Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms

Investigating the association between nitrate dosing and nitrite generation by the human oral microbiota in continuous culture

The generation of nitrite by the oral microbiota is believed to contribute to healthy cardiovascular function, with oral nitrate reduction to nitrite associated with systemic blood pressure regulation. There is the potential to manipulate the composition or activities of the oral microbiota to a higher nitrate-reducing state through nitrate supplementation. The current study examined microbial community composition and enzymatic responses to nitrate supplementation in sessile oral microbiota grown in continuous culture. Nitrate reductase (NaR) activity and nitrite concentrations were not significantly different to tongue-derived inocula in model biofilms. These were generally dominated by Streptococcus spp., initially, and a single nitrate supplementation resulted in the increased relative abundance of the nitrate-reducing genera Veillonella, Neisseria, and Proteus spp. Nitrite concentrations increased concomitantly and continued to increase throughout oral microbiota development. Continuous nitrate supplementation, over a 7-day period, was similarly associated with an elevated abundance of nitrate-reducing taxa and increased nitrite concentration in the perfusate. In experiments in which the models were established in continuous low or high nitrate environments, there was an initial elevation in nitrate reductase, and nitrite concentrations reached a relatively constant concentration over time similar to the acute nitrate challenge with a similar expansion of Veillonella and Neisseria. In summary, we have investigated nitrate metabolism in continuous culture oral biofilms, showing that nitrate addition increases nitrate reductase activity and nitrite concentrations in oral microbiota with the expansion of putatively NaR-producing taxa.IMPORTANCEClinical evidence suggests that blood pressure regulation can be promoted by nitrite generated through the reduction of supplemental dietary nitrate by the oral microbiota. We have utilized oral microbiota models to investigate the mechanisms responsible, demonstrating that nitrate addition increases nitrate reductase activity and nitrite concentrations in oral microbiota with the expansion of nitrate-reducing taxa.

Effects of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans on Modeling Subgingival Microbiome and Impairment of Oral Epithelial Barrier

Periodontitis is an exemplar of dysbiosis associated with the coordinated action of multiple members within the microbial consortium. The polymicrobial synergy and dysbiosis hypothesis proposes a dynamic host-microbiome balance, with certain modulators capable of disrupting eubiosis and driving shifts towards dysbiosis within the community. However, these factors remain to be explored. We established a Porphyromonas gingivalis- or Aggregatibacter actinomycetemcomitans-modified subgingival microbiome model and 16S rRNA sequencing revealed that P. gingivalis and A. actinomycetemcomitans altered the microbiome structure and composition indicated by α and β diversity metrics. P. gingivalis increased the subgingival dysbiosis index (SDI), while A. actinomycetemcomitans resulted in a lower SDI. Furthermore, P. gingivalis-stimulated microbiomes compromised epithelium function and reduced expression of tight junction proteins, whereas A. actinomycetemcomitans yielded mild effects. In conclusion, by inoculating P. gingivalis, we created dysbiotic microcosm biofilms in vitro resembling periodontitis-related subgingival microbiota, exhibiting enhanced dysbiosis and impaired epithelium integrity.

Influence of Lactobacillus reuteri, Bifidobacterium animalis subsp. lactis, and prebiotic inulin on dysbiotic dental biofilm composition ex vivo

BACKGROUND

Probiotic bacterial supplementation has shown promising results in the treatment of periodontitis and the maintenance of periodontal health. The purpose of this investigation was to evaluate the influence of Lactobacillus reuteri or Bifidobacterium animalis subsp. lactis supplementation with and without prebiotic inulin on biofilm composition using an ex vivo biofilm model.

METHODS

Subgingival plaque specimens from three periodontitis-affected human donors were used to grow biofilms on hydroxyapatite disks in media supplemented with varying combinations of prebiotic inulin, Lactobacillus reuteri, and Bifidobacterium animalis subsp. lactis. Relative abundances of bacterial genera present in mature biofilms were evaluated using 16S rRNA next-generation sequencing. Diversity metrics of microbial communities were evaluated using a next-generation microbiome bioinformatics platform.

RESULTS

Inulin supplementation produced statistically significant dose-dependent increases in relative abundances of Lactobacillus and Bifidobacterium species (p < 0.001) with concomitant decreases in relative abundances of Streptococcus, Veillonella, Fusobacterium, Parvimonas, and Prevotella species (p < 0.001). Inoculation with L. reuteri or B. animalis subsp. lactis increased the relative abundance of only the supplemented probiotic genera (p < 0.05). Supplemental inulin led to a statistically significant decrease in biofilm alpha diversity (p < 0.001).

CONCLUSIONS

The described ex vivo model appears suitable for investigating the effects of probiotic bacteria, prebiotic oligosaccharides, and combinations thereof on biofilm composition and complexity. Within the limitations imposed by this model, results from the present study underscore the potential for prebiotic inulin to modify biofilm composition favorably. Additional research further elucidating biologic rationale and controlled clinical research defining therapeutic benefits is warranted.

