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Virtual screening of plant compounds and nonsteroidal anti-inflammatory drugs for inhibition of quorum sensing and biofilm formation in Salmonella.
Almeida, FA, Vargas, ELG, Carneiro, DG, Pinto, UM, Vanetti, MCD
Microbial pathogenesis. 2018;:369-388
Abstract
Salmonella belongs to the Enterobacteriaceae family which is widely distributed in the environment due to its adaptive capacity to stress conditions. In addition, Salmonella is able to perform a type of cell-to-cell communication called quorum sensing, which leads to differential gene expression. The quorum sensing system mediated by AI-1, acyl homoserine lactones (AHLs), is incomplete in Salmonella because the luxI homolog gene, which encodes for AI-1 synthase, is missing in the genome. However, a homologue of LuxR, known as SdiA, is present and allows the detection of signaling molecules produced by other species of bacteria, leading to regulation of gene expression, mainly related to virulence and biofilm formation. Thus, in view of the importance of quorum sensing on the physiology regulation of microorganisms, the aim of the present study was to perform a virtual screening of plant compounds and nonsteroidal anti-inflammatory drugs (NASIDs) for inhibition of quorum sensing by molecular docking and biofilm formation in Salmonella. In general, most plant compounds and all NSAIDs bound in, at least, one of the three modeled structures of SdiA proteins of Salmonella Enteritidis PT4 578. In addition, many tested compounds had higher binding affinities than the AHLs and the furanones which are inducers and inhibitors of quorum sensing, respectively. The Z-phytol and lonazolac molecules were good candidates for the in vitro inhibition tests of quorum sensing mediated by AI-1 and biofilm formation in Salmonella. Thus, this study directs future prospecting of plant extracts for inhibition of quorum sensing mechanism depending on AHL and biofilm formation. In addition, the use of inhibitors of quorum sensing and biofilm formation can be combined with antibiotics for better treatment efficacy, as well as the use of these compounds to design new drugs.
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Oral fungal-bacterial biofilm models in vitro: a review.
Chevalier, M, Ranque, S, Prêcheur, I
Medical mycology. 2018;(6):653-667
Abstract
Inclusion of fungi as commensals in oral biofilm is an important innovation in oral biology, and this work aimed to review the literature on the available biofilm and related disease in vitro models. Actually, thousands of bacterial and around one hundred of fungal phylotypes can colonize the oral cavity. Taxonomic profiling combined with functional expression analysis has revealed that Candida albicans, Streptococcus mutans and prominent periodontopathogens are not always present or numerically important in candidiasis, caries, or periodontitis lesions. However, C. albicans combined with Streptococcus spp. co-increase their virulence in invasive candidiasis, early childhood caries or peri-implantitis. As Candida species and many other fungi are also members of oral microcosms in healthy individuals, mixed fungal-bacterial biofilm models are increasingly valuable investigative tools, and new fungal-bacterial species combinations need to be investigated. Here we review the key points and current methods for culturing in vitro mixed fungal-bacterial models of oral biofilms. According to ecosystem under study (health, candidiasis, caries, periodontitis), protocol design will select microbial strains, biofilm support (polystyrene plate, cell culture, denture, tooth, implant), pre-treatment support (human or artificial saliva) and culture conditions. Growing mixed fungal-bacterial biofilm models in vitro is a difficult challenge. But reproducible models are needed, because oral hygiene products, food and beverage, medication, licit and illicit drugs can influence oral ecosystems. So, even though most oral fungi and bacteria are not cultivable, in vitro microbiological models should still be instrumental in adapting oral care products, dietary products and care protocols to patients at higher risk of oral diseases. Microbial biofilm models combined with oral epithelial cell cultures could also aid in understanding the inflammatory reaction.
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What are the advantages of living in a community? A microbial biofilm perspective!
