Proteomic profiling of host-biofilm interactions in an oral infection model resembling the periodontal pocket

Microfluidic organ-on-chip systems for periodontal research: advances and future directions

Advances in tissue engineering and microfluidic technologies have enabled the development of sophisticated in vitro models known as organ-on-a-chip (OoC) or microphysiological systems. These systems enable to potential to simulate the dynamic interactions between host tissues and their microenvironment including microbes, biomaterials, mechanical forces, pharmaceutical, and consumer-care products. These fluidic technologies are increasingly being utilized to investigate host-microbe and host-material interactions in oral health and disease. Of interest is their application in understanding periodontal disease, a chronic inflammatory condition marked by the progressive destruction of periodontal tissues, including gingiva, periodontal ligament, and alveolar bone. The pathogenesis of periodontal disease involves a complex interplay between microbial dysbiosis and host immune responses, which can lead to a loss of dental support structures and contribute to systemic conditions such as cardiovascular disease, diabetes, and inflammatory bowel disease. This provides a comprehensive overview of the latest developments in millifluidic and microfluidic systems designed to emulate periodontal host-microbe and host-material interactions. We discuss the critical engineering and biological considerations in designing these platforms, their applications in studying oral biofilms, periodontal tissue responses, and their potential to unravel disease mechanisms and therapeutic targets in periodontal disease.

Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids

Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.

Oral host-microbe interactions investigated in 3D organotypic models

The oral cavity is inhabited by abundant microbes which continuously interact with the host and influence the host's health. Such host-microbe interactions (HMI) are dynamic and complex processes involving e.g. oral tissues, microbial communities and saliva. Due to difficulties in mimicking the in vivo complexity, it is still unclear how exactly HMI influence the transition between healthy status and disease conditions in the oral cavity. As an advanced approach, three-dimensional (3D) organotypic oral tissues (epithelium and mucosa/gingiva) are being increasingly used to study underlying mechanisms. These in vitro models were designed with different complexity depending on the research questions to be answered. In this review, we summarised the existing 3D oral HMI models, comparing designs and readouts, discussing applications as well as future perspectives.

Biofabrication Strategies for Oral Soft Tissue Regeneration

Gingival recession, a prevalent condition affecting the gum tissues, is characterized by the exposure of tooth root surfaces due to the displacement of the gingival margin. This review explores conventional treatments, highlighting their limitations and the quest for innovative alternatives. Importantly, it emphasizes the critical considerations in gingival tissue engineering leveraging on cells, biomaterials, and signaling factors. Successful tissue-engineered gingival constructs hinge on strategic choices such as cell sources, scaffold design, mechanical properties, and growth factor delivery. Unveiling advancements in recent biofabrication technologies like 3D bioprinting, electrospinning, and microfluidic organ-on-chip systems, this review elucidates their precise control over cell arrangement, biomaterials, and signaling cues. These technologies empower the recapitulation of microphysiological features, enabling the development of gingival constructs that closely emulate the anatomical, physiological, and functional characteristics of native gingival tissues. The review explores diverse engineering strategies aiming at the biofabrication of realistic tissue-engineered gingival grafts. Further, the parallels between the skin and gingival tissues are highlighted, exploring the potential transfer of biofabrication approaches from skin tissue regeneration to gingival tissue engineering. To conclude, the exploration of innovative biofabrication technologies for gingival tissues and inspiration drawn from skin tissue engineering look forward to a transformative era in regenerative dentistry with improved clinical outcomes.

Microbial diagnostics in periodontal diseases

Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.

Utility of gingival crevicular fluid components for periodontal diagnosis

Periodontal diseases are highly prevalent chronic diseases, and severe periodontitis creates functional and esthetic problems and decreases self-esteem for a large percentage of the older population worldwide. In many cases of periodontitis, there is no distinct tell-tale pain that motivates a patient to seek treatment, rather the signs become clinically detectable late, and typically when the disease has progressed to a problematic level for the life of the dentition. Early periodontal screening and diagnostics tools will provide early recognition of periodontal diseases and facilitate timely management of the disease to reduce tooth loss. To this goal, gingival crevicular fluid is easily sampled, can be repeatedly and non-invasively collected, and can be tested for potential biomarkers. Moreover, the site specificity of periodontal diseases enhances the usefulness of gingival crevicular fluid sampled from specific sites as a biofluid for diagnosis and longitudinal monitoring of periodontal diseases. The present review aimed to provide up-to-date information on potential diagnostic biomarkers with utility that can be assayed from gingival crevicular fluid samples, focusing on what is new and useful and providing only general historic background textually and in a tabulated format.

