Nanofibers with genotyped Bacillus strains exhibiting antibacterial and immunomodulatory activity.

Biofilm-associated diseases such as periodontitis are widespread and challenging to treat which calls for new strategies for their effective management. Probiotics represent a promising approach for targeted treatment of dysbiosis in biofilm and modulation of host immune response. In this interdisciplinary study, nanofibers with two autochthonous Bacillus strains 27.3.Z and 25.2.M were developed. The strains were isolated from the oral microbiota of healthy individuals, and their genomes were sequenced and screened for genes associated with antimicrobial and immunomodulatory activities, virulence factors, and transferability of resistance to antibiotics. Spores of two Bacillus strains were incorporated individually or in combination into hydrophilic poly(ethylene oxide) (PEO) and composite PEO/alginate nanofibers. The nanofiber mats were characterised by a high loading of viable spores (> 7 log CFU/mg) and they maintained viability during electrospinning and 6 months of storage at room temperature. Spores were rapidly released from PEO nanofibers, while presence of alginate in the nanofibers prolonged their release. All formulations exhibited swelling, followed by transformation of the nanofiber mat into a hydrogel and polymer erosion mediating spore release kinetics. The investigated Bacillus strains released metabolites, which were not cytotoxic to peripheral blood mononuclear cells (PBMCs) in vitro. Moreover, their metabolites exhibited antibacterial activity against two periodontopathogens, an antiproliferative effect on PBMCs, and inhibition of PBMC expression of proinflammatory cytokines. In summary, the developed nanofiber-based delivery system represents a promising therapeutic approach to combat biofilm-associated disease on two fronts, namely via modulation of the local microbiota with probiotic bacteria and host immune response with their metabolites.

Effect of olive-processing technology on the utilization of olive mill pomace as a soil amendment.

In the Mediterranean basin, the treatment and disposal of olive mill pomace (OMP) remain a salient environmental issue for the olive oil-producing industry. This study assesses the effects of olive-processing technology (three-phase and two-phase systems) on the potential use of OMP as a soil amendment. Samples from 12 Croatian olive mills were analyzed for their total phenolic content (TPC), residual oil fraction, and elemental concentration. The samples were profiled using Fourier transform infrared spectroscopy (FT-IR) and structurally characterized using scanning electron microscopy-energy-dispersive X-ray spectroscopy (EDS). Compared to three-phase samples, two-phase OMP was more acidic (pH 4.5 vs. 5.0), with a higher TPC (3835 vs. 1576 mg/kg fresh weight), oil content (11.7% vs. 7.5% d.w., where d.w. is dry weight), electrical conductivity (EC, 5.1 vs. 3.0 mS/cm), and levels of calcium (Ca, 1.34 vs. 1.20 g/kg d.w.) and copper (Cu, 10.4 vs. 7.0 mg/kg d.w.). Similar values of carbon/nitrogen (C/N; 61 vs. 72), N (10 vs. 8.1 g/kg d.w.), phosphorus (1040 vs. 691 mg/kg d.w.), and potassium (K, 13.7 vs. 8.1 g/kg d.w.) were observed. The amounts of chromium, copper, nickel, and zinc were below EC limits in both cases. The EDS mapping revealed that Ca was concentrated at sharp-edged OMP particles while K was evenly distributed, suggesting that pelletized OMP compost is preferable for amending soil to obtain a homogeneous distribution of nutrients. It was also possible to distinguish between OMPs based on oil and lignin absorption bands in their FT-IR spectra. According to the obtained results, composting is recommended for both types of OMP to produce a safe product for amendment purposes.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Modification of bacterial cells for in vivo remotely guided systems.

