Multiscale spatial segregation analysis in digital images of biofilms

Quantifying the degree of spatial segregation of two bacterial strains in mixed biofilms is an important topic in microbiology. Spatial segregation is dependent on spatial scale as two strains may appear to be well mixed if observed from a distance, but a closer look can reveal strong separation. Typically, this information is encoded in a digital image that represents the binary system, e.g., a microscopy image of a two species biofilm. To decode spatial segregation information, we have developed quantitative measures for evaluating the degree of the spatial scale-dependent segregation of two bacterial strains in a digital image. The constructed algorithm is based on the new segregation measures and overcomes drawbacks of existing approaches for biofilm segregation analysis. The new approach is implemented in a freely available software and was successfully applied to biofilms of two strains and bacterial suspensions for detection of the different spatial scale-dependent segregation levels.

Biofilm Removal from In Vitro Narrow Geometries Using Single and Dual Pulse Er:YAG Laser Photoacoustic Irrigation

The disinfection and removal of biofilm from titanium dental implants remains a great challenge in oral medicine. Here we present results of novel photoacoustic irrigation laser modalities for biofilm removal in model geometries mimicking the peri-implant pocket. The efficacy of single pulse (Er:YAG-SSP) and dual pulse (Er:YAG-AutoSWEEPS) photoacoustic irrigation modalities were determined for Enterococcus faecalis biofilm decontamination from titanium surfaces in narrow cylindrical and square gap geometries. The density of bacteria as well as the number of live bacteria were determined prior and after different photoacoustic treatments. Both SSP and AutoSWEEPS photoacoustic irrigation techniques removed at least 92% of biofilm bacteria during the 10 s photoacoustic treatment. The effectiveness of cleaning was better in the narrow square gap geometry compared to the cylindrical geometry. The dual pulse Er:YAG-AutoSWEEPS photoacoustic irrigation showed better results compared to SSP modality. No chemical adjuvants were needed to boost the effectiveness of the photoacoustic irrigation in the saline solution. The results imply that photoacoustic irrigation is an efficient cleaning method for debridement and decontamination in narrow geometries and should be considered as a new therapeutic option for the treatment of peri-implant diseases.

New Phage-Derived Antibacterial Enzyme PolaR Targeting Rothia spp

Rothia is an opportunistic pathogen, particularly life-threatening for the immunocompromised. It is associated with pneumonia, endocarditis, peritonitis and many other serious infections, including septicemia. Of note, Rothia mucilaginousa produces metabolites that support and increase overgrowth of Pseudomonas aeruginosa, one of the ESKAPE bacteria. Endolysins are considered as antibacterial enzymes derived from bacteriophages that selectively and efficiently kill susceptible bacteria without harming human cells or the normal microbiome. Here, we applied a computational analysis of metagenomic sequencing data of the gastric mucosa phageome extracted from human patients' stomach biopsies. A selected candidate anti-Rothia sequence was produced in an expression system, purified and confirmed as a Rothia mucilaginosa- and Rothia dentocariosa-specific endolysin PolaR, able to destroy bacterial cells even when aggregated, as in a biofilm. PolaR had no cytotoxic or antiproliferative effects on mammalian cells. PolaR is the first described endolysin selectively targeting Rothia species, with a high potential to combat infections caused by Rothia mucilaginosa and Rothia dentocariosa, and possibly other bacterial groups. PolaR is the first antibacterial enzyme selected from the gastric mucosa phageome, which underlines the biological complexity and probably underestimated biological role of the phageome in the human gastric mucosa.

Thermal and Rheological Properties of Gluten-Free, Starch-Based Model Systems Modified by Hydrocolloids

