The authors have taken the liberty of presenting this manuscript in two parts. The first is a brief primer on microbial ecology, because, although the importance of microbial ecology in periodontal diseases is widely recognized, most of us do not know precisely what is meant by the term. The second section is a rather extensive overview of current studies of oral microbial ecology based almost entirely on recent in vivo studies.

https://laurieximenez.files.wordpress.com/2011/02/ref-2_socransky-2005_p2000.pdf

Periodontal microbial ecology.

Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia: The 'red complex', a prototype polybacterial pathogenic consortium in periodontitis

Recent advancements in the periodontal research field are consistent with a new model of pathogenesis according to which periodontitis is initiated by a synergistic and dysbiotic microbial community rather than by select 'periopathogens', such as the 'red complex'. In this polymicrobial synergy, different members or specific gene combinations within the community fulfill distinct roles that converge to shape and stabilize a disease-provoking microbiota. One of the core requirements for a potentially pathogenic community to arise involves the capacity of certain species, termed 'keystone pathogens', to modulate the host response in ways that impair immune surveillance and tip the balance from homeostasis to dysbiosis. Keystone pathogens also elevate the virulence of the entire microbial community through interactive communication with accessory pathogens. Other important core functions for pathogenicity require the expression of diverse molecules (e.g. appropriate adhesins, cognate receptors, proteolytic enzymes and proinflammatory surface structures/ligands), which in combination act as community virulence factors to nutritionally sustain a heterotypic, compatible and proinflammatory microbial community that elicits a non-resolving and tissue-destructive host response. On the basis of the fundamental concepts underlying this model of periodontal pathogenesis, that is, polymicrobial synergy and dysbiosis, we term it the PSD model.

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Beyond the red complex and into more complexity: the polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology.

Studies from the 1960s indicated that increased microbial diversity and a succession in the predominant bacterial species in plaque correlate with the appearance of gingival inflammation and the development of periodontal disease. In the past few years, molecular characterization of the microflora found in various sites of the oral cavity of different subjects has detected around 700 bacterial species or phylotypes (1, 63, 93). Some of these species are considered commensal and a positive feature of our healthy microflora, while others are considered pathogenic. The colonization of pathogenic bacteria is probably dependent upon the interaction of pathogens and commensal organisms. The clinical relevance and periodontal microbial ecology of these bacteria have been presented in an outstanding, comprehensive review (101). The discussion in the present article centers on interactions among bacterial species and how these interactions contribute to the development of plaque and ultimately to the formation of periodontopathogenic communities. Interactions among human oral bacteria are integral to the development of plaque. From the early stages of colonization to the formation of mature supragingival and subgingival plaque, a diverse array of bacterial species colonizes into densely populated communities. Interactions among different bacterial cell types are proposed to drive the maturation of plaque. These interactions occur at several levels, including physical contact, metabolic exchange, small-signal-molecule-mediated communication and exchange of genetic material. A principal feature of human oral bacteria is their ability to interact by coaggregation with other oral bacteria (48). Coaggregation is defined as the specific cell-to-cell recognition that occurs between genetically distinct cell types. Each cell type bears on its surface one or more types of coaggregation mediator, which are called adhesins and receptors (described below). The adhesins and receptors confer a particular set of coaggregation properties. Coaggregation partnerships are central to the development of biodiversity in supragingival and subgingival plaque. Coaggregations effect changes in populations, from low diversity in initial communities of supragingival plaque to high diversity in subgingival plaque. This article will provide an overview of the physical and metabolic interactions that occur among the oral microflora in the context of plaque development.

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Bacterial interactions and successions during plaque development.

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth’s soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.

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Challenges in microbial ecology: building predictive understanding of community function and dynamics

It has been difficult to conduct large scale studies of microbiologically complex ecosystems using conventional microbiological techniques. Molecular identification techniques in new probe-target formats, such as checkerboard DNA-DNA hybridization, permit enumeration of large numbers of species in very large numbers of samples. Digoxigenin-labeled whole genomic probes to 40 common subgingival species were tested in a checkerboard hydridization format. Chemifluorescent signals resulting from the hybridization reactions were quantified using a Fluorimager and used to evaluate sensitivity and specificity of the probes. Sensitivity of the DNA probes was adjusted to detect 10 4 cells. In all, 93.5% of potential cross-reactions to 80 cultivable species exhibited signals <5% of that detected for the homologous probe signal. Competitive hybridization and probes prepared by subtraction hybridization and polymerase chain reaction were effective in minimizing cross-reactions for closely related taxa. To demonstrate utility, the technique was used to evaluate 8887 subgingival plaque samples from 79 periodontally healthy and 272 chronic periodontitis subjects and 8126 samples from 166 subjects taken prior to and after periodontal therapy. Significant differences were detected for many taxa for mean counts, proportion of total sample, and percentage of sites colonized between samples from periodontally healthy and periodontitis subjects. Further, significant reductions were observed post therapy for many subgingival species including periodontal pathogens. DNA probes used in the checkerboard DNA-DNA format provide a useful tool for the enumeration of bacterial species in microbiologically complex systems.