Microphysiological Modeling of Gingival Tissues and Host-Material Interactions Using Gingiva-on-Chip

Gingiva plays a crucial barrier role at the interface of teeth, tooth-supporting structures, microbiome, and external agents. To mimic this complex microenvironment, an in vitro microphysiological platform and biofabricated full-thickness gingival equivalents (gingiva-on-chip) within a vertically stacked microfluidic device is developed. This design allowed long-term and air-liquid interface culture, and host-material interactions under flow conditions. Compared to static cultures, dynamic cultures on-chip enabled the biofabrication of gingival equivalents with stable mucosal matrix, improved epithelial morphogenesis, and barrier features. Additionally, a diseased state with disrupted barrier function representative of gingival/oral mucosal ulcers is modeled. The apical flow feature is utilized to emulate the mechanical action of mouth rinse and integrate the assessment of host-material interactions and transmucosal permeation of oral-care formulations in both healthy and diseased states. Although the gingiva-on-chip cultures have thicker and more mature epithelium, the flow of oral-care formulations induced increased tissue disruption and cytotoxic features compared to static conditions. The realistic emulation of mouth rinsing action facilitated a more physiological assessment of mucosal irritation potential. Overall, this microphysiological system enables biofabrication of human gingiva equivalents in intact and ulcerated states, providing a miniaturized and integrated platform for downstream host-material and host-microbiome applications in gingival and oral mucosa research.

Proteomic profile of human gingival crevicular fluid reveals specific biological and molecular processes during clinical progression of periodontitis

BACKGROUND AND OBJECTIVE

There is no clear understanding of molecular events occurring in the periodontal microenvironment during clinical disease progression. Our aim was to explore qualitative and quantitative differences in gingival crevicular fluid (GCF) protein profiles from patients diagnosed with periodontitis between non-progressive and progressive periodontal sites.

METHODS

Five systemically healthy patients diagnosed with periodontitis were monitored weekly in their progression of the disease and GCF samples from 10 candidate sites were obtained. Two groups of five sites, matched from an equal number of teeth, were selected from the five patients: Progression (PG) and Non-Progression (NP). Global protein identification was performed with high-throughput proteomic approaches and label-free analysis determined their relative abundances. Proteins were identified by Proteome Discoverer v2.4 and searched against human SwissProt protein databases. Enrichment bioinformatic analyses were performed in STRING-DB and ShinyGO environment.

RESULTS

1504 and 1500 proteins were identified in NP and PG respectively. Forty-eight proteins were exclusively identified in PG, while 52 were identified in NP. Moreover, 35 proteins were more abundant in PG and 29 proteins in NP (twofold change, p < .05). The NP group was mainly represented by proteins from "response to biotic stimuli and other organisms," "processes of cell death regulation," "peptidase regulation," "protein ubiquitination," and "ribosomal activity" GO categories. The most represented GO categories of the PG group were "assembly of multiprotein complexes," "catabolic processes," "lipid metabolism," and "binding to hemoglobin and haptoglobin."

CONCLUSIONS

There are quantitative and qualitative differences in the proteome of GCF from periodontal sites according to the status of clinical progression of periodontitis. Progressive periodontitis sites are characterized by a protein profile associated with catabolic processes, immune response, and response to cellular stress, while stable periodontitis sites show a protein profile mainly related to wound repair and healing processes, cell death regulation, and chaperone-mediated autophagy. Understanding the etiopathogenic role of these profiles in progressive periodontitis may help to develop new diagnostic and therapeutic approaches.

Potential Clinical Application of Organs-on-a-Chip in Periodontal Diseases: A Systematic Review of In Vitro Studies

The periodontium is a unique organ from the standpoint of building an organ-on-a-chip (OoC) since it is a system that is continually threatened by microorganisms, their noxious compounds, and antigenic components. At the same time, periodontal health depends on a balanced connection between the host and the bacteria in the oral cavity, which is a complex micro-ecological environment. The objective of this systematic review of in vitro studies is to revise the potential clinical application of OoC in periodontal diseases. PRISMA was used to guide this analysis. The review framework made use of several databases, including SCOPUS, PubMed/MEDLINE, SCIELO, and LILACS as well as the gray literature. This systematic review comprised seven studies. The clinical efficacy of OoC in periodontal diseases was observed in models of the gingival crevice for the research of periodontitis, periodontal medication analysis, the interaction of multiple microbial species, pH measurements in in situ-grown biofilm, testing antimicrobial reagents, evaluation of mucosal interactions with microorganisms, and a device for quantitative exploration of microorganisms. OoC has the potential to advance our understanding of periodontal diseases by providing a more accurate representation of the oral microenvironment and enabling the development of new treatments.

