Although biofilm can improve bacteria stress tolerance, regulating biofilm formation in Z. mobilis is still a challenge. In this work, we constructed a pathway by heterologous expressing pfs and luxS from Escherichia coli in Z. mobilis to produce AI-2 (autoinducer 2), a universal quorum-sensing signal molecule, to control cell morphology for enhancing stress tolerance. Unexpectedly, the results suggested that neither endogenous AI-2 nor exogenous AI-2 promoted biofilm formation, while heterologous expression of pfs can significantly raise biofilm. Therefore, we proposed that the main factor in assisting biofilm formation was the product accumulated due to heterologous expression of pfs, like methylated DNA. Consequently, ZM4::pfs produced more biofilm, which presented an enhanced tolerance to acetic acid. All these findings provide a novel strategy to improve the stress tolerance of Z. mobilis by enhancing biofilm formation for efficient production of lignocellulosic ethanol and other value-added chemical products.

Response mechanism of microbial community during anaerobic biotransformation of marine toxin domoic acid

Domoic acid (DA) is a potent neurotoxin produced by toxigenic Pseudo-nitzschia blooms and quickly transfers to the benthic anaerobic environment by marine snow particles. DA anaerobic biotransformation is driven by microbial interactions, in which trace amounts of DA can cause physiological stress in marine microorganisms. However, the underlying response mechanisms of microbial community to DA stress remain unclear. In this study, we utilized an anaerobic marine DA-degrading consortium GLY (using glycine as co-substrate) to systematically investigate the global response mechanisms of microbial community during DA anaerobic biotransformation.16S rRNA gene sequencing and metatranscriptomic analyses were applied to measure microbial community structure, function and metabolic responses. Results showed that DA stress markedly changed the composition of main species, with increased levels of Firmicutes and decreased levels of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several genera of tolerated bacteria (Bacillus and Solibacillus) were increased, while, Stenotrophomonas, Sphingomonas and Acinetobacter were decreased. Metatranscriptomic analyses indicated that DA stimulated the expression of quorum sensing, extracellular polymeric substance (EPS) production, sporulation, membrane transporters, bacterial chemotaxis, flagellar assembly and ribosome protection in community, promoting bacterial adaptation ability under DA stress. Moreover, amino acid metabolism, carbohydrate metabolism and lipid metabolism were modulated during DA anaerobic biotransformation to reduce metabolic burden, increase metabolic demands for EPS production and DA degradation. This study provides the new insights into response of microbial community to DA stress and its potential impact on benthic microorganisms in marine environments.

Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities

Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.

Optimization of environmental factors in a dual in vitro biofilm model of Candida albicans-Streptococcus mutans

The biofilm formation of Streptococcus mutans-Candida albicans is an important virulence factor for dental caries. The purpose of this study was to determine the effect of some environmental conditions on the biofilm formation like inoculation concentration, temperature, sugar, amino acid, metal ions and saliva, and then establish a persistent in vitro biofilm model for further research. Based on the single factor experiment, the factors participating in the biofilm formation including sugar, inoculation concentration, and saliva increased the biofilm mass, while amino acid, metal ions, temperatures reduced biofilm mass. Optimal conditions for biofilm formation were the inoculation dosage of S. mutans and C. albicans of 10⁸ and 10⁷ , respectively, the addition of 0·3 g l^-1 sucrose and sterile saliva. These results contribute to a deep understanding of the factors involved in oral biofilm formation of the important cariogenic pathogen S. mutans and the opportunistic pathogen C. albicans to study better for biofilm and promote the design of new therapeutic approaches. The present research also provides a model for evaluating the therapeutic potential for drugs in the future.

Molecular genetics for probiotic engineering: dissecting lactic acid bacteria

The composition of the gut microbiome is greatly influenced by nutrition and dietary alterations which can also induce large temporary microbial shifts. However, the molecular mechanisms that promote these changes remain to be determined. Species of the family Lactobacillaceae and Bacillus species are genetically manipulatable bacteria that are naturally found in the human gastrointestinal (GI) tract and are often considered models of beneficial microbiota. Here, we identify specific conserved molecular pathways that play a key role in host colonization by beneficial members of the microbiota. In particular, we highlight three pathways important to the success of lactic acid bacteria (LAB) in the GI tract: glycolysis and fermentation, microbial communication via membrane vesicles, and condition-dependent antibiotic production. We elaborate on how the understanding of these circuits can lead to the development of novel therapeutic approaches to combat GI tract infections.

Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation

Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.

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.

Bacterial signalling mechanism: An innovative microbial intervention with multifaceted applications in microbial electrochemical technologies: A review

Microbial electrochemical technologies (METs) are a set of inventive tools that generate value-added by-products with concomitant wastewater remediation. However, due to the bottlenecks, like higher fabrication cost and inferior yield of resources, these inventive METs are still devoid of successful field-scale implementation. In this regard, application of quorum sensing (QS) mechanism to improve the power generation of the METs has gained adequate attention. The QS is an intercellular signalling mechanism that controls the bacterial social network in its vicinity via the synthesis of diffusible signal molecules labelled as auto inducers, thus ameliorating yield of valuables produced through METs. This state-of-the-art review elucidates different types of QS molecules and their working mechanism with the special focus on the widespread application of QS in the field of METs for their performance enhancement. Thus, this review intends to guide the researchers in rendering scalability to METs by integrating innovative QS mechanisms into them.

Cut the noise or couple up: Coordinating circadian and synthetic clocks

Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.

Two Lysine Sites That Can Be Malonylated Are Important for LuxS Regulatory Roles in Bacillus velezensis

S-ribosylhomocysteine lyase (LuxS) has been shown to regulate bacterial multicellular behaviors, typically biofilm formation. However, the mechanisms for the regulation are still mysterious. We previously identified a malonylation modification on K124 and K130 of the LuxS in the plant growth-promoting rhizobacterium B. velezensis (FZB42). In this work, we investigated the effects of the two malonylation sites on biofilm formation and other biological characteristics of FZB42. The results showed that the K124R mutation could severely impair biofilm formation, swarming, and sporulation but promote AI-2 production, suggesting inhibitory effects of high-level AI-2 on the features. All mutations (K124R, K124E, K130R, and K130E) suppressed FZB42 sporulation but increased its antibiotic production. The double mutations generally had a synergistic effect or at least equal to the effects of the single mutations. The mutation of K130 but not of K124 decreased the in vitro enzymatic activity of LuxS, corresponding to the conservation of K130 among various Bacillus LuxS proteins. From the results, we deduce that an alternative regulatory circuit may exist to compensate for the roles of LuxS upon its disruption. This study broadens the understanding of the biological function of LuxS in bacilli and underlines the importance of the two post-translational modification sites.

Molecular Characterization and Biofilm Formation Study of Contaminant Bacteria Isolated from Domiaty and Hungarian Cheeses in Jeddah City

The aim was to study the microbiological quality of Domiaty and Hungarian cheeses, molecular identification and biofilm formation of some selected contaminant bacteria. Samples were collected from two M and P big markets in Jeddah City through the period from February to October 2018, nine visits for two types of natural cheese. Results showed that the total bacterial counts (CFU/ml) from Domiaty cheese from two markets (M and P) were 0.1 x 105, 8 x 105 and 1 x 10 5 CFU/ml respectively (3 visits of M market) and 4 x 106, 0.4 x 106, 6.5 x 103, 1 x 103, 0.1 x 103 and 0.1 x 103 CFU/ml respectively (six samples from 6 visits from P market). Results showed that the total bacterial counts (CFU/ml) from Hungarian cheese were 1.5 x 10 5, 1x 10 4, 11 x 10 4 and 4 x10 6 CFU/ml respectively from (4 visits of M market) and 0.18 x 104, 3 x 106, 22 x 106, 6 x 106 and 5 x 104 CFU/ml respectively (5 visits from P market).Different bacterial isolates from cheese were identified by morphology and biochemical test. Bacterial isolates from cheeses were identified by VITEK MS as follow: Serratia liquefaciens (D6-1, D6-2, D14-1, D13-1 and D13-2), and Pseudomonas fluorescens (D14-2) were isolated from Domiaty cheese while Enterococcus faecium (H11-2), Serratia liquefaciens (H15-1) and Streptococcus thermophilus (H14-1) were isolated from Hungarian cheese. Some selected bacterial isolates were identified by 16S rRNA. Isolates were belong to MK757978 (Raoultilla terrigena (D15-1)), MK757979 (Bacillus cereus (D16-1)), MK757980 (Enterococcus faecalis (H10-2)), MK757982 (Enterococcus fiscalism (H11-1)), MK757981 (Serratia liquefactions (H13-1)), MK757984 (Anoxybacillus flavithermus (H17-1). All bacterial isolates have been tested for the formation of biofilm using a Tissue Culture Plate (TCP). Results revealed 12.5% and 46.15% of high biofilm formation respectively for bacterial isolates of Domiaty and Hungarian cheeses.

