Bacterial diversity within the human subgingival crevice

Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients

Bacteria are involved in the onset and progression of periodontitis. A promising molecular technique, denaturing gradient gel electrophoresis (DGGE), to study microbial population dynamics in the subgingival pocket is presented. Twenty-three samples were taken from the subgingival pockets of nine patients and six healthy family members. From four periodontitis patients, 12 samples were evaluated before, 1 day after and 3 months after treatment. Part of the 16S rRNA gene of all bacteria was amplified by PCR and separated by DGGE, creating banding patterns representative of the community structure. Shifts in composition and diversity of the microbial population could be determined semiquantitatively, and this showed that treatment resulted in a decrease in the diversity of the population. After 3 months a microbial population 33-47% different from the population before treatment had re-established. Intense bands representing Exiguobacterium aurantiacum were present in 13 out of 25 samples, indicating that this species may play a role in periodontal disease.

Bacterial coaggregation: an integral process in the development of multi-species biofilms

Coaggregation is a process by which genetically distinct bacteria become attached to one another via specific molecules. Cumulative evidence suggests that such adhesion influences the development of complex multi-species biofilms. Once thought to occur exclusively between dental plaque bacteria, there are increasing reports of coaggregation between bacteria from other biofilm communities in several diverse habitats. A general role for coaggregation in the formation of multi-species biofilms is discussed.

Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients

The primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. Our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-cultivated species of the oral cavity. Tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjects with halitosis, defined as an organoleptic score of 2 or more and volatile sulfur compound levels greater than 200 ppb. 16S rRNA genes from DNA isolated from tongue dorsum scrapings were amplified by PCR with universally conserved bacterial primers and cloned into Escherichia coli. Typically, 50 to 100 clones were analyzed from each subject. Fifty-one strains isolated from the tongue dorsa of healthy subjects were also analyzed. Partial sequences of approximately 500 bases of cloned inserts from the 16S rRNA genes of isolates were compared with sequences of known species or phylotypes to determine species identity or closest relatives. Nearly complete sequences of about 1,500 bases were obtained for potentially novel species or phylotypes. In an analysis of approximately 750 clones, 92 different bacterial species were identified. About half of the clones were identified as phylotypes, of which 29 were novel to the tongue microbiota. Fifty-one of the 92 species or phylotypes were detected in more than one subject. Those species most associated with healthy subjects were Streptococcus salivarius, Rothia mucilaginosa, and an uncharacterized species of Eubacterium (strain FTB41). Streptococcus salivarius was the predominant species in healthy subjects, as it represented 12 to 40% of the total clones analyzed from each healthy subject. Overall, the predominant microbiota on the tongue dorsa of healthy subjects was different from that on the tongue dorsa of subjects with halitosis. Those species most associated with halitosis were Atopobium parvulum, a phylotype (clone BS095) of Dialister, Eubacterium sulci, a phylotype (clone DR034) of the uncultivated phylum TM7, Solobacterium moorei, and a phylotype (clone BW009) of STREPTOCOCCUS: On the basis of our ongoing efforts to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species that colonize the oral cavity, there are now over 600 species.

Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis

Terminal restriction fragment-length polymorphism (T-RFLP) analysis was applied to characterize oral bacterial flora in saliva from 18 healthy subjects and 18 patients with periodontitis. The 16S rRNA genes (rDNAs) of oral bacteria and spirochaetes in saliva were amplified by PCR with a 6'carboxy-fluorescein (6-FAM)-labelled universal forward primer (27F) and a universal reverse primer (1492R) or the Spirochaeta-selective reverse primer. The 16S rDNAs were digested with restriction enzymes with 4 bp recognition sites (HhaI or MspI) and analysed by using an automated DNA sequencer. T-RFLP patterns were numerically analysed using a computer program. From analysis of the oral bacterial community, patterns derived from periodontally healthy subjects and patients with periodontitis were grouped into different clusters, though with some uncertainty. Samples from patients with periodontitis tended to cluster into their respective types (aggressive and chronic periodontitis), although this was not very clear. Analysis of spirochaetal community using T-RFLP showed that the patterns derived from patients with periodontitis were grouped more as compared with the analysis of the oral bacterial community. These results suggest that samples from patients with periodontitis contain an unexpected diversity. T-RFLP patterns of 16S rDNAs from saliva samples of two periodontally healthy subjects over a 5-week period showed host-specific relatively stable oral bacterial flora. Our study indicates that T-RFLP analysis is useful for the assessment of diversity of oral bacterial flora and rapid comparison of the community structure between subjects with and without periodontitis.

