Bacterial diversity within the human subgingival crevice

Capnocytophaga canimorsus: a human pathogen feeding at the surface of epithelial cells and phagocytes

Capnocytophaga canimorsus, a commensal bacterium of the canine oral flora, has been repeatedly isolated since 1976 from severe human infections transmitted by dog bites. Here, we show that C. canimorsus exhibits robust growth when it is in direct contact with mammalian cells, including phagocytes. This property was found to be dependent on a surface-exposed sialidase allowing C. canimorsus to utilize internal aminosugars of glycan chains from host cell glycoproteins. Although sialidase probably evolved to sustain commensalism, by releasing carbohydrates from mucosal surfaces, it also contributed to bacterial persistence in a murine infection model: the wild type, but not the sialidase-deficient mutant, grew and persisted, both when infected singly or in competition. This study reveals an example of pathogenic bacteria feeding on mammalian cells, including phagocytes by deglycosylation of host glycans, and it illustrates how the adaptation of a commensal to its ecological niche in the host, here the dog's oral cavity, contributes to being a potential pathogen.

Capnocytophaga canimorsus is a commensal bacterium of dogs/cats oral flora, which causes rare but severe infections in humans that have been bitten or simply licked by a dog/cat. Fulminant septicemia and peripheral gangrene are most common symptoms. Although splenectomy has been identified as a predisposing factor, some 40% of the patients have no immunosuppression history. C. canimorsus belongs to the phylum Bacteroidetes, which includes many commensals of the human gut flora but few pathogens. C. canimorsus has been shown previously to be immunosuppressive and to resist phagocytosis by macrophages. Here, we show that this bacterium feeds on surface-exposed glycoproteins from cultured mammalian cells. This property, which was found to depend on a bacterial surface-exposed sialidase, suggests that in its natural niche—the dog's oral cavity—C. canimorsus may feed on the dog's mucosal cells. Moreover, we found that C. canimorsus also feeds on phagocytes and that sialidase contributes to persistence and virulence in a mouse infection model. Thus, by adapting to its ecological niche, C. canimorsus also developed the potential to persist within the tissues of an infected host. This observation nicely illustrates how commensalism and pathogenesis are two faces of the same coin.

Prokaryote-eukaryote interactions identified by using Caenorhabditis elegans

Prokaryote-eukaryote interactions are ubiquitous and have important medical and environmental significance. Despite this, a paucity of data exists on the mechanisms and pathogenic consequences of bacterial-fungal encounters within a living host. We used the nematode Caenorhabditis elegans as a substitute host to study the interactions between two ecologically related and clinically troublesome pathogens, the prokaryote, Acinetobacter baumannii, and the eukaryote, Candida albicans. After co-infecting C. elegans with these organisms, we observed that A. baumannii inhibits filamentation, a key virulence determinant of C. albicans. This antagonistic, cross-kingdom interaction led to attenuated virulence of C. albicans, as determined by improved nematode survival when infected with both pathogens. In vitro coinfection assays in planktonic and biofilm environments supported the inhibitory effects of A. baumannii toward C. albicans, further showing a predilection of A. baumannii for C. albicans filaments. Interestingly, we demonstrate a likely evolutionary defense by C. albicans against A. baumannii, whereby C. albicans inhibits A. baumannii growth once a quorum develops. This counteroffensive is at least partly mediated by the C. albicans quorum-sensing molecule farnesol. We used the C. elegans-A. baumannii-C. albicans coinfection model to screen an A. baumannii mutant library, leading to the identification of several mutants attenuated in their inhibitory activity toward C. albicans. These findings present an extension to the current paradigm of studying monomicrobial pathogenesis in C. elegans and by use of genetic manipulation, provides a whole-animal model system to investigate the complex dynamics of a polymicrobial infection.

Colloquium paper: microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity

The study of elevational diversity gradients dates back to the foundation of biogeography. Although elevational patterns of plant and animal diversity have been studied for centuries, such patterns have not been reported for microorganisms and remain poorly understood. Here, in an effort to assess the generality of elevational diversity patterns, we examined soil bacterial and plant diversity along an elevation gradient. To gain insight into the forces that structure these patterns, we adopted a multifaceted approach to incorporate information about the structure, diversity, and spatial turnover of montane communities in a phylogenetic context. We found that observed patterns of plant and bacterial diversity were fundamentally different. While bacterial taxon richness and phylogenetic diversity decreased monotonically from the lowest to highest elevations, plants followed a unimodal pattern, with a peak in richness and phylogenetic diversity at mid-elevations. At all elevations bacterial communities had a tendency to be phylogenetically clustered, containing closely related taxa. In contrast, plant communities did not exhibit a uniform phylogenetic structure across the gradient: they became more overdispersed with increasing elevation, containing distantly related taxa. Finally, a metric of phylogenetic beta-diversity showed that bacterial lineages were not randomly distributed, but rather exhibited significant spatial structure across the gradient, whereas plant lineages did not exhibit a significant phylogenetic signal. Quantifying the influence of sample scale in intertaxonomic comparisons remains a challenge. Nevertheless, our findings suggest that the forces structuring microorganism and macroorganism communities along elevational gradients differ.