Microbial Biofilms in the Food Industry-A Comprehensive Review

Biofilms, present as microorganisms and surviving on surfaces, can increase food cross-contamination, leading to changes in the food industry’s cleaning and disinfection dynamics. Biofilm is an association of microorganisms that is irreversibly linked with a surface, contained in an extracellular polymeric substance matrix, which poses a formidable challenge for food industries. To avoid biofilms from forming, and to eliminate them from reversible attachment and irreversible stages, where attached microorganisms improve surface adhesion, a strong disinfectant is required to eliminate bacterial attachments. This review paper tackles biofilm problems from all perspectives, including biofilm-forming pathogens in the food industry, disinfectant resistance of biofilm, and identification methods. As biofilms are largely responsible for food spoilage and outbreaks, they are also considered responsible for damage to food processing equipment. Hence the need to gain good knowledge about all of the factors favouring their development or growth, such as the attachment surface, food matrix components, environmental conditions, the bacterial cells involved, and electrostatic charging of surfaces. Overall, this review study shows the real threat of biofilms in the food industry due to the resistance of disinfectants and the mechanisms developed for their survival, including the intercellular signalling system, the cyclic nucleotide second messenger, and biofilm-associated proteins.

Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

BACKGROUND

Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity.

RESULTS

The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes.

CONCLUSIONS

Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

Exploring interfacial dynamics in homodimeric S-ribosylhomocysteine lyase (LuxS) from Vibrio cholerae through molecular dynamics simulations

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme. The dynamics of the interfacial region were investigated in terms of inter-residual contacts and the associated interface area of the enzyme in its ligand-free and ligand–bound states which produced characteristics contrast in the interfacial dynamics. Moreover, the binding patterns of the two inhibitors (RHC and KRI) to the enzyme forming two different enzyme–ligand complexes were analyzed which pointed towards a varying inhibition potential of the inhibitors as also revealed by the free energies of ligand binding. It is shown that KRI is a more potent inhibitor than RHC – a substrate analogue, showing correlation with experimental data. Moreover, the role of a loop in chain B of the enzyme was found to facilitate the binding of RHC similar to that of the substrate, while KRI demonstrates a differing binding pattern. The computation of the free energy of binding for the two ligands was also carried out via thermodynamic integration which ultimately served to correlate the dynamical properties with the inhibition potential of two different ligands against the enzyme. Furthermore, this successful study provides a rational to suggest novel LuxS inhibitors which could become promising candidates to treat the diseases caused by a broad variety of bacterial species.

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme.

Growth effects in oregano plants (Origanum vulgare L.) assessment through inoculation of bacteria isolated from crop fields located on desert soils

Bacteria can establish beneficial interactions with plants by acting as growth promoters and enhancing stress tolerance during plant interactions. Likewise, bacteria can develop multispecies communities where multiple interactions are possible. In this work, we assessed the physiological effects of three bacteria isolated from an arid environment (Bacillus niacini, Bacillus megaterium, and Moraxella osloensis) applied as single species or as a consortium on oregano (Origanum vulgare L.) plants. Moreover, we assessed the quorum-sensing (QS) signaling activity to determine the molecular communication between plant-growth-promoting bacteria. The plant inoculation with B. megaterium showed a positive effect on morphometric and physiologic parameters. However, no synergistic effects were observed when a bacterial consortium was inoculated. Likewise, activation of QS signaling in biofilm assays was observed only for interspecies interaction within the Bacillus genus, not for either interaction with M. osloensis. These results suggest a neutral or antagonistic interaction for interspecific bacterial biofilm establishment, as well as for the interaction with oregano plants when bacteria were inoculated in a consortium. In conclusion, we were able to determine that the bacterial interactions are not always positive or synergistic, but they also might be neutral or antagonistic.