Culture-independent molecular analysis of microbial constituents of the healthy human outer ear

Molecular-phylogenetic sequence analyses have provided a new perspective on microbial communities by allowing the detection and identification of constituent microorganisms in the absence of cultivation. In this study we used broad-specificity amplification of ribosomal DNA (rDNA) genes to survey organisms present in the human outer ear canal. Samples were obtained from 24 individuals, including members of three extended families, in order to survey the resident microbiota and to examine microbial population structures in individuals related by familial or household associations. To examine the stability of the microbial populations, one individual was sampled four times and another twice over a 14-month period. We found that a distinct set of microbial types was present in the majority of the subjects sampled. The two most prevalent rDNA sequence types that were identified in multiple individuals corresponded closely to those of Alloiococcus otitis and Corynebacterium otitidis, commonly thought to be associated exclusively with infections of the middle ear. Our results suggest, therefore, that the outer ear canal may serve as a reservoir for normally commensal microbes that can contribute to pathogenesis upon introduction into the middle ear. Alternatively, culture analyses of diseases of the middle ear may have been confounded by these contaminating commensal organisms.

Identification of bacteria in acute endodontic infections and their antimicrobial susceptibility

OBJECTIVE

The purpose of the study was to identify the bacterial composition of the microbiota from acute endodontic abscesses/cellulitis and their antimicrobial susceptibilities.

STUDY DESIGN

Purulence from 17 patients with acute endodontic abscesses/cellulitis was obtained by needle aspiration and processed under anaerobic conditions. Bacteria were isolated and identified by biochemical or molecular methods. The antimicrobial susceptibility of isolated bacteria was determined by using the Etest.

RESULTS

All 17 aspirates contained a mix of microorganisms. A total of 127 strains of bacteria were isolated. Of 127 strains, 80 strains were anaerobes and 47 strains were aerobes. The mean number of strains per sample was 7.5 (range, 3 to 13). The average number of viable bacteria was 6.37 x 10(7) (range, 10(4) to 10(8)) colony-forming units/mL. Strict anaerobes and microaerophiles were the dominant bacteria in 82% (14 of 17) of the cases. The genera of bacteria most frequently encountered were Prevotella and Streptococcus. Prevotella and Peptostreptococcus were frequently found to dominate the mixture. The combination of Prevotella and Streptococcus was found in 53% (9 of 17). The previously reported uncultured Prevotella clone PUS9.180 was frequently identified. The percentage of bacteria susceptible/intermediate for each antibiotic in this study was penicillin V, 81% (95 of 118); metronidazole, 88% (51 of 58); amoxicillin, 85% (100 of 118); amoxicillin + clavulanic acid, 100% (118 of 118); and clindamycin, 89% (105 of 118).

CONCLUSIONS

The present results confirm the existence of mixed infection with the predominance of anaerobic bacteria in acute endodontic abscesses/cellulitis. The frequency of uncultured Prevotella clone PUS9.180 suggests the possible key role of this Prevotella species in acute endodontic infections. Penicillin V still possesses antimicrobial activity against the majority of bacteria isolated from acute endodontic infections. However, if penicillin V therapy has failed to be effective, the combination of penicillin V with metronidazole or amoxicillin with clavulanic acid is recommended. Switching to clindamycin is another good alternative.

Are there naturally occurring pleomorphic bacteria in the blood of healthy humans?

Dark-field microscopy of blood from healthy individuals revealed the existence of pleomorphic microorganisms. These bacteria exhibited limited growth and susceptibility to antibiotics and could be detected by fluorescent in situ hybridization and flow cytometry. They were further characterized by analysis of their 16S rRNA and gyrB genes.

New technologies, human-microbe interactions, and the search for previously unrecognized pathogens

Evidence suggests that a significant number of clinically important microbial pathogens remain unrecognized. Observations from the natural world, from patterns of disease in human populations, from the bedside, and from the clinical laboratory all contribute to this body of evidence. A variety of acute and chronic neurologic syndromes illustrate this point; despite features of infection, most cases of aseptic meningitis, encephalitis, and cerebral vasculitis cannot be assigned a microbiologic diagnosis. The development and clinical application of molecular methods have led to the discovery of novel members of the endogenous normal flora as well as putative disease agents. Current challenges include the establishment of criteria for disease causation and further characterization of the human microbiome during states of health. These challenges and the goal of understanding microbial contributions to inflammatory disease may be addressed effectively through the thoughtful integration of modern technologies and clinical insight.

How host-microbial interactions shape the nutrient environment of the mammalian intestine

Humans and other mammals are colonized by a vast, complex, and dynamic consortium of microorganisms. One evolutionary driving force for maintaining this metabolically active microbial society is to salvage energy from nutrients, particularly carbohydrates, that are otherwise nondigestible by the host. Much of our understanding of the molecular mechanisms by which members of the intestinal microbiota degrade complex polysaccharides comes from studies of Bacteroides thetaiotaomicron, a prominent and genetically manipulatable component of the normal human and mouse gut. Colonization of germ-free mice with B. thetaiotaomicron has shown how this anaerobe modifies many aspects of intestinal cellular differentiation/gene expression to benefit both host and microbe. These and other studies underscore the importance of understanding precisely how nutrient metabolism serves to establish and sustain symbiotic relationships between mammals and their bacterial partners.