Santos, ALSD, Galdino, ACM, Mello, TP, Ramos, LS, Branquinha, MH, Bolognese, AM, Columbano Neto, J, Roudbary, M
Memorias do Instituto Oswaldo Cruz. 2018;(9):e180212
Abstract
Biofilm formation is the preferred mode of growth lifestyle for many microorganisms, including bacterial and fungal human pathogens. Biofilm is a strong and dynamic structure that confers a broad range of advantages to its members, such as adhesion/cohesion capabilities, mechanical properties, nutritional sources, metabolite exchange platform, cellular communication, protection and resistance to drugs (e.g., antimicrobials, antiseptics, and disinfectants), environmental stresses (e.g., dehydration and ultraviolet light), host immune attacks (e.g., antibodies, complement system, antimicrobial peptides, and phagocytes), and shear forces. Microbial biofilms cause problems in the hospital environment, generating high healthcare costs and prolonged patient stay, which can result in further secondary microbial infections and various health complications. Consequently, both public and private investments must be made to ensure better patient management, as well as to find novel therapeutic strategies to circumvent the resistance and resilience profiles arising from biofilm-associated microbial infections. In this work, we present a general overview of microbial biofilm formation and its relevance within the biomedical context.
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Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism.
Sheraton, MV, Yam, JKH, Tan, CH, Oh, HS, Mancini, E, Yang, L, Rice, SA, Sloot, PMA
Antimicrobial agents and chemotherapy. 2018;(5)
Abstract
Segregation of bacteria based on their metabolic activities in biofilms plays an important role in the development of antibiotic resistance. Mushroom-shaped biofilm structures, which are reported for many bacteria, exhibit topographically varying levels of multiple drug resistance from the cap of the mushroom to its stalk. Understanding the dynamics behind the formation of such structures can aid in design of drug delivery systems, antibiotics, or physical systems for removal of biofilms. We explored the development of metabolically heterogeneous Pseudomonas aeruginosa biofilms using numerical models and laboratory knockout experiments on wild-type and chemotaxis-deficient mutants. We show that chemotactic processes dominate the transformation of slender and hemispherical structures into mushroom structures with a signature cap. Cellular Potts model simulation and experimental data provide evidence that accelerated movement of bacteria along the periphery of the biofilm, due to nutrient cues, results in the formation of mushroom structures and bacterial segregation. Multidrug resistance of bacteria is one of the most threatening dangers to public health. Understanding the mechanisms of the development of mushroom-shaped biofilms helps to identify the multidrug-resistant regions. We decoded the dynamics of the structural evolution of bacterial biofilms and the physics behind the formation of biofilm structures as well as the biological triggers that produce them. Combining in vitro gene knockout experiments with in silico models showed that chemotactic motility is one of the main driving forces for the formation of stalks and caps. Our results provide physicists and biologists with a new perspective on biofilm removal and eradication strategies.
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5.
Application of phototrophic biofilms: from fundamentals to processes.
Strieth, D, Ulber, R, Muffler, K
Bioprocess and biosystems engineering. 2018;(3):295-312
Abstract
Biotechnological production of valuables by microorganisms is commonly achieved by cultivating the cells as suspended solids in an appropriate liquid medium. However, the main portion of these organisms features a surface-attached growth in their native habitats. The utilization of such biofilms shows significant challenges, e.g. concerning control of pH, nutrient supply, and heat/mass transfer. But the use of biofilms might also enable novel and innovative production processes addressing robustness and strength of the applied biocatalyst, for example if variable conditions might occur in the process or a feedstock (substrate) is changed in its composition. Besides the robustness of a biofilm, the high density of the immobilized biocatalyst facilitates a simple separation of the catalyst and the extracellular product, whereas intracellular target compounds occur in a concentrated form; thus, expenses for downstream processing can be drastically reduced. While phototrophic organisms feature a fabulous spectrum of metabolites ranging from biofuels to biologically active compounds, the low cell density of phototrophic suspension cultures is still limiting their application for production processes. The review is focusing on pro- and eukaryotic microalgae featuring the production of valuable compounds and highlights requirements for their cultivation as phototrophic biofilms, i.e. setup as well as operation of biofilm reactors, and modeling of phototrophic growth.
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6.
Bistable emergence of oscillations in growing Bacillus subtilis biofilms.