Proteomics analysis of urine and catheter-associated biofilms in spinal cord injury patients

After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and frequent catheter-associated urinary tract infections (CAUTI). One determinant of infection success and treatment resistance is production of catheter-associated biofilms, composed of microorganisms and host- and microbial-derived components. To better understand the biofilm microenvironment, we performed proteomics analysis of catheter-associated biofilms and paired urine samples from four people with SCI with chronic indwelling urinary catheters. We developed a novel method for the removal of adhered cellular components on catheters that contained both human and microbial homologous proteins. Proteins from seven microbial species were identified including: Escherichia coli, Klebsiella species (spp), Enterococcus spp, Proteus mirabilis, Pseudomonas spp, Staphylococcus spp, and Candida spp. Peptides identified from catheter biofilms were assigned to 4,820 unique proteins, with 61% of proteins assigned to the biofilm-associated microorganisms, while the remainder were human-derived. Contrastingly, in urine, only 51% were assigned to biofilm-associated microorganisms and 4,554 proteins were identified as a human-derived. Of the proteins assigned to microorganisms in the biofilm and paired urine, Enterococcus, Candida spp, and P. mirabilis had greater associations with the biofilm phase, whereas E. coli and Klebsiella had greater associations with the urine phase, thus demonstrating a significant difference between the urine and adhered microbial communities. The microbial proteins that differed significantly between the biofilm and paired urine samples mapped to pathways associated with amino acid synthesis, likely related to adaptation to high urea concentrations in the urine, and growth and protein synthesis in bacteria in the biofilm. Human proteins demonstrated enrichment for immune response in the catheter-associated biofilm. Proteomic analysis of catheter-associated biofilms and paired urine samples has the potential to provide detailed information on host and bacterial responses to chronic indwelling urinary catheters and could be useful for understanding complications of chronic indwelling catheters including CAUTIs, urinary stones, and catheter blockages.

Periodontal microbiology and microbial etiology of periodontal diseases: Historical concepts and contemporary perspectives

This narrative review summarizes the collective knowledge on periodontal microbiology, through a historical timeline that highlights the European contribution in the global field. The etiological concepts on periodontal disease culminate to the ecological plaque hypothesis and its dysbiosis-centered interpretation. Reference is made to anerobic microbiology and to the discovery of select periodontal pathogens and their virulence factors, as well as to biofilms. The evolution of contemporary molecular methods and high-throughput platforms is highlighted in appreciating the breadth and depth of the periodontal microbiome. Finally clinical microbiology is brought into perspective with the contribution of different microbial species in periodontal diagnosis, the combination of microbial and host biomarkers for this purpose, and the use of antimicrobials in the treatment of the disease.

Modeling Crevicular Fluid Flow and Host-Oral Microbiome Interactions in a Gingival Crevice-on-Chip

Gingival crevice and gingival crevicular fluid (GCF) flow play a crucial role at the gingiva-oral microbiome interface which contributes toward maintaining the balance between gingival health and periodontal disease. Interstitial flow of GCF strongly impacts the host-microbiome interactions and tissue responses. However, currently available in vitro preclinical models largely disregard the dynamic nature of gingival crevicular microenvironment, thus limiting the progress in the development of periodontal therapeutics. Here, a proof-of-principle "gingival crevice-on-chip" microfluidic platform to culture gingival connective tissue equivalent (CTE) under dynamic interstitial fluid flow mimicking the GCF is described. On-chip co-culture using oral symbiont (Streptococcus oralis) shows the potential to recapitulate microbial colonization, formation of biofilm-like structures at the tissue-microbiome interface, long-term co-culture, and bacterial clearance secondary to simulated GCF (s-GCF) flow. Further, on-chip exposure of the gingival CTEs to the toll-like receptor-2 (TLR-2) agonist or periodontal pathogen Fusobacterium nucleatum demonstrates the potential to mimic early gingival inflammation. In contrast to direct exposure, the induction of s-GCF flow toward the bacterial front attenuates the secretion of inflammatory mediators demonstrating the protective effect of GCF flow. This proposed in vitro platform offers the potential to study complex host-microbe interactions in periodontal disease and the development of periodontal therapeutics under near-microphysiological conditions.

Oral microbiome interactions with gingival gene expression patterns for apoptosis, autophagy and hypoxia pathways in progressing periodontitis