Amylase-binding protein B of Streptococcus gordonii is an extracellular dipeptidyl-peptidase

The oral commensal bacterium Streptococcus gordonii interacts with salivary amylase via two amylase-binding proteins, AbpA and AbpB. Based on sequence analysis, the 20-kDa AbpA protein is unique to S. gordonii, whereas the 82-kDa AbpB protein appears to share sequence homology with other bacterial dipeptidases. The aim of this study was to verify the peptidase activity of AbpB and further explore its potential functions. The abpB gene was cloned, and histidine-tagged AbpB (His-AbpB) was expressed in Escherichia coli and purified. Its amylase-binding activity was verified in an amylase ligand binding assay, and its cross-reactivity was verified with an anti-AbpB antibody. Both recombinant His-AbpB and partially purified native AbpB displayed dipeptidase activity and degraded human type VI collagen and fibrinogen, but not salivary amylase. Salivary amylase precipitates not only AbpA and AbpB but also glucosyltransferase G (Gtf-G) from S. gordonii supernatants. Since Streptococcus mutans also releases Gtf enzymes that could also be involved in multispecies plaque interactions, the effect of S. gordonii AbpB on S. mutans Gtf-B activity was also tested. Salivary amylase and/or His-AbpB caused a 1.4- to 2-fold increase of S. mutans Gtf-B sucrase activity and a 3- to 6-fold increase in transferase activity. An enzyme-linked immunosorbent assay verified the interaction of His-AbpB and amylase with Gtf-B. In summary, AbpB demonstrates proteolytic activity and interacts with and modulates Gtf activity. These activities may help explain the crucial role AbpB appears to play in S. gordonii oral colonization.

Do you have a probiotic in your future?

The possibility of using microbes to maintain health, and to prevent or treat disease is a topic as old as microbiology. However, one factor impeding the introduction of effective probiotics has been our very limited understanding of the composition of the human microbiome, as well as the biological requirements for these organisms. With advances in understanding the microbiome and its metagenome in humans and other mammals, we now can build a more robust scientific basis to develop probiotic strategies. Increasing knowledge of intramicrobial competition and cooperation, as well as host-microbe cross-signaling, will facilitate design of new probiotics and the modeling of their deployment, leading to eventual clinical trials.

Ibis T5000: a universal biosensor approach for microbiology

The Ibis T5000 couples nucleic acid amplification to high-performance electrospray mass spectrometry and base-composition analysis and enables the identification and quantification of all known bacteria, all major groups of pathogenic fungi and the major families of viruses that cause disease in humans and animals. Here, Ecker and colleagues describe this new technology.

We describe a new technology, the Ibis T5000, for the identification of pathogens in clinical and environmental samples. The Ibis T5000 couples nucleic acid amplification to high-performance electrospray ionization mass spectrometry and base-composition analysis. The system enables the identification and quantification of a broad set of pathogens, including all known bacteria, all major groups of pathogenic fungi and the major families of viruses that cause disease in humans and animals, along with the detection of virulence factors and antibiotic resistance markers.

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.

Streptococcal antagonism in oral biofilms: Streptococcus sanguinis and Streptococcus gordonii interference with Streptococcus mutans

Biofilms are polymicrobial, with diverse bacterial species competing for limited space and nutrients. Under healthy conditions, the different species in biofilms maintain an ecological balance. This balance can be disturbed by environmental factors and interspecies interactions. These perturbations can enable dominant growth of certain species, leading to disease. To model clinically relevant interspecies antagonism, we studied three well-characterized and closely related oral species, Streptococcus gordonii, Streptococcus sanguinis, and cariogenic Streptococcus mutans. S. sanguinis and S. gordonii used oxygen availability and the differential production of hydrogen peroxide (H(2)O(2)) to compete effectively against S. mutans. Interspecies antagonism was influenced by glucose with reduced production of H(2)O(2). Furthermore, aerobic conditions stimulated the competence system and the expression of the bacteriocin mutacin IV of S. mutans, as well as the H(2)O(2)-dependent release of heterologous DNA from mixed cultures of S. sanguinis and S. gordonii. These data provide new insights into ecological factors that determine the outcome of competition between pioneer colonizing oral streptococci and the survival mechanisms of S. mutans in the oral biofilm.

Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease

Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H(2)-metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of methanogens and sulfate reducers being significantly elevated in severe cases. In addition, antagonistic interactions among the three microbial groups indicated that they may function as alternative syntrophic partners of secondary fermenting periodontal pathogens.

Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease

Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H(2)-metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of methanogens and sulfate reducers being significantly elevated in severe cases. In addition, antagonistic interactions among the three microbial groups indicated that they may function as alternative syntrophic partners of secondary fermenting periodontal pathogens.

Salivary Genomics, Transcriptomics and Proteomics: The Emerging Concept of the Oral Ecosystem and their Use in the Early Diagnosis of Cancer and other Diseases

There is an increasingly growing interest world-wide for the genomics, transcriptomics and proteomics of saliva and the oral cavity, since they provide a non-invasive source of unprecedently rich genetic information. The complexity of oral systems biology goes much beyond the human genome, transcriptome and proteome revealed by oral mucosal cells, gingival crevicular fluid, and saliva, and includes the complexity of the oral microbiota, the symbiotic assembly of bacterial, fungal and other microbial flora in the oral cavity. In our review we summarize the recent information on oral genomics, transcriptomics and proteomics, of both human and microbial origin. We also give an introduction and practical advice on sample collection, handling and storage for analysis. Finally, we show the usefulness of salivary and oral genomics in early diagnosis of cancer, as well as in uncovering other systemic diseases, infections and oral disorders. We close the review by highlighting a number of possible exploratory pathways in this emerging, hot research field.