Martinez-Corral, R, Liu, J, Süel, GM, Garcia-Ojalvo, J
Proceedings of the National Academy of Sciences of the United States of America. 2018;(36):E8333-E8340
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Abstract
Biofilm communities of Bacillus subtilis bacteria have recently been shown to exhibit collective growth-rate oscillations mediated by electrochemical signaling to cope with nutrient starvation. These oscillations emerge once the colony reaches a large enough number of cells. However, it remains unclear whether the amplitude of the oscillations, and thus their effectiveness, builds up over time gradually or if they can emerge instantly with a nonzero amplitude. Here we address this question by combining microfluidics-based time-lapse microscopy experiments with a minimal theoretical description of the system in the form of a delay-differential equation model. Analytical and numerical methods reveal that oscillations arise through a subcritical Hopf bifurcation, which enables instant high-amplitude oscillations. Consequently, the model predicts a bistable regime where an oscillating and a nonoscillating attractor coexist in phase space. We experimentally validate this prediction by showing that oscillations can be triggered by perturbing the media conditions, provided the biofilm size lies within an appropriate range. The model also predicts that the minimum size at which oscillations start decreases with stress, a fact that we also verify experimentally. Taken together, our results show that collective oscillations in cell populations can emerge suddenly with nonzero amplitude via a discontinuous transition.
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Amyloid-Like β-Aggregates as Force-Sensitive Switches in Fungal Biofilms and Infections.
Lipke, PN, Klotz, SA, Dufrene, YF, Jackson, DN, Garcia-Sherman, MC
Microbiology and molecular biology reviews : MMBR. 2018;(1)
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Abstract
Cellular aggregation is an essential step in the formation of biofilms, which promote fungal survival and persistence in hosts. In many of the known yeast cell adhesion proteins, there are amino acid sequences predicted to form amyloid-like β-aggregates. These sequences mediate amyloid formation in vitro. In vivo, these sequences mediate a phase transition from a disordered state to a partially ordered state to create patches of adhesins on the cell surface. These β-aggregated protein patches are called adhesin nanodomains, and their presence greatly increases and strengthens cell-cell interactions in fungal cell aggregation. Nanodomain formation is slow (with molecular response in minutes and the consequences being evident for hours), and strong interactions lead to enhanced biofilm formation. Unique among functional amyloids, fungal adhesin β-aggregation can be triggered by the application of physical shear force, leading to cellular responses to flow-induced stress and the formation of robust biofilms that persist under flow. Bioinformatics analysis suggests that this phenomenon may be widespread. Analysis of fungal abscesses shows the presence of surface amyloids in situ, a finding which supports the idea that phase changes to an amyloid-like state occur in vivo. The amyloid-coated fungi bind the damage-associated molecular pattern receptor serum amyloid P component, and there may be a consequential modulation of innate immune responses to the fungi. Structural data now suggest mechanisms for the force-mediated induction of the phase change. We summarize and discuss evidence that the sequences function as triggers for protein aggregation and subsequent cellular aggregation, both in vitro and in vivo.
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Extracellular matrix influence in Streptococcus mutans gene expression in a cariogenic biofilm.
Florez Salamanca, EJ, Klein, MI
Molecular oral microbiology. 2018;(2):181-193
Abstract
Caries etiology is biofilm-diet-dependent. Biofilms are highly dynamic and structured microbial communities enmeshed in a three-dimensional extracellular matrix. The study evaluated the expression dynamics of Streptococcus mutans genes associated with exopolysaccharides (EPS) (gtfBCD, gbpB, dexA), lipoteichoic acids (LTA) (dltABCD, SMU_775c) and extracellular DNA (eDNA) (lytST, lrgAB, ccpA) during matrix development within a mixed-species biofilm of S. mutans, Actinomyces naeslundii and Streptococcus gordonii. Mixed-species biofilms using S. mutans strains UA159 or ΔgtfB formed on saliva-coated hydroxyapatite discs were submitted to a nutritional challenge (providing an abundance of sucrose and starch). Biofilms were removed at eight developmental stages for gene expression analysis by quantitative polymerase chain reaction. The pH of spent culture media remained acidic throughout the experimental periods, being lower after sucrose and starch exposure. All genes were expressed at all biofilm developmental phases. EPS- and LTA-associated genes had a similar expression profile for both biofilms, presenting lower levels of expression at 67, 91 and 115 hours and a peak of expression at 55 hours, but having distinct expression magnitudes, with lower values for ΔgtfB (eg, fold-difference of ~382 for gtfC and ~16 for dltB at 43 hours). The eDNA-associated genes presented different dynamics of expression between both strains. In UA159 biofilms lrgA and lrgB genes were highly expressed at 29 hours (which were ~13 and ~5.4 times vs ΔgtfB, respectively), whereas in ΔgtfB biofilms an inverse relationship between lytS and lrgA and lrgB expression was detected. Therefore, the deletion of gtfB influences dynamics and magnitude of expression of genes associated with matrix main components.
