How to study biofilms: technological advancements in clinical biofilm research

Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.

Efficacy of Endodontic Disinfection Protocols in an E. faecalis Biofilm Model-Using DAPI Staining and SEM

The aim of this study was to investigate the antimicrobial efficacy of different disinfection protocols in a novel Enterococcus faecalis biofilm model based on a visualization method and to evaluate the potential alteration of dentinal surface. A total of 120 extracted human premolars were allocated to 6 groups with different irrigation protocols. The assessment of the effectiveness of each protocol and the alteration of dentinal surface were visualized by using SEM and fluorescence microscopy (DAPI). A dense E. faecalis biofilm with a penetration depth of 289 μm (medial part of the root canal) and 93 μm (apical part) validated that the biofilm model had been successfully implemented. A significant difference between the 3% NaOCl groups and all the other groups in both observed parts of the root canal (p < 0.05) was detected. However, the SEM analysis revealed that the dentinal surface in the 3% NaOCl groups was severely altered. The established biofilm model and the visualization method based on DAPI are appropriate for bacterial quantification and evaluation of the depth effect of different disinfection protocols in the root canal system. The combination of 3% NaOCl with 20% EDTA or MTAD with PUI allows the decontamination of deeper dentine zones within the root canal but simultaneously alters the dentinal surface.

Antibacterial Electrodeposited Copper-Doped Calcium Phosphate Coatings for Dental Implants

Dental implants provide a good solution for the replacement of tooth roots. However, the full restoration of tooth functions relies on the bone-healing period before positioning the abutment and the crown on the implant, with the associated risk of post-operative infection. This study aimed at developing a homogeneous and adherent thin calcium phosphate antibacterial coating on titanium dental implants by electrodeposition to favor both implant osseointegration and to limit peri-implantitis. By combining global (XRD, FTIR-ATR, elemental titration) and local (SEM, Raman spectroscopy on the coating surface and thickness) characterization techniques, we determined the effect of electrodeposition time on the characteristics and phases content of the coating and the associated mechanism of its formation. The 1-min-electrodeposited CaP coating (thickness: 2 ± 1 μm) was mainly composed of nano-needles of octacalcium phosphate. We demonstrated its mechanical stability after screwing and unscrewing the dental implant in an artificial jawbone. Then, we showed that we can reach a high copper incorporation rate (up to a 27% Cu/(Cu+Ca) molar ratio) in this CaP coating by using an ionic exchange post-treatment with copper nitrate solution at different concentrations. The biological properties (antibiofilm activity and cytotoxicity) were tested in vitro using a model of mixed bacteria biofilm mimicking peri-implantitis and the EN 10993-5 standard (direct contact), respectively. An efficient copper-doping dose was determined, providing an antibiofilm property to the coating without cytotoxic side effects. By combining the electrodeposition and copper ionic exchange processes, we can develop an antibiofilm calcium phosphate coating on dental implants with a tunable thickness and phases content.

Ex vivo evaluation of antibiotic sensitivity in samples from endodontic infections

Objective

To develop an in vitro model for real-time monitoring of endodontic biofilm growth and evaluate the ex vivo effect of antibiotics on biofilm growth.

Material and Methods

Root canal samples were taken from 40 patients and inoculated into 96-well plates in a system that measures biofilm growth through electrical impedance. Biofilm bacterial composition at the genus and species level was analyzed by Illumina sequencing. ANCOM-BC corrected data were used to compare bacterial composition after antibiotic treatment through compositional analysis, and to compare microbiological with clinical data.

Results

The stationary phase was reached at 8 hours. The biofilm formed had a similar bacterial composition to the inoculum, and Enterococcus faecalis was virtually absent from the samples. The bacterial composition and the effect of antibiotics were sample-dependent. Metronidazole was the antibiotic that most inhibited biofilm formation and azithromycin the one that inhibited it in the highest percentage of cases. The antibiotic effect could not be related to the biofilm original bacterial composition.

Conclusions

The impedance system allowed real-time monitoring of endodontic biofilm formation, and we propose it as a model for ex vivo evaluation of the whole biofilm susceptibility to antimicrobials, as opposed to evaluating antibiotic sensitivity of specific bacterial isolates.