Detection of novel oral phylotypes associated with periodontitis

A phylogenetic approach based on 16S rRNA (rDNA) has been recently applied to investigate the diversity of cultivable and uncultivable species in the human oral cavity without cultivation. In a previous study [Sakamoto et al. (2000) Microbiol. Immunol. 44, 643-652], we identified a number of novel oral phylotypes, representing as yet uncultured organisms. The purpose of this study was to design specific PCR primers for five phylotypes AP12, AP21, AP24, AP50, and RP58, which are deeply branched particularly in the phylogenetic tree, and determine the prevalence of these phylotypes in 45 patients with periodontitis and 18 healthy subjects. The specificity of each primer was validated by the sequence analysis of PCR products obtained from saliva and subgingival plaque samples. Among phylotypes tested, phylotype AP24, which is closely related to oral clone DA014 reported previously [Paster et al. (2001) J. Bacteriol. 183, 3770-3783], was significantly associated with saliva and subgingival plaque samples from patients with periodontitis (P<0.01), but the difference was not statistically significant in the presence of other phylotypes. These data suggest that phylotype AP24 may play an important role in periodontal disease.

Molecular and cultural analysis of the microflora associated with endodontic infections

Cultural studies have indicated that a subset of the oral microflora is responsible for endodontic infections. Approximately 50% of oral bacteria are unculturable, so it is likely that currently unknown bacteria are present in such infections. In this study, cultural and molecular analyses were performed on the microflora in aspirate samples collected from 5 infected root canals. 16S rDNA sequences from 261 isolates and 624 clones were identified by comparison with database sequences. Sixty-five taxa were identified, of which 26 were found by the molecular method alone. A mean of 20.2 taxa was found in each sample. A new species of Dialister was the only organism present in all 5 samples. Twenty-seven novel taxa were detected, 18 of which belonged to the phylum Firmicutes and 8 to Bacteroidetes. Culture-independent, molecular analysis has revealed a more diverse microflora associated with endodontic infections than that revealed by cultural methods alone.

Communication among oral bacteria

Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities.

Bacterial and yeast flora of root surface caries in elderly, ethnic Chinese

OBJECTIVES

Root caries is emerging as a significant problem in the middle aged and elderly. As little data is available on the microbiology of root caries in Chinese cohorts, we evaluated 30 such lesions in elderly, institutionalized, ethnic Chinese.

METHODS

Samples of carious dentine were aseptically taken from root caries lesions of 18 subjects (five males and 13 females, mean age 79.67 +/- 8.57). The cultivable bacteria, both aerobic and anaerobic, were isolated and identified using standard methods and commercial identification kits. The yeasts were isolated on Sabouraud's agar and identified using the API system.

RESULTS

The main findings were: (1) of the total isolates, 91.09% were Gram-positive and 8.91% were Gram-negative microorganisms; (2) the proportions of cocci and rods were 36.68 and 63.31%, respectively; (3) the predominant groups of organisms isolated were Streptococcus spp., Lactobacillus spp., Staphylococcus spp. and Actinomyces spp. with isolation frequencies of 100, 90.00, 73.33 and 63.33%, respectively; (4) the isolation frequency of yeasts belonging to Candida spp. (63.33%) was notably high although the proportion of yeasts within each sample was low (0.01%). Candida dubliniensis, a newly identified yeast species particularly prevalent in HIV infection, comprised 14.29% of yeasts.

CONCLUSIONS

This study provides baseline information on the microbiologic features of root caries in the elderly, ethnic Chinese. Whilst our data on the most predominant bacteria isolated in root caries concur with those from other regions of the world the isolation of C. dubliniensis from these lesions has not been documented before.

Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

The human gastrointestinal (GI) tract harbors a complex community of bacterial cells in the mucosa, lumen, and feces. Since most attention has been focused on bacteria present in feces, knowledge about the mucosa-associated bacterial communities in different parts of the colon is limited. In this study, the bacterial communities in feces and biopsy samples from the ascending, transverse, and descending colons of 10 individuals were analyzed by using a 16S rRNA approach. Flow cytometric analysis indicated that 10(5) to 10(6) bacteria were present in the biopsy samples. To visualize the diversity of the predominant and the Lactobacillus group community, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was performed. DGGE analysis and similarity index comparisons demonstrated that the predominant mucosa-associated bacterial community was host specific and uniformly distributed along the colon but significantly different from the fecal community (P < 0.01). The Lactobacillus group-specific profiles were less complex than the profiles reflecting the predominant community. For 6 of the 10 individuals the community of Lactobacillus-like bacteria in the biopsy samples was similar to that in the feces. Amplicons having 99% sequence similarity to the 16S ribosomal DNA of Lactobacillus gasseri were detected in the biopsy samples of nine individuals. No significant differences were observed between healthy and diseased individuals. The observed host-specific DGGE profiles of the mucosa-associated bacterial community in the colon support the hypothesis that host-related factors are involved in the determination of the GI tract microbial community.