Oral mucosal tissues must react with and respond to microbes comprising the oral microbiome ecology. This study examined the interaction of the microbiome with transcriptomic footprints of apoptosis, autophagy and hypoxia pathways during periodontitis. Adult Macaca mulatta (n = 18; 12-23 years of age) exhibiting a healthy periodontium at baseline were used to induce progressing periodontitis through ligature placement around premolar/molar teeth. Gingival tissue samples collected at baseline, 0·5, 1 and 3 months of disease and at 5 months for disease resolution were analysed via microarray. Bacterial samples were collected at identical sites to the host tissues and analysed using MiSeq. Significant changes in apoptosis and hypoxia gene expression occurred with initiation of disease, while autophagy gene changes generally emerged later in disease progression samples. These interlinked pathways contributing to cellular homeostasis showed significant correlations between altered gene expression profiles in apoptosis, autophagy and hypoxia with groups of genes correlated in different directions across health and disease samples. Bacterial complexes were identified that correlated significantly with profiles of host genes in health, disease and resolution for each pathway. These relationships were more robust in health and resolution samples, with less bacterial complex diversity during disease. Using these pathways as cellular responses to stress in the local periodontal environment, the data are consistent with the concept of dysbiosis at the functional genomics level. It appears that the same bacteria in a healthy microbiome may be interfacing with host cells differently than in a disease lesion site and contributing to the tissue destructive processes.

Metaproteome and metabolome of oral microbial communities

The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.

A review of co-culture models to study the oral microenvironment and disease

Co-cultures allow for the study of cell-cell interactions between different eukaryotic species or with bacteria. Such an approach has enabled researchers to more closely mimic complex tissue structures. This review is focused on co-culture systems modelling the oral cavity, which have been used to evaluate this unique cellular environment and understand disease progression. Over time, these systems have developed significantly from simple 2D eukaryotic cultures and planktonic bacteria to more complex 3D tissue engineered structures and biofilms. Careful selection and design of the co-culture along with critical parameters, such as seeding density and choice of analysis method, have resulted in several advances. This review provides a comparison of existing co-culture systems for the oral environment, with emphasis on progression of 3D models and the opportunity to harness techniques from other fields to improve current methods. While filling a gap in navigating this literature, this review ultimately supports the development of this vital technique in the field of oral biology.

Host-microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome

Periodontal studies using transcriptomics, proteomics, and metabolomics encompass the collection of mRNA transcripts, proteins, and small-molecule chemicals in the context of periodontal health and disease. The number of studies using these approaches has significantly increased in the last decade and they have provided new insight into the pathogenesis and host-microbe interactions that define periodontal diseases. This review provides an overview of current molecular findings using -omic approaches that underlie periodontal disease, including modulation of the host immune response, tissue homeostasis, and complex metabolic processes of the host and the oral microbiome. Integration of these -omic approaches will broaden our perspective of the molecular mechanisms involved in periodontal disease, advancing and improving the diagnosis and treatment of various stages and forms of periodontal disease.

Three-Dimensional In Vitro Oral Mucosa Models of Fungal and Bacterial Infections

Oral mucosa is the target tissue for many microorganisms involved in periodontitis and other infectious diseases affecting the oral cavity. Three-dimensional (3D) in vitro and ex vivo oral mucosa equivalents have been used for oral disease modeling and investigation of the mechanisms of oral bacterial and fungal infections. This review was conducted to analyze different studies using 3D oral mucosa models for the evaluation of the interactions of different microorganisms with oral mucosa. In this study, based on our inclusion criteria, 43 articles were selected and analyzed. Different types of 3D oral mucosa models of bacterial and fungal infections were discussed in terms of the biological system used, culture conditions, method of infection, and the biological endpoints assessed in each study. The critical analysis revealed some contradictory reports in this field of research in the literature. Challenges in recovering bacteria from oral mucosa models were further discussed, suggesting possible future directions in microbiomics, including the use of oral mucosa-on-a-chip. The potential use of these 3D tissue models for the evaluation of the effects of antiseptic agents on bacteria and oral mucosa was also addressed. This review concluded that there were many aspects that would require optimization and standardization with regard to using oral mucosal models for infection by microorganisms. Using new technologies-such as microfluidics and bioreactors-could help to reproduce some of the physiologically relevant conditions and further simulate the clinical situation. Impact statement Tissue-engineered or commercial models of the oral mucosa are very useful for the study of diseases that involve the interaction of microorganisms and oral epithelium. In this review, challenges in recovering bacteria from oral mucosa models, the potential use of these three-dimensional tissue models for the evaluation of the effects of antiseptic agents, and future directions in microbiomics are discussed.

A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility

Several proteins and peptides in saliva were shown to stimulate gingival wound repair, but the role of salivary metabolites in this process remains unexplored. In vitro gingival re-epithelialization kinetics were determined using unstimulated saliva samples from healthy individuals collected during an experimental gingivitis study. Elastic net regression with stability selection identified a specific metabolite signature in a training dataset that was associated with the observed re-epithelialization kinetics and enabled its prediction for all saliva samples obtained in the clinical study. This signature encompassed ten metabolites, including plasmalogens, diacylglycerol and amino acid derivatives, which reflect enhanced host-microbe interactions. This association is in agreement with the positive correlation of the metabolite signature with the individual’s gingival bleeding index. Remarkably, intra-individual signature-variation over time was associated with elevated risk for gingivitis development. Unravelling how these metabolites stimulate wound repair could provide novel avenues towards therapeutic approaches in patients with impaired wound healing capacity.