Novel microarray design strategy to study complex bacterial communities

Assessing bacterial flora composition appears to be of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, the environment, and the food industry. We report here the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains approximately 9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes (<or=1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared.

Environmental influences on biofilm development

Bacterial biofilms are found under diverse environmental conditions, from sheltered and specialized environments found within mammalian hosts to the extremes of biological survival. The process of forming a biofilm and the eventual return of cells to the planktonic state involve the coordination of vast amounts of genetic information. Nevertheless, the prevailing evidence suggests that the overall progression of this cycle within a given species or strain of bacteria responds to environmental conditions via a finite number of key regulatory factors and pathways, which affect enzymatic and structural elements that are needed for biofilm formation and dispersal. Among the conditions that affect biofilm development are temperature, pH, O2 levels, hydrodynamics, osmolarity, the presence of specific ions, nutrients, and factors derived from the biotic environment. The integration of these influences ultimately determines the pattern of behavior of a given bacterium with respect to biofilm development. This chapter will present examples of how environmental conditions affect biofilm development, most of which come from studies of species that have mammalian hosts.

Interspecies interactions within oral microbial communities

While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning "system thinking" and "holism." Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name "dental plaque," oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios.

Antigen capture of Porphyromonas gingivalis by human macrophages is enhanced but killing and antigen presentation are reduced by endotoxin tolerance

The innate and the adaptive arms of the mucosal immune system must be coordinated to facilitate the control of pathogenic invasion while maintaining immune homeostasis. Toll-like receptors, able to activate the cell to produce bactericidal and inflammatory cytokines but also able to upregulate antigen (Ag)-presenting and costimulatory molecules, are particularly important in this regard. We have previously shown that the chronically infected oral mucosa is in a state of endotoxin tolerance, as evidenced by the downregulation of Toll-like receptors 2 and 4 and of inflammatory cytokines and the upregulation of SH2-containing inositol phosphatase, an inhibitor of NF-kappaB signaling. In the present study, we hypothesized that endotoxin tolerance would influence the ability of human macrophages to engage in Ag capture and killing of the oral pathogen Porphyromonas gingivalis and to upregulate costimulatory molecules and stimulate autologous T-cell proliferation. We show that uptake, but not killing, of P. gingivalis 381 is enhanced by endotoxin tolerance. Reduced killing is possibly due to a reduction of the intracellular lysosomes. We further show that the expression of the Ag-presenting molecule HLA-DR and costimulatory molecules CD40 and CD86 is dampened by endotoxin tolerance to the constitutive level. This, along with our previous evidence for reduction in immunostimulatory cytokines, is consistent with the observed decrease in the induction of autologous CD4(+) T-cell proliferation by endotoxin-tolerized macrophages. Overall, these studies suggest that endotoxin tolerance, as observed in the inflamed oral mucosa, potentiates the innate Ag capture activity of macrophages but diminishes the potential of human macrophages to initiate the adaptive immune response. In conclusion, endotoxin tolerance, while helpful in bacterial clearance and in surmounting excessive inflammatory tissue damage, could potentially reduce the (protective) adaptive immune response during chronic infections such as periodontitis.

Identification of oral bacterial species associated with halitosis

BACKGROUND

The authors examined the tongue bacteria associated with oral halitosis (bad breath originating from the oral cavity), focusing on noncultivable bacteria-bacteria that cannot be identified by bacterial culture techniques.

METHODS

The authors took samples from the dorsal tongue surface of eight adult subjects with halitosis and five control subjects who did not have halitosis. They identified the bacteria in these samples by using both anaerobic culture and direct amplification of 16S ribosomal DNA, a method that can identify both cultivable and noncultivable microorganisms. They analyzed the resulting microbiological data using chi(2) and correlation coefficient tests.

RESULTS

Clinical measures of halitosis were correlated highly with each other and with tongue coating scores. Of 4,088 isolates and phylotypes identified from the 13 subjects, 32 species including 13 noncultivable species were found only in subjects with halitosis. Solobacterium moorei was present in all subjects with halitosis but not in any control subjects.

CONCLUSIONS

Subjects with halitosis harbor some bacterial species on their dorsal tongue surfaces that are distinct from bacterial species found in control subjects. This finding is consistent with the hypothesis that halitosis has a microbial etiology.

CLINICAL IMPLICATIONS

Like other oral diseases with microbial etiology, halitosis may be amenable to specific and nonspecific antimicrobial therapy targeted toward the bacteria associated with it.

Susceptibility of various oral bacteria to antimicrobial peptides and to phagocytosis by neutrophils

BACKGROUND AND OBJECTIVE

The aim of this study was to compare the susceptibility of nonperiodontopathic and periodontopathic bacteria to major defense mechanisms for bacterial clearance in gingival sulcus.