Investigation of an anaerobic microbial community associated with a corneal ulcer by denaturing gradient gel electrophoresis and 16S rDNA sequence analysis

The bacterial community manifested in a corneal ulcer was investigated with culture-independent techniques. DNA was extracted from the eye swab, 200-bp fragments spanning the hypervariable V3 region of the 16S rRNA gene (16S rDNA) were amplified by broad-range PCR and genetic fingerprinting of the total bacterial community was performed by denaturing gradient gel electrophoresis (DGGE). Additionally, 16S rDNA clone libraries containing 1500-bp fragments were constructed, clones were screened by DGGE and sequenced. Microorganisms were phylogenetically most closely related to the Cytophaga/Flavobacterium/Bacteroides phylum (eight clones), Fusobacteria (four clones), spirochetes (three clones) and to the low G+C Gram-positive bacteria (two clones). Low sequence similarity values less than 93% to sequences of known bacteria indicated that some bacteria belonged to hitherto unknown genera. Bacteria which were detected in the healthy eye of the same patient, were phylogenetically related to the low G+C and high G+C Gram-positive bacteria (two clones) and to the Proteobacteria (one clone). To our knowledge, this is the first time that such a complex and anaerobic bacterial community normally found in subgingival crevices is reported to play a role in corneal ulceration. Previous treatment of the ulcer with several topical antibiotics had shown no effect for six months. The followed culture-independent identification of spirochetes and Gram-negative, anaerobic bacilli facilitated the appropriate treatment with topical penicillin G, which stopped further destruction of the eye. Results demonstrated that 16S rDNA genotyping in combination with DGGE fingerprinting are appropriate molecular methods for the investigation of severe bacterial infections which might not be detected by conventional cultivation.

Characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques

The bacterial community associated with black band disease (BBD) of the scleractinian corals Diploria strigosa, Montastrea annularis and Colpophyllia natans was examined using culture-independent techniques. Two complementary molecular screening techniques of 16S rDNA genes [amplified 16S ribosomal DNA restriction analysis (ARDRA) of clone libraries and denaturing gradient gel electrophoresis (DGGE)] were used to give a comprehensive characterization of the community. Findings support previous studies indicating low bacterial abundance and diversity associated with healthy corals. A single cyanobacterial ribotype was present in all the diseased samples, but this was not the same as that identified from Phormidium corallyticum culture isolated from BBD. The study confirms the presence of Desulfovibrio spp. and sulphate-reducing bacteria that have previously been associated with the BBD consortium. However, the species varied between diseased coral samples. We found no evidence of bacteria from terrestrial, freshwater or human sources in any of the samples. We report the presence of previously unrecognized potential pathogens [a Cytophaga sp. and an alpha-proteobacterium identified as the aetiological agent of juvenile oyster disease (JOD)] that were consistently present in all the diseased coral samples. The molecular biological approach described here gives an increasingly comprehensive and more precise picture of the bacterial population associated with BBD. To understand the pathogenesis of BBD, our attention should be focused on the pervasive ribotypes identified in this study (the Cyanobacterium sp., the Cytophaga sp. and the JOD pathogen).

Molecular analysis of bacterial species associated with childhood caries

Although substantial epidemiologic evidence links Streptococcus mutans to caries, the pathobiology of caries may involve more complex communities of bacterial species. Molecular methods for bacterial identification and enumeration now make it possible to more precisely study the microbiota associated with dental caries. The purpose of this study was to compare the bacteria found in early childhood caries (ECC) to those found in caries-free children by using molecular identification methods. Cloning and sequencing of bacterial 16S ribosomal DNAs from a healthy subject and a subject with ECC were used for identification of novel species or uncultivated phylotypes and species not previously associated with dental caries. Ten novel phylotypes were identified. A number of species or phylotypes that may play a role in health or disease were identified and warrant further investigation. In addition, quantitative measurements for 23 previously known bacterial species or species groups were obtained by a reverse capture checkerboard assay for 30 subjects with caries and 30 healthy controls. Significant differences were observed for nine species: S. sanguinis was associated with health and, in order of decreasing cell numbers, Actinomyces gerencseriae, Bifidobacterium, S. mutans, Veillonella, S. salivarius, S. constellatus, S. parasanguinis, and Lactobacillus fermentum were associated with caries. These data suggest that A. gerencseriae and other Actinomyces species may play an important role in caries initiation and that a novel Bifidobacterium may be a major pathogen in deep caries. Further investigation could lead to the identification of targets for biological interventions in the caries process and thereby contribute to improved prevention of and treatment for this significant public health problem.

