Intermicrobial Interactions as a Driver for Community Composition and Stratification of Oral Biofilms

A novel multiplex fluorescent-labeling method for the visualization of mixed-species biofilms in vitro

In nature, bacteria usually exist as mixed-species biofilms, where they engage in a range of synergistic and antagonistic interactions that increase their resistance to environmental challenges. Biofilms are a major cause of persistent infections, and dispersal from initial foci can cause new infections at distal sites thus warranting further investigation. Studies of development and spatial interactions in mixed-species biofilms can be challenging due to difficulties in identifying the different bacterial species in situ. Here, we apply CellTrace dyes to studies of biofilm bacteria and present a novel application for multiplex labeling, allowing identification of different bacteria in mixed-species, in vitro biofilm models. Oral bacteria labeled with CellTrace dyes (far red, yellow, violet, and CFSE [green]) were used to create single- and mixed-species biofilms, which were analyzed with confocal spinning disk microscopy (CSDM). Biofilm supernatants were studied with flow cytometry (FC). Both Gram-positive and Gram-negative bacteria were well labeled and CSDM revealed biofilms with clear morphology and stable staining for up to 4 days. Analysis of CellTrace labeled cells in supernatants using FC showed differences in the biofilm dispersal between bacterial species. Multiplexing with different colored dyes allowed visualization of spatial relationships between bacteria in mixed-species biofilms and relative coverage by the different species was revealed through segmentation of the CSDM images. This novel application, thus, offers a powerful tool for studying structure and composition of mixed-species biofilms in vitro.IMPORTANCEAlthough most chronic infections are caused by mixed-species biofilms, much of our knowledge still comes from planktonic cultures of single bacterial species. Studies of formation and development of mixed-species biofilms are, therefore, required. This work describes a method applicable to labeling of bacteria for in vitro studies of biofilm structure and dispersal. Critically, labeled bacteria can be multiplexed for identification of different species in mixed-species biofilms using confocal spinning disk microscopy, facilitating investigation of biofilm development and spatial interactions under different environmental conditions. The study is an important step in increasing the tools available for such complex and challenging studies.

Human saliva modifies growth, biofilm architecture, and competitive behaviors of oral streptococci

The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example is the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions between S. mutans and several species of oral bacteria. However, these experiments were carried out in a medium without human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight Streptococcus species individually and found saliva to positively benefit growth rates while negatively influencing biofilm biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors of S. mutans in coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures of S. mutans and Streptococcus oralis with and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, with S. mutans upregulating carbohydrate uptake and utilization pathways while S. oralis upregulated genome features related to peptide uptake and glycan foraging. S. mutans also upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese leading to an advantage over its opponent. Our report highlights observable changes in microbial behaviors through leveraging environmental- and host-supplied resources over their competitors.

IMPORTANCE

Dental caries (tooth decay) is the most prevalent disease for both children and adults nationwide. Caries are initiated from demineralization of the enamel due to organic acid production through the metabolic activity of oral bacteria growing in biofilm communities attached to the tooth's surface. Mutans group streptococci are closely associated with caries development and initiation of the cariogenic cycle, which decreases the amount of acid-sensitive, health-associated commensal bacteria while selecting for aciduric and acidogenic species that then further drives the disease process. Defining the exchanges that occur between mutans group streptococci and oral commensals in a condition that closely mimics their natural environment is of critical need toward identifying factors that can influence odontopathogen establishment, persistence, and outgrowth. The goal of our research is to develop strategies, potentially through manipulation of microbial interactions characterized here, that prevent the emergence of mutans group streptococci while keeping the protective flora intact.

Pine-Oil-Derived Sodium Resinate Inhibits Growth and Acid Production of Streptococcus mutans In Vitro

S. mutans is a key pathogen in dental caries initiation and progression. It promotes oral biofilm dysbiosis and biofilm acidification. Sodium resinate is a salt of pine-oil-derived resin which has antimicrobial properties. Pine-oil-derived resin consists of terpenes, diterpenes, and abietic acids. The aim of this study was to determine the effects of pine (Pinus sylvestris) oil resinate (RS) on growth and acid production of cariogenic S. mutans strains in planktonic form and biofilm. The S. mutans type strain NCTC10449 and clinical isolate CI2366 were grown on 96-well plates for testing of RS effects on growth and biofilm formation, and on plates with integrated pH-sensitive optical ensors for real-time measurements of the effects of RS on bacterial acid production. We found that even short-time exposure to RS inhibits the growth and acid production of S. mutans in the planktonic phase and biofilms. In addition, RS was able to penetrate the biofilm matrix and reduce acid production inside S. mutans biofilm. RS thus shows potential as a novel antibacterial agent against cariogenic bacteria in biofilm.

Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats

Container aquatic habitats host a community of aquatic insects, primarily mosquito larvae that browse on container surface microbial biofilm and filter-feed on microorganisms in the water column. We examined how the bacterial communities in these habitats respond to feeding by larvae of two container-dwelling mosquito species, Culex pipiens and Cx. restuans. We also investigated how the microbiota of these larvae is impacted by intra- and interspecific interactions. Microbial diversity and richness were significantly higher in water samples when mosquito larvae were present, and in Cx. restuans compared to Cx. pipiens larvae. Microbial communities of water samples clustered based on the presence or absence of mosquito larvae and were distinct from those of mosquito larvae. Culex pipiens and Cx. restuans larvae harbored distinct microbial communities when reared under intraspecific conditions and similar microbial communities when reared under interspecific conditions. These findings demonstrate that mosquito larvae play a major role in structuring the microbial communities in container habitats and that intra- and interspecific interactions in mosquito larvae may shape their microbiota. This has important ecological and public health implications since larvae of the two mosquito species are major occupants of container habitats while the adults are vectors of West Nile virus.

Magnetic Hydroxyapatite-Coated Iron-Chromium Microspheres for Dental Surface Polishing and Plaque Removal

This research aimed to engineer magnetic hydroxyapatite-coated iron-chromium (HAp-FeCr) microspheres to enhance dental surface polishing and plaque elimination. Utilizing a tailored sol-gel approach, the HAp-FeCr microspheres were synthesized and exhaustively characterized via scanning electron microscopy, energy-dispersive X-ray spectroscopy, ζ-potential, X-ray diffractometry, and X-ray photoelectron spectroscopy methodologies. Key findings showcased that these microspheres retained their magnetic properties post-HAp coating, as evidenced by the magnetization curves. An innovative magnetic polishing system was developed, incorporating these microspheres and a 2000 rpm magnet. Comparative evaluations between traditional air-powder polishing and the proposed magnetic technique demonstrated the latter's superiority. Notably, the magnetic polishing led to a substantial reduction in dental plaque on the tooth surface, decreasing bacterial adhesion and early biofilm formation by Streptococcus gordonii and Lactobacillus acidophilus, where the most pronounced effects were observed in samples with elevated HAp content. A significant 60% reduction in dental plaque was achieved with the magnetic method relative to air-powder polishing. Furthermore, the HAp-FeCr microspheres' biocompatibility was verified through cytotoxicity tests and animal studies. In essence, the magnetic HAp-FeCr microspheres present a novel and efficient strategy for dental treatments, holding immense potential for improving oral health.