Pressure Cycling Technology Assisted Mass Spectrometric Quantification of Gingival Tissue Reveals Proteome Dynamics during the Initiation and Progression of Inflammatory Periodontal Disease

Understanding the progression of periodontal tissue destruction is at the forefront of periodontal research. The authors aimed to capture the dynamics of gingival tissue proteome during the initiation and progression of experimental (ligature-induced) periodontitis in mice. Pressure cycling technology (PCT), a recently developed platform that uses ultra-high pressure to disrupt tissues, is utilized to achieve efficient and reproducible protein extraction from ultra-small amounts of gingival tissues in combination with liquid chromatography-tandem mass spectrometry (MS). The MS data are processed using Progenesis QI and the regulated proteins are subjected to METACORE, STRING, and WebGestalt for functional enrichment analysis. A total of 1614 proteins with ≥2 peptides are quantified with an estimated protein false discovery rate of 0.06%. Unsupervised clustering analysis shows that the gingival tissue protein abundance is mainly dependent on the periodontitis progression stage. Gene ontology enrichment analysis reveals an overrepresentation in innate immune regulation (e.g., neutrophil-mediated immunity and antimicrobial peptides), signal transduction (e.g., integrin signaling), and homeostasis processes (e.g., platelet activation and aggregation). In conclusion, a PCT-assisted label-free quantitative proteomics workflow that allowed cataloging the deepest gingival tissue proteome on a rapid timescale and provided novel mechanistic insights into host perturbation during periodontitis progression is applied.

Virulence and Pathogenicity Properties of Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is a periodontal pathogen colonizing the oral cavity of a large proportion of the human population. It is equipped with several potent virulence factors that can cause cell death and induce or evade inflammation. Because of the large genetic diversity within the species, both harmless and highly virulent genotypes of the bacterium have emerged. The oral condition and age, as well as the geographic origin of the individual, influence the risk to be colonized by a virulent genotype of the bacterium. In the present review, the virulence and pathogenicity properties of A. actinomycetemcomitans will be addressed.

Proteomic Investigations of In Vitro and In Vivo Models of Periodontal Disease

Proteomics has currently been a developing field in periodontal diseases to obtain protein information of certain samples. Periodontal disease is an inflammatory disorder that attacks the teeth, connective tissues, and alveolar bone within the oral cavity. Proteomics information can provide proteins that are differentially expressed in diseased or healthy samples. This review provides insight into approaches researching single species, multi species, bacteria, non-human, and human models of periodontal disease for proteomics information. The approaches that have been taken include gel electrophoresis and qualitative and quantitative mass spectrometry. This review is carried out by extracting information about in vitro and in vivo studies of proteomics in models of periodontal diseases that have been carried out in the past two decades. The research has concentrated on a relatively small but well-known group of microorganisms. A wide range of models has been reviewed and conclusions across the breadth of these studies are presented in this review.

Periodontal disease: From the lenses of light microscopy to the specs of proteomics and next-generation sequencing

Periodontal disease entails the inflammatory destruction of the tooth supporting (periodontal) tissues as a result of polymicrobial colonization of the tooth surface in the form of biofilms. Extensive data collected over the past decades on this chronic disease demonstrate that its progression is infrequent and episodic, and the susceptibility to it can vary among individuals. Physical assessments of previously occurring damage to periodontal tissues remain the cornerstone of detection and diagnosis, whereas traditionally used diagnostic procedures do neither identify susceptible individuals nor distinguish between disease-active and disease-inactive periodontal sites. Thus, more sensitive and accurate "measurable biological indicators" of periodontal diseases are needed in order to place diagnosis (e.g., the presence or stage) and management of the disease on a more rational less empirical basis. Contemporary "omics" technologies may help unlock the path to this quest. High throughput nucleic acid sequencing technologies have enabled us to examine the taxonomic distribution of microbial communities in oral health and disease, whereas proteomic technologies allowed us to decipher the molecular state of the host in disease, as well as the interactive cross-talk of the host with the microbiome. The newly established field of metaproteomics has enabled the identification of the repertoire of proteins that oral microorganisms use to compete or co-operate with each other. Vast such data is derived from oral biological fluids, including gingival crevicular fluid and saliva, which is progressively completed and catalogued as the analytical technologies and bioinformatics tools progressively advance. This chapter covers the current "omics"-derived knowledge on the microbiome, the host and their "interactome" with regard to periodontal diseases, and addresses challenges and opportunities ahead.