Enterococcus faecalis Shields Porphyromonas gingivalis in Dual-Species Biofilm in Oxic Condition

Aim: To develop a reproducible biofilm model consisting of Enterococcus faecalis (E. faecalis) and Porphyromonas gingivalis (P. gingivalis) and to evaluate the interaction between the two bacterial species. Methodology: E. faecalis and P. gingivalis were grown in mono-culture, sequential, and co-culture models for 96 h in a 96-well polystyrene microtiter plate under both aerobic and anaerobic conditions separately. The viability of the two bacterial species in the biofilms was quantified by polymerase chain reaction (qPCR). Biofilm thickness and protein contents were measured using confocal laser scanning microscopy (CLSM). Two-way analysis of variance (ANOVA) was performed to analyze cell viability and biofilm thickness among different culture models cultivated under either aerobic or anaerobic conditions. The level of significance was set at p < 0.05. Results: Different culture models tested did not show any significant difference between the viable cell counts of both E. faecalis and P. gingivalis cultivated under aerobic and anaerobic conditions (p > 0.05). Biofilm was significantly thicker (p < 0.05) in the co-culture models compared to the mono-culture and sequential models. Protein contents in the biofilms were more pronounced when both bacterial species were co-cultured under aerobic conditions. Conclusions: E. faecalis appeared to shield P. gingivalis and support its continued growth in oxic (aerobic) conditions. The co-culture model of E. faecalis and P. gingivalis produced a significantly thicker biofilm irrespective of the presence or absence of oxygen, while increased protein contents were only observed in the presence of oxygen.

In-vitro evaluation of the anti-cariogenic effect of a hybrid coating associated with encapsulated sodium fluoride and stannous chloride in nanoclays on enamel

OBJECTIVE

The aim of this study is to test, in vitro, the anti-cariogenic effect of experimental hybrid coatings, with nano clays of halloysite or bentonite, loaded with sodium fluoride or with a combination of sodium fluoride and stannous chloride, respectively.

METHODOLOGY

The varnish Fluor Protector (1,000 ppm of F-) was used as positive control and no treatment was the negative control. Enamel specimens (5 mm × 5 mm) were obtained from bovine teeth. The specimens (n=10) had their surfaces divided into two halves (5 mm × 2.5 mm each), in which one half received one of the treatments (Hybrid; Hybrid + NaF; Hybrid + NaF + SnCl2; Hybrid + NaF Loaded; Hybrid + NaF + SnCl2 Loaded). The specimens were submitted to a cariogenic challenge using a biofilm model (S. mutans UA159, for 5 days). Enamel surfaces both under and adjacent to the treated area were analyzed for mineral loss and lesion depth, by transverse microradiography. The pH of the medium was measured twice a day, and the fluoride release was analyzed. Additional specimens were submitted to confocal analysis.

RESULTS

Data were statistically analyzed by two-way ANOVA followed by Tukey test (α=0.05). None of hybrid groups were able to reduce the lesion depth; the Hybrid + NaF group, however, was able to reduce mineral loss differing from the negative control (p=0.008). The groups showed no significant difference in the pH measurement and fluoride release. Confocal analysis confirmed that for all groups the biofilm growth was similar.

CONCLUSION

None of the hybrid groups reduced lesion depth, but the Hybrid + NaF group was able to promote protection against mineral loss.

Novel Cyclic Lipopeptides Fusaricidin Analogs for Treating Wound Infections

Both acute and chronic cutaneous wounds are often difficult to treat due to the high-risk for bacterial contamination. Once hospitalized, open wounds are at a high-risk for developing hospital-associated infections caused by multi drug-resistant bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. Treating these infections is challenging, not only because of antibiotic resistance, but also due to the production of biofilms. New treatment strategies are needed that will help in both stimulating the wound healing process, as well as preventing and eliminating bacterial wound infections. Fusaricidins are naturally occurring cyclic lipopeptides with antimicrobial properties that have shown to be effective against a variety of fungi and Gram-positive bacteria, with low toxicity. Continuing with our efforts toward the identification of novel cyclic lipopeptides Fusaricidin analogs, herein we report the synthesis and evaluation of the antimicrobial activity for two novel cyclic lipopeptides (CLP), CLP 2605-4 and CLP 2612-8.1 against methicillin resistant S. aureus and P. aeruginosa, respectively, in in vivo porcine full thickness wound model. Both CLPs were able to reduce bacterial counts by approximately 3 log CFU/g by the last assessment day. Peptide 2612-8.1 slightly enhanced the wound healing, however, wounds treated with peptide 2605-4, have shown higher levels of inflammation and impaired wound healing process. This study highlights the importance of identifying new antimicrobials that can combat bacterial infection while not impeding tissue repair.