The Evolving Microbiome of Dental Caries

Dental caries is a significant oral and public health problem worldwide, especially in low-income populations. The risk of dental caries increases with frequent intake of dietary carbohydrates, including sugars, leading to increased acidity and disruption of the symbiotic diverse and complex microbial community of health. Excess acid production leads to a dysbiotic shift in the bacterial biofilm composition, demineralization of tooth structure, and cavities. Highly acidic and acid-tolerant species associated with caries include Streptococcus mutans, Lactobacillus, Actinomyces, Bifidobacterium, and Scardovia species. The differences in microbiotas depend on tooth site, extent of carious lesions, and rate of disease progression. Metagenomics and metatranscriptomics not only reveal the structure and genetic potential of the caries-associated microbiome, but, more importantly, capture the genetic makeup of the metabolically active microbiome in lesion sites. Due to its multifactorial nature, caries has been difficult to prevent. The use of topical fluoride has had a significant impact on reducing caries in clinical settings, but the approach is costly; the results are less sustainable for high-caries-risk individuals, especially children. Developing treatment regimens that specifically target S. mutans and other acidogenic bacteria, such as using nanoparticles, show promise in altering the cariogenic microbiome, thereby combatting the disease.

Synergistic metabolism of salivary MUC5B in oral commensal bacteria during early biofilm formation

IMPORTANCE

The study of bacterial interactions and salivary-mediated regulation of early dental biofilm activity is of interest for understanding oral microbial adaptation to environmental cues and biofilm maturation. Findings in oral commensals can prove useful from the perspectives of both oral and systemic health of the host, as well as the understanding of general microbial biofilm physiology. The knowledge may provide a basis for the development of prognostic biomarkers, or development of new treatment strategies, related to oral health and disease and possibly also to other biofilm-induced conditions. The study is also an important step toward developing the methodology for similar studies in other species and/or growth conditions.

Human Saliva Modifies Growth, Biofilm Architecture and Competitive Behaviors of Oral Streptococci

The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example are the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions between S. mutans and several species of oral bacteria. However, these experiments were carried out in a medium that was absent of human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight streptococci species individually, and found saliva to positively benefit growth rates while negatively influencing biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors of S. mutans in coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures of S. mutans and Streptococcus oralis with and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, with S. mutans upregulating carbohydrate uptake and utilization pathways while S. oralis upregulated genome features related to peptide uptake and glycan foraging. S. mutans also upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese to give it an advantage over its opponent. Our report highlights observable changes in microbial behaviors via leveraging environmental- and host-supplied resources over their competitors.

pH-Responsive Biomaterials for the Treatment of Dental Caries-A Focussed and Critical Review

Dental caries is a common and costly multifactorial biofilm disease caused by cariogenic bacteria that ferment carbohydrates to lactic acid, demineralizing the inorganic component of teeth. Therefore, low pH (pH 4.5) is a characteristic signal of the localised carious environment, compared to a healthy oral pH range (6.8 to 7.4). The development of pH-responsive delivery systems that release antibacterial agents in response to low pH has gained attention as a targeted therapy for dental caries. Release is triggered by high levels of acidogenic species and their reduction may select for the establishment of health-associated biofilm communities. Moreover, drug efficacy can be amplified by the modification of the delivery system to target adhesion to the plaque biofilm to extend the retention time of antimicrobial agents in the oral cavity. In this review, recent developments of different pH-responsive nanocarriers and their biofilm targeting mechanisms are discussed. This review critically discusses the current state of the art and innovations in the development and use of smart delivery materials for dental caries treatment. The authors' views for the future of the field are also presented.

Simultaneous Chemical Mapping of Live Biofilm Microenvironmental pH and Hydrogen Peroxide in Real Time with a Triple Scanning Electrochemical Microscopy Tip

Dental plaque biofilm is a complex ecosystem. The distribution of microbial species in the biofilm is heavily influenced by local chemical interactions that result from diverse metabolic activities and the nature of the released molecules. As a relevant example, H2O2-producing bacteria can antagonize disease-associated bacteria, leading to the maintenance of a healthy oral microbiome. Herein, we report the development of a triple-sensor (redox, pH, and H2O2) scanning electrochemical microscopy (SECM) tip capable of simultaneously mapping the pH and H2O2 concentration produced by a dental plaque-derived multispecies biofilm grown on hydroxyapatite. The pH sensor of the triple SECM tip showed a near Nernstian slope of -71.1 ± 2 mV/pH (N = 3), whereas the H2O2 sensor showed a slope of -0.052 ± 0.002 nA/μM H2O2 at pH 7.2 and a detection limit of 1.0 ± 0.2 μM (N = 7). There is no significant difference in the sensitivities of H2O2 sensors at pH 6.2, 7.2, and 8.2 at 95% CI (N = 7). The pH and H2O2 sensors demonstrated excellent reversibility with response times of 3 and 5 s, respectively, along with reliable stability over 4 h at 37 °C. The sensors did not show any cross talk between pH and H2O2 concentration ([H2O2]) measurements, highlighting the accuracy and versatility of the SECM tip. Simultaneous chemical imaging of pH and [H2O2] across the biofilm revealed a clustered distribution of local H2O2 concentrations, ranging from 0 to 17 μM. Conversely, the local pH remained constant at 7.2. The relation of local chemical profiles and the distribution of bacterial species within the oral microbiome was experimentally investigated in the context of bacterial H2O2 antagonism. The benefit of clustered H2O2 production was that the total area of H2O2 produced by smaller clusters was 67% more than that of a single cluster with the same starting number of bacteria. Thus, this triple SECM tip can potentially be used to study local molecular mechanisms that result in dysbiosis of the oral microbiome.

Streptococcus salivarius as an Important Factor in Dental Biofilm Homeostasis: Influence on Streptococcus mutans and Aggregatibacter actinomycetemcomitans in Mixed Biofilm

A disturbed balance within the dental biofilm can result in the dominance of cariogenic and periodontopathogenic species and disease development. Due to the failure of pharmacological treatment of biofilm infection, a preventive approach to promoting healthy oral microbiota is necessary. This study analyzed the influence of Streptococcus salivarius K12 on the development of a multispecies biofilm composed of Streptococcus mutans, S. oralis and Aggregatibacter actinomycetemcomitans. Four different materials were used: hydroxyapatite, dentin and two dense polytetrafluoroethylene (d-PTFE) membranes. Total bacteria, individual species and their proportions in the mixed biofilm were quantified. A qualitative analysis of the mixed biofilm was performed using scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The results showed that in the presence of S. salivarius K 12 in the initial stage of biofilm development, the proportion of S. mutans was reduced, which resulted in the inhibition of microcolony development and the complex three-dimensional structure of the biofilm. In the mature biofilm, a significantly lower proportion of the periodontopathogenic species A. actinomycetemcomitans was found in the salivarius biofilm. Our results show that S. salivarius K 12 can inhibit the growth of pathogens in the dental biofilm and help maintain the physiological balance in the oral microbiome.