Gingival Exudatome Dynamics Implicate Inhibition of the Alternative Complement Pathway in the Protective Action of the C3 Inhibitor Cp40 in Nonhuman Primate Periodontitis

Periodontitis is a prevalent chronic inflammatory disease associated with dysbiosis. Although complement inhibition has been successfully used to treat periodontitis in animal models, studies globally analyzing inflamed tissue proteins to glean insight into possible mechanisms of action are missing. Using quantitative shotgun proteomics, we aimed to investigate differences in composition of inflammatory gingival tissue exudate ("gingival crevicular fluid"; GCF), before and after local administration of an inhibitor of the central complement component, C3, in nonhuman primates. The C3 inhibitor, Cp40 (also known as AMY-101) was administered locally in the maxillary gingival tissue of cynomolgus monkeys with established periodontitis, either once a week (1×-treatment; n = 5 animals) or three times per week (3×-treatment; n = 10 animals), for 6 weeks followed by another 6 weeks of observation in the absence of treatment. 45 GCF samples were processed for FASP digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Data were processed using the ProgenesisQI software. The statistical significance of differences between the groups was determined by RM-ANOVA, and a protein expression change was considered as a true regulation at >2-fold and p < 0.05. The human orthologues were subjected to Gene Ontology analyses using PANTHER. Data are available via ProteomeXchange with identifier PXD009502. 573 proteins with >2 peptides were longitudinally quantified. Both 3× and 1× administration of Cp40 resulted in significant down-regulation of dozens of proteins during the 6-week course of treatment as compared to baseline. Following drug withdrawal at 6 weeks, more than 50% of the down-regulated proteins showed increased levels at week 12. The top scored pathway was "complement activation, alternative pathway", and several proteins involved in this pathway were down-regulated at 6 weeks. We mapped the proteomic fingerprint changes in local tissue exudate of cynomolgus monkey periodontitis in response to C3 inhibition and identified the alternative pathway of complement activation and leukocyte degranulation as main targets, which are thus likely to play significant roles in periodontal disease pathogenesis. Label-free quantitative proteomics strategies utilizing GCF are powerful tools for the identification of treatment targets and providing insights into disease mechanisms.

Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm

Microorganisms frequently coexist in complex multispecies communities, where they distribute non-randomly, reflective of the social interactions that occur. It is therefore important to understand how social interactions and local spatial organization influences multispecies biofilm succession. Here the localization of species pairs was analyzed in three dimensions in a reproducible four-species biofilm model, to study the impact of spatial positioning of individual species on the temporal development of the community. We found, that as the biofilms developed, species pairs exhibited distinct intermixing patterns unique to the four-member biofilms. Higher biomass and more intermixing were found in four-species biofilms compared to biofilms with fewer species. Intriguingly, in local regions within the four member biofilms where Microbacterium oxydans was scant, both biomass and intermixing of all species were lowered, compared to regions where M. oxydans was present at typical densities. Our data suggest that Xanthomonas retroflexus and M. oxydans, both low abundant biofilm-members, intermixed continuously during the development of the four-species biofilm, hereby facilitating their own establishment. In turn, this seems to have promoted distinct spatial organization of Stenotrophomonas rhizophila and Paenibacillus amylolyticus enabling enhanced growth of all four species. Here local intermixing of bacteria advanced the temporal development of a multi-species biofilm.

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community

Microbial biofilms are omnipresent in nature and relevant to a broad spectrum of industries ranging from bioremediation and food production to biomedical applications. To date little is understood about how multi-species biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we apply a meta-proteomics approach to investigate the mechanisms influencing biofilm formation in a model consortium of four bacterial soil isolates; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. Protein abundances in community and single species biofilms were compared to describe occurring inter-species interactions and the resulting changes in active metabolic pathways. To obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for generating reduced reference proteomes for spectral database searches. Meta-proteomics profiling indicated that community development is dependent on cooperative interactions between community members facilitating cross-feeding on specific amino acids. Opposite regulation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, indicate that competition for limited resources also affects community development. Overall our results demonstrate the multitude of pathways involved in biofilm formation in mixed communities.

The making of a miscreant: tobacco smoke and the creation of pathogen-rich biofilms