MATERIAL AND METHODS

Twenty strains of 13 oral bacterial species were studied for their susceptibility to phagocytosis by human neutrophils and to the antimicrobial peptides LL-37 and human beta defensin-3. The minimum inhibitory concentrations of LL-37 and human beta defensin-3 were determined by a liquid dilution assay, and susceptibility to phagocytosis was examined by a flow cytometric phagocytosis assay.

RESULTS

The minimum inhibitory concentrations of LL-37 and human beta defensin-3 varied greatly, depending on the strain and species. Although a significant difference between the non- and periodontopathic groups was not observed, the red-complex bacteria were more resistant to LL-37 than the others (p=0.004). The susceptibility of oral bacteria to phagocytosis was quite variable, depending on the species but not on the strains. The periodontopathic bacteria, especially Actinobacillus actinomycetemcomitans and the red-complex triad, were more resistant to phagocytosis than were the nonperiodontopathic bacteria (p=0.0003). In addition, bacteria resistant both to antimicrobial peptides and to phagocytosis were more common in the periodontopathic group.

CONCLUSION

Our results indicate that immune evasion may contribute to the pathogenicity of some periodontopathic bacteria.

Clinical characteristics and microbiota of progressing slight chronic periodontitis in adults

AIM

This study sought clinical and microbial risk indicators for progressing slight periodontitis.

MATERIAL AND METHODS

One hundred and seventeen periodontally healthy or slight periodontitis adults (20-40 years) were monitored clinically at 6-month intervals followed by supragingival cleaning. Inter-proximal sites with >1.5 mm increase in clinical attachment over 18 months were considered disease active. Subgingival plaque was analysed by 78 16S rDNA and 38 whole-genomic DNA probes and by PCR to Porphyromonas gingivalis and Tannerella forsythia. Characteristics were compared between active and inactive subjects.

RESULTS

Twenty-two subjects showed disease activity principally at molars. Mean baseline gingival and plaque indices, bleeding on probing, probing depth and clinical attachment level (CAL) were higher in active subjects. DNA probes detected species and not-yet-cultivated phylotypes from chronic periodontitis, although few species were associated with active subjects. By PCR P. gingivalis (p=0.007) and T. forsythia (p=0.075) were detected more frequently during monitoring in active subjects. Stepwise logistic analysis associated baseline levels of gingival index, clinical attachment and bleeding with subsequent clinical attachment loss.

CONCLUSIONS

Gingivitis and CAL were significantly associated with progressing slight periodontitis in 20--40-year-old adults. Species associated with moderate and advanced chronic periodontitis were detected in slight periodontitis.

Identification of Tannerella forsythia antigens specifically expressed in patients with periodontal disease

Molecular pathogenesis of Tannerella forsythia, a putative periodontal pathogen, has not yet been adequately elucidated due to limited information on its virulence factors. Here, identification of in vivo expressed antigens of T. forsythia is reported using in vivo-induced antigen technology (IVIAT). Among 13 000 recombinant clones screened, 16 positive clones were identified that reacted reproducibly with sera obtained from patients with periodontal disease. DNA sequences from 12 of these in vivo-induced genes were determined. IVIAT-identified protein antigens of T. forsythia include: BspA, a well-defined virulence factor of T. forsythia; enzymes involved in housekeeping functions (tRNA synthetases, glycine hydroxymethyltransferase, and glucoside glucohydrolase); enzymes implicated in tissue destruction (dipeptidyl peptidase IV); a DNA mismatch repair protein; and putative outer membrane proteins of unknown function. The in vivo gene expression of these IVIAT-identified antigens was confirmed by a quantitative real-time PCR analysis. This is, to the best of the authors' knowledge, the first report using IVIAT in T. forsythia. It is anticipated that detailed analysis of the in vivo-induced genes identified by IVIAT in this study will lead to a better understanding of the molecular mechanisms mediating periodontal infection by T. forsythia.

Microbiologic investigations for head and neck infections

A variety of methods, including direct examination of stained smears, antigen detection, routine and special cultures, and histopathologic evaluation are available for investigation of head and neck infections. Newer rapid molecular techniques with increased sensitivity and specificity are becoming available at many centers. Evaluation of specific causes in head and neck infections is complicated by the tendency for polymicrobial infections, difficulty in obtaining adequate specimens, and the presence of a diverse endogenous microflora at various mucosal sites that also can include true pathogens. These aspects of laboratory investigation for head and neck infections are reviewed in this article.

The Impact of a Low-Frequency Chlorhexidine Rinsing Schedule on the Subgingival Microbiota (the TEETH clinical trial)

BACKGROUND

Information on the efficacy of chlorhexidine (CHX) rinsing on the subgingival microbiota is limited. This study tested if intermittent CHX rinsing over 5 years had an impact on the subgingival microbiota.

METHODS

Subgingival plaque samples were analyzed by the checkerboard DNA-DNA hybridization method in a double-blind randomized CHX rinse study.

RESULTS

A total of 210 subjects were included. The mean age of the subjects was 71.7 (+/- 4.1) years, and 56.2% were women. Evidence of alveolar bone loss was found in 39% of subjects. Bacterial loads were not correlated significantly with probing depth. At year 5, subjects in the CHX rinse group with no evidence of bone loss presented with lower total bacterial counts than control subjects with no bone loss. The levels of the following bacteria were significantly lower in the CHX group: Lactobacillus acidophilus (P <0.05), Eikenella corrodens (P <0.05), Fusobacterium nucleatum sp. nucleatum (P <0.01), Treponema denticola (P <0.05), Leptotrichia buccalis (P <0.05), and Eubacterium saburreum (P <0.05). No differences in bacterial loads were found between CHX and control rinse subjects with alveolar bone loss.