Who is in the driver's seat? Parvimonas micra: An understudied pathobiont at the crossroads of dysbiotic disease and cancer

Recent advances in our understanding of microbiome composition at sites of inflammatory dysbiosis have triggered a substantial interest in a variety of historically understudied bacteria, especially among fastidious obligate anaerobes. A plethora of new evidence suggests that these microbes play outsized roles in establishing synergistic polymicrobial infections at many different sites in the human body. Parvimonas micra is a prime example of such an organism. Despite being almost completely uncharacterized at the genetic level, it is one of the few species commonly detected in abundance at multiple mucosal sites experiencing either chronic or acute inflammatory diseases, and more recently, it has been proposed as a discriminating biomarker for multiple types of malignancies. In the absence of disease, P. micra is commonly found in low abundance, typically residing within the oral cavity and gastrointestinal tract. P. micra exhibits the typical features of an inflammophilic organism, meaning its growth actually benefits from active inflammation and inflammatory tissue destruction. In this mini-review, we will describe our current understanding of this underappreciated but ubiquitous pathobiont, specifically focusing upon the role of P. micra in polymicrobial inflammatory dysbiosis and cancer as well as the key emerging questions regarding its pathobiology. Through this timely work, we highlight Parvimonas micra as a significant driver of disease and discuss its unique position at the crossroads of dysbiosis and cancer.

Biofilm ecology associated with dental caries: Understanding of microbial interactions in oral communities leads to development of therapeutic strategies targeting cariogenic biofilms

A biofilm is a sessile community characterized by cells attached to the surface and organized into a complex structural arrangement. Dental caries is a biofilm-dependent oral disease caused by infection with cariogenic pathogens, such as Streptococcus mutans, and associated with frequent exposure to a sugar-rich diet and poor oral hygiene. The virulence of cariogenic biofilms is often associated with the spatial organization of S. mutans enmeshed with exopolysaccharides on tooth surfaces. However, in the oral cavity, S. mutans does not act alone, and several other microbes contribute to cariogenic biofilm formation. Microbial communities in cariogenic biofilms are spatially organized into complex structural arrangements of various microbes and extracellular matrices. The balance of microbiota diversity with reduced diversity and a high proportion of acidogenic-aciduric microbiota within the biofilm is closely related to the disease state. Understanding the characteristics of polymicrobial biofilms and the association of microbial interactions within the biofilm (e.g., symbiosis, cooperation, and competition) in terms of their potential role in the pathogenesis of oral disease would help develop new strategies for interventions in virulent biofilm formation.

Application of fluoride disturbs plaque microecology and promotes remineralization of enamel initial caries

Background

The caries-preventive effect of topical fluoride application has been corroborated by a number of clinical studies. However, the effect of fluoride on oral microecology remains unclear.

Objective

To monitor the effect of fluoride on dental plaque microecology and demineralization/remineralization balance of enamel initial caries.

Methods

Three-year-old children were enrolled and treated with fluoride at baseline and 6 months. International Caries Detection and Assessment System II indices of 52 subjects were measured at baseline, 3, 6, and 12 months. Supragingival plaque samples of 12 subjects were collected at baseline, 3 and 14 days for 16S rRNA sequencing.

Results

Changes in microbial community structure were observed at 3 days after fluoridation. Significant changes in the relative abundance of microorganisms were observed after fluoride application, especially Capnocytophaga, unidentified Prevotellaceae and Rothia. Functional prediction revealed that cell movement, carbohydrate and energy metabolism were affected significantly after fluoride application. Fluoride significantly inhibited enamel demineralization and promoted remineralization of early demineralized caries enamel at 3 months.

Conclusion

Fluoride application significantly inhibited the progression of enamel initial caries and reversed the demineralization process, possibly by disturbing dental plaque microecology and modulating the physicochemical action of demineralization/remineralization. This deepened our understanding of caries-preventive effects and mechanisms of fluoride.

Microbiota of preterm infant develops over time along with the first teeth eruption

Objective

The temporal growth of the infant microbiome in the early years of life influences short- and long-term infant health. The aim of this longitudinal study was to investigate bacterial dynamics in the microbiome of preterm infants during tooth eruption.

Methods

Saliva samples from normally delivered (n = 24) and preterm infants (n = 31) were collected 30 days after birth and after the eruption of two primary mandibular incisors. Based on Illumina MiSeq Sequencing of the 16S rRNA gene, the dynamic microbial changes of newborns at two-time points were investigated. Meanwhile, the Human Oral Microbiome Database was adopted for assigning taxonomy.

Results

Using alpha and beta diversity analyses, different shift patterns of microbiome structures in preterm and healthy participants and bacterial diversity over time were observed. The relative abundance and shifts trend, along with the two lower primary central incisors eruption, of core oral flora varies in full-term and preterm groups, including Gemella spp., Rothia mucilaginosa, Veillonella atypica, etc. Several microorganisms colonize later in the oral microbiome development of premature babies, such as Gemella spp. In addition to teeth eruption, the growth of the saliva microbiome in preterm infants could be influenced by breastfeeding durations and birth weight.

Conclusion

This study provided insights into how the oral microbiota changes during tooth eruption in preterm infants and how the colonization of the oral cavity with bacteria in preterm infants differs significantly from that in full-term infants.

Interspecies competition in oral biofilms mediated by Streptococcus gordonii extracellular deoxyribonuclease SsnA

Extracellular DNA (eDNA) is a key component of many microbial biofilms including dental plaque. However, the roles of extracellular deoxyribonuclease (DNase) enzymes within biofilms are poorly understood. Streptococcus gordonii is a pioneer colonizer of dental plaque. Here, we identified and characterised SsnA, a cell wall-associated protein responsible for extracellular DNase activity of S. gordonii. The SsnA-mediated extracellular DNase activity of S. gordonii was suppressed following growth in sugars. SsnA was purified as a recombinant protein and shown to be inactive below pH 6.5. SsnA inhibited biofilm formation by Streptococcus mutans in a pH-dependent manner. Further, SsnA inhibited the growth of oral microcosm biofilms in human saliva. However, inhibition was ameliorated by the addition of sucrose. Together, these data indicate that S. gordonii SsnA plays a key role in interspecies competition within oral biofilms. Acidification of the medium through sugar catabolism could be a strategy for cariogenic species such as S. mutans to prevent SsnA-mediated exclusion from biofilms.

Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication

Food fermentation is driven by microorganisms, which usually coexist as multispecies biofilms. The activities and interactions of functional microorganisms and pathogenic bacteria in biofilms have important implications for the quality and safety of fermented foods. It was verified that the biofilm lifestyle benefited the fitness of microorganisms in harsh environments and intensified the cooperation and competition between biofilm members. This review focuses on multispecies biofilm formation, microbial interactions and communication in biofilms, and the application of multispecies biofilms in food fermentation. Microbial aggregation and adhesion are important steps in the early stage of multispecies biofilm formation. Different biofilm-forming abilities and strategies among microorganisms lead to several types of multispecies biofilm formation. The spatial distribution of multispecies biofilms reflects microbial interactions and biofilm function. Then, we discuss the intrinsic factors and external manifestations of multispecies biofilm system succession. Several typical interspecies cooperation and competition modes and mechanisms of microbial communication were reviewed in this review. The main limitations of the studies included in this review are the relatively small number of studies of biofilms formed by functional microorganisms during fermentation and the lack of direct evidence for the formation process of multispecies biofilms and microbial interactions and communication within biofilms. This review aims to provide the food industry with a sufficient understanding of multispecies biofilms in food fermentation. Practical Application: Meanwhile, it offers a reference value for better controlling and utilizing biofilms during food fermentation process, and the improvement of the yield, quality, and safety of fermented products including Chinese Baijiu, cheeese,kefir, soy sauce, kombucha, and fermented olive.

The Microbiome in Periodontitis and Diabetes

Objectives

To perform a comprehensive and integrative review of the available literature on the potential changes in the microbiome of healthy and individuals with diabetes under periodontal health and disease.

Materials and Methods

The review was conducted by two independent reviewers. Indexed electronic databases (PubMed/Medline, Cochrane Library, Web of Science and Scopus) were searched, including articles published in English and dated from 5 years ago until December 2021. A manual search also was performed to identify co-related articles. Following the removal of duplicates and eligibility criteria, the articles were included in tables for analysis and described in the manuscript.

Results

According to this review, diabetes mellitus was associated with significant changes in the subgingival and salivary microbiome, either in its association with periodontitis or in cases of periodontal health. In addition to affecting microbial diversity in terms of taxonomy, metagenomic studies have shown that this endocrine disorder may also be directly related to increased pathogenicity in the oral microbiome.

Conclusion

Although the reviewed studies demonstrate important differences in the subgingival and salivary microbiome composition because of diabetes mellitus, further studies are needed to clarify the real effects of hyperglycemia on oral microbial profiles and support new diagnostic approaches and innovative treatments.

In vitro efficacy of a non‐instrumentation technique to remove intracanal multispecies biofilm

Aim

The aim of this study was to assess the efficacy of a non‐instrumentation technique to disinfect root canals infected by a human dental plaque‐derived multispecies biofilm.

Methodology

Twenty‐two mandibular incisors were accessed, autoclaved and inoculated with dental plaque. The Center for Disease Control biofilm reactor was used to promote contamination of the root canal space. In the conventional technique (control), the specimens were instrumented until size 35/04 and irrigated with 6% NaOCl. In the non‐instrumentation technique, a glide path was established using K‐files size 10–20 and specimens were immediately cleaned with the GentleWave System. Samples were obtained for culture and 16S rRNA gene sequencing. Differences in abundances of genera were evaluated using Kruskal–Wallis test, and differences in alpha diversity were compared using anova. Alpha and beta diversity indices were calculated using mothur. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray–Curtis dissimilarity was used to measure beta diversity. Differences in community composition were evaluated using analysis of similarity with Bonferroni correction for multiple comparisons.

Results

The total numbers of reads in biological samples ranged from 126 to 45 286. Significantly fewer reads were obtained from samples following cleaning by either method (p < .0001), and significantly fewer reads were obtained in post‐cleaning samples following conventional versus non‐instrumentation cleaning regiment (p = .002). Communities in pre‐treatment samples were similar in both groups; however, significantly greater relative abundances of Streptococcus, Veillonella and Campylobacter were observed following cleaning using non‐instrumentation technique (Kruskal–Wallis p = .009, .033, and .001, respectively). Whilst no significant differences were observed in Shannon alpha diversity, the Chao1 index was significantly lower in post‐cleaning samples.

Conclusions

Significant shifts in composition were observed following cleaning by using both regimens, but the impact of this change was greater following a conventional cleaning technique.

A Correlation Study of the Microbiota Between Oral Cavity and Tonsils in Children With Tonsillar Hypertrophy

Tonsillar hypertrophy is a common disease in 3-to-6-year-old children, which may cause serve symptoms like airway obstruction. Microbiological factors play an important role in the etiology of tonsillar hypertrophy. As the starting point of digestive and respiratory tracts, the microbial composition of the oral cavity is not only unique but also closely related to the resident microbiota in other body sites. Here we reported a correlation study of the microbiota between oral cavity and tonsils in children with tonsillar hypertrophy. Saliva, supragingival plaque, and wiped samples from the tonsil surface were collected from both tonsillar hypertrophy patients and participants with healthy tonsils and were then analyzed using Illumina Miseq Sequencing of the 16S rRNA gene. In the tonsillar hypertrophic state, more genera were detected on the tonsil surface than in the tonsil parenchyma, with more intra-microbiota correlations. When tonsillar hypertrophy occurred, both the oral cavity and tonsil surface endured microbiome shift with increased genera category and more active bacterial interactions. Over half of the newly detected genera from the tonsillar hypertrophic state were associated with infection and inflammation process or exhibited antibiotic-resistant characters. Of each individual, the microbial composition and structure of saliva seemed more similar to that of the tonsil surface, compared with the supragingival plaque. In salivary microbiota, genus Johnsonella might be relative with the healthy state of tonsils, while Pseudoxanthomonas might be relative with tonsillar hypertrophy. Our study supported the link between oral microbiota with the healthy and hypertrophic states of tonsils and may provide new directions for future researches in the specific role of oral microbiota in the etiology of tonsil diseases.

Temporal development of the infant oral microbiome

The human oral microbiome is becoming recognized as playing roles in health and disease well beyond the oral cavity over the lifetime of the individual. The oral microbiome is hypothesized to result from specific colonization events followed by a reproducible and ordered development of complex bacterial communities. Colonization events, proliferation, succession and subsequent community development are dependent on a range of host and environmental factors, most notably the neonate diet. It is now becoming apparent that early childhood and prenatal influences can have long term effects on the development of human oral microbiomes. In this review, the temporal development of the infant human oral microbiome is examined, with the effects of prenatal and postnatal influences and the roles of specific bacteria. Dietary and environmental factors, especially breastfeeding, have a significant influence on the development of the infant oral microbiome. The evidence available regarding the roles and functions of early colonizing bacteria is still limited, and gaps in knowledge where further research is needed to elucidate these specific roles in relation to health and disease still exist.