Obtaining good-quality gluten-free products represents a technological challenge; thus, it is important to understand how and why the addition of hydrocolloids influences the properties of starch-based products. To obtain insight into the physicochemical changes imparted by hydrocolloids on gluten-free dough, we prepared several suspensions with different corn starch/potato starch/hydroxpropyl methyl cellulose/xanthan gum/water ratios. Properties of the prepared samples were determined by differential scanning calorimetry and rheometry. Samples with different corn/potato starch ratios exhibited different thermal properties. Xanthan gum and HPMC (hydroxypropyl methyl cellulose) exhibited a strong influence on the rheological properties of the mixtures since they increased the viscosity and elasticity. HPMC and xanthan gum increased the temperature of starch gelatinization, as well as they increased the viscoelasticity of the starch model system. Although the two hydrocolloids affected the properties of starch mixtures in the same direction, the magnitude of their effects was different. Our results indicate that water availability, which plays a crucial role in the starch gelatinization process, could be modified by adding hydrocolloids such as, hydroxypropyl methyl cellulose and xanthan gum. By adding comparatively small amounts of the studied hydrocolloids to starch, one can achieve similar thermo-mechanical effects by the addition of gluten. Understanding these effects of hydrocolloids could contribute to the development of better quality gluten-free bread with optimized ingredient content.

A Novel Artificial Hemoglobin Carrier Based on Heulandite-Calcium Mesoporous Aluminosilicate Particles

Tetraethyl-orthosilicate (TEOS)-based nanoparticles are most extensively used as a silica-based hemoglobin carrier system. However, TEOS-based nanoparticles induce adverse effects on the hemoglobin structure. Therefore, a heulandite-calcium-based carrier was investigated as a novel silica-based hemoglobin carrier system. The heulandite-calcium mesoporous aluminosilicate particles (MSPs) were fabricated by a patented tribo-mechanical activation process, according to the manufacturer, and its structure was assessed by X-ray diffraction analysis. Upon hemoglobin encapsulation, alternation in the secondary and tertiary structure was observed. The hemoglobin-particle interactions do not cause heme degradation or decreased activity. Once encapsulated inside the particle pores, the hemoglobin shows increased thermal stability, and higher loading capacity per gram of particles (by a factor of >1.4) when compared to TEOS-based nanoparticles. Futhermore, we introduced a PEGlyted lipid bilayer which significantly decreases the premature hemoglobin release and increases the colloidal stability. The newly developed hemoglobin carrier shows no cytotoxicity to human umbilical vein endothelial cells (HUVEC).

Surfactin Facilitates Horizontal Gene Transfer in Bacillus subtilis

Genetic competence for the uptake and integration of extracellular DNA is a key process in horizontal gene transfer (HGT), one of the most powerful forces driving the evolution of bacteria. In several species, development of genetic competence is coupled with cell lysis. Using Bacillus subtilis as a model bacterium, we studied the role of surfactin, a powerful biosurfactant and antimicrobial lipopeptide, in genetic transformation. We showed that surfactin itself promotes cell lysis and DNA release, thereby promoting HGT. These results, therefore, provide evidence for a fundamental mechanism involved in HGT and significantly increase our understanding of the spreading of antibiotic resistance genes and diversification of microbial communities in the environment.

Photoacoustic removal of Enterococcus faecalis biofilms from titanium surface with an Er:YAG laser using super short pulses

Biofilms that grow on implant surfaces pose a great risk and challenge for the dental implant survival. In this work, we have applied Er:YAG photoacoustic irrigation using super short pulses (Er:YAG-SSP) to remove biofilms from the titanium surfaces in the non-contact mode. Mature Enterococcus faecalis biofilms were treated with saline solution, chlorhexidine, and hydrogen peroxide, or photoacoustically with Er:YAG-SSP for 10 or 60 s. The number of total and viable bacteria as well as biofilm surface coverage was determined prior and after different treatments. Er:YAG-SSP photoacoustic treatment significantly increases the biofilm removal rate compared to saline or chemically treated biofilms. Up to 92% of biofilm-covered surface can be cleaned in non-contact mode during 10 s without the use of abrasives or chemicals. In addition, Er:YAG-SSP photoacoustic irrigation significantly decreases the number of viable bacteria that remained on the titanium surface. Within the limitations of the present in vitro model, the ER:YAG-SSP seems to constitute an efficient therapeutic option for quick debridement and decontamination of titanium implants without using abrasives or chemicals.