CONCLUSIONS

Older subjects with or without periodontitis carry a large variety of bacteria associated with periodontitis. Intermittent rinsing with CHX may provide a preventive benefit in reducing levels of bacteria but only in subjects without alveolar bone loss.

Mite-related bacterial antigens stimulate inflammatory cells in rosacea

BACKGROUND

Patients with papulopustular rosacea have a higher density of Demodex folliculorum mites on their faces than normal subjects but the role, if any, of their mites in initiating inflammation is disputed. Selective antibiotics are effective in reducing the inflammatory changes of papulopustular rosacea, but their mode of action is unknown.

OBJECTIVES

To investigate whether a D. folliculorum-related bacterium was capable of expressing antigens that could stimulate an inflammatory immune response in patients with rosacea.

METHODS

A bacterium (Bacillus oleronius) was isolated from a D. folliculorum mite extracted from the face of a patient with papulopustular rosacea, and was investigated further.

RESULTS

This bacterium produced antigens capable of stimulating peripheral blood mononuclear cells proliferation in 16 of 22 (73%) patients with rosacea but only five of 17 (29%) control subjects (P = 0.0105). This antigenic preparation was fractionated into 70 subfractions and the proteins in each fraction were visualized by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Western blot analysis revealed the presence of two antigenic proteins of size 62 and 83 kDa in fractions when probing with sera from patients with rosacea. No immunoreactivity to these proteins was recorded when probing with sera from control patients. Two-dimensional electrophoretic separation was used to isolate these proteins and matrix-assisted laser desorption/ionization time-of-flight analysis was employed to identify the relevant peptides. The 62-kDa immunoreactive protein shared amino acid sequence homology with an enzyme involved in carbohydrate metabolism and signal transduction while the 83-kDa protein was similar to bacterial heat shock proteins.

CONCLUSIONS

Antigenic proteins related to a bacterium (B. oleronius), isolated from a D. folliculorum mite, have the potential to stimulate an inflammatory response in patients with papulopustular rosacea.

Use of a DNA microarray for simultaneous detection of antibiotic resistance genes among staphylococcal clinical isolates

We developed a multiplex asymmetric PCR (MAPCR)-based DNA microarray assay for characterization of the clinically relevant antibiotic resistance genes leading to penicillin, methicillin, aminoglycoside, macrolide, lincosamide, and streptogramin B (MLS(B)) resistance in staphylococci. The DNA-based assay involves detection of specific conserved regions of the mecA, blaZ (methicillin and penicillin resistance), aac(6')-Ie-aph(2'') (aminoglycoside resistance), ermA and ermC genes (MLS(B) resistance), and the msrA gene (macrolide and streptogramin B resistance). The microarray uses a variable sequence region of the 16S rRNA gene to broadly differentiate between Staphylococcus aureus and other coagulase-negative staphylococci (CoNS). The performance of the microarray was validated with a total of 178 clinically important S. aureus and 237 CoNS isolates, with correlations of 100% for S. aureus to CoNS discrimination and more than 90% for antibiotic resistance between the genotypic analysis determined by the microarray and the phenotype determined by standard methods of species identification and susceptibility testing. The major discrepant results were 17 mecA-positive CoNS and 60 aac(6')-Ie-aph(2'')-positive CoNS isolates measured by microarray that were susceptible to the corresponding antibiotics based on disk diffusion assay. Overall, this microarray-based assay offers a simultaneous, fast (< or =5 h), and accurate identification of antibiotic resistance genes from a single colony, as well as species classification. Our extensive validation of the microarray suggests that it may be a useful tool to complement phenotypic susceptibility testing in clinical laboratories and to survey the spread of antibiotic resistance determinants in epidemiological studies.

Bacterial diversity in aphthous ulcers

INTRODUCTION

Recurrent aphthous ulcers are common lesions of the oral mucosa of which the etiology is unknown. This study aimed to estimate the bacterial diversity in the lesions and in control mucosa in pooled samples using a culture-independent molecular approach.

METHODS

Samples were collected from ten healthy individuals and ten individuals with a clinical history of recurrent aphthous ulcers. After DNA extraction, the 16S ribosomal RNA bacterial gene was amplified by polymerase chain reaction with universal primers; amplicons were cloned, sequenced and matched to the GenBank database.

RESULTS

A total of 535 clones were analyzed, defining 95 bacterial species. We identified 62 putative novel phylotypes. In recurrent aphthous ulcer lesions 57 phylotypes were detected, of which 11 were known species. Control samples had 38 phylotypes, five of which were already known. Only three species or phylotypes were abundant and common to both groups (Gemella haemolysans, Streptococcus mitis strain 209 and Streptococcus pneumoniae R6). One genus was found only in recurrent aphthous ulcer samples (Prevotella) corresponding to 16% of all lesion-derived clones.

CONCLUSION

The microbiota found in recurrent aphthous ulcers and in the control groups diverged markedly and the rich variety of genera found can provide a new starting point for individual qualitative and quantitative analyses of bacteria associated with this oral condition.