Unseen forces: the influence of bacteria on animal development

The diversity of developmental programs present in animal phyla first evolved within the world's oceans, an aquatic environment teeming with an abundance of microbial life. All stages in the life histories of these early animals became adapted to microorganisms bathing their tissues, and countless examples of animal-bacterial associations have arisen as a result. Thus far, it has been difficult for biologists to design ways of determining the extent to which these associations have influenced the biology of animals, including their developmental patterns. The following review focuses on an emerging field, the goal of which is to understand the influence of bacteria on animal developmental programs. This integrative area of research is undergoing a revolution that has resulted from advances in technology and the development of suitable animal-bacterial systems for the study of these complex associations. In this contribution, the current status of the field is reviewed and the emerging research horizons are examined.

Broad-range bacterial detection and the analysis of unexplained death and critical illness

Broad-range rDNA polymerase chain reaction (PCR) provides an alternative, cultivation-independent approach for identifying pathogens. In 1995, the Centers for Disease Control and Prevention initiated population-based surveillance for unexplained life-threatening infections (Unexplained Death and Critical Illness Project [UNEX]). To address the causes of UNEX cases, we examined 59 specimens from 46 cases by using broad-range bacterial 16S rDNA PCR and phylogenetic analysis of amplified sequences. Specimens from eight cases yielded sequences from Neisseria meningitidis (cerebrospinal fluid from two patients with meningitis), Streptococcus pneumoniae (cerebrospinal fluid from one patient with meningitis2 and pleural fluid from two patients with pneumonia), or Stenotrophomonas maltophilia (bone marrow aspirate from one patient with pneumonia). Streptococcus pneumoniae rDNA sequence microheterogeneity was found in one pleural fluid specimen, suggesting the presence of multiple strains. In conclusion, known bacterial pathogens cause some critical illnesses and deaths that fail to be explained with traditional diagnostic methods.

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

The design and evaluation of a set of universal primers and probe for the amplification of 16S rDNA from the Domain Bacteria to estimate total bacterial load by real-time PCR is reported. Broad specificity of the universal detection system was confirmed by testing DNA isolated from 34 bacterial species encompassing most of the groups of bacteria outlined in Bergey's Manual of Determinative Bacteriology. However, the nature of the chromosomal DNA used as a standard was critical. A DNA standard representing those bacteria most likely to predominate in a given habitat was important for a more accurate determination of total bacterial load due to variations in 16S rDNA copy number and the effect of generation time of the bacteria on this number, since rapid growth could result in multiple replication forks and hence, in effect, more than one copy of portions of the chromosome. The validity of applying these caveats to estimating bacterial load was confirmed by enumerating the number of bacteria in an artificial sample mixed in vitro and in clinical carious dentine samples. Taking these parameters into account, the number of anaerobic bacteria estimated by the universal probe and primers set in carious dentine was 40-fold greater than the total bacterial load detected by culture methods, demonstrating the utility of real-time PCR in the analysis of this environment.

Chemokines and the tissue-specific migration of lymphocytes

Tissue-selective trafficking of memory and effector T and B lymphocytes is mediated by unique combinations of adhesion molecules and chemokines. The discovery of several related epithelial-expressed chemokines (TECK/CCL25 in small intestine, CTACK/CCL27 in skin, and MEC/CCL28 in diverse mucosal sites) now highlights an important role for epithelial cells in controlling homeostatic lymphocyte trafficking, including the localization of cutaneous and intestinal memory T cells, and of IgA plasma cells. Constitutively expressed epithelial chemokines may help determine the character of local immune responses and contribute to the systemic organization of the immune system.

Oral health care in the 21st century: implications for dental and medical education

The past decade has been turbulent for dental education, marked by debate about the future directions of the curriculum and the profession itself. The bulk of the dental school curriculum is still devoted to tooth restoration or replacement techniques, although the need for these procedures has declined. Some dental educators now advocate an oral physician model as the desired direction for the profession, with expanded training in systemic disease pathophysiology and a practice scope that extends beyond exclusive focus on the teeth and supporting structures. Proponents of this model contend for curriculum time with faculty who desire to maintain a technical focus. The outcome of this curricular tug-of-war has implications for medical education, because many oral health problems now fall into the overlapping educational and patient care environments of physicians, dentists, and other health care providers. Will physicians perceive the new dentist as an encroachment on territory or as a resource to enhance patient care? Within dentistry, the traditions of tooth restoration and prosthodontics shape the profession's culture. Are dental educators ready to reconfigure a curriculum that is deeply intertwined with the professional identity of 150,000 U.S. dentists practicing today? To stimulate thinking about these issues, the authors analyze the responses of dental education to changes in the public's oral health and to calls for curricular reform, propose strategies for modifying the way dentists are prepared for their professional responsibilities, and explore the sociology of change in academic institutions, because elements of dental education targeted for reform are revered components of school culture.