The Antibacterial Effects of New N-Alkylpyridinium Salts on Planktonic and Biofilm Bacteria

An increasing microbial resistance to known antibiotics raises a demand for new antimicrobials. In this study the antimicrobial properties of a series of new N-Alkylpyridinium quaternary ammonium compounds (QACs) with varying alkyl chain lengths were evaluated for several nosocomial pathogens. The chemical identities of the new QACs were determined by NMR, LC-MS, and HRMS. All the planktonic bacteria tested were susceptible to the new QACs as evaluated by MIC and MBC assays. The antimicrobial effect was most pronounced against Staphylococcus aureus clinical isolates. Live/dead staining CLSM was used to test the effectiveness of the QACs in biofilms. The effectiveness was up to 10-fold lower than in the plankton. When QACs were used as irrigants in Er:YAG – SSP photoacoustic steaming, their effectiveness significantly increased. The combined use of irrigants and photoacoustic streaming increased biofilm removal from the surface and increased the killing rate of the cells remaining on the surface. This may allow for a shorter chemical exposure time and lower dosage of QACs used in applications. The results demonstrate that the new QACs have potential to be applied as antibacterial compounds effective against planktonic and biofilm bacteria as well as irrigants in removal of difficult-to-reach biofilms.

Liposome destruction by hydrodynamic cavitation in comparison to chemical, physical and mechanical treatments

Liposomes are widely applied in research, diagnostics, medicine and in industry. In this study we show for the first time the effect of hydrodynamic cavitation on liposome stability and compare it to the effect of well described chemical, physical and mechanical treatments. Fluorescein loaded giant 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid vesicles were treated with hydrodynamic cavitation as promising method in inactivation of biological samples. Hydrodynamic treatment was compared to various chemical, physical and mechanical stressors such as ionic strength and osmolarity agents (glucose, Na⁺, Ca²⁺, and Fe³⁺), free radicals, shear stresses (pipetting, vortex mixing, rotational shear stress), high pressure, electroporation, centrifugation, surface active agents (Triton X-100, ethanol), microwave irradiation, heating, freezing-thawing, ultrasound (ultrasonic bath, sonotrode). The fluorescence intensity of individual fluorescein loaded lipid vesicles was measured with confocal laser microscopy. The distribution of lipid vesicle size, vesicle fluorescence intensity, and the number of fluorescein loaded vesicles was determined before and after treatment with different stressors. The different environmental stressors were ranked in order of their relative effect on liposome fluorescein release. Of all tested chemical, physical and mechanical treatments for stability of lipid vesicles, the most detrimental effect on vesicles stability had hydrodynamic cavitation, vortex mixing with glass beads and ultrasound. Here we showed, for the first time that hydrodynamic cavitation was among the most effective physico-chemical treatments in destroying lipid vesicles. This work provides a benchmark for lipid vesicle robustness to a variety of different physico-chemical and mechanical parameters important in lipid vesicle preparation and application.

Viscoelastic response of Escherichia coli biofilms to genetically altered expression of extracellular matrix components

How the viscoelastic properties of the extracellular matrix affect the various biological functions conferred by biofilms is an important question in microbiology. In this study, the viscoelastic response of Escherichia coli biofilms to the genetically altered expression of extracellular matrix components was studied. Biofilms of the wild type E. coli MG1655 and its mutant strains producing different amounts of extracellular matrix components (curli, colanic acid, and poly-β-1,6-N-acetyl-d-glucosamine) were used to examine the viscoelastic behavior of biofilms grown at the solid-atmosphere interface. The results suggest that the presence of curli proteins dominates biofilm mechanical behavior. The rheological data indicate that the cohesive energy of the biofilm was the highest in the wild type strain. The results demonstrate the importance of extracellular matrix composition for biofilm mechanical properties. We propose that by genetically altering the expression of extracellular matrix polymers, bacteria are able to modulate the mechanical properties of their local environment in accordance with bulk environmental conditions.

An early mechanical coupling of planktonic bacteria in dilute suspensions

It is generally accepted that planktonic bacteria in dilute suspensions are not mechanically coupled and do not show correlated motion. The mechanical coupling of cells is a trait that develops upon transition into a biofilm, a microbial community of self-aggregated bacterial cells. Here we employ optical tweezers to show that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion. The strength of the coupling increases with the growth of liquid bacterial culture. The matrix responsible for the mechanical coupling is composed of cell debris and extracellular polymer material. The fragile network connecting cells behaves as viscoelastic liquid of entangled extracellular polymers. Our findings point to physical connections between bacteria in dilute bacterial suspensions that may provide a mechanistic framework for understanding of biofilm formation, osmotic flow of nutrients, diffusion of signal molecules in quorum sensing, or different efficacy of antibiotic treatments at low and high bacterial densities.Planktonic bacteria are untethered to surfaces or to each other, and thus are expected to move independently when at low cell densities. Here Sretenovic et al. show, using optical tweezers, that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion.