In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities

Numerous in vitro biofilm model systems are available to study oral biofilms. Over the past several decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed for the increased generalizability of in vitro oral biofilm studies. The integration of contemporary systems with confocal microscopy and 16S rRNA community profiling has enhanced the capabilities of in vitro biofilm model systems to quantify biofilm architecture and analyse microbial community composition. In this review, we describe several model systems relevant to modern in vitro oral biofilm studies: the constant depth film fermenter, Sorbarod perfusion system, drip-flow reactor, modified Robbins device, flowcells and microfluidic systems. We highlight how combining these systems with confocal microscopy and community composition analysis tools aids exploration of oral biofilm development under different conditions and in response to antimicrobial/anti-biofilm agents. The review closes with a discussion of future directions for the field of in vitro oral biofilm imaging and analysis.

The microbiome of oral cavity patients with periodontitis, adhesive and biofilm forming properties

The microbiome of oral cavity in healthy people and patients with periodontitis was analyzed to determine their adhesive properties and the ability to form biofilms. The study involved 2 groups: healthy, 18 people, and an experimental group, 20 patients with chronic generalized periodontitis moderate severity of the disease. The average age of the studied people was 35-45 years. Material - dental plaque, scraping from the mucous membrane of the back of the tongue, the contents of the periodontal groove and periodontal pocket, as well as oral fluid. The main method of diagnostic was bacteriological. The average adhesion index (AAI) was used to determine adhesion level of microorganisms to epithelial cells of oral cavity’s mucous membrane. The microbiota’s ability to form biofilm was tested on glass and plastic surface. The microbiota of oral cavity of patients with periodontitis was characterized by decrease in the frequency of bacteria of the genera: Streptococcus, Peptostreptococcus, Peptococcus, and an increase in Staphylococcus aureus, Veillonella spp., Bacillus spp. The microbiota of the oral cavity of patients with generalized periodontitis has a greater ability to adhere to the cells of the mucous membrane than in healthy people, while their ability to form biofilms and exhibit pathogenic properties is enhanced. The biofilm formation of microorganisms in healthy and sick people differs both on glass and on plastic surfaces.

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.

Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro

Developing a laboratory model of oral polymicrobial communities is essential for in vitro studies of the transition from healthy to diseased oral plaque. SHI medium is an enriched growth medium capable of supporting in vitro biofilms with similar diversity to healthy supragingival inocula; however, this medium does not maintain the diversity of gram‐negative bacteria more associated with subgingival plaque. Here, we systematically modified SHI medium components to investigate the impacts of varying nutrients and develop a medium capable of supporting a specific disease‐state subgingival community. A diseased subgingival plaque sample was inoculated in SHI medium with increasing concentrations of sucrose (0%, 0.1%, 0.5%), fetal bovine serum (FBS) (0%, 10%, 20%, 30%, 50%), and mucin (0.1, 2.5, 8.0 g/L) and grown for 48 hrs, then the 16S rRNA profiles of the resulting biofilms were examined. In total, these conditions were able to capture 89 of the 119 species and 43 of the 51 genera found in the subgingival inoculum. Interestingly, biofilms grown in high sucrose media, although dominated by acidogenic Firmicutes with a low final pH, contained several uncultured taxa from the genus Treponema, information that may aid culturing these periodontitis‐associated fastidious organisms. Biofilms grown in a modified medium (here named subSHI‐v1 medium) with 0.1% sucrose and 10% FBS had a high diversity closest to the inoculum and maintained greater proportions of many gram‐negative species of interest from the subgingival periodontal pocket (including members of the genera Prevotella and Treponema, and the Candidate Phyla Radiation phylum Saccharibacteria), and therefore best represented the disease community.

Modeling Normal and Dysbiotic Subgingival Microbiomes: Effect of Nutrients

Screening for microbiome modulators requires availability of a high-throughput in vitro model that replicates subgingival dysbiosis and normobiosis, with a tool to measure microbial dysbiosis. Here, we tested various formulations to grow health- and periodontitis-associated subgingival microbiomes in parallel, and we describe a new subgingival dysbiosis index. Subgingival plaque samples pooled from 5 healthy subjects and, separately, 5 subjects with periodontitis were used to inoculate a Calgary Biofilm Device containing saliva-conditioned, hydroxyapatite-coated pegs. Microbiomes were grown for 7 d on either nutrient-rich media-including a modification of SHI medium, brain-heart infusion (BHI) supplemented with hemin and vitamin K, and a blend of SHI and BHI, each at 3 sucrose concentrations (0%, 0.05% and 0.1%)-or nutrient-limited media (saliva with 5%, 10%, or 20% inactivated human serum). The microbiomes were assessed for biomass, viability, and 16S rRNA profiles. In addition to richness and diversity, a dysbiosis index was calculated as the ratio of the sum of relative abundances of disease-associated species to that of health-associated species. The supplemented BHI and blend of SHI and BHI resulted in the highest biomass, whereas saliva-serum maximized viability. Distinct groups of bacteria were enriched in the different media. Regardless of medium type, the periodontitis-derived microbiomes showed higher species richness and alpha diversity and clustered with their inoculum separate from the health-derived microbiomes. Microbiomes grown in saliva-serum showed the highest species richness and the highest similarity to the clinical inocula in both health and disease. However, inclusion of serum reduced alpha diversity and increased dysbiosis in healthy microbiomes in a dose-dependent manner, mainly due to overenrichment of Porphyromonas species. The modification of SHI stood second in terms of species richness and diversity but resulted in low biomass and viability and significantly worsened dysbiosis in the periodontitis-derived microbiomes. Overall, saliva with 5% human serum was optimal for replicating subgingival microbiomes from health and disease.