Microbial ecology of human skin in health and disease

Cultivation of human skin reveals numerous bacteria and at least one fungus to be normal inhabitants of this ecosystem; however, most of our knowledge about the microbiology of human skin was acquired decades ago. Modern techniques employing nucleic acid-based microbial identification methods demonstrate the limitations of cultivation for appreciating microbial diversity in many ecosystems. The application of modern molecular methods to the study of skin may offer new perspectives on the resident microfora, and new insights into the causes of antibiotic responsive dermatologic conditions, such as acne and rosacea.

Applied Evolution

▪ Abstract  Evolutionary biology is widely perceived as a discipline with relevance that lies purely in academia. Until recently, that perception was largely true, except for the often neglected role of evolutionary biology in the improvement of agricultural crops and animals. In the past two decades, however, evolutionary biology has assumed a broad relevance extending far outside its original bounds. Phylogenetics, the study of Darwin's theory of “descent with modification,” is now the foundation of disease tracking and of the identification of species in medical, pharmacological, or conservation settings. It further underlies bioinformatics approaches to the analysis of genomes. Darwin's “evolution by natural selection” is being used in many contexts, from the design of biotechnology protocols to create new drugs and industrial enzymes, to the avoidance of resistant pests and microbes, to the development of new computer technologies. These examples present opportunities for education of the public and for nontraditional career paths in evolutionary biology. They also provide new research material for people trained in classical approaches.

Molecular identification of microorganisms from endodontic infections

A relatively wide range of bacteria have been isolated from root canals using standard culture techniques. However, only 50% of the bacteria in the oral cavity are cultivable (S. S. Socransky et al., Arch. Oral Biol. 8:278-280, 1963); hence, bacterial diversity in endodontic infections is underestimated. This study used a PCR-based 16S rRNA gene assay, followed by cloning and sequencing of 16S rRNA amplicons from a small subset of samples to assess the diversity of bacteria present in infected root canals. A total of 41 clinical samples from 15 de novo and 26 refractory cases of endodontic infections were assessed. Of these samples, 44% were positive by culture and 68% were positive by PCR. Eight samples were selected for further analysis. Of these, the two de novo cases yielded sequences related to those of the genera Enterococcus, Lactobacillus, Propionibacterium, and Streptococcus and two clones were related to previously uncultivated bacteria, while the sinus-associated, de novo case yielded sequences related to those of the genera Lactobacillus, Pantoea, Prevotella, and Selenomonas. The five refractory cases produced clones which were related to the genera Capnocytophaga, Cytophaga, Dialister, Eubacterium, Fusobacterium, Gemella, Mogibacterium, Peptostreptococcus, Prevotella, Propionibacterium, Selenomonas, Solobacterium, Streptococcus, and Veillonella and two clones representing previously uncultivated bacteria. The phylogenetic positions of several clones associated with the Clostridiaceae and Sporomusa subgroups of the Firmicutes grouping are also shown. This study demonstrates that molecular techniques can detect the presence of bacteria in endodontic infections when culture techniques yield a negative result and can be used to identify a wider range of endodontic-infection-related bacteria including the presence of previously unidentified or unculturable bacteria.

Mutualism versus independence: strategies of mixed-species oral biofilms in vitro using saliva as the sole nutrient source

During initial dental plaque formation, the ability of a species to grow when others cannot would be advantageous, and enhanced growth through interspecies and intergeneric cooperation could be critical. These characteristics were investigated in three coaggregating early colonizers of the tooth surface (Streptococcus gordonii DL1, Streptococcus oralis 34, and Actinomyces naeslundii T14V). Area coverage and cell cluster size measurements showed that attachment of A. naeslundii and of S. gordonii to glass flowcells was enhanced by a salivary conditioning film, whereas attachment of S. oralis was hindered. Growth experiments using saliva as the sole carbon and nitrogen source showed that A. naeslundii was unable to grow either in planktonic culture or as a biofilm, whereas S. gordonii grew under both conditions. S. oralis grew planktonically, but to a much lower maximum cell density than did S. gordonii; S. oralis did not grow reproducibly as a biofilm. Thus, only S. gordonii possessed all traits advantageous for growth as a solitary and independent resident of the tooth. Two-species biofilm experiments analyzed by laser confocal microscopy showed that neither S. oralis nor A. naeslundii grew when coaggregated pairwise with S. gordonii. However, both S. oralis and A. naeslundii showed luxuriant, interdigitated growth when paired together in coaggregated microcolonies. Thus, the S. oralis-A. naeslundii pair formed a mutualistic relationship, potentially contact dependent, that allows each to grow where neither could survive alone. S. gordonii, in contrast, neither was hindered by nor benefited from the presence of either of the other strains. The formation of mutually beneficial interactions within the developing biofilm may be essential for certain initial colonizers to be retained during early plaque development, whereas other initial colonizers may be unaffected by neighboring cells on the substratum.