Root Caries Preventive Effect of Varnishes Containing Fluoride or Fluoride + Chlorhexidine/Cetylpyridinium Chloride In Vitro

Caries preventive varnishes containing only fluoride might differ from those containing a combination of fluoride and antimicrobial components in terms of mineralization properties and their impact on the cariogenic biofilm. We compared a fluoride and a fluoride + chlorhexidine (CHX)/cetylpyridinium chloride (CPC) varnish on root caries formation in vitro. One hundred bovine root dentin samples were allocated to five groups (n = 20/group): (1) 7700 ppm fluoride varnish (Fluorprotector S (F)), (2) experimental placebo varnish for F (F-P), (3) 1400 ppm fluoride + 0.3% CHX/0.5% CPC varnish (Cervitec F (CF)), (4) experimental placebo varnish for CF (CF-P), (5) untreated control. Cariogenic challenge was provided using a multi-station, continuous-culture 3-species (Streptococcus mutans (SM), Lactobacillus rhamnosus (LR), Actinomyces naeslundii (AN)) biofilm model for 10 days. Mineral loss (ΔZ) was evaluated using transversal microradiography and bacterial counts in the biofilm assessed as colony-forming units. Fluorescence in situ hybridization (FISH) and confocal microscopy were performed to assess the three-dimensional biofilm architecture. Mean ± SD (vol% × μm) ΔZ was significantly lower for F (9133 ± 758) and CF (9835 ± 1677) compared to control (11362 ± 919) (p < 0.05), without significant differences between F and CF. SM counts were significantly lower and LR counts significantly higher in F- and CF-biofilms compared to control. AN counts were significantly higher in the F-biofilms than in all other groups. According to FISH, SM and LR invaded dentinal tubules only in the control-group. In the CF-group, the basal biofilm layer did not contain SM and AN. Both F and CF varnishes had similar caries-preventive effects and a considerable impact on biofilm structure and composition.

Manipulation of Saliva-Derived Microcosm Biofilms To Resemble Dysbiotic Subgingival Microbiota

In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators.

Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and reestablish a health-associated microbiota, a high-throughput in vitro multispecies biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rRNA gene amplicon sequencing as well as measurement of dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principal-component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis to saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder a microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies.

IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in a dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large-scale evaluation of strategies that can potentially modulate microbial ecology.

Probiotic Effects on Multispecies Biofilm Composition, Architecture, and Caries Activity In Vitro

While probiotics have been tested for their anti-caries effect in vitro and also clinically, there is a lack of understanding of their effects on complex dental biofilms. We assessed two probiotics, Lactobacillus reuteri and Streptococcus oligofermentans, on a continuous-cultured model containing Streptococcus mutans, Lactobacillus rhamnosus and Actinomyces naeslundii. Cariogenic biofilms were grown on bovine enamel specimens and daily challenged with L. reuteri or S. oligofermentans whole culture (LC/SC) or cell-free supernatant (LS/SS) or medium only (negative control, NC) (n = 21/group) for 10 days. Biofilm was assessed via counting colony-forming units, quantitative polymerase chain reaction, and fluorescence in situ hybridization. Caries activity was determined by pH measurements and by assessing mineral loss (ΔZ) using transverse microradiography. Both LC and SC significantly reduced total and strain-specific cariogenic bacterial numbers (p < 0.05). ΔZ was reduced in LC (mean ± SD: 1846.67 ± 317.89) and SC (3315.87 ± 617.30) compared to NC (4681.48 ± 495.18, p < 0.05). No significant reductions in bacterial numbers and ΔZ was induced by supernatants. Biofilm architecture was not considerably affected by probiotic applications. Viable probiotics L. reuteri and S. oligofermentans, but not their culture supernatants, could reduce the caries activity of multi-species biofilms in vitro.

Kinetics of anaerobic methane oxidation coupled to denitrification in the membrane biofilm reactor

Anaerobic oxidation of methane coupled to denitrification (AOM-D) in a membrane biofilm reactor (MBfR), a platform used for efficiently coupling gas delivery and biofilm development, has attracted attention in recent years due to the low cost and high availability of methane. However, experimental studies have shown that the nitrate-removal flux in the CH₄ -based MBfR (<1.0 g N/m² -day) is about one order of magnitude smaller than that in the H₂ -based MBfR (1.1-6.7 g N/m² -day). A one-dimensional multispecies biofilm model predicts that the nitrate-removal flux in the CH₄ -based MBfR is limited to <1.7 g N/m² -day, consistent with the experimental studies reported in the literature. The model also determines the two major limiting factors for the nitrate-removal flux: The methane half-maximum-rate concentration (K₂ ) and the specific maximum methane utilization rate of the AOM-D syntrophic consortium (k_max2 ), with k_max2 being more important. Model simulations show that increasing k_max2 to >3 g chemical oxygen demand (COD)/g cell-day (from its current 1.8 g COD/g cell-day) and developing a new membrane with doubled methane-delivery capacity (D_m ) could bring the nitrate-removal flux to ≥4.0 g N/m² -day, which is close to the nitrate-removal flux for the H₂ -based MBfR. Further increase of the maximum nitrate-removal flux can be achieved when D_m and k_max2 increase together.

Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action

Biofilm refers to the complex, sessile communities of microbes found either attached to a surface or buried firmly in an extracellular matrix as aggregates. The biofilm matrix surrounding bacteria makes them tolerant to harsh conditions and resistant to antibacterial treatments. Moreover, the biofilms are responsible for causing a broad range of chronic diseases and due to the emergence of antibiotic resistance in bacteria it has really become difficult to treat them with efficacy. Furthermore, the antibiotics available till date are ineffective for treating these biofilm related infections due to their higher values of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), which may result in in-vivo toxicity. Hence, it is critically important to design or screen anti-biofilm molecules that can effectively minimize and eradicate biofilm related infections. In the present article, we have highlighted the mechanism of biofilm formation with reference to different models and various methods used for biofilm detection. A major focus has been put on various anti-biofilm molecules discovered or tested till date which may include herbal active compounds, chelating agents, peptide antibiotics, lantibiotics and synthetic chemical compounds along with their structures, mechanism of action and their respective MICs, MBCs, minimum biofilm inhibitory concentrations (MBICs) as well as the half maximal inhibitory concentration (IC₅₀) values available in the literature so far. Different mode of action of anti biofilm molecules addressed here are inhibition via interference in the quorum sensing pathways, adhesion mechanism, disruption of extracellular DNA, protein, lipopolysaccharides, exopolysaccharides and secondary messengers involved in various signaling pathways. From this study, we conclude that the molecules considered here might be used to treat biofilm-associated infections after significant structural modifications, thereby investigating its effective delivery in the host. It should also be ensured that minimum effective concentration of these molecules must be capable of eradicating biofilm infections with maximum potency without posing any adverse side effects on the host.

Effectiveness of implant surface debridement using particle beams at differing air pressures

Because implant surface decontamination is challenging, air powder abrasive systems have been suggested as an alternative debridement method. This in vitro study investigated the effectiveness of different powder formulations and air pressures in cleaning implant surfaces and the extent of surface damage. A validated ink model of implant biofilm was used. Sterile 4.1 × 10 mm Grade 4 titanium implants were coated in a blue indelible ink to form a uniform, visually detectable biofilm-like layer over the implant threads and mounted into a bone replica material with bony defects to approximate peri-implantitis. Air powder abrasive treatments were undertaken using glycine, sodium bicarbonate, or calcium carbonate powder at air pressures of 25, 35, 45, and 55 psi. Digital macro photographs of the threads were stitched to give composite images of the threads, so the amount of ink remaining could be quantified as the residual area and expressed as a percentage. Implant surfaces were also examined with scanning electron microscopy to grade the surface changes. No treatment cleaned all the surface of the threads. The powders were ranked in order of decreasing effectiveness and decreasing surface change into the same sequence of calcium carbonate followed by sodium bicarbonate followed by glycine. Higher air pressure improved cleaning and increased surface change, with a plateau effect evident. All powders caused some level of surface alteration, with rounding of surface projections most evident. With air powder abrasive systems, there is a trade-off between cleaning efficacy and surface damage. Using this laboratory model, sodium bicarbonate and calcium carbonate powders were the most effective for surface cleaning when used at air pressures as low as 25 psi.

XTT assay of ex vivo saliva biofilms to test antimicrobial influences

OBJECTIVE

Many dental diseases are attributable to biofilms. The screening of antimicrobial substances, in particular, requires a high sample throughput and a realistic model, the evaluation must be as quick and as simple as possible. For this purpose, a colorimetric assay of the tetrazolium salt XTT (sodium 3'-[1-[(phenylamino)-carbony]-3,4-tetrazolium]-bis(4-methoxy-6-nitro)benzene-sulfonic acid hydrate) converted by saliva biofilms is recommended. Cleavage of XTT by dehydrogenase enzymes of metabolically active cells in biofilms yields a highly colored formazan product which is measured photometrically.

MATERIALS AND METHOD

The suitability of the XTT assay for detecting the vitality of ex vivo saliva biofilms was tested to determine the efficacy of chlorhexidine and ozone versus saliva biofilms grown on titanium discs.

RESULTS

The XTT method lends itself to testing the vitality of microorganisms in saliva biofilms. The sensitivity of the arrays requires a specific minimum number of pathogens, this number being different for planktonic bacteria and those occurring in biofilms. The antibacterial effect after treatment with chlorhexidine or ozone was measured by XTT conversion that was significantly reduced. The antimicrobial efficacy of 60 s 0.5% and 0.1% chlorhexidine treatment was equal and comparable with 60 s ozone treatment.

CONCLUSION

The XTT assay is a suitable method to determine the vitality in saliva biofilms, permitting assessment of the efficacy of antimicrobial substances. Its quick and easy applicability renders it especially suitable for screening.