Polymicrobial synergy stimulates Porphyromonas gingivalis survival and gingipain expression in a multi-species subgingival community

Background

Dysbiosis in subgingival microbial communities, resulting from increased inflammatory transudate from the gingival tissues, is an important factor in initiation and development of periodontitis. Dysbiotic communities are characterized by increased numbers of bacteria that exploit the serum-like transudate for nutrients, giving rise to a proteolytic community phenotype. Here we investigate the contribution of interactions between members of a sub-gingival community to survival and development of virulence in a serum environment—modelling that in the subgingival pocket.

Methods

Growth and proteolytic activity of three Porphyromonas gingivalis strains in nutrient broth or a serum environment were assessed using A₆₀₀ and a fluorescent protease substrate, respectively. Adherence of P. gingivalis strains to serum-coated surfaces was studied with confocal microscopy and 2D-gel electrophoresis of bacterial supernatants used to investigate extracellular proteins. A model multi-species sub-gingival community containing Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra with wild type or isogenic mutants of P. gingivalis was then created and growth and proteolytic activity in serum assessed as above. Community composition over time was monitored using culture techniques and qPCR.

Results

The P. gingivalis strains showed different growth rates in nutrient broth related to the level of proteolytic activity (largely gingipains) in the cultures. Despite being able to adhere to serum-coated surfaces, none of the strains was able to grow alone in a serum environment. Together in the subgingival consortium however, all the included species were able to grow in the serum environment and the community adopted a proteolytic phenotype. Inclusion of P. gingivalis strains lacking gingipains in the consortium revealed that community growth was facilitated by Rgp gingipain from P. gingivalis.

Conclusions

In the multi-species consortium, growth was facilitated by the wild-type and Rgp-expressing strains of P. gingivalis, suggesting that Rgp is involved in delivery of nutrients to the whole community through degradation of complex protein substrates in serum. Whereas they are constitutively expressed by P. gingivalis in nutrient broth, gingipain expression in the model periodontal pocket environment (serum) appeared to be orchestrated through signaling to P. gingivalis from other members of the community, a phenomenon which then promoted growth of the whole community.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01971-9.

Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis

Cell-cell adhesion between oral bacteria plays a key role in the development of polymicrobial communities such as dental plaque. Oral streptococci such as Streptococcus gordonii and Streptococcus oralis are important early colonizers of dental plaque and bind to a wide range of different oral microorganisms, forming multispecies clumps or "coaggregates." S. gordonii actively responds to coaggregation by regulating gene expression. To further understand these responses, we assessed gene regulation in S. gordonii and S. oralis following coaggregation in 25% human saliva. Coaggregates were formed by mixing, and after 30 min, RNA was extracted for dual transcriptome sequencing (RNA-Seq) analysis. In S. oralis, 18 genes (6 upregulated and 12 downregulated) were regulated by coaggregation. Significantly downregulated genes encoded functions such as amino acid and antibiotic biosynthesis, ribosome, and central carbon metabolism. In total, 28 genes were differentially regulated in Streptococcus gordonii (25 upregulated and 3 downregulated). Many genes associated with transporters and a two-component (NisK/SpaK) regulatory system were upregulated following coaggregation. Our comparative analyses of S. gordonii-S. oralis with different previously published S. gordonii pairings (S. gordonii-Fusobacterium nucleatum and S. gordonii-Veillonella parvula) suggest that the gene regulation is specific to each pairing, and responses do not appear to be conserved. This ability to distinguish between neighboring bacteria may be important for S. gordonii to adapt appropriately during the development of complex biofilms such as dental plaque. IMPORTANCE Dental plaque is responsible for two of the most prevalent diseases in humans, dental caries and periodontitis. Controlling the formation of dental plaque and preventing the transition from oral health to disease requires a detailed understanding of microbial colonization and biofilm development. Streptococci are among the most common colonizers of dental plaque. This study identifies key genes that are regulated when oral streptococci bind to one another, as they do in the early stages of dental plaque formation. We show that specific genes are regulated in two different oral streptococci following the formation of mixed-species aggregates. The specific responses of S. gordonii to coaggregation with S. oralis are different from those to coaggregation with other oral bacteria. Targeting the key genes that are upregulated during interspecies interactions may be a powerful approach to control the development of biofilm and maintain oral health.

The oral microbiome: Role of key organisms and complex networks in oral health and disease

States of oral health and disease reflect the compositional and functional capacities of, as well as the interspecies interactions within, the oral microbiota. The oral cavity exists as a highly dynamic microbial environment that harbors many distinct substrata and microenvironments that house diverse microbial communities. Specific to the oral cavity, the nonshedding dental surfaces facilitate the development of highly complex polymicrobial biofilm communities, characterized not only by the distinct microbes comprising them, but cumulatively by their activities. Adding to this complexity, the oral cavity faces near-constant environmental challenges, including those from host diet, salivary flow, masticatory forces, and introduction of exogenous microbes. The composition of the oral microbiome is shaped throughout life by factors including host genetics, maternal transmission, as well as environmental factors, such as dietary habits, oral hygiene practice, medications, and systemic factors. This dynamic ecosystem presents opportunities for oral microbial dysbiosis and the development of dental and periodontal diseases. The application of both in vitro and culture-independent approaches has broadened the mechanistic understandings of complex polymicrobial communities within the oral cavity, as well as the environmental, local, and systemic underpinnings that influence the dynamics of the oral microbiome. Here, we review the present knowledge and current understanding of microbial communities within the oral cavity and the influences and challenges upon this system that encourage homeostasis or provoke microbiome perturbation, and thus contribute to states of oral health or disease.

Dynamic Change in Oral Microbiota of Children With Cleft Lip and Palate After Alveolar Bone Grafting

To investigate the longitudinal influence of alveolar bone grafting on the oral microbiota of children with cleft lip and palate (CLP).

Twenty-eight children with nonsyndromic CLP were recruited and underwent secondary alveolar bone grafting at the first time. Unstimulated saliva and plaque samples were collected from the subjects preoperatively and at 2 days, 1 month, and 3 months postoperatively. The v3-v4 hypervariable regions of the 16S rRNA gene from bacterial DNA were sequenced using the Illumina MiSeq sequencing platform.

The alpha diversity of the saliva and plaque microbiota was significantly decreased at 2 days postoperatively and then increased at 1 and 3 months postoperatively. The saliva and plaque microbiota compositions at 2 days postoperatively differed from those at the other time points, and the microbiota compositions at 1 and 3 months postoperatively showed a gradual shift toward the preoperative composition. The saliva, but not plaque, microbiota composition 3 months postoperatively was similar to that preoperatively.