We have previously reported that oral biofilms in clinically healthy smokers are pathogen-rich, and that this enrichment occurs within 24 h of biofilm formation. The present investigation aimed to identify a mechanism by which smoking creates this altered community structure. By combining in vitro microbial–mucosal interface models of commensal (consisting of Streptococcus oralis, Streptococcus sanguis, Streptococcus mitis, Actinomyces naeslundii, Neisseria mucosa and Veillonella parvula) and pathogen-rich (comprising S.oralis, S.sanguis, S.mitis, A.naeslundii, N.mucosa and V.parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, Filifactor alocis, Dialister pneumosintes, Selenonomas sputigena, Selenominas noxia, Catonella morbi, Parvimonas micra and Tannerella forsythia) communities with metatranscriptomics, targeted proteomics and fluorescent microscopy, we demonstrate that smoke exposure significantly downregulates essential metabolic functions within commensal biofilms, while significantly increasing expression of virulence genes, notably lipopolysaccharide (LPS), flagella and capsule synthesis. By contrast, in pathogen-rich biofilms several metabolic pathways were over-expressed in response to smoke exposure. Under smoke-rich conditions, epithelial cells mounted an early and amplified pro-inflammatory and oxidative stress response to these virulence-enhanced commensal biofilms, and a muted early response to pathogen-rich biofilms. Commensal biofilms also demonstrated early and widespread cell death. Similar results were observed when smoke-free epithelial cells were challenged with smoke-conditioned biofilms, but not vice versa. In conclusion, our data suggest that smoke-induced transcriptional shifts in commensal biofilms triggers a florid pro-inflammatory response, leading to early commensal death, which may preclude niche saturation by these beneficial organisms. The cytokine-rich, pro-oxidant, anaerobic environment sustains inflammophilic bacteria, and, in the absence of commensal antagonism, may promote the creation of pathogen-rich biofilms in smokers.

Tobacco smoke inhibits the metabolism of beneficial bacteria in biofilms, while activating specific genes in pathogenic bacteria. This suggests a mechanism to explain how smoking quickly leads to the formation of damaging biofilms in the mouth and respiratory tract. Purnima Kumar and colleagues at Ohio State University, USA studied the effect of tobacco smoke on cultured biofilms used to model those that form on mucous membranes. They detected specific and varied changes in the activity of genes, proteins and metabolism that allowed pathogenic bacteria to displace beneficial “commensal” bacteria. The research suggests the transition toward pathogen-rich biofilms may contribute to the health effects of smoking by causing increased inflammation of mucous membranes and the production of damaging oxidant chemicals. Further research should investigate the chemical constituents of smoke responsible for these effects.

Saliva-Derived Commensal and Pathogenic Biofilms in a Human Gingiva Model

In vitro models that closely mimic human host-microbiome interactions can be a powerful screening tool for antimicrobials and will hold great potential for drug validation and discovery. The aim of this study was to develop an organotypic oral mucosa model that could be exposed to in vitro cultured commensal and pathogenic biofilms in a standardized and scalable manner. The oral mucosa model consisted of a tissue-engineered human gingiva equivalent containing a multilayered differentiated gingiva epithelium (keratinocytes) grown on a collagen hydrogel, containing gingiva fibroblasts, which represented the lamina propria. Keratinocyte and fibroblast telomerase reverse transcriptase–immortalized cell lines were used to overcome the limitations of isolating cells from small biopsies when scalable culture experiments were required. The oral biofilms were grown under defined conditions from human saliva to represent 3 distinct phenotypes: commensal, gingivitis, and cariogenic. The in vitro grown biofilms contained physiologic numbers of bacterial species, averaging >70 operational taxonomic units, including 20 differentiating operational taxonomic units. When the biofilms were applied topically to the gingiva equivalents for 24 h, the gingiva epithelium increased its expression of elafin, a protease inhibitor and antimicrobial protein. This increased elafin expression was observed as a response to all 3 biofilm types, commensal as well as pathogenic (gingivitis and cariogenic). Biofilm exposure also increased secretion of the antimicrobial cytokine CCL20 and inflammatory cytokines IL-6, CXCL8, and CCL2 from gingiva equivalents. This inflammatory response was far greater after commensal biofilm exposure than after pathogenic biofilm exposure. These results show that pathogenic oral biofilms have early immune evasion properties as compared with commensal oral biofilms. The novel host-microbiome model provides an ideal tool for future investigations of gingiva responses to commensal and pathogenic biofilms and for testing novel therapeutics.

Immunization with alkyl hydroperoxide reductase subunit C reduces Fusobacterium nucleatum load in the intestinal tract

Fusobacterium nucleatum (Fn) is an important tumour-associated bacterium in colorectal cancer (CRC). The antioxidant protein alkyl hydroperoxide reductase subunit C (AhpC) can induce strong antibacterial immune response during various pathogen infections. Our study aimed to evaluate the efficacy of Fn-AhpC as a candidate vaccine. In this work, by western blot analysis, we showed that Fn-AhpC recombinant protein could be recognized specifically by antibodies present in the sera of CRC patients; using the mouse Fn-infection model, we observed that systemic prophylactic immunization with AhpC/alum conferred significant protection against infection in 77.3% of mice. In addition, we measured the anti-AhpC antibody level in the sera of CRC patients and found that there was no obvious increase of anti-AhpC antibodies in the early-stage CRC group. Furthermore, we treated Fn with the sera from both immunized mice and CRC patients and found that sera with high anti-AhpC antibodies titre could inhibit Fn growth. In conclusion, our findings support the use of AhpC as a potential vaccine candidate against inhabitation or infection of Fn in the intestinal tract, which could provide a practical strategy for the prevention of CRC associated with Fn infection.