Combination of beneficial bacteria improves blueberry production and soil quality

Blueberry is an important agricultural crop with high nutritional, health, and economic value. Despite the well-studied blueberry cultivation methods and soil requirements, little is known about how beneficial bacteria function in organic blueberry cultivation systems and their effects on acidic soils. In this study, a single bacteria Bacillus amyloliquefaciens JC65 and three biocontrol bacteria consortiums containing JC65 were applied to organic system. The effect of bacteria to blueberry growth, yield, fruit quality, and soil quality was investigated. A consortium of three mixed Bacillus (B. amyloliquefaciens JC65, B. licheniforims HS10 and B. subtilis 7ze3) showed the highest growth improvement efficiency. The bacterial inoculation increased blueberry leaf chlorophyll content, net photosynthetic rate by 21.50%, 13.21% at 30 days, and increased average plant height by 2.72% at 69 days. Compared with the control, the inoculated plants showed an increased yield of 14.56%. Interestingly, blueberry fruit quality was also improved with supplement of the bacterial consortium. Fruit anthocyanin, soluble sugar, vitamin C, soluble solids, and soluble protein content were increased by 5.99%, 4.21%, 17.31%, 2.41%, and 21.65%, respectively. Besides, beneficial bacterial consortium also enables sustainable agriculture by improving soil ammonium nitrogen and organic matter by 3.77% and 2.96% after blueberry planting. In conclusion, the combination of beneficial bacteria showed a synergistic activity in organic system to promote the blueberry yield, fruit quality, and soil nutrient preservation.

Mitigating Milk-Associated Bacteria through Inducing Zinc Ions Antibiofilm Activity

Dairy products are a sector heavily impacted by food loss, often due to bacterial contaminations. A major source of contamination is associated with the formation of biofilms by bacterial species adopted to proliferate in milk production environment and onto the surfaces of milk processing equipment. Bacterial cells within the biofilm are characterized by increased resistance to unfavorable environmental conditions and antimicrobial agents. Members of the Bacillus genus are the most commonly found spoilage microorganisms in the dairy environment. It appears that physiological behavior of these species is somehow depended on the availability of bivalent cations in the environment. One of the important cations that may affect the bacterial physiology as well as survivability are Zn²⁺ ions. Thus, the aim of this study was to examine the antimicrobial effect of Zn²⁺ ions, intending to elucidate the potential of a zinc-based antibacterial treatment suitable for the dairy industry. The antimicrobial effect of different doses of ZnCl₂ was assessed microscopically. In addition, expression of biofilm related genes was evaluated using RT-PCR. Analysis of survival rates following heat treatment was conducted in order to exemplify a possible applicative use of Zn²⁺ ions. Addition of zinc efficiently inhibited biofilm formation by B. subtilis and further disrupted the biofilm bundles. Expression of matrix related genes was found to be notably downregulated. Microscopic evaluation showed that cell elongation was withheld when cells were grown in the presence of zinc. Finally, B. cereus and B. subtilis cells were more susceptible to heat treatment after being exposed to Zn²⁺ ions. It is believed that an anti-biofilm activity, expressed in downregulation of genes involved in construction of the extracellular matrix, would account for the higher sensitivity of bacteria during heat pasteurization. Consequently, we suggest that Zn²⁺ ions can be of used as an effective antimicrobial treatment in various applications in the dairy industry, targeting both biofilms and vegetative bacterial cells.

Potential of N2 Gas Flushing to Hinder Dairy-Associated Biofilm Formation and Extension

Worldwide, the dairy sector remains of vital importance for food production despite severe environmental constraints. The production and handling conditions of milk, a rich medium, promote inevitably the entrance of microbial contaminants, with notable impact on the quality and safety of raw milk and dairy products. Moreover, the persistence of high concentrations of microorganisms (especially bacteria and bacterial spores) in biofilms (BFs) present on dairy equipment or environments constitutes an additional major source of milk contamination from pre- to post-processing stages: in dairies, BFs represent a major concern regarding the risks of disease outbreaks and are often associated with significant economic losses. One consumption trend toward "raw or low-processed foods" combined with current trends in food production systems, which tend to have more automation and longer processing runs with simultaneously more stringent microbiological requirements, necessitate the implementation of new and obligatory sustainable strategies to respond to new challenges regarding food safety. Here, in light of studies, performed mainly with raw milk, that considered dominant "planktonic" conditions, we reexamine the changes triggered by cold storage alone or combined with nitrogen gas (N2) flushing on bacterial populations and discuss how the observed benefits of the treatment could also contribute to limiting BF formation in dairies.

Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure

In the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment.

Strain variability in biofilm formation: A food safety and quality perspective

The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as "strain variability", are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.

Evaluation of two fixation techniques for direct observation of biofilm formation of Bacillus subtilis in situ, on Congo red agar, using scanning electron microscopy

BACKGROUND AND AIM

Direct observation, scanning electron microscopy (SEM) is a common method used for the observations of biofilms. N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide) (EDC) fixation method has proven to be a valuable fixation method in the observation of these biofilms. Still, it entails a method of biofilm fixation that can damage slim structures, leading to the impossible observation of biofilm development. In contrast, alcian blue and lysine (ABL) fixation technique appears more glycocalyx of biofilm, fully preserved samples, which may provide much insight into the development of B. subtilis biofilms.

MATERIALS AND METHODS

Here, the evaluation of the fixation of ABL technique for the study of B. subtilis biofilms was carried out in situ, on Congo red agar. In doing so, the comparison to commonly use conventional EDC technique for sample fixation, and observation was carried out. Observations were based on SEM over 30 samples.

RESULTS

Overall, ABL technique provided excellent observation of biofilms formed in situ, on Congo red agar, and revealed slime structures, which have not been observed, much in standard EDC fixation or earlier in other studies of these biofilms in B. subtilis.

CONCLUSION

This study reported the appropriate use of ABL in the fixation technique for the preservation of biofilm of B. subtilis.

Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana

Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant-microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields.

The impact of Paenibacillus polymyxa HY96-2 luxS on biofilm formation and control of tomato bacterial wilt

The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation and biocontrol efficacy against Ralstonia solanacearum by Paenibacillus polymyxa HY96-2. luxS mutants were constructed and assayed for biofilm formation of the wild-type (WT) strain and luxS mutants of P. polymyxa HY96-2 in vitro and in vivo. The results showed that luxS positively regulated the biofilm formation of HY96-2. Greenhouse experiments of tomato bacterial wilt found that from the early stage to late stage postinoculation, the biocontrol efficacy of the luxS deletion strain was the lowest with 50.70 ± 1.39% in the late stage. However, the luxS overexpression strain had the highest biocontrol efficacy with 75.66 ± 1.94% in the late stage. The complementation of luxS could restore the biocontrol efficacy of the luxS deletion strain with 69.84 ± 1.09% in the late stage, which was higher than that of the WT strain with 65.94 ± 2.73%. Therefore, we deduced that luxS could promote the biofilm formation of P. polymyxa HY96-2 and further promoted its biocontrol efficacy against R. solanacearum.

Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts

Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.

Creating an in vivo bifunctional gene expression circuit through an aptamer-based regulatory mechanism for dynamic metabolic engineering in Bacillus subtilis

Aptamer-based regulatory biosensors can dynamically regulate the expression of target genes in response to ligands and could be used in dynamic metabolic engineering for pathway optimization. However, the existing aptamer-ligand biosensors can only function with non-complementary DNA elements that cannot replicate in growing cells. Here, we construct an aptamer-based synthetic regulatory circuit that can dynamically upregulate and downregulate the expression of target genes in response to the ligand thrombin at transcriptional and translational levels, respectively, and further used this system to dynamically engineer the synthesis of 2'-fucosyllactose (2'-FL) in Bacillus subtilis. First, we demonstrated the binding of ligand molecule thrombin with the aptamer can induce the unwinding of fully complementary double-stranded DNA. Based on this finding, we constructed a bifunctional gene expression regulatory circuit using ligand thrombin-bound aptamers. The expression of the reporter gene ranged from 0.084- to 48.1-fold. Finally, by using the bifunctional regulatory circuit, we dynamically upregulated the expression of key genes fkp and futC and downregulated the expression of gene purR, resulting in the significant increase of 2'-FL titer from 24.7 to 674 mg/L. Compared with the other pathway-specific dynamic engineering systems, here the constructed aptamer-based regulatory circuit is independent of pathways, and can be generally used to fine-tune gene expression in other microbes.