It was shown recently that bacterial strains, which can act specifically against malignant cells, can be used efficiently in cancer therapy. Many appropriate bacterial strains are either pathogenic or invasive and there is a substantial shortage of methods with which to monitor in vivo the distribution of bacteria used in this way. Here, it is proposed to use a Layer-by-Layer (LbL) approach that can encapsulate individual bacterial cells with fluorescently labeled polyelectrolytes (PE)s and magnetite nanoparticles (NP)s. The NP enable remote direction in vivo to the site in question and the labeled shells in the far-red emission spectra allow non-invasive monitoring of the distribution of bacteria in the body. The magnetic entrapment of the modified bacteria causes the local concentration of the bacteria to increase by a factor of at least 5. The PEs create a strong barrier, and it has been shown in vitro experiments that the division time of bacterial cells coated in this way can be regulated, resulting in control of their invasion into tissues. That animals used in the study survived and did not suffer septic shock, which can be attributed to PE capsules that prevent release of endotoxins from bacterial cells.

Isolation, Identification, and Selection of Bacteria With Proof-of-Concept for Bioaugmentation of Whitewater From Wood-Free Paper Mills.

In the wood-free paper industry, whitewater is usually a mixture of additives for paper production. We are currently lacking an efficient, cost-effective purification technology for their removal. In closed whitewater cycles the additives accumulate, causing adverse production problems, such as the formation of slime and pitch. The aim of our study was to find an effective bio-based strategy for whitewater treatment using a selection of indigenous bacterial isolates. We first obtained a large collection of bacterial isolates and then tested them individually by simple plate and spectrophotometric methods for their ability to degrade the papermaking additives, i.e., carbohydrates, resin acids, alkyl ketene dimers, polyvinyl alcohol, latex, and azo and fluorescent dyes. We examined correlation between carbon source use, genera, and inoculum source of isolates using two multivariate methods: principal component analysis and FreeViz projection. Of the 318 bacterial isolates, we selected a consortium of four strains (Xanthomonadales bacterium sp. CST37-CF, Sphingomonas sp. BLA14-CF, Cellulosimicrobium sp. AKD4-BF and Aeromonas sp. RES19-BTP) that degrade the entire spectrum of tested additives by means of dissolved organic carbon measurements. A proof-of-concept study on a pilot scale was then performed by immobilizing the artificial consortium of the four strains and inserting them into a 33-liter, tubular flow-through reactor with a retention time of < 15 h. The consortium caused an 88% reduction in the COD of the whitewater, even after 21 days.

Microbial competition reduces metabolic interaction distances to the low µm-range.

Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 µm-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15 µm away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells' product affinity, to show that within producer-receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low µm-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.

Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level.

Confinement of bacterial cells in a matrix or in capsules is an integral part of many biotechnological applications. Here, the well-known layer-by-layer method of deposition of a polyelectrolyte film a few nanometers in thickness to confine separated bacterial cells in permeable and physically durable shells has been examined. Due to the physical properties of such a confinement, we found that this method enables investigation of effects of physical barriers against mass gain and cell division. Using the method of time-lapse confocal microscopy, we observed a prolonged lag phase, dependent on the number of polyelectrolyte layers. In the confinement, both the GFP fluorescent signal from the leaking T7 promoter and the cell size were increased by factors of more than five and two, respectively. This creates a paradigm shift that enables use of mechanical entrapment for control of bacterial cell physiology and opens possibilities of controlling the division rate as well as gene expression. These effects can be attributed to the perturbation of the sensing of the cell size, which results in disproportional synthesis of a cell envelope impinging the intracellular material and compels cells to grow rapidly. In addition, the charged surface of cells enables prolonged intercellular physical interaction and results in spherically shaped microcolonies.

Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms.

Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC-related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water-proof rubber elastomer barrier. The artificial biofilm is constructed layer-by-layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular-biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC-related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.

Sustained release of antimicrobials from double-layer nanofiber mats for local treatment of periodontal disease, evaluated using a new micro flow-through apparatus.