Bacterial colonization immediately after installation on oral titanium implants

BACKGROUND

Information on bacterial colonization immediately after dental implant insertion is limited.

AIMS

(1) To assess the early colonization on titanium implants immediately after placement and throughout the first 12 post-surgical weeks, (2) to compare the microbiota at interproximal subgingival implant and adjacent tooth sites.

MATERIAL AND METHODS

Subgingival plaque samples from implant and neighbouring teeth were studied by checkerboard DNA-DNA hybridization before surgery, 30 min after implant placement, and 1, 2, 4, 8, and 12 weeks after surgery.

RESULTS

Comparing bacterial loads at implant sites between 30 min after placement with 1-week data showed that only the levels of Veillonella parvula (P<0.05) differed with higher loads at week 1 post-surgically. Week 12 data demonstrated significantly higher bacterial loads for 15/40 species at tooth sites compared with pre-surgery (P-values varying between 0.05 and 0.01). Between the period immediately after surgery and 12 weeks at implant sites, 29/40 species was more commonly found at 12 weeks. Included among these bacteria at implant sites were Porphyromonas gingivalis (P<0.05), Tannerella forsythia, (P<0.01), and Treponema denticola (P<0.001). Immediately post-surgery 5.9% of implants, and 26.2% of teeth, and at week 12, 15% of implants, and 39.1% of teeth harbored Staphylococcus aureus. Comparing tooth and implant sites, significantly higher bacterial loads were found at tooth sites for 27/40 species after 30 min following implant placement. This difference increased to 35/40 species at 12 weeks post-surgically.

CONCLUSIONS

Bacterial colonization occurred within 30 min after implant placement. Early colonization patterns differed between implant and tooth surfaces.

A novel exclusion mechanism for carbon resource partitioning in Aggregatibacter actinomycetemcomitans

The bacterium Aggregatibacter actinomycetemcomitans is a common commensal of the human oral cavity and the putative causative agent of the disease localized aggressive periodontitis. A. actinomycetemcomitans is a slow-growing bacterium that possesses limited metabolic machinery for carbon utilization. This likely impacts its ability to colonize the oral cavity, where growth and community composition is mediated by carbon availability. We present evidence that in the presence of the in vivo relevant carbon substrates glucose, fructose, and lactate A. actinomycetemcomitans preferentially metabolizes lactate. This preference for lactate exists despite the fact that A. actinomycetemcomitans grows faster and obtains higher cell yields during growth with carbohydrates. The preference for lactate is mediated by a novel exclusion mechanism in which metabolism of lactate inhibits carbohydrate uptake. Coculture studies reveal that A. actinomycetemcomitans utilizes lactate produced by the oral bacterium Streptococcus gordonii, suggesting the potential for cross-feeding in the oral cavity.

Streptococcus oligofermentans inhibits Streptococcus mutans through conversion of lactic acid into inhibitory H2O2: a possible counteroffensive strategy for interspecies competition

The oral microbial flora contains over 500 different microbial species that often interact as a means to compete for limited space and nutritional resources. Streptococcus mutans, a major caries-causing pathogen, is a species which tends to interact competitively with other species in the oral cavity, largely due to its ability to generate copious quantities of the toxic metabolite, lactic acid. However, during a recent clinical study, we discovered a novel oral streptococcal species, Streptococcus oligofermentans, whose abundance appeared to be inversely correlated with that of S. mutans within dental plaque samples and thus suggested a possible antagonistic relationship with S. mutans. In this study, we used a defined in vitro interspecies interaction assay to confirm that S. oligofermentans was indeed able to inhibit the growth of S. mutans. Interestingly, this inhibitory effect was relatively specific to S. mutans and was actually enhanced by the presence of lactic acid. Biochemical analyses revealed that S. oligofermentans inhibited the growth of S. mutans via the production of hydrogen peroxide with lactic acid as the substrate. Further genetic and molecular analysis led to the discovery of the lactate oxidase (lox) gene of S. oligofermentans as responsible for this biological activity. Consequently, the lox mutant of S. oligofermentans also showed dramatically reduced inhibitory effects against S. mutans and also exhibited greatly impaired growth in the presence of the lactate produced by S. mutans. These data indicate that S. oligofermentans possesses the capacity to convert its competitor's main 'weapon' (lactic acid) into an inhibitory chemical (H(2)O(2)) in order to gain a competitive growth advantage. This fascinating ability may be an example of a counteroffensive strategy used during chemical warfare within the oral microbial community.

The division "Synergistes"

The "Synergistes" group of organisms are a phylogenetic cluster of Gram-negative anaerobes related to Synergistes jonesii, sufficiently distinct from all other phyla to be considered a distinct phylum or Division. They are widely distributed in nature although normally only a minor constituent of the bacterial community in each habitat. They have evolved to adapt to each habitat, and therefore exhibit a wide range of physiological and biochemical characteristics, although all cultivable taxa so far studied have the ability to degrade amino acids. They are found in the human mouth where they appear to be more numerous in tooth and gum disease than health. They have also been found in the human gut and soft tissue infections. Their role in human disease has yet to be established but improved knowledge of the characteristics that enable their identification should increase the likelihood of their recognition when present at diseased sites.