The effect of secondary alveolar bone grafting on the plaque microbiota in children with CLP lasted longer than the saliva microbiota. Alveolar bone grafting altered the saliva microbiota in children with CLP within 3 months postoperatively.

Evaluation of Periodontal Risk Factors with Quantitative Light-Induced Fluorescence Based Fluorescent Plaque Index, in Comparison to Radiographic and Oral Health Habit Scoring: A Retrospective Case Study

The aim of this study was to evaluate periodontal risk factors with oral health habits and fluorescent plaque index (FPI) using quantitative light-induced fluorescence (QLF) images, and to evaluate their effect on the degree of radiographic bone loss (RBL). Selected were 276 patients over 19 years of age to complete the questionnaire for oral health habit and take QLF images, periapical and panoramic radiographs. Oral health habit score, age, and sex showed a statistically significant correlation with FPI. FPI showed a lower value as the oral health habit score increased and the age decreased. Moreover, females showed lower FPI values than did males. RBL showed a statistically significant positive correlation with age but did not show any correlation with oral health habit scores and sex. There was no correlation between FPI and RBL. The results of this study suggest that the clinical use of QLF allows plaque detection by non-invasive procedures and can aid in a more objective estimation for oral hygiene status.

Streptococcus salivarius K12 inhibits Candida albicans aggregation, biofilm formation and dimorphism

Candida albicans causes candidiasis, particularly in immunocompromised patients. Streptococcus salivarius K12 (K12) is a probiotic isolated from a healthy oral cavity. The study aimed to determine the effect of K12 on C. albicans aggregation, biofilm formation and dimorphism. C. albicans ATCC MYA-4901, acquired immunodeficiency syndrome (AIDS) isolate (ALC2), and oral cancer isolate (ALC3) and K12 were used in the study. All C. albicans strains and K12 were grown in yeast peptone dextrose agar and brain heart infusion agar, respectively, prior to aggregation, biofilm and dimorphism assays. Auto-aggregation of C. albicans MYA-4901 and ALC2 was categorised as high, while the co-aggregation of the strains was low in the presence of K12. C. albicans total cell count decreased significantly when co-cultured with K12 compared with monocultured C. albicans biofilm (p < 0.05). Inhibition of yeast-to-hyphae transition was also observed when co-cultured with K12. In conclusion, K12 inhibits C. albicans aggregation, biofilm formation and dimorphism.

Bacteria autoaggregation: how and why bacteria stick together

Autoaggregation, adherence between identical bacterial cells, is important for colonization, kin and kind recognition, and survival of bacteria. It is directly mediated by specific interactions between proteins or organelles on the surfaces of interacting cells or indirectly by the presence of secreted macromolecules such as eDNA and exopolysaccharides. Some autoaggregation effectors are self-associating and present interesting paradigms for protein interaction. Autoaggregation can be beneficial or deleterious at specific times and niches. It is, therefore, typically regulated through transcriptional or post-transcriptional mechanisms or epigenetically by phase variation. Autoaggregation can contribute to bacterial adherence, biofilm formation or other higher-level functions. However, autoaggregation is only required for these phenotypes in some bacteria. Thus, autoaggregation should be detected, studied and measured independently using both qualitative and quantitative in vitro and ex vivo methods. If better understood, autoaggregation holds the potential for the discovery of new therapeutic targets that could be cost-effectively exploited.

Bacterial adhesion to biomaterials: What regulates this attachment? A review

•

Bacterial adhesion to the surface of dental materials play a significant role in infections.

•

The factors that govern microbial attachment involves different types of physical-chemical interactions and biological processes.

•

Studying bacterial adhesion makes it possible to understand the mechanisms involved in attachment and helps in the search for technologies that promote antibacterial surfaces.

Bacterial attachment to biomaterials is of great interest to the medical and dental field due to its impact on dental implants, dental prostheses, and others, leading to the need to introduce methods for biofilm control and mitigation of infections. Biofilm adhesion is a multifactorial process and involves characteristics relevant to the bacterial cell as well as biological, chemical, and physical properties relative to the surface of biomaterials. Bacteria encountered different environmental conditions during their growth and developed interspecies communication strategies, as well as various mechanisms to detect the environment and facilitate survival, such as chemical sensors or physical detection mechanisms. However, the factors that govern microbial attachment to surfaces are not yet fully understood. In order to understand how bacteria interact with surfaces, as well as to characterize the physical-chemical properties of bacteria adhesins, and to determine their interrelation with the adhesion to the substrate, in recent years new techniques of atomic force microscopy (AFM) have been developed and helped by providing quantitative results. Thus, the purpose of this review is to gather current studies about the factors that regulate microbial adhesion to surfaces in order to offer a guide to studies to obtain technologies that provide an antimicrobial surface.

Spatial scale in analysis of the dental plaque microbiome

Ecologists have long recognized the importance of spatial scale in understanding structure-function relationships among communities of organisms within their environment. Here, we review historical and contemporary studies of dental plaque community structure in the context of three distinct scales: the micro (1-10 µm), meso (10-100 µm) and macroscale (100 µm to ≥1 cm). Within this framework, we analyze the compositional nature of dental plaque at the macroscale, the molecular interactions of microbes at the microscale, and the emergent properties of dental plaque biofilms at the mesoscale. Throughout our analysis of dental plaque across spatial scales, we draw attention to disease and health-associated structure-function relationships and include a discussion of host immune involvement in the mesoscale structure of periodontal disease-associated biofilms. We end with a discussion of two filamentous organisms, Fusobacterium nucleatum and Corynebacterium matruchotii, and their relevant contributions in structuring dental plaque biofilms.

Mimicking biofilm formation and development: Recent progress in in vitro and in vivo biofilm models

Biofilm formation in living organisms is associated to tissue and implant infections, and it has also been linked to the contribution of antibiotic resistance. Thus, understanding biofilm development and being able to mimic such processes is vital for the successful development of antibiofilm treatments and therapies. Several decades of research have contributed to building the foundation for developing in vitro and in vivo biofilm models. However, no such thing as an "all fit" in vitro or in vivo biofilm models is currently available. In this review, in addition to presenting an updated overview of biofilm formation, we critically revise recent approaches for the improvement of in vitro and in vivo biofilm models.

Bacterial coaggregation in aquatic systems

The establishment of a sessile community is believed to occur in a sequence of steps where genetically distinct bacteria can become attached to partner cells via specific molecules, in a process known as coaggregation. The presence of bacteria with the ability to autoaggregate and coaggregate has been described for diverse aquatic systems, particularly freshwater, drinking water, wastewater, and marine water. In these aquatic systems, coaggregation already demonstrated a role in the development of complex multispecies sessile communities, including biofilms. While specific molecular aspects on coaggregation in aquatic systems remain to be understood, clear evidence exist on the impact of this mechanism in multispecies biofilm resilience and homeostasis. The identification of bridging bacteria among coaggregating consortia has potential to improve the performance of wastewater treatment plants and/or to contribute for the development of strategies to control undesirable biofilms. This study provides a comprehensive analysis on the occurrence and role of bacterial coaggregation in diverse aquatic systems. The potential of this mechanism in water-related biotechnology is further described, with particular emphasis on the role of bridging bacteria.

