Development and experimental evaluation of a steady-state, multispecies biofilm model

A steady-state model for quantifying the space competition in multispecies biofilms is developed. The model includes multiple active species, inert biomass, substrate utilization and diffusion within the biofilm, external mass transport, and detachment phenomena. It predicts the steady-state values of biofilm thickness, species distribution, and substrate fluxes. An experimental evaluation is carried out in completely mixed biofilm reactors in which slow-growing nitrifying bacteria compete with acetate-utilizing heterotrophs. The experimental results show that the model successfully describes the space competition. In particular, increasing acetate concentrations causes NH(4) (+)-N fluxes to decrease, because nitrifiers are forced deeper into the biofilm, where they experience greater mass-transport resistance.     

Mini-review: efficacy of lytic bacteriophages on multispecies biofilms

There is potential for phages to prevent and control bacterial biofilms, but few studies have examined the effect of phages on the multispecies biofilms that characterize most bacterial infections. This paper reviews the mechanism of action of phages, the evidence supporting the view that phage therapy will be effective against bacterial targets and the opposite viewpoint, phage application approaches, and the comparative advantage of phage therapy in multispecies biofilms. The few reports measuring the actions of lytic phages against multispecies biofilms are also reviewed. The authors are cautiously optimistic about the application of phages against their targets when in multispecies biofilms because some lysis mechanisms do not require species specificity.     

The green alga Dicytosphaeria ocellata and its organic extracts alter natural bacterial biofilm communities

Surfaces immersed in the marine environment are under intense fouling pressure by a number of invertebrates and algae. The regulation of this fouling can often be attributed to the bacterial biofilm that quickly develops on the surface of any available substratum in the ocean. The bacterial community composition on the surface of the green alga Dictyosphaeria ocellata was investigated and compared to those found on two other green algae, Batophora oerstedii and Cladophoropsis macromeres, and on a reference surface from three sites along the Florida Keys. Although the bacterial community composition of D. ocellata was not consistent across the sites, it was significantly different from the other algae and the reference surface at two of the three sites tested. Methanol extracts of D. ocellata significantly affected the abundance of bacteria and composition of the bacterial community on Phytagel? plates when compared to solvent controls, suggesting that the alga regulates the bacterial community by producing active metabolites.     

Degradation of toluene by a mixed population of archetypal aerobes, microaerophiles, and denitrifiers: laboratory sand column experiment and multispecies biofilm model formulation

An experiment was conducted in a saturated sand column with three bacterial strains that have different growth characteristics on toluene, Pseudomonas putida F1 which degrades toluene only under aerobic conditions, Thauera aromatica T1 which degrades toluene only under denitrifying conditions, and Ralstonia pickettii PKO1 has a facultative nature and can perform nitrate-enhanced biodegradation of toluene under hypoxic conditions (DO <2 mg/L). Steady-state concentration profiles showed that oxygen and nitrate appeared to be utilized simultaneously, regardless of the dissolved oxygen concentration and the results from fluorescent in-situ hybridization (FISH) indicated that PKO1 maintained stable cells numbers throughout the column, even when the pore water oxygen concentration was high. Since PKO1's growth rate under aerobic condition is much lower than that of F1, except under hypoxic conditions, these observations were not anticipated. Therefore these observations require a mechanistic explanation that can account for localized low oxygen concentrations under aerobic conditions. To simulate the observed dynamics, a multispecies biofilm model was implemented. This model formulation assumes the formation of a thin biofilm that is composed of the three bacterial strains. The individual strains grow in response to the substrate and electron acceptor flux from bulk fluid into the biofilm. The model was implemented such that internal changes in bacterial composition and substrate concentration can be simulated over time and space. The model simulations from oxic to denitrifying conditions compared well to the experimental profiles of the chemical species and the bacterial strains, indicating the importance of accounting for the biological activity of individual strains in biofilms that span different redox conditions.     

Development of a multispecies periodontal biofilm model within a stirred bioreactor

Abstract

The objective of this work was to develop a subgingival biofilm model using a stirred bioreactor. Discs of bovine teeth were adapted to a stirred bioreactor filled with a culture medium containing bacterial species associated with periodontal health or disease. After anaerobic incubation, the biofilms growing on the substratum surfaces were collected and analyzed. The mean number of Colony-forming Units (CFUs) varied, but with no difference between 3 and 7?days of biofilm formation (p?>?0.05). Scanning Electron Microscopy (SEM) analysis showed a uniform biofilm layer covering the cement layer of the root surface containing bacteria with diverse morphology. In checkerboard DNA-DNA hybridization, bacterial species were identified in both biofilms. In conclusion, a subgingival biofilm model was developed using a stirred bioreactor, allowing the in vitro reproduction of complex microbial communities. This is an advanced model that may be useful to mimic complex clinical periodontal biofilms.     

Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces

Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3 approximately 15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that gamma-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured gamma-Proteobacteria) were predominant in the community during 0 approximately 9 h, while the ratio of alpha-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured alpha-Proteobacteria) increased 2.6 approximately 4.8 folds during 24 approximately 36 h of the biofilm formation, emerging as the most predominant group. Previously, alpha-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of gamma-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation.     

Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes

Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has provided useful structural information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinases to provide a structurally based sequence alignment: alpha-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat mast cell protease 2 (RMCP2). The root mean square differences in alpha-carbon atom positions among these four structures when compared in a pairwise fashion range from 0.79 to 0.97 A for structurally equivalent residues. The sequences of the two lymphocyte enzymes were then aligned to these proteinases using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. With RMCP2 as a template for CCP1 and the two enzymes RMCP2 and BT as templates for HF, the molecular models were constructed. Intramolecular steric clashes that resulted from the replacement of amino acid side chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angles in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginine residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 position of the substrate. Both CCP1 and HF have a free cysteine in the segment of polypeptide 88 to 93.(ABSTRACT TRUNCATED AT 400 WORDS)     

口腔静态生物膜模型研究进展北大核心CSCD

口腔静态生物膜模型是体外模拟口腔微生态环境的重要手段,因其成本低、通量高、可靠性好、操作容易等优点,已成为研究各种口腔疾病的发病机制,测试各种药物、口腔护理用品、食品的重要工具。建立口腔静态生物膜模型,可根据研究目的,选择不同的装置、接种源、培养基、基质和培养条件,并通过测定生物量、代谢活性、群落结构以及进行可视化分析等多种方法评价生物膜的生长情况。本文汇总了近年来报道的口腔静态生物膜模型建立和评价的方法学要素,并分析讨论了各种方法的适用范围,希望有助于相关领域研究和生产实践的开展。     

Streptomyces-derived actinomycin D inhibits biofilm formation by Staphylococcus aureus and its hemolytic activity

Staphylococcus aureus is a versatile human pathogen that produces diverse virulence factors, and its biofilm cells are difficult to eradicate due to their inherent ability to tolerate antibiotics. The anti-biofilm activities of the spent media of 252 diverse endophytic microorganisms were investigated using three S. aureus strains. An attempt was made to identify anti-biofilm compounds in active spent media and to assess their anti-hemolytic activities and hydrophobicities in order to investigate action mechanisms. Unlike other antibiotics, actinomycin D (0.5 μg ml^?1) from Streptomyces parvulus significantly inhibited biofilm formation by all three S. aureus strains. Actinomycin D inhibited slime production in S. aureus and it inhibited hemolysis by S. aureus and caused S. aureus cells to become less hydrophobic, thus supporting its anti-biofilm effect. In addition, surface coatings containing actinomycin D prevented S. aureus biofilm formation on glass surfaces. Given these results, FDA-approved actinomycin D warrants further attention as a potential antivirulence agent against S. aureus infections.     

The HIV aspartyl protease inhibitor ritonavir impairs planktonic growth,biofilm formation and proteolytic activity in Trichosporon spp.

This study evaluated the effect of the protease inhibitor ritonavir (RIT) on Trichosporon asahii and Trichosporon inkin. Susceptibility to RIT was assessed by the broth microdilution assay and the effect of RIT on protease activity was evaluated using azoalbumin as substrate. RIT was tested for its anti-biofilm properties and RIT-treated biofilms were assessed regarding protease activity, ultrastructure and matrix composition. In addition, antifungal susceptibility, surface hydrophobicity and biofilm formation were evaluated after pre-incubation of planktonic cells with RIT for 15 days. RIT (200 μg ml^?1) inhibited Trichosporon growth. RIT (100 μg ml^?1) also reduced protease activity of planktonic and biofilm cells, decreased cell adhesion and biofilm formation, and altered the structure of the biofilm and the protein composition of the biofilm matrix. Pre-incubation with RIT (100 μg ml^?1) increased the susceptibility to amphotericin B, and reduced surface hydrophobicity and cell adhesion. These results highlight the importance of proteases as promising therapeutic targets and reinforce the antifungal potential of protease inhibitors.     

Dextranase from Arthrobacter oxydans KQ11-1 inhibits biofilm formation by polysaccharide hydrolysis

Dental plaque is a biofilm of water-soluble and water-insoluble polysaccharides, produced primarily by Streptococcus mutans. Dextranase can inhibit biofilm formation. Here, a dextranase gene from the marine microorganism Arthrobacter oxydans KQ11-1 is described, and cloned and expressed using E. coli DH5α competent cells. The recombinant enzyme was then purified and its properties were characterized. The optimal temperature and pH were determined to be 60°C and 6.5, respectively. High-performance liquid chromatography data show that the final hydrolysis products were glucose, maltose, maltotriose, and maltotetraose. Thus, dextranase can inhibit the adhesive ability of S. mutans. The minimum biofilm inhibition and reduction concentrations (MBIC₅₀ and MBRC₅₀) of dextranase were 2 U ml^?1 and 5 U ml^?1, respectively. Scanning electron microscopy and confocal laser scanning microscope (CLSM) observations confirmed that dextranase inhibited biofilm formation and removed previously formed biofilms.     