Periodontal disease is a widespread chronic condition associated with degradation of periodontal tissues that requires more effective approaches for its treatment. Thus, the aim was to develop a nanodelivery system for local application of antimicrobials, with evaluation in vitro using a newly developed micro flow-through apparatus that simulates local in-vivo conditions in the periodontal pocket: small resting volume, and low gingival crevicular fluid flow rate. We successfully developed a double-layer nanofiber mat composed of a chitosan/ poly(ethylene) oxide nanofiber layer with 30% ciprofloxacin, and a poly(ε-caprolactone) nanofiber layer with 5% metronidazole. The precisely designed composition enabled sustained in-vitro release of the antimicrobials according to their specific drug release mechanisms. The rate-limiting step of ciprofloxacin release was its own low solubility at pH 7.4, when there was excess of solid drug present in the delivery system. In contrast, sustained release of metronidazole was due to slow penetration of dissolution medium through the hydrophobic poly(ε-caprolactone) nanofiber layer. The double-layer nanofiber mat developed showed antibacterial activity against Escherichia coli and Aggregatibacter actinomycetemcomitans based on plate antibiogram assays. The antimicrobial concentrations released from the nanofiber mats determined using the developed apparatus were above the minimal inhibitory concentrations against the periodontal pathogens for up to 7 days, which is valuable information for prediction of the efficacy of the nanodelivery system. Although this apparatus was specifically designed for characterization of formulations associated with treatments for periodontal disease, its applicability is much wide, as for development of any delivery system for application at target sites that have similar local conditions.

Medium-Dependent Antibacterial Properties and Bacterial Filtration Ability of Reduced Graphene Oxide.

Toxicity of reduced graphene oxide (rGO) has been a topic of multiple studies and was shown to depend on a variety of characteristics of rGO and biological objects of interest. In this paper, we demonstrate that when studying the same dispersions of rGO and fluorescent Escherichia coli (E. coli) bacteria, the outcome of nanotoxicity experiments also depends on the type of culture medium. We show that rGO inhibits the growth of bacteria in a nutrition medium but shows little effect on the behavior of E. coli in a physiological saline solution. The observed effects of rGO on E. coli in different media could be at least partially rationalized through the adsorption of bacteria and nutrients on the dispersed rGO sheets, which is likely mediated via hydrogen bonding. We also found that the interaction between rGO and E. coli is medium-dependent, and in physiological saline solutions they form stable flocculate structures that were not observed in nutrition media. Furthermore, the aggregation of rGO and E. coli in saline media was observed regardless of whether the bacteria were alive or dead. Filtration of the aggregate suspensions led to nearly complete removal of bacteria from filtered liquids, which highlights the potential of rGO for the filtration and separation of biological contaminants, regardless of whether they include live or dead microorganisms.

Effect of GO on bacterial cells: Role of the medium type and electrostatic interactions.

Graphene and graphene oxide (GO) both being two-dimensional materials are gaining popularity among researchers as a promising nanomaterial for various medical and biological applications. The aim of this study is to elucidate the influence of nanostructured GO sheets on viability of a model species of gram-negative E. coli bacteria transformed with pRSET-emGFP plasmid in in vitro experiments. It was shown that GO at concentrations between 0.0025 and 2.5 g/l in growth medium inhibits growth of bacterial colonies, while in physiological saline solution (PS) this effect decreases dramatically to the point of complete disappearance. It was shown that in order to obtain a pronounced antibacterial effect one needs to introduce high concentrations of GO into the media (up to 2.5 g/l), which can be important for development of antibacterial materials for biomedical applications. Some of the obtained data provide clear evidence to electrostatic nature of interaction between bacterial and GO sheets. A number of previous papers suggested the process of biofilms formation by bacteria as the primary reason for aggregation between graphene-like materials and bacterial cells. However, formation of flocculent structures consisting of GO and dead bacteria and accompanied with decrease in zeta-potential of particles in the suspension to 18 mV proves that electrostatic interactions play the major role in aggregation. The obtained data can be used for employing GO and similar materials in new systems for water-purification from biological contaminants. Besides, our results stress the importance of accounting for the conditions in which goods and coatings containing graphene-like materials as an antibacterial agent are used, as well as unification of the experimental conditions.