Oral Microbiome Geography: Micron-Scale Habitat and Niche

The mouth presents a multiplicity of local environments in communication with one another via saliva. The spatial organization of microbes within the mouth is shaped by opposing forces in dynamic equilibrium-salivary flow and adhesion, shedding and colonization-and by interactions among and between microbes and the host. Here we review recent evidence confirming that oral microbes are specialized for individual habitats within the mouth and that microbial habitats and niches are defined by micron-scale gradients in combination with short- and long-range interactions. Micron-scale structure illuminates the roles of individual taxa and provides insight into their community ecology and potential pathogenicity.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

Antimicrobial Effects of Essential Oils on Oral Microbiota Biofilms: The Toothbrush In Vitro Model

The present investigation intended to evaluate the bacteriostatic and bactericidal abilities of clove, oregano and thyme essential oils against oral bacteria in planktonic and biofilm states. Furthermore, aiming to mimic everyday conditions, a toothbrush in vitro model was developed. Determination of the minimum inhibitory concentration, minimum bactericidal concentration, minimum biofilm inhibitory concentration and minimum biofilm eradication concentration were achieved using the microdilution procedure. To simulate the toothbrush environment, nylon fibers were inoculated with oral bacteria, which, after incubation to allow biofilm development, were submitted to contact with the essential oils under study. Thyme and oregano essential oils revealed promising antimicrobial effects, both in growth inhibition and the destruction of cells in planktonic and biofilm states, while clove essential oil showed a weaker potential. Regarding the toothbrush in vitro model, observation of the nylon fibers under a magnifying glass proved the essential oil anti-biofilm properties. Considering the effects observed using the in vitro toothbrush model, a realistic approximation to oral biofilm establishment in an everyday use object, a putative application of essential oils as toothbrush sanitizers to help prevent the establishment of bacterial biofilm can be verified.

Tea extracts modulate oral biofilm development by altering bacterial hydrophobicity and aggregation

OBJECTIVES

This study aims to investigate the effects of tea extracts on biofilm formation by oral streptococci and the potential mechanisms behind the effects.

DESIGN

We examined the effects of five types of tea extracts (green, oolong, black, pu-erh and chrysanthemum tea) on cell surface hydrophobicity and auto-aggregation of three different streptococcal species (Streptococcus mutans, Streptococcus salivarius and Streptococcus mitis) and evaluated their biofilm formation on four disparate hard surfaces (glass, stainless steel, hydroxyapatite and titanium). The correlation between biofilm formation and the cellular properties were investigated in order to study the mechanisms by which the tea extracts affect biofilm formation.

RESULTS

Results show that the tea extracts reduced cell surface hydrophobicity (by up to 57.9 %) and, in some cases, altered cellular auto-aggregation (by up to 12 %) and biofilm formation (by up to 2.61 log CFU cm^-2). Specifically, oolong tea extract was found to enhance biofilm formation by increasing cellular auto-aggregation and pu-erh tea extract retarded biofilm formation by increasing auto-aggregation. Biofilm formation correlated well to cell surface hydrophobicity and auto-aggregation in combination, but not to either one alone as determined by multiple linear regression analysis.

CONCLUSIONS

Tea extracts have the ability to modulate streptococcal biofilm formation by altering cell surface hydrophobicity and cellular aggregation.

A polymicrobial biofilm model for testing the antimicrobial potential of a nisin-biogel for canine periodontal disease control

BACKGROUND

Periodontal disease (PD) in dogs is prompted by the establishment of a polymicrobial biofilm at the tooth surface and a subsequent host inflammatory response. Several strategies may be used for PD control, including dental hygiene home care procedures, like toothbrushing, special diet and chew toys that reduce dental plaque accumulation, or professional periodontal treatments. Aiming at PD control, a biogel composed by nisin and guar-gum was previously developed. This work aimed to establish an in vitro model mimicking the PD-associated biofilms and to evaluate the nisin-biogel inhibitory activity against this polymicrobial biofilm by determining its Minimum Biofilm Inhibitory (MBIC) and Eradication Concentrations (MBEC). Bacterial species tested included Neisseria zoodegmatis CCUG 52598T, Corynebacterium canis CCUG 58627T, Porphyromonas cangingivalis DSMZ VPB 4874, Peptostreptococcus canis CCUG 57081 and an Enterococcus faecalis isolate belonging to a collection of oral bacteria obtained from dogs with PD. Before establishing the biofilm, coaggregation between species was determined by optical density measurement after 2 and 24 hours. Nisin-biogel MBIC and MBEC values regarding the polymicrobial biofilm were determined using a modified version of the Calgary biofilm pin lid device, after confirming the presence of the five bacterial species by Fluorescent In Situ Hybridization.

RESULTS

Only 40% of the bacterial dual suspensions were able to coaggregate at 2 hours, but all species tested exhibited a coaggregation percentage higher than 30% at 24 hours. It was possible to establish a 48 h polymicrobial biofilm model composed by the five bacterial species selected. This model was used to determine nisin-biogel MBIC (26.39 ± 5.89 µg/mL) and MBEC (62.5 ± 27.73 µg/mL) values.

CONCLUSIONS

Our results showed that the nisin-biogel can inhibit and eradicate PD multispecies biofilms. As this in vitro model mimics an in vivo periodontal polymicrobial biofilm, our results reinforce the potential of the application of nisin-biogel for canine PD control.

Omics and interspecies interaction

Interspecies interactions are key determinants in biofilm behavior, ecology, and architecture. The cellular responses of microorganisms to each other at transcriptional, proteomic, and metabolomic levels ultimately determine the characteristics of biofilm and the corresponding implications for health and disease. Advances in omics technologies have revolutionized our understanding of microbial community composition and their activities as a whole. Large-scale analyses of the complex interaction between the many microbial species residing within a biofilm, however, are currently still hampered by technical and bioinformatics challenges. Thus, studies of interspecies interactions have largely focused on the transcriptional and proteomic changes that occur during the contact of a few prominent species, such as Porphyromonas gingivalis, Streptococcus mutans, Candida albicans, and a few others, with selected partner species. Expansion of available tools is necessary to grow the revealing, albeit limited, insight these studies have provided into a profound understanding of the nature of individual microbial responses to the presence of others. This will allow us to answer important questions including: Which intermicrobial interactions orchestrate the myriad of cooperative, synergistic, antagonistic, manipulative, and other types of relationships and activities in the complex biofilm environment, and what are the implications for oral health and disease?