Microproteome of dentoalveolar tissues

Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues. Using the LCM-LC-MS/MS approach, a total of 243 proteins was identified from all tissues, 193 proteins in DC, 147 in AB, and 135 proteins DE. Ninety proteins (37% of total) were common to all tissues, whereas 52 proteins (21%) were overlapping in only two. Also, 101 (42%) proteins were exclusively detected in DC (60), AB (15), or DE (26). Identification in all tissues of expected ECM proteins including collagen alpha-1(I) chain (COL1A1), collagen alpha-1(XII) chain (COL12A1), biglycan (BGN), asporin (ASPN), lumican (LUM), and fibromodulin (FMOD), served to validate the approach. Principal component analysis (PCA) and hierarchical clustering identified a high degree of similarity in DC and AB proteomes, whereas DE presented a distinct dataset. Exclusively and differentially identified proteins were detected from all three tissues. The protein-protein interaction network (interactome) of DC was notable for its inclusion of several indicators of metabolic function (e.g. mitochondrial proteins, protein synthesis, and calcium transport), possibly reflecting cementocyte activity. The DE proteome included known and novel mineralization regulators, including matrix metalloproteinase 20 (MMP-20), 5' nucleotidase (NT5E), and secreted phosphoprotein 24 (SPP-24 or SPP-2). Application of the LCM-LC-MS/MS approach to dentoalveolar tissues would be of value in many experimental designs, including developmental studies of transgenic animals, investigation of treatment effects, and identification of novel regenerative factors.

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus

Anaeroglobus geminatus is a relatively newly discovered putative pathogen, with a potential role in the microbial shift associated with periodontitis, a disease that causes inflammatory destruction of the periodontal tissues, and eventually tooth loss. This study aimed to introduce A. geminatus into a polymicrobial biofilm model of relevance to periodontitis, and monitor the proteomic responses exerted to the rest of the biofilm community. A. geminatus was grown together with another 10-species in a well-established "subgingival" in vitro biofilm model. Its effects on the other species were quantitatively evaluated by qPCR and label-free proteomics. A. geminatus caused a significant increase in P. intermedia numbers, but not the other species in the biofilm. Whole cell proteome profiling of the biofilms by LC-MS/MS identified a total of 3213 proteins. Label-free quantitative proteomics revealed that 187 proteins belonging to the other 10 species were differentially abundant when A. geminatus was present in the biofilm. The species with most up-regulated and down-regulated proteins were P. intermedia and S. oralis, respectively. Regulated proteins were of primarily of ribosomal origin, and other affected categories involved proteolysis, carbon metabolism and iron transport. In conclusion, A. geminatus can be successfully grown in a polymicrobial biofilm community, causing quantitative proteomic shifts commensurate with increased virulence properties.

Er:YAG Laser and Cyclosporin A Effect on Cell Cycle Regulation of Human Gingival Fibroblast Cells

Introduction: Periodontitis is a set of inflammatory disorders characterized by periodontal attachment loss and alveolar bone resorption. Because of deficiency in periodontitis mechanical therapy, this study was aimed to explore the molecular influence of the erbiumdoped: yttrium aluminum garnet (Er:YAG) laser and cyclosporin A (CsA) on human gingival fibroblasts (HGFs) for improvement in periodontal diseases therapy. Methods: We focused on articles that studied the proteome profiles of HGFs after treatment with laser irradiation and application of CsA. The topological features of differentially expressed proteins were analyzed using Cytoscape Version 3.4.0 followed by module selection from the protein-protein interaction (PPI) network using Cluster ONE plugin. In addition, we performed gene ontology (GO) enrichment analysis for the densely connected region and key proteins in both PPI networks. Results: Analysis of PPI network of Er:YAG laser irradiation on HGFs lead to introducing YWHAZ, VCP, HNRNPU, YWHAE, UBA52, CLTC, FUS and IGHG1 as key proteins while similar analysis revealed that ACAT1, CTSD, ALDOA, ANXA2, PRDX1, LGALS3, ARHGDI and EEF1A1 are the crucial proteins related to the effect of drug. GO enrichment analysis of hubbottleneck proteins of the 2 networks showed the different significant biological processes and cellular components. The functional enrichments of module of Er:YAG laser network are included as fatty acid transmembrane transport, cytokinesis, regulation of RNA splicing and asymmetric protein localization. There are not any significant clusters in network of HGF treated by CsA. Conclusion: The results indicate that there are 2 separate biomarker panels for the 2 treatment methods.