Mycobacterium smegmatis biofilm formation and sliding motility are affected by the serine/threonine protein kinase PknF

Eighteen 'eukaryotic-like' serine/threonine kinases are present in the Mycobacterium smegmatis genome. One of them encoded by the ORF 3677 demonstrates high similarity to the Mycobacterium tuberculosis protein kinase PknF. A merodiploid strain was generated, which showed reduced growth associated with irregular cell structure. The merodiploid strain displayed altered colony morphology, defective sliding motility and biofilm formation. These data indicate a role for PknF in biofilm formation, possibly associated with alterations in glycopeptidolipid composition.     

Activity of disinfectants against multispecies biofilms formed by Staphylococcus aureus,Candida albicans and Pseudomonas aeruginosa

Microbial biofilms are a serious threat to human health. Recent studies have indicated that many clinically relevant biofilms are polymicrobial. In the present study, multispecies biofilms were grown in a reproducible manner in a 96-well microtiter plate. The efficacy of nine commercially available disinfectants against Staphylococcus aureus, Candida albicans, and Pseudomonas aeruginosa in multispecies biofilms was determined and compared. The results showed that the direction and the magnitude of the effect in a multispecies biofilm depend on the strain and the disinfectant used and challenge the common belief that organisms in multispecies biofilms are always less susceptible than in monospecies biofilms.     

大蒜素对白色念珠菌生物被膜形成的作用

生物被膜的形成是白色念珠菌产生耐药性的重要原因之一。本研究首先构建白色念珠菌体外生物被膜模型,通过倒置显微镜和甲基四氮盐（XTT）法检测大蒜素对白色念珠菌生物被膜形成的影响,同时采用实时荧光定量PCR法（qRT-PCR）对白色念珠菌生物被膜相关基因ALS1、ALS3、HWP1、MP65、SUN41的表达水平进行检测。结果显示,当大蒜素浓度≥12.5μg/mL时,白色念珠菌生物被膜的生长被抑制,并且在生物被膜形成的早期,大蒜素干预能有效抑制其形成;大蒜素能下调白色念珠菌生物被膜相关基因ALS1、ALS3、HWP1、MP65、SUN41的表达水平。研究结果提示,大蒜素可有效抑制体外白色念珠菌生物被膜的形成,可能与其下调生物被膜相关基因的表达有关。     

Investigations of Rhizobium biofilm formation

The development of nitrogen-fixing nodules of the Rhizobium-legume symbiosis, especially the early stages of root hair deformation and curling, infection thread formation, and nodule initiation, has been well studied from a genetic standpoint. In contrast, the factors important for the colonization of surfaces by rhizobia, including roots-an important prerequisite for nodule formation-have not been as thoroughly investigated. We developed conditions for analyzing the ability of two fast-growing rhizobia, Sinorhizobium meliloti and Rhizobium leguminosarum bv. viciae, to produce biofilms on abiotic surfaces such as glass, plastic microtiter plates, sand and soil as a prelude to characterizing the genes important for aggregation and attachment. Factors involved in adherence to abiotic surfaces are likely to be used in rhizobial attachment to legume root cells. In this report, we show that S. meliloti exopolysaccharide-deficient mutants as well as exopolysaccharide overproducers exhibit reduced biofilm phenotypes that show parallels with their nodulation abilities. We also investigated two flagella-less S. meliloti mutants and found them to have reduced biofilming capabilities. To investigate whether there was a symbiotic phenotype, we tested one of the Fla- mutants on two different S. meliloti hosts, alfalfa and white sweetclover, and found that nodule formation was significantly delayed on the latter.     