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Biofilms and beyond: expanding echinocandin utility.
Larkin, EL, Dharmaiah, S, Ghannoum, MA
The Journal of antimicrobial chemotherapy. 2018;(suppl_1):i73-i81
Abstract
Echinocandins have been in use for over 15 years, starting with the first approval in 2001. Current trends, such as increasing resistance to fluconazole and shifts toward non-albicans spp. of Candida, suggest a growing role for echinocandins, as reflected by recent (2016) updates to guidelines that recommend echinocandins as first-line treatment for candidaemia. The efficacy, tolerability, and safety of echinocandins and their target site of action (1,3-β-d-glucan synthesis) have prompted research into potential new uses, such as for treatment of biofilm infections, MDR Candida auris and dermatophytes. Moreover, new mycobiome discoveries linking inflammatory bowel disease (IBD; for instance Crohn's disease) to fungi have led to preliminary but encouraging data regarding echinocandin therapy and treatment of IBD. In this article, we will review the available evidence and potential utility of echinocandins and 1,3-β-d-glucan synthesis inhibition in these areas of emerging interest.
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Susceptibility patterns and the role of extracellular DNA in Staphylococcus epidermidis biofilm resistance to physico-chemical stress exposure.
Olwal, CO, Ang'ienda, PO, Onyango, DM, Ochiel, DO
BMC microbiology. 2018;(1):40
Abstract
BACKGROUND Over 65% of human infections are ascribed to bacterial biofilms that are often highly resistant to antibiotics and host immunity. Staphylococcus epidermidis is the predominant cause of recurrent nosocomial and biofilm-related infections. However, the susceptibility patterns of S. epidermidis biofilms to physico-chemical stress induced by commonly recommended disinfectants [(heat, sodium chloride (NaCl), sodium hypochlorite (NaOCl) and hydrogen peroxide (H2O2)] in domestic and human healthcare settings remains largely unknown. Further, the molecular mechanisms of bacterial biofilms resistance to the physico-chemical stresses remain unclear. Growing evidence demonstrates that extracellular DNA (eDNA) protects bacterial biofilms against antibiotics. However, the role of eDNA as a potential mechanism underlying S. epidermidis biofilms resistance to physico-chemical stress exposure is yet to be understood. Therefore, this study aimed to evaluate the susceptibility patterns of and eDNA release by S. epidermidis biofilm and planktonic cells to physico-chemical stress exposure. RESULTS S. epidermidis biofilms exposed to physico-chemical stress conditions commonly recommended for disinfection [heat (60 °C), 1.72 M NaCl, solution containing 150 μL of waterguard (0.178 M NaOCl) in 1 L of water or 1.77 M H2O2] for 30 and 60 min exhibited lower log reductions of CFU/mL than the corresponding planktonic cells (p < 0.0001). The eDNA released by sub-lethal heat (50 °C)-treated S. epidermidis biofilm and planktonic cells was not statistically different (p = 0.8501). However, 50 °C-treated S. epidermidis biofilm cells released significantly increased eDNA than the untreated controls (p = 0.0098). The eDNA released by 0.8 M NaCl-treated S. epidermidis biofilm and planktonic cells was not significantly different (p = 0.9697). Conversely, 5 mM NaOCl-treated S. epidermidis biofilms exhibited significantly increased eDNA release than the corresponding planktonic cells (p = 0.0015). Further, the 50 μM H2O2-treated S. epidermidis biofilms released significantly more eDNA than the corresponding planktonic cells (p = 0.021). CONCLUSIONS S. epidermidis biofilms were less susceptible to physico-chemical stress induced by the four commonly recommended disinfectants than the analogous planktonic cells. Further, S. epidermidis biofilms enhanced eDNA release in response to the sub-lethal heat and oxidative stress exposure than the corresponding planktonic cells suggesting a role of eDNA in biofilms resistance to the physico-chemical stresses.