Effect of Silver Diamine Fluoride Treatment on Microbial Profiles of Plaque Biofilms from Root/Cervical Caries Lesions

Purpose: To assess the effect of silver diamine fluoride (SDF) on microbial profiles present in plaque from root/cervical carious lesions, and its association with caries lesion arrest. Materials and Methods: Twenty patients with at least one soft cavitated root/cervical carious lesion were included. One lesion/patient was randomly selected and treated with 38% SDF. Supragingival plaque samples were harvested at preintervention and 1 month postintervention. Using an MiSeq platform, 16S rDNA sequencing of the V3-V4 regions was used to determine bacterial profiles. Clinical evaluation of lesion hardness was used to evaluate arrest. t tests, principal component analysis (PCA), multidimensional scaling (MDS), and generalized linear models (GLMs) tests were used for statistical comparisons. Results: From a total of 40 plaque samples, 468 probe targets were observed. Although 60% of lesions became hard postintervention, PCA and MDS tests showed no distinct pre- and postintervention groups. In addition, pre- and postintervention differences in diversity (Shannon index) of microbial profiles between patients with and without lesion arrest were not statistically different. A likelihood ratio test for pre- versus postintervention differences within patients, i.e., adjusting for differences between patients using negative binomial GLMs, showed 17 bacterial taxa with significant differences (FDR <0.05). Conclusion: Although 60% of lesions hardened after SDF treatment, this was not directly due to either overall statistically significant differences in microbial profiles or differences in microbial diversity. Nevertheless, there was a trend with some acid-producing species in that their relative abundance was reduced postintervention. The negative binomial GLMs showed 17 bacterial taxa that were significantly different after SDF treatment.

Preterm birth associated with periodontal and dental indicators: a pilot case-control study in a developing country

Introduction: Preterm delivery is a multifactorial health problem that represents a serious public health problem around the world. In recent years, there has been an increase in scientific evidence suggesting associations between oral health status (mainly periodontal disease and tooth loss) and an increased risk of systemic diseases and various adverse pregnancy outcomes. This study explores the association between indicators of oral health and preterm delivery in a sample of Mexican pregnant women.Materials and methods: A case-control study was carried out with 111 pregnant (36 cases, 75 controls) who received prenatal care and delivered in an obstetric hospital in Pachuca, Mexico. Clinical files were reviewed to obtain the necessary information for the variables studied. The dependent variable was preterm delivery and the independent variables were gingivitis, periodontitis, DMFT index and its components, the number of decayed teeth with pulpal exposure or endodontic lesions, age of the mother, education, alcohol use, smoking status, number of gestations, and sex of the newborn.Results: The average ages were similar between the cases and the controls (24.29 ± 5.42 versus 24.89 ± 5.67, p = .5781). Significant differences were observed with gingivitis (p < .01) and periodontitis (p < .001). In addition, when the severity of gingivitis or periodontitis increased, the percentage of cases of preterm delivery increased (p < .01). The average number of teeth lost was higher among the cases than among the controls (1.33 ± 1.89 versus 0.81 ± 1.82, p < .05).Conclusions: It was found that gingivitis, periodontitis, and tooth loss were associated with preterm delivery. It is necessary to carry out actions aimed at the preservation of oral health in pregnant patients to avoid adverse results. These findings indicate a likely association, but it needs to be confirmed by large and well-designed studies.

Microcosm biofilms cultured from different oral niches in periodontitis patients

Objective: Periodontal diseases are triggered by dysbiotic microbial biofilms. Therefore, it is essential to develop appropriate biofilm models. Aim of the present study was to culture microcosm biofilms inoculated from different niches in periodontitis patients and compare their microbial composition to those inoculated from subgingival plaque. Methods: Saliva, subgingival plaque, tongue and tonsils were sampled in five periodontitis patients to serve as inocula for culturing biofilms in vitro in an active attachment model. Biofilms were grown for 14 or 28 d and analyzed for their microbial composition by 16S rDNA sequencing. Results: As classified by HOMD, all biofilms were dominated by periodontitis-associated taxa, irrespective which niche had been used for inoculation. There was a low similarity between 14 d biofilms and their respective inocula (Bray-Curtis similarity 0.26), while biofilms cultured for 14 and 28 d shared high similarity (0.69). Principal components analysis showed much stronger clustering per patient than per niche indicating that the choice of patients may be more crucial than choice of the respective niches in these patients. Conclusion: Saliva, tongue scrapings or tonsil swabs may represent sufficient alternative inocula for growing microcosm biofilms resembling periodontitis-associated microbial communities in cases when sampling subgingival plaque is not possible.