环境因子对水霉菌生物膜形成的影响

【目的】体外构建水霉菌(Saprolegnia)生物膜(Biofilm,BF),研究环境因子对其生物膜形成的影响。【方法】采用改良的微孔板法研究静置培养条件下寄生水霉(Saprolegnia parasitica)ATCC200013在96孔酶标板上的成膜情况,CCK-8法(Cell Counting Kit-8)定量检测生物膜中水霉菌的活力。【结果】水霉菌的生物膜的OD450值在培养24 h达到峰值,48 h后趋于稳定。随着初始孢子浓度升高,水霉菌生物膜OD450值升高,差异显著(P0.05)。20-25°C生物膜形成量最多,OD450值显著高于其他温度组(P0.05)。在起始pH值为4-11的沙氏葡萄糖液体培养基中,水霉菌均能形成生物膜。在培养基中加入0.12 mmol/L以上CaCl2,能促进生物膜形成;添加0.03-2.00 mmol/L MgCl2,水霉菌生物膜形成量与未添加MgCl2对照组无显著性差异;Cu2+对水霉菌生物膜的形成有显著影响,0.5 mmol/L以上添加处理几乎不形成生物膜;NaCl能明显抑制水霉菌生物膜的形成,当NaCl质量分数低于0.12%时,对生物膜形成的影响较小(P0.05)。水霉菌在鲫皮和肌肉提取液包被后生物膜形成量与对照组相比无显著性差异,而鲫表皮黏液、鳃黏液包被后生物膜的形成量明显减少。【结论】研究首次采用微孔板法体外构建水霉菌生物膜,发现其生物膜的形成与多种环境因素有着密切的关系。这为了解水霉菌生物膜的形成规律提供了一定参考,为水霉菌生物膜的进一步研究奠定了基础。     

Prevention of biofilm formation by polymer modification

Bacterial biofilm formation on synthetic polymers plays an important role in industry and in modern medicine, leading, for example, to difficult-to-treat infections caused by colonized foreign bodies. Prevention of biofilm formation is a necessary step in the successful prophylaxis of such infections. One approach is to inhibit bacterial adherence by polymer surface modification. We have investigated polymer modification by glow discharge treatment in order to study the influence of the modified surface on bacterial adherence. Surface roughness, surface charge density and contact angles of the modified polymers were determined and related to the adherence ofStaphylococcus epidermidis KH6. Although no influence of surface roughness and charge density on bacterial adherence was noticed, a correlation between the free enthalpy of adhesion (estimated from contact angle measurements) and adherence was observed. There seems to exist a certain minimum bacterial adherence, independent of the nature of the polymer surface. Modified polymers with negative surface charge allow for bacterial adherence close to the adherence minimum. These polymers could be improved further by the ionic bonding of silver ions to the surface. Such antimicrobial polymers are able to prevent bacterial colonization, which is a prerequisite for biofilm formation. It is suggested that modification of polymers and subsequent surface coupling of antimicrobials might be an effective approach for the prevention of bacterial biofilm formation.     

PH826噬菌体与抗生素联用有效抑制多重耐药铜绿假单胞菌生物被膜的形成

【目的】铜绿假单胞菌(Pseudomonas aeruginosa)是一种重要的革兰氏阴性病原体,可以加重囊性纤维化患者的肺部感染,最终会导致患者的死亡。然而由于多重耐药(multi-drug resistant,MDR)和泛耐药(pan-drug resistant, PDR)铜绿假单胞菌菌株的出现,使其防控变得更为严峻。【方法】从养殖场污水中分离能有效裂解多重耐药铜绿假单胞菌的噬菌体,研究其形态特征、生物学特性、宿主谱范围、基因组特征和体外抑菌能力等,并采用噬菌体和抗生素联用的方法进行生物被膜的抑制试验。【结果】透射电子显微镜的形态分析和基因组分析结合表明,该噬菌体属于Nankokuvirus病毒属。生物学特性试验表明,PH826具有广泛的温度稳定性(4-60℃)和pH稳定性(3.0-11.0)。宿主谱测试显示,PH826可以裂解13株铜绿假单胞菌(包括人源和动物源),体外抑菌试验显示,PH826在感染复数(multiplicity of infection, MOI)分别为10、1、0.1时对铜绿假单胞菌均有强烈的裂解作用。根据基因组分析,PH826噬菌体的基因组大小为87 95...     

Phylogenetic analysis of a biofilm bacterial population in a water pipeline in the Gulf of Mexico

The aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the Gulf of Mexico used to inject marine water into the oil reservoir. Several aerobic and heterotrophic bacteria were isolated and identified by 16S rRNA gene sequence analysis. Metagenomic DNA was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16S rRNA gene metagenomic library. Denaturing gradient gel electrophoresis profiles and ribosomal libraries exhibited a limited bacterial diversity. Most of the species detected in the ribosomal library or isolated from the pipeline were assigned to Proteobacteria (Halomonas spp., Idiomarina spp., Marinobacter aquaeolei, Thalassospira sp., Silicibacter sp. and Chromohalobacter sp.) and Bacilli (Bacillus spp. and Exiguobacterium spp.). This is the first report that associates some of these bacteria with a corrosive biofilm. It is relevant that no sulfate-reducing bacteria were isolated or detected by a PCR-based method. The diversity and relative abundance of bacteria from water pipeline biofilms may contribute to an understanding of the complexity and mechanisms of metal corrosion during marine water injection in oil secondary recovery.