Mixed-species biofilms in the food industry: Current knowledge and novel control strategies

Attachment of microorganisms to food contact surfaces and the subsequent formation of biofilms may cause equipment damage, food spoilage and even diseases. Mixed-species biofilms are ubiquitous in the food industry and they generally exhibit higher resistance to disinfectants and antimicrobials compared to single-species biofilms. The physiology and metabolic activity of microorganisms in mixed-species biofilms are however rather complicated to study, and despite targeted research efforts, the potential role of mixed-species biofilms in food industry is still rather unexplored. In this review, we summarize recent studies in the context of bacterial social interactions in mixed-species biofilms, resistance to disinfectants, detection methods, and potential novel strategies to control the formation of mixed-species biofilms for enhanced food safety and food quality.

Interference With Quorum-Sensing Signal Biosynthesis as a Promising Therapeutic Strategy Against Multidrug-Resistant Pathogens

Faced with the global health threat of increasing resistance to antibiotics, researchers are exploring interventions that target bacterial virulence factors. Quorum sensing is a particularly attractive target because several bacterial virulence factors are controlled by this mechanism. Furthermore, attacking the quorum-sensing signaling network is less likely to select for resistant strains than using conventional antibiotics. Strategies that focus on the inhibition of quorum-sensing signal production are especially attractive because the enzymes involved are expressed in bacterial cells but are not present in their mammalian counterparts. We review here various approaches that are being taken to interfere with quorum-sensing signal production via the inhibition of autoinducer-2 synthesis, PQS synthesis, peptide autoinducer synthesis, and N-acyl-homoserine lactone synthesis. We expect these approaches will lead to the discovery of new quorum-sensing inhibitors that can help to stem the tide of antibiotic resistance.

Biofilms in Food Processing Environments: Challenges and Opportunities

This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.

Insights into Bacterial Milk Spoilage with Particular Emphasis on the Roles of Heat-Stable Enzymes, Biofilms, and Quorum Sensing

Milk spoilage caused by psychrotrophic bacteria and their heat-stable enzymes is a serious challenge for the dairy industry. In many studies, spoilage has been explored based on the simplistic view of undesirable enzymes produced by planktonic cells. Recently, biofilms and quorum sensing (QS) have been suggested as important factors in the deterioration of milk, which opens new avenues for investigation of the processes and challenges. Production and heat stability of enzymes are enhanced in biofilms, mainly because of inherent differences in physiological states and protective shielding by extracellular polymeric substances. QS plays a key role in modulating expression of hydrolytic enzymes and biofilm formation. To date, few studies have been conducted to investigate the complex interplays of enzyme production, biofilm formation, and QS. This review provides novel insights into milk spoilage with particular emphasis on the roles of biofilms and QS and summarizes potential effective strategies for controlling the spoilage of milk.

Cell wall associated protein TasA provides an initial binding component to extracellular polysaccharides in dual-species biofilm

Many bacteria in biofilm surround themselves by an extracellular matrix composed mainly of extracellular polysaccharide (EP), proteins such as amyloid-like fibers (ALF) and nucleic acids. While the importance of EP in attachment and acceleration of biofilm by a number of different bacterial species is well established, the contribution of ALF to attachment in multispecies biofilm remains unknown. The study presented here aimed to investigate the role of TasA, a precursor for ALF, in cell-cell interactions in dual-species biofilms of Bacillus subtilis and Streptococcus mutans. Expression of major B. subtilis matrix operons was significantly up-regulated in the presence of S. mutans during different stages of biofilm formation, suggesting that the two species interacted and modulated gene expression in each other. Wild-type B. subtilis expressing TasA adhered strongly to S. mutans biofilm, while a TasA-deficient mutant was less adhesive and consequently less abundant in the dual-species biofilm. Dextran, a biofilm polysaccharide, induced aggregation of B. subtilis and stimulated adhesion to S. mutans biofilms. This effect was only observed in the wild-type strain, suggesting that interactions between TasA and dextran-associated EP plays an important role in inter-species interactions during initial stages of multispecies biofilm development.