The in vivo dynamics of Streptococcus spp., Actinomyces naeslundii, Fusobacterium nucleatum and Veillonella spp. in dental plaque biofilm as analysed by five-colour multiplex fluorescence in situ hybridization

The formation and composition of dental plaque biofilm in vivo are important factors which influence the development of gingivitis, caries and periodontitis. Studying dental plaque biofilm in in vitro models can cause an oversimplification of the real conditions in the oral cavity. In this study, bovine enamel slabs were fixed in an individual acrylic appliance in situ to quantify dental plaque formation and composition using multiplex fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy. Each of the five oligonucleotide probes used for FISH was specific for either eubacteria or one of four frequently isolated bacterial constituents belonging to early and late colonizers of tooth surfaces. The thickness of formed biofilm increased from 14.9+/-5.0 microm after 1 day to 49.3+/-11.6 microm after 7 days. Streptococcus spp. were predominant in 1-day-old dental plaque and decreased significantly after 7 days (P=0.0061). Compared to the first day, Fusobacterium nucleatum decreased after 2 days and increased significantly after 7 days (P=0.0006). The decreases of Actinomyces naeslundii content on day 2 and day 7 were significant (P=0.0028). Changes in Veillonella spp. were not significant during the study period (P >0.05). The results showed that an in vivo observation period of 7 days was required to detect significant changes in Streptococcus spp. and F. nucleatum. The multiplex FISH used is suitable for analysing the dynamics of four important bacterial constituents in the oral biofilm in epidemiological studies.

Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry

Newly emergent infectious diseases are a global public health problem. The population dense regions of Southeast Asia are the epicenter of many emerging diseases, as evidenced by the outbreak of Nipah, SARS, avian influenza (H5N1), Dengue, and enterovirus 71 in this region in the past decade. Rapid identification, epidemiologic surveillance, and mitigation of transmission are major challenges in ensuring public health safety. Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI-MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. This approach is capable of automated analysis of more than 1,500 PCR reactions a day. It is applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens and will facilitate rapid characterization of known and emerging pathogens.

Phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections

Phylogenetic analysis of bacterial and archaeal 16S rRNA was used to examine polymicrobial communities within infected root canals of 20 symptomatic and 14 asymptomatic patients. Nucleotide sequences from approximately 750 clones amplified from each patient group with universal bacterial primers were matched to the Ribosomal Database Project II database. Phylotypes from 37 genera representing Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were identified. Results were compared to those obtained with species-specific primers designed to detect Prevotella intermedia, Porphyromonas gingivalis, Porphyromonas endodontalis, Peptostreptococcus micros, Enterococcus sp., Streptococcus sp., Fusobacterium nucleatum, Tannerella forsythensis and Treponema denticola. Since members of the domain Archaea have been implicated in the severity of periodontal disease, and a recent report confirms that archaea are present in endodontic infections, 16S archaeal primers were also used to detect which patients carried these prokaryotes, to determine if their presence correlated with severity of the clinical symptoms. A Methanobrevibacter oralis-like species was detected in one asymptomatic and one symptomatic patient. DNA from root canals of these two patients was further analysed using species-specific primers to determine bacterial cohabitants. Trep. denticola was detected in the asymptomatic but not the symptomatic patient. Conversely, Porph. endodontalis was found in the symptomatic but not the asymptomatic patient. All other species except enterococci were detected with the species-specific primers in both patients. These results confirm the presence of archaea in root canals and provide additional insights into the polymicrobial communities in endodontic infections associated with clinical symptoms.

Evolution of species interactions in a biofilm community

Biofilms are spatially structured communities of microbes whose function is dependent on a complex web of symbiotic interactions. Localized interactions within these assemblages are predicted to affect the coexistence of the component species, community structure and function, but there have been few explicit empirical analyses of the evolution of interactions. Here we show, with the use of a two-species community, that selection in a spatially structured environment leads to the evolution of an exploitative interaction. Simple mutations in the genome of one species caused it to adapt to the presence of the other, forming an intimate and specialized association. The derived community was more stable and more productive than the ancestral community. Our results show that evolution in a spatially structured environment can stabilize interactions between species, provoke marked changes in their symbiotic nature and affect community function.

Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia

Trauma intensive care unit (TICU) patients requiring mechanical respiratory support frequently develop ventilator-associated pneumonia (VAP). Oral and oropharyngeal bacteria are believed to be responsible for many cases of VAP, but definitive evidence of this relationship is lacking. Earlier studies used conventional culture-based methods for identification of bacterial pathogens, but these methods are insufficient, as some bacteria may be uncultivable or difficult to grow. The purpose of this study was to use a culture-independent molecular approach to analyze and compare the bacterial species colonizing the oral cavity and the lungs of TICU patients who developed VAP. Bacterial samples were acquired from the dorsal tongue and bronchoalveolar lavage fluid of 16 patients. Bacterial DNA was extracted, and the 16S rRNA genes were PCR amplified, cloned into Escherichia coli, and sequenced. The sequencing data revealed the following: (i) a wide diversity of bacterial species in both the oral and pulmonary sites, some of them novel; (ii) known and putative respiratory pathogens colonizing both the oral cavity and lungs of 14 patients; and (iii) a number of bacterial pathogens (e.g., Dialister pneumosintes, Haemophilus segnis, Gemella morbillorum, and Pseudomonas fluorescens) in lung samples that had not been reported previously at this site when culture-based methods were used. Our data indicate that the dorsal surface of the tongue serves as a potential reservoir for bacterial species involved in VAP. Furthermore, it is clear that the diversity of bacterial pathogens for VAP is far more complex than the current literature suggests.