Metatranscriptomic analyses of the oral microbiome

Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.

Dental black plaque: metagenomic characterization and comparative analysis with white-plaque

Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles "orally healthy" communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.

Signaling Natural Products from Human Pathogenic Bacteria

Natural products from microorganisms are important small molecules that play roles in various biological processes like cellular growth, motility, nutrient acquisition, stress response, biofilm formation, and defense. It is hypothesized that pathogens exploit these molecules to regulate virulence and persistence during infections. Here, we present selected examples of signaling natural products from human pathogenic bacteria that use these metabolites to gain a competitive advantage. Targeting these signaling systems provides novel strategies to antimicrobial treatments.

The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease

The human oral cavity harbors diverse communities of microbes that live as biofilms: highly ordered, surface-associated assemblages of microbes embedded in an extracellular matrix. Oral microbial communities contribute to human health by fine-tuning immune responses and reducing dietary nitrate. Dental caries and periodontal disease are together the most prevalent microbially mediated human diseases worldwide. Both of these oral diseases are known to be caused not by the introduction of exogenous pathogens to the oral environment, but rather by a homeostasis breakdown that leads to changes in the structure of the microbial communities present in states of health. Both dental caries and periodontal disease are mediated by synergistic interactions within communities, and both diseases are further driven by specific host inputs: diet and behavior in the case of dental caries and immune system interactions in the case of periodontal disease. Changes in community structure (taxonomic identity and abundance) are well documented during the transition from health to disease. In this review, changes in biofilm physical structure during the transition from oral health to disease and the concomitant relationship between structure and community function will be emphasized.

Detection of dental plaque and its potential pathogenicity using quantitative light-induced fluorescence

Quantitative light-induced fluorescence (QLF) technology can detect some dental plaque as red fluorescence. This in vivo study aimed to identify the microbial characteristics of red fluorescent (RF) dental plaque using 16S rRNA gene sequencing and evaluate the correlations between RF plaque and the clinical symptoms of dental diseases. Paired supragingival plaque samples collected from each 10 subjects and consisted of RF and non-RF dental plaques as observed by QLF technology using a 405 nm blue light source for excitation. The characteristics of the bacterial communities in the RF and non-RF plaque samples were compared by sequencing analysis. An increase in microbial diversity was observed in RF plaque compared with the non-RF plaque. There were significant differences in the community compositions between the 2 types of dental plaque. Periodontopathic bacteria were significantly more abundant in the RF plaque than non-RF plaque. The fluorescence intensity of RF plaque was significantly related to the proportion of the periodontopathic bacterial community and the presence of gingival inflammation. In conclusion, the plaque red fluorescence is associated with changes in the microbial composition and enrichment of periodontopathic pathogens, which suggests that RF plaque detected by QLF technology could be used as a risk indicator for gingival inflammation.

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq

Many oral bacteria form macroscopic clumps known as coaggregates when mixed with a different species. It is thought that these cell-cell interactions are critical for the formation of mixed-species biofilms such as dental plaque. Here, we assessed the impact of coaggregation between two key initial colonizers of dental plaque, Streptococcus gordonii and Veillonella parvula, on gene expression in each partner. These species were shown to coaggregate in buffer or human saliva. To monitor gene regulation, coaggregates were formed in human saliva and, after 30 minutes, whole-transcriptomes were extracted for sequencing and Dual RNA-Seq analysis. In total, 272 genes were regulated in V. parvula, including 39 genes in oxidoreductase processes. In S. gordonii, there was a high degree of inter-sample variation. Nevertheless, 69 genes were identified as potentially regulated by coaggregation, including two phosphotransferase system transporters and several other genes involved in carbohydrate metabolism. Overall, these data indicate that responses of V. parvula to coaggregation with S. gordonii are dominated by oxidative stress-related processes, whereas S. gordonii responses are more focussed on carbohydrate metabolism. We hypothesize that these responses may reflect changes in the local microenvironment in biofilms when S. gordonii or V. parvula immigrate into the system.

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.

Streptococcus gordonii Challisin protease is required for sensing cell--cell contact with Actinomyces oris

The ability of microorganisms to regulate gene expression is thought to be critical for survival and growth during the development of polymicrobial biofilms such as dental plaque. The commensal dental plaque colonizer, Streptococcus gordonii, responds to cell--cell contact (coaggregation) with Actinomyces oris by regulating >20 genes, including those involved in arginine biosynthesis. We hypothesized that an S. gordonii extracellular protease is critical for sensing by providing amino acids that modulate gene expression. S. gordonii coaggregated strongly with A. oris in buffer, saliva or chemically defined medium (CDM). In wild-type S. gordonii, expression of arginine biosynthesis genes argC and argG increased within two hours' growth in CDM in monocultures, but not following coaggregation with A. oris. By contrast, coaggregation of A. oris with an S. gordonii mutant lacking sgc, encoding the extracellular protease Challisin, resulted in increases in argC and argG gene expression that were similar to monocultures. Genetic complementation of sgc restored the ability of S. gordonii to sense coaggregation with A. oris. Coaggregation enabled growth of S. gordonii in low/no arginine and disruption of sgc did not affect this ability. We propose that extracellular bacterial proteases may be key mediators of cell--cell contact sensing by diverse microbial species.

Streptococcus mutans yidC1 and yidC2 Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties

YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen Streptococcus mutans are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either yidC results in changes to the structure and physical properties of the EPS matrix produced by S. mutans , ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial yidC orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.

In Sickness and in Health-What Does the Oral Microbiome Mean to Us? An Ecological Perspective

The oral microbiome is natural and has a symbiotic relationship with the host by delivering important benefits. In oral health, a dynamic balance is reached between the host, the environment, and the microbiome. However, the frequent intake of sugar and/or reductions in saliva flow results in extended periods of low pH in the biofilm, which disrupts this symbiotic relationship. Such conditions inhibit the growth of beneficial species and drive the selection of bacteria with an acid-producing/acid-tolerating phenotype, thereby increasing the risk of caries (dysbiosis). A more detailed understanding of the interdependencies and interactions that exist among the resident microbiota in dental biofilms, and an increased awareness of the relationship between the host and the oral microbiome, is providing new insights and fresh opportunities to promote symbiosis and prevent dysbiosis. These include modifying the oral microbiome (e.g., with prebiotics and probiotics), manipulating the oral environment to selectively favor the growth of beneficial species, and moderating the growth and metabolism of the biofilm to reduce the likelihood of dysbiosis. Evidence is provided to suggest that the regular provision of interventions that deliver small but relevant benefits, consistently over a prolonged period, can support the maintenance of a symbiotic oral microbiome.

Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition

BACKGROUND

The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.

RESULTS

Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations.

CONCLUSIONS

We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.