Identification of diacetonamine from soybean curd residue as a sporulation-inducing factor toward Bacillus spp

Under bioassay-guided investigation, a sporulation-inducing factor (SIF) toward Bacillus spp. was searched for in methanol (MeOH) extracts of soybean curd residues, and diacetonamine (1) was identified as the active compound. SIF was first isolated as a monoacetylated derivative (2, 4.1 mg from 655 g soybean curd residues), and its chemical structure was elucidated by field desorption mass spectrometry, electron ionization mass spectrometry, and nuclear magnetic resonance (NMR) analyses. After 48-h incubation, 40 µM diacetonamine hydrochloride (1b) exhibited sporulation-inducing activity with 35% sporulation frequency toward a Bacillus amyloliquefaciens wild-type strain (AHU 2170), whereas 40 µM diacetone acrylamide (3) showed 99% sporulation induction, which was much higher than that of 1b. Although Bacillus megaterium NBRC 15308 was sporulated by the treatment with 400 µM 1b with 36 and 70% sporulation frequency after 72- and 96-h incubation respectively, 3 at the same concentration showed only 2% sporulation after 72-h incubation. Hence, diacetonamine (1) was characterized as a genuine SIF from soybean curd residues, but it was uncertain whether 1 is a natural product or an artifact. Spores of B. amyloliquefaciens induced by 1b survived after treatment with heating at 95 °C for 10 min, also suggesting that 1 is genuine SIF in soybean curd residue. As sporulation induction is likely linked to activation of antibiotic production in some spore-forming Firmicutes bacteria, compound 1 would be a possible chemical tool to develop an effective fermentation technology in Bacillus species.

Bacillus subtilis Biofilm Development - A Computerized Study of Morphology and Kinetics

Biofilm is commonly defined as accumulation of microbes, embedded in a self-secreted extra-cellular matrix, on solid surfaces or liquid interfaces. In this study, we analyze several aspects of Bacillus subtilis biofilm formation using tools from the field of image processing. Specifically, we characterize the growth kinetics and morphological features of B. subtilis colony type biofilm formation and compare these in colonies grown on two different types of solid media. Additionally, we propose a model for assessing B. subtilis biofilm complexity across different growth conditions. GFP-labeled B. subtilis cells were cultured on agar surfaces over a 4-day period during which microscopic images of developing colonies were taken at equal time intervals. The images were used to perform a computerized analysis of few aspects of biofilm development, based on features that characterize the different phenotypes of B. subtilis colonies. Specifically, the analysis focused on the segmented structure of the colonies, consisting of two different regions of sub-populations that comprise the biofilm – a central “core” region and an “expanding” region surrounding it. Our results demonstrate that complex biofilm of B. subtillis grown on biofilm-promoting medium [standard lysogeny broth (LB) supplemented with manganese and glycerol] is characterized by rapidly developing three-dimensional complex structure observed at its core compared to biofilm grown on standard LB. As the biofilm develops, the core size remains largely unchanged during development and colony expansion is mostly attributed to the expansion in area of outer cell sub-populations. Moreover, when comparing the bacterial growth on biofilm-promoting agar to that of colonies grown on LB, we found a significant decrease in the GFP production of colonies that formed a more complex biofilm. This suggests that complex biofilm formation has a diminishing effect on cell populations at the biofilm core, likely due to a combination of reduced metabolic rate and increased levels of cell death within this region.

Enrichment of milk with magnesium provides healthier and safer dairy products

Biofilms on the surfaces of milk-processing equipment are often a major source of contamination of dairy products. Members of the genus Bacillus appear to be among the most commonly found bacteria in dairy farms and processing plants. Bacillus species may thrive in dairy farm equipment and in dairy products since they can form robust biofilms during growth within milk. We found that fortification of milk with magnesium mitigated biofilm formation by Bacillus species, and thus could notably reduce dairy product spoilage. We also show that the mode of action of Mg²⁺ ions is specific to inhibition of transcription of genes involved in biofilm formation. Our further findings indicate that in the presence of Mg²⁺ bacterial cells are hypersensitive to the heat pasteurization applied during milk processing. Additionally, we demonstrated that enrichment of milk with magnesium improved technological properties of milk products such as soft cheeses. Finally, we report that there is a notable increase in the intestinal bioavailability potential of magnesium from supplemented milk compared with that from non-supplemented milk.