Bacterial diversity in human subgingival plaque

The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria. Subgingival plaque was analyzed from healthy subjects and subjects with refractory periodontitis, adult periodontitis, human immunodeficiency virus periodontitis, and acute necrotizing ulcerative gingivitis. 16S ribosomal DNA (rDNA) bacterial genes from DNA isolated from subgingival plaque samples were PCR amplified with all-bacterial or selective primers and cloned into Escherichia coli. The sequences of cloned 16S rDNA inserts were used to determine species identity or closest relatives by comparison with sequences of known species. A total of 2,522 clones were analyzed. Nearly complete sequences of approximately 1,500 bases were obtained for putative new species. About 60% of the clones fell into 132 known species, 70 of which were identified from multiple subjects. About 40% of the clones were novel phylotypes. Of the 215 novel phylotypes, 75 were identified from multiple subjects. Known putative periodontal pathogens such as Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola were identified from multiple subjects, but typically as a minor component of the plaque as seen in cultivable studies. Several phylotypes fell into two recently described phyla previously associated with extreme natural environments, for which there are no cultivable species. A number of species or phylotypes were found only in subjects with disease, and a few were found only in healthy subjects. The organisms identified only from diseased sites deserve further study as potential pathogens. Based on the sequence data in this study, the predominant subgingival microbial community consisted of 347 species or phylotypes that fall into 9 bacterial phyla. Based on the 347 species seen in our sample of 2,522 clones, we estimate that there are 68 additional unseen species, for a total estimate of 415 species in the subgingival plaque. When organisms found on other oral surfaces such as the cheek, tongue, and teeth are added to this number, the best estimate of the total species diversity in the oral cavity is approximately 500 species, as previously proposed.

Commensal host-bacterial relationships in the gut

One potential outcome of the adaptive coevolution of humans and bacteria is the development of commensal relationships, where neither partner is harmed, or symbiotic relationships, where unique metabolic traits or other benefits are provided. Our gastrointestinal tract is colonized by a vast community of symbionts and commensals that have important effects on immune function, nutrient processing, and a broad range of other host activities. The current genomic revolution offers an unprecedented opportunity to identify the molecular foundations of these relationships so that we can understand how they contribute to our normal physiology and how they can be exploited to develop new therapeutic strategies.

Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis

Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.

Does blood of healthy subjects contain bacterial ribosomal DNA?

Real-time PCR methods with primers and a probe targeting conserved regions of the bacterial 16S ribosomal DNA (rDNA) revealed a larger amount of rDNA in blood specimens from healthy individuals than in matched reagent controls. However, the origins and identities of these blood-associated bacterial rDNA sequences remain obscure.

Intracellular Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis in buccal epithelial cells collected from human subjects

The mouth may provide an accessible model for studying bacterial interactions with human cells in vivo. Using fluorescent in situ hybridization and laser scanning confocal microscopy, we found that human buccal epithelial cells from 23 of 24 subjects were infected with intracellular bacteria, including the periodontal pathogens Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis, as well as other species which have yet to be identified. Buccal cell invasion may allow fastidious anaerobes to establish themselves in aerobic sites that otherwise present an unfavorable environment. Exfoliated buccal epithelial cells might provide a protected route for bacterial transmission between different oral sites within and between hosts.

Oral microbial communities: biofilms, interactions, and genetic systems

Oral microbial-plaque communities are biofilms composed of numerous genetically distinct types of bacteria that live in close juxtaposition on host surfaces. These bacteria communicate through physical interactions called coaggregation and coadhesion, as well as other physiological and metabolic interactions. Streptococci and actinomyces are the major initial colonizers of the tooth surface, and the interactions between them and their substrata help establish the early biofilm community. Fusobacteria play a central role as physical bridges that mediate coaggregation of cells and as physiological bridges that promote anaerobic microenvironments which protect coaggregating strict anaerobes in an aerobic atmosphere. New technologies for investigating bacterial populations with 16S rDNA probes have uncovered previously uncultured bacteria and have offered an approach to in situ examination of the spatial arrangement of the participant cells in oral-plaque biofilms. Flow cells with saliva-coated surfaces are particularly useful for studies of biofilm formation and observation. The predicted sequential nature of colonization of the tooth surface by members of different genera can be investigated by using these new technologies and imaging the cells in situ with confocal scanning laser microscopy. Members of at least seven genera now can be subjected to genetic studies owing to the discovery of gene-transfer systems in these genera. Identification of contact-inducible genes in streptococci offers an avenue to explore bacterial responses to their environment and leads the way toward understanding communication among inhabitants of a multispecies biofilm.