Functionalization of titania nanotubes with electrophoretically deposited silver and calcium phosphate nanoparticles: Structure, composition and antibacterial assay.

Herein TiO2 nanotubes (NTs) were fabricated via electrochemical anodization and coated with silver and calcium phosphate (CaP) nanoparticles (NPs) by electrophoretic deposition. Scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) revealed that Ag and CaP NPs were successfully deposited onto the TiO2 NTs. Using X-ray diffraction, only anatase and Ti were observed after deposition of Ag and CaP NPs. However, X-ray photoelectron spectroscopy (XPS) analysis revealed that the binding energy (BE) of the Ag and CaP NP core levels corresponded to metallic Ag, hydroxyapatite and amorphous calcium phosphate, based on the knowledge that CaP NPs synthesized by precipitation have the nanocrystalline structure of hydroxyapatite. The application of Ag NPs allows for decreasing the water contact angle and thus increasing the surface free energy. It was concluded that the CaP NP surfaces are superhydrophilic. A significant antimicrobial effect was observed on the TiO2 NT surface after the application of Ag NPs and/or CaP NPs compared with that of the pure TiO2 NTs. Thus, fabrication of TiO2 NTs, Ag NPs and CaP NPs with PEI is promising for diverse biomedical applications, such as in constructing a biocompatible coating on the surface of Ti that includes an antimicrobial effect.

Nanofibers with Incorporated Autochthonous Bacteria as Potential Probiotics for Local Treatment of Periodontal Disease.

The conventional treatment of periodontal disease does not solve the high incidence of recolonization of periodontal pockets by pathogens. Here, we introduce an innovative concept of incorporating autochthonous bacteria as potential probiotics into nanofibers for local treatment. We selected and isolated the strain 25.2.M from the oral microbiota of healthy volunteers. It was identified as Bacillus sp. based on 16S rRNA sequence analyses. The strain is nonpathogenic, produces antimicrobial substances, and can grow over the periodontal pathogen Aggregatibacter actinomycetemcomitans in vitro, making it a promising probiotic candidate. The strain 25.2.M was successfully incorporated into the nanofibers in the form of spores (107 CFU/mg), the viabilities of which were exceptional (max. change of 1 log unit) both during electrospinning and after 12 months of storage. The release of the bacteria was delayed from chitosan/poly(ethylene oxide) compared to poly(ethylene oxide) nanofibers, and the antimicrobial activity against A. actinomycetemcomitans was confirmed. The developed nanodelivery system for administration into periodontal pockets thus offers a promising approach for the inhibition of periodontal pathogens and restoration of healthy oral microbiota.

Novel electrospun fibers with incorporated commensal bacteria for potential preventive treatment of the diabetic foot.

AIM: A novel electrospun biocompatible nanofibrous material loaded with commensal bacteria for potential preventive treatment of the diabetic foot was developed. MATERIALS & METHODS: Two biocompatible polymers (carboxymethylcellulose and polyethylene oxide) were combined with a bacterium isolate from the skin located between the toes of a healthy adult (identified using a matrix-assisted laser desorption/ionization mass spectrometry-based method as a strain of Staphylococcus epidermidis). Higher bacteria loads in the material were assured through their encapsulation in polyethylenimine. The nanofibrous material was characterized using scanning electron microscopy, zeta-potential measurements and through evaluation of cell growth and viability. RESULTS & DISCUSSION: nanometer formation was confirmed using scanning electron microscopy, while the zeta-potential measurements revealed successful bacteria encapsulation. Viable and sufficiently growing cells were confirmed prior and after their incorporation. CONCLUSION: The prepared materials were proven suitable to deliver viable commensal bacteria in a comparable share to the Staphylococcaceae in the foot microbiome making this approach promising for preventive diabetic foot treatment.

Development of probiotic-loaded microcapsules for local delivery: Physical properties, cell release and growth.