Use of checkerboard DNA–DNA hybridization to study complex microbial ecosystems

The treatment of periodontitis/peri-implantitis involves the reduction/eradication of periopathogens. After therapy, beneficial and pathogenic species recolonize the subgingival area. The dynamics of recolonization and especially the role of the supragingival environment in this process are still not well-understood. This prospective, split-mouth study followed the early colonization of 'pristine' pockets created during implant surgery (16 partially edentulous patients), to record the time needed before a complex subgingival flora could be established with the supragingival area as the single source. Four subgingival plaque samples were taken from shallow and medium pockets around implants (test), and neighboring teeth (undisturbed microbiota as reference) 1, 2, and 4 wks after abutment connection. Checkerboard DNA-DNA hybridization and culture data revealed a complex microbiota (including several pathogenic species) in the pristine pockets within a wk, with a minimal increase in counts up to 4 wks. Analysis of these data demonstrated that, even with the supragingival environment as the single source for colonizing bacteria, a complex subgingival microbiota can develop within 1 wk.

Initial Subgingival Colonization of ‘Pristine’ Pockets

Teles FR, Teles RP, Uzel NG, Song XQ, Torresyap G, Socransky SS, Haffajee AD. Early microbial succession in redeveloping dental biofilms in periodontal health and disease. J Periodont Res 2012; 47: 95–104. © 2011 John Wiley & Sons A/S



Background and Objective:  The development of dental biofilms after professional plaque removal is very rapid. However, it is not clear whether most bacterial species return at similar rates in periodontally healthy and periodontitis subjects or if there are differences in bacterial recolonization between supragingival and subgingival biofilms in periodontal health and disease.



Material and Methods:  Supragingival and subgingival plaque samples were taken separately from 28 teeth in 38 healthy and 17 periodontitis subjects immediately after professional cleaning. Samples were taken again from seven teeth in randomly selected quadrants after 1, 2, 4 and 7 d of no oral hygiene and analyzed using checkerboard DNA–DNA hybridization. The percentage of DNA probe counts were averaged within subjects at each time-point. Ecological succession was determined using a modified moving-window analysis.



Results:  Succession in supragingival biofilms from subjects with periodontitis and from healthy individuals was similar. At 1 d, Streptococcus mitis and Neisseria mucosa showed increased proportions, followed by Capnocytophaga gingivalis, Eikenella corrodens, Veillonella parvula and Streptococcus oralis at 1–4 d. At 4–7 d, Campylobacter rectus, Campylobacter showae, Prevotella melaninogenica and Prevotella nigrescens became elevated. Subgingival plaque redevelopment was slower and very different from supragingival plaque redevelopment. Increased proportions were first observed for S. mitis, followed by V. parvula and C. gingivalis and, at 7 d, by Capnocytophaga sputigena and P. nigrescens. No significant increase in the proportions of periodontal pathogens was observed in any of the clinical groups or locations.



Conclusion:  There is a defined order in bacterial species succession in early supragingival and subgingival biofilm redevelopment after professional cleaning.

Early microbial succession in redeveloping dental biofilms in periodontal health and disease

Uzel NG, Teles FR, Teles RP, Song XQ, Torresyap G, Socransky SS, Haffajee AD. Microbial shifts during dental biofilm re-development in the absence of oral hygiene in periodontal health and disease. J Clin Peridontol 2011; doi: 10.1111/j.1600-051X.2011.01730.x.

Abstract
Aim: To monitor microbial shifts during dental biofilm re-development.

Materials and methods: Supra- and subgingival plaque samples were taken separately from 28 teeth in 38 healthy and 17 periodontitis subjects at baseline and immediately after tooth cleaning. Samples were taken again from seven teeth in randomly selected quadrants during 1, 2, 4 and 7 days of no oral hygiene. Samples were analysed using checkerboard DNA–DNA hybridization. Species counts were averaged within subjects at each time point. Significant differences in the counts between healthy and periodontitis subjects were determined using the Mann–Whitney test.

Results: The total supra- and subgingival counts were significantly higher in periodontitis on entry and reached or exceeded the baseline values after day 2. Supragingival counts of Veillonella parvula, Fusobacterium nucleatum ss vincentii and Neisseria mucosa increased from 2 to 7 days. Subgingival counts were greater for Actinomyces, green and orange complex species. Significant differences between groups in supragingival counts occurred for 17 of 41 species at entry, 0 at day 7; for subgingival plaque, these values were 39/41 taxa at entry, 17/41 at day 7.

Conclusions: Supragingival plaque re-development was similar in periodontitis and health, but subgingival species recolonization was more marked in periodontitis.

Microbial shifts during dental biofilm re-development in the absence of oral hygiene in periodontal health and disease.

Background: Surfaces and fluids can affect oral bacterial colonization. The aim of this study is to compare redeveloping biofilms on natural teeth and dentures.Methods: Supragingival plaque samples were taken from 55 dentate individuals and the denture teeth of 62 edentulous individuals before and after professional cleaning. Also, samples from seven “teeth” (samples included dentures) in randomly selected quadrants were collected after 1, 2, 4, and 7 days of no oral hygiene. Samples were analyzed using checkerboard DNA-DNA hybridization. Counts and proportions of 41 bacterial taxa were determined at each time point, and significant differences were determined using the Mann-Whitney U test. Ecological succession was determined using a modified moving window analysis.Results: Mean total DNA probe counts were similar precleaning but were higher in dentate individuals at all post-cleaning visits (P <0.01). Precleaning edentate biofilms had higher counts and proportions of Streptococcus mitis, Streptococcus o...

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N. G. Uzel

Papers

Use of checkerboard DNA–DNA hybridization to study complex microbial ecosystems

Initial Subgingival Colonization of ‘Pristine’ Pockets

Early microbial succession in redeveloping dental biofilms in periodontal health and disease

Microbial shifts during dental biofilm re-development in the absence of oral hygiene in periodontal health and disease.

Comparison of microbial changes in early redeveloping biofilms on natural teeth and dentures.