Automated fluorescent in situ hybridization for the specific detection and quantification of oral streptococci in dental plaque

Our aim was to develop a rapid fluorescent in situ hybridization (FISH) assay for the identification of different oral groups of streptococci in dental plaque and to combine it with digital image analysis for the automated enumeration of target cells. Cy3-labeled oligonucleotide probes specific for 16S rRNA gene sequences of the anginosus, mitis, mutans, and salivarius groups of streptococci were hybridized under stringent conditions with bacterial cultures or supragingival plaque samples that had been permeabilized with lysozyme. Probe specificity was determined with strains from 30 different species, mainly of oral origin. Results showed that probes ANG541, MIT447, SSP001, and SAL090 with specificity for the anginosus, mitis, mutans, and salivarius groups, respectively, the pan-reactive streptococcal probe STR405, the S. mutans specific probe MUT590, and the S. sobrinus specific probe SOB174 were well-suited for the identification of cultured streptococci. Probes STR405, MIT447 and SSP001 were then successfully applied to enumerate automatically bacteria of the recognized taxa in 144 supragingival plaque samples. On the average, total streptococci accounted for 8.2%, streptococci of the mitis and mutans groups for 3.9 and 1.7%, respectively, of the plaques. The combined application of FISH and automated image analysis provides an objective time-saving alternative to culture or PCR for the enumeration of selected oral streptococci in dental plaque.

Saliva and dental plaque

Dental plaque is being redefined as oral biofilm. Diverse overlapping microbial consortia are present on all oral tissues. Biofilms are structured, displaying features like channels and projections. Constituent species switch back and forth between sessile and planktonic phases. Saliva is the medium for planktonic suspension. Several major functions can be defined for saliva in relation to oral biofilm. It serves as a medium for transporting planktonic bacteria within and between mouths. Bacteria in transit may be vulnerable to negative selection. Salivary agglutinins may prevent reattachment to surfaces. Killing by antimicrobial proteins may lead to attachment of dead cells. Salivary proteins form conditioning films on all oral surfaces. This contributes to positive selection for microbial adherence. Saliva carries chemical messengers which allow live adherent cells to sense a critical density of conspecifics. Growth begins, and thick biofilms may become resistant to antimicrobial substances. Salivary macromolecules may be catabolized, but salivary flow also may clear dietary substrates. Salivary proteins act in ways that benefit both host and microbe. All have multiple functions, and many do the same job. They form heterotypic complexes, which may exist in large micelle-like structures. These issues make it useful to compare subjects whose saliva functions differently. We have developed a simultaneous assay for aggregation, killing, live adherence, and dead adherence of oral species. Screening of 149 subjects has defined high killing/low adherence, low killing/high adherence, high killing/high adherence, and low killing/low adherence groups. These will be evaluated for differences in their flora.

Evolving together: the biology of symbiosis, part 1

Symbioses, prolonged associations between organisms often widely separated phylogenetically, are more common in biology than we once thought and have been neglected as a phenomenon worthy of study on its own merits. Extending along a dynamic continuum from antagonistic to cooperative and often involving elements of both antagonism and mutualism, symbioses involve pathogens, commensals, and mutualists interacting in myriad ways over the evolutionary history of the involved "partners." In this first of 2 parts, some remarkable examples of symbiosis will be explored, from the coral-algal symbiosis and nitrogen fixation to the great diversity of dietary specializations enabled by the gastrointestinal microbiota of animals.

Organization, structure, and variability of the rRNA operon of the Whipple's disease bacterium (Tropheryma whippelii)

Whipple's disease is a systemic disorder associated with a cultivation-resistant, poorly characterized actinomycete, Tropheryma whippelii. We determined a nearly complete rRNA operon sequence of T. whippelii from specimens from 3 patients with Whipple's disease, as well as partial operon sequences from 43 patients. Variability was observed in the 16S-23S rRNA spacer sequences, leading to the description of five distinct sequence types. One specimen contained two spacer sequence types, raising the possibility of a double infection. Secondary structure models for the primary rRNA transcript and mature rRNAs revealed rare or unique features.

Microbiology: intimate strangers

A more robust view of the diversity of prokaryotes has come from sequencing rRNAs amplified directly from environmental samples. This approach has now been used to examine microbial communities in the human body, revealing populations rich in undescribed species whose impact on humans remains to be determined.