The delivery of probiotics to different sites of action within the human body might help to prevent and treat several diseases. Here, we describe a microcapsule-based system for delivery of probiotic bacteria, as vegetative cells or spores, which promotes their prolonged survival and efficient revival, and successful colonisation of the target surface. This system is proposed for local delivery into periodontal pockets. Encapsulation of the probiotic bacteria was based on alginate crosslinking with calcium ions. This was performed by prilling the polymer dispersion supplemented with the probiotic using membrane vibration technology, followed by chitosan coating by polyelectrolyte complexation. The microcapsules were 120-150 µm in diameter, and were dried by lyophilisation. The chitosan coating increased the specific surface area and improved the bioadhesion potential, with no negative impact on viability and growth kinetics of the probiotic bacteria. Chitosan represents a barrier, which promotes sustained release of the probiotic bacteria. Vegetative bacteria were encapsulated at 2 × 108 CFU/g dry microcapsules, which represented ~5% of the prepared microcapsules, with stable viability for at least 2 months. Encapsulation of bacterial spores was greater, at 2 × 1010 CFU/g dry microcapsules, achieving 100% of microcapsules with incorporated revivable spores.

DNA structure at the plasmid origin-of-transfer indicates its potential transfer range.

Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efficiently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.html .

Cyanogenic Pseudomonas spp. strains are concentrated in the rhizosphere of alpine pioneer plants.

HCN producing bacteria have previously been isolated from alpine mineral soil and their ecophysiology was presumed to be associated with mineral weathering. Nevertheless, the high ecological patchiness of the alpine environment calls for an extensive and detailed analysis of the spatial distribution of HCN producing bacterial populations and their associated weathering traits. Our results of such an analysis showed that primarily the rhizosphere of pioneer plants was rich in HPPs, harbouring the most potent HCN producers. HCN production incidence and intensity were dependent on the plant-associated microhabitat and type of bedrock/mineral soil, however the HCN+ phenotype was not associated with one of the particular genotypes which we determined by BOX-PCR. In HPP isolates, HCN production most commonly co-occurred with the production of hydroxamate-type siderophores, but was less often associated with inorganic phosphate solubilization activity and the production of catechol-type siderophores. These observations indicate that a plant's physiotype, not species, provide physicochemical conditions that determine selective pressure, which enables the growth of Pseudomonas spp. with a random genotype, but phenotypically predetermined to increase mineral weathering via a particular combination of phosphate solubilization and iron complexation with siderophores and HCN.

Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water.

Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 µg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units.

Hydrogen Cyanide in the Rhizosphere: Not Suppressing Plant Pathogens, but Rather Regulating Availability of Phosphate.

Plant growth promoting rhizobacteria produce chemical compounds with different benefits for the plant. Among them, HCN is recognized as a biocontrol agent, based on its ascribed toxicity against plant pathogens. Based on several past studies questioning the validity of this hypothesis, we have re-addressed the issue by designing a new set of in vitro experiments, to test if HCN-producing rhizobacteria could inhibit the growth of phytopathogens. The level of HCN produced by the rhizobacteria in vitro does not correlate with the observed biocontrol effects, thus disproving the biocontrol hypothesis. We developed a new concept, in which HCN does not act as a biocontrol agent, but rather is involved in geochemical processes in the substrate (e.g., chelation of metals), indirectly increasing the availability of phosphate. Since this scenario can be important for the pioneer plants living in oligotrophic alpine environments, we inoculated HCN producing bacteria into sterile mineral sand together with germinating plants and showed that the growth of the pioneer plant French sorrel was increased on granite-based substrate. No such effect could be observed for maize, where plantlets depend on the nutrients stored in the endosperm. To support our concept, we used KCN and mineral sand and showed that mineral mobilization and phosphate release could be caused by cyanide in vitro. We propose that in oligotrophic alpine environments, and possibly elsewhere, the main contribution of HCN is in the sequestration of metals and the consequential indirect increase of nutrient availability, which is beneficial for the rhizobacteria and their plant hosts.

Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability.

DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.