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis

The soil bacterium Bacillus subtilis is often found in association with plants in the rhizosphere. Previously, plant polysaccharides have been shown to stimulate formation of root-associated multicellular communities, or biofilms, in this bacterium, yet the underlying mechanism is not fully understood. A five-gene gan operon (ganSPQAB) in B. subtilis has recently been shown to be involved in utilization of the plant-derived polysaccharide galactan. Despite these findings, molecular details about the regulation of the operon and the role of the operon in biofilm formation remain elusive. In this study, we performed comprehensive genetic analyses on the regulation of the gan operon. We show that this operon is regulated both by a LacI-like transcription repressor (GanR), which directly binds to pairs of inverted DNA repeats in the promoter region of the operon, and by the catabolite control protein A (CcpA). Derepression can be triggered by the presence of the inducer β-1,4-galactobiose, a hydrolysis product of galactan, or in situ when B. subtilis cells are associated with plant roots. In addition to the transcriptional regulation, the encoded ß-galactosidase GanA (by ganA), which hydrolyzes ß-1,4-galactobiose into galactose, is inhibited at the enzymatic level by the catalytic product galactose. Thus, the galactan utilization pathway is under complex regulation involving both positive and negative feedback mechanisms in B. subtilis. We discuss about the biological significance of such complex regulation as well as a hypothesis of biofilm induction by galactan via multiple mechanisms.

New Weapons to Fight Old Enemies: Novel Strategies for the (Bio)control of Bacterial Biofilms in the Food Industry

Biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, DNA and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. Biofilm formation enhances the ability of the producer/s to persist in a given environment. Pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem for the healthcare and food industries, as their biofilm-forming ability protects them from common cleaning processes and allows them to remain in the environment post-sanitation. In the food industry, persistent bacteria colonize the inside of mixing tanks, vats and tubing, compromising food safety and quality. Strategies to overcome bacterial persistence through inhibition of biofilm formation or removal of mature biofilms are therefore necessary. Current biofilm control strategies employed in the food industry (cleaning and disinfection, material selection and surface preconditioning, plasma treatment, ultrasonication, etc.), although effective to a certain point, fall short of biofilm control. Efforts have been explored, mainly with a view to their application in pharmaceutical and healthcare settings, which focus on targeting molecular determinants regulating biofilm formation. Their application to the food industry would greatly aid efforts to eradicate undesirable bacteria from food processing environments and, ultimately, from food products. These approaches, in contrast to bactericidal approaches, exert less selective pressure which in turn would reduce the likelihood of resistance development. A particularly interesting strategy targets quorum sensing systems, which regulate gene expression in response to fluctuations in cell-population density governing essential cellular processes including biofilm formation. This review article discusses the problems associated with bacterial biofilms in the food industry and summarizes the recent strategies explored to inhibit biofilm formation, with special focus on those targeting quorum sensing.

Bacillus cereus Biofilms-Same, Only Different

Bacillus cereus displays a high diversity of lifestyles and ecological niches and include beneficial as well as pathogenic strains. These strains are widespread in the environment, are found on inert as well as on living surfaces and contaminate persistently the production lines of the food industry. Biofilms are suspected to play a key role in this ubiquitous distribution and in this persistency. Indeed, B. cereus produces a variety of biofilms which differ in their architecture and mechanism of formation, possibly reflecting an adaptation to various environments. Depending on the strain, B. cereus has the ability to grow as immersed or floating biofilms, and to secrete within the biofilm a vast array of metabolites, surfactants, bacteriocins, enzymes, and toxins, all compounds susceptible to act on the biofilm itself and/or on its environment. Within the biofilm, B. cereus exists in different physiological states and is able to generate highly resistant and adhesive spores, which themselves will increase the resistance of the bacterium to antimicrobials or to cleaning procedures. Current researches show that, despite similarities with the regulation processes and effector molecules involved in the initiation and maturation of the extensively studied Bacillus subtilis biofilm, important differences exists between the two species. The present review summarizes the up to date knowledge on biofilms produced by B. cereus and by two closely related pathogens, Bacillus thuringiensis and Bacillus anthracis. Economic issues caused by B. cereus biofilms and management strategies implemented to control these biofilms are included in this review, which also discuss the ecological and functional roles of biofilms in the lifecycle of these bacterial species and explore future developments in this important research area.