Structure and Dynamics of a Model Polymer Mixture Mimicking a Levan-Based Bacterial Biofilm of Bacillus subtilis

In this paper, we report on the structure and dynamics of biologically important model polymer mixtures that mimic the extracellular polymeric matrix in native biofilm of Bacillus subtilis. This biofilm is rich in nonionic polysaccharide levan, but also contains other biopolymers such as DNA and proteins in small concentrations. Aiming to identify the contribution of each component to the formation of the biofilm, our investigations encompassed dynamic rheology, small-angle X-ray scattering, dynamic light scattering, microscopy, densitometry, and sound velocity measurements. As it turned out, this very powerful combination of techniques is able to provide solid results on the dynamical and structural aspects of the microbiologically and chemically complex biofilm formations. Macroscopic rheological measurements revealed that the addition of DNA to levan solution increased the viscosity, pseudoplasticity, and elasticity of the system. The addition of protein contributed similarly, but also increased the rigidity of the system. This confirms that the presence of minor biofilm components is essential for biofilm formation. DNA and proteins appear to confine levan molecules within their supramolecular structure and, in this way, restrict the role of levan to merely a filling agent. These findings were complemented by small-angle X-ray scattering data, which provided insight into the structure on a molecular scale. One of the essential goals of this work was to compare the structural properties of the native biofilm and synthetic biofilm mixture.

Viscoelastic properties of levan-DNA mixtures important in microbial biofilm formation as determined by micro- and macrorheology

We studied the viscoelastic properties of homogeneous and inhomogeneous levan-DNA mixtures using optical tweezers and a rotational rheometer. Levan and DNA are important components of the extracellular matrix of bacterial biofilms. Their viscoelastic properties influence the mechanical as well as molecular-transport properties of biofilm. Both macro- and microrheology measurements in homogeneous levan-DNA mixtures revealed pseudoplastic behavior. When the concentration of DNA reached a critical value, levan started to aggregate, forming clusters of a few microns in size. Microrheology using optical tweezers enabled us to measure local viscoelastic properties within the clusters as well as in the DNA phase surrounding the levan aggregates. In phase-separated levan-DNA mixtures, the results of macro- and microrheology differed significantly. The local viscosity and elasticity of levan increased, whereas the local viscosity of DNA decreased. On the other hand, the results of bulk viscosity measurements suggest that levan clusters do not interact strongly with DNA. Upon treatment with DNase, levan aggregates dispersed. These results demonstrate the advantages of microrheological measurements compared to bulk viscoelastic measurements when the materials under investigation are complex and inhomogeneous, as is often the case in biological samples.

Evaluating SAXS Results on Aqueous Solutions of Various Bacterial Levan utilizing the String-of-Beads Model

Polysaccharide levan is a homopolymer of fructose and is an important component of plants, yeast, fungi and some bacterial biofilms. In this paper we report on the structural properties of aqueous solutions of bacterial levan utilizing smallangle X-ray scattering and light microscopy. In addition to commercially available levan isolated from Zymomonas mobilis and Erwinia herbicola, we also studied levan isolated and purified from the biofilm of Bacillus subtilis. The smallangle X-ray scattering data were analyzed by the string-of-beads model that revealed qualitative differences in the structure of levan molecules. Levan can be represented as a semi-flexible chain that interacts intra- and inter-molecularly and therefore forms various suprastructures on larger size scales. Increasing the concentration of levan makes the levan structure more compact, which was observed on the nano as well as on the micro scale. The structures with most homogeneously distributed polymer local density were found in B. subtilis levan solutions.

ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes

The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand. Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013). After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions. The census data show that in addition to B. subtilis and close relatives, 20 comQXPA-like loci are predicted to occur outside the B. subtilis clade. These include some species of Clostridiales order, but none outside the phylum Firmicutes. Characteristic gene-overlap patterns were observed in comQXPA loci, which were different for the B. subtilis-like and non-B. subtilis-like clades. Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

Structure and dynamics of a polysaccharide matrix: aqueous solutions of bacterial levan

The polysaccharide levan is a homopolymer of fructose and appears in nature as an important structural component of some bacterial biofilms. This paper reports the structural and dynamic properties of aqueous solutions of levan of various origin obtained from dynamic rheological, small-angle X-ray scattering, static and dynamic light scattering, as well as density and sound velocity measurements, determination of polymer branching after per-O-methylation, and microscopy. Besides samples of commercially available levan from Zymomonas mobilis and Erwinia herbicola, we also isolated, purified, and studied a levan sample from the biofilm of Bacillus subtilis. The results of dynamic rheological and light scattering measurements revealed very interesting viscoelastic properties of levan solutions even at very low polymer concentrations. The findings were complemented by small-angle X-ray scattering data that revealed some important differences in the structure of the aqueous levan solutions at the molecular level. Besides presenting detailed dynamic and structural results on the polysaccharide systems of various levans, one of the essential goals of this work was to point out the level of structural information that may be obtained for such polymer systems by combining basic physicochemical, rheological, and various light scattering techniques.

Private link between signal and response in Bacillus subtilis quorum sensing

Bacteria coordinate their behavior using quorum sensing (QS), whereby cells secrete diffusible signals that generate phenotypic responses associated with group living. The canonical model of QS is one of extracellular signaling, where signal molecules bind to cognate receptors and cause a coordinated response across many cells. Here we study the link between QS input (signaling) and QS output (response) in the ComQXPA QS system of Bacillus subtilis by characterizing the phenotype and fitness of comQ null mutants. These lack the enzyme to produce the ComX signal and do not activate the ComQXPA QS system in other cells. In addition to the activation effect of the signal, however, we find evidence of a second, repressive effect of signal production on the QS system. Unlike activation, which can affect other cells, repression acts privately: the de-repression of QS in comQ cells is intracellular and only affects mutant cells lacking ComQ. As a result, the QS signal mutants have an overly responsive QS system and overproduce the secondary metabolite surfactin in the presence of the signal. This surfactin overproduction is associated with a strong fitness cost, as resources are diverted away from primary metabolism. Therefore, by acting as a private QS repressor, ComQ may be protected against evolutionary competition from loss-of-function mutations. Additionally, we find that surfactin participates in a social selection mechanism that targets signal null mutants in coculture with signal producers. Our study shows that by pleiotropically combining intracellular and extracellular signaling, bacteria may generate evolutionarily stable QS systems.

Structure of bacterial extracellular polymeric substances at different pH values as determined by SAXS

Extracellular polymeric substances (EPS) play an important role in cell aggregation, cell adhesion, and biofilm formation, and protect cells from a hostile environment. The EPS was isolated by trichloroacetic acid/ethanol extraction from broth culture of a marine bacterium isolate. The EPS was composed of glucose and galactose as determined by HPLC and TLC; the protein content was on average 15 +/- 5% of EPS dry mass. The solution structure of EPS at different values of pH was revealed by small-angle x-ray scattering. Scattering curves of EPS solutions (0.4%, w/v) consistently showed two nearly linear log-log regions with slopes a and b in the q-ranges from 0.06 nm(-1) to 0.26 nm(-1), and from 0.27 nm(-1) to 0.88 nm(-1), respectively. Slope a was sensitive to pH changes whereas slope b was not. The observed sensitivity to pH was not a consequence of ionic strength variation with pH, as checked by salt addition. The pH variation causes major rearrangements of EPS structure mainly at length scales above 24 nm. To get a better understanding of the pH effect on EPS structure, the original model proposed by Geissler was refined into a mathematical model that enabled fitting of the experimental scattering curves in the pH range from 0.7 to 11.0. The model describes EPS structure as a network of randomly coiled polymeric chains with denser domains of polymeric chains. The results obtained from the model indicate that dense domains increase in average size from 19 nm at pH 11.0 to 52 nm at pH 0.7. The average distance between the polysaccharide chains at pH 0.7 was 2.3 nm, which indicates a compact EPS structure. Swelling was found to be at a maximum around pH = 8.8, where the average distance between the chains was 4.8 nm.