Molecular analysis of human forearm superficial skin bacterial biota

The microbial ecology of human skin is complex, but little is known about its species composition. We examined the diversity of the skin biota from the superficial volar left and right forearms in six healthy subjects using broad-range small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones. For the initial 1,221 clones analyzed, 182 species-level operational taxonomic units (SLOTUs) belonging to eight phyla were identified, estimated as 74.0% [95% confidence interval (C.I.), approximately 64.8-77.9%] of the SLOTUs in this ecosystem; 48.0 +/- 12.2 SLOTUs were found in each subject. Three phyla (Actinobacteria, Firmicutes, and Proteobacteria) accounted for 94.6% of the clones. Most (85.3%) of the bacterial sequences corresponded to known and cultivated species, but 98 (8.0%) clones, comprising 30 phylotypes, had <97% similarity to prior database sequences. Only 6 (6.6%) of the 91 genera and 4 (2.2%) of the 182 SLOTUs, respectively, were found in all six subjects. Analysis of 817 clones obtained 8-10 months later from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numbering 65). Only four (3.4%) of the 119 genera (Propionibacteria, Corynebacteria, Staphylococcus, and Streptococcus) were observed in each subject tested twice, but these genera represented 54.4% of all clones. These results show that the bacterial biota in normal superficial skin is highly diverse, with few well conserved and well represented genera, but otherwise low-level interpersonal consensus.

Targeted profiling of oral bacteria in human saliva and in vitro biofilms with quantitative real-time PCR

An in vitro plaque model based on the use of human salivary bacteria and tooth-like surfaces was previously developed for studying the formation of oral biofilm and its use for pre-clinical testing of candidate antimicrobial or antiplaque agents. In this study, a quantitative Taqman PCR assay (QPCR) was developed to compare the bacterial compositions of in vitro biofilms to parent saliva samples, and to determine the relative contributions of different species in the formation of the oral biofilm. In addition, the growth inhibition of saliva-derived plaque was evaluated by chlorhexidine. With this assay, which consisted of primer/probe sets targeting either 16S rDNA sequences present in public databases or cloned ribosomal intergenic spacer region (ISR) sequences, 15 oral bacteria derived from saliva as well as those that were responsible for biofilm formation in an in vitro plaque model were rapidly identified and quantified. Among the target organisms were Actinobacillus actinomycetemcomitans, Eikenella corrodens, Fusobacterium nucleatum, Lactobacillus acidophilus, Micromonas micros, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus mutans, Streptococcus sobrinus, Tannerella forsythensis, and Veillonella parvula. Primer and probe sets developed were both sensitive and specific. The relative profiles of a number of bacteria in 45-h-old biofilms were determined and, when compared to saliva samples, it was found that most of the bacteria identified in saliva also populated the in vitro plaque, including some anaerobes. Brief exposure of biofilms to chlorhexidine resulted in significant losses in viability. This new broad spectrum QPCR assay in combination with the in vitro plaque model will be of significant value in the quantitative study of the microbial composition of human saliva, saliva-derived plaque, and pre-clinical evaluation of potential antimicrobial and antiplaque molecules.

Denaturing gradient gel electrophoresis as a diagnostic tool in periodontal microbiology

Bacteria play an important role in the initiation and progression of periodontal diseases and are part of a biofilm, which can contain over 100 different species. The aim of the present study was to show the potential of denaturing gradient gel electrophoresis (DGGE) as a tool for the detection of clinically relevant species and to compare the results of detection by DGGE with those by PCR and culturing. Hybridization of the bands from the DGGE profiles with species-specific probes was developed to confirm the band positions in the marker obtained with reference strains. The sensitivities of DGGE compared to those of cultivation for the detection of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythensis were 100, 100, 88, and 100%, respectively; and the sensitivities of DGGE compared to those of PCR were 100, 90, 88, and 96%, respectively. DGGE as a diagnostic tool could easily be extended to other species, as shown for Treponema denticola, which could be detected in 48% of the samples. Three different groups of A. actinomycetemcomitans serotypes could be distinguished by DGGE (i.e., a group comprising serotypes a, d, e, and f; a group comprising serotype b; and a group comprising serotype c). Amplicons from P. gingivalis and T. denticola migrated to the same position in the gel, and P. intermedia produced multiple bands. In the present study we show that the DGGE profiles represent clinically relevant species which can be detected by hybridization with species-specific probes. With DGGE, large numbers of samples can be analyzed for different species simultaneously, and DGGE may be a good alternative in periodontal microbial diagnostics.

Molecular approaches to the role of the microbiota in inflammatory bowel disease

The microbiota plays a crucial role in experimental models of inflammatory bowel disease, but the exact mechanisms of its effects are unknown. These studies took two molecular approaches to this question. The first used amplification of the 16s ribosomal DNA to define microbial diversity in the colon. Although there were differences in colitic and non-colitic mice, we could not determine whether this was primary or secondary to the disease. The second approach used serologic expression cloning to identify the microbial proteins stimulating the pathogenic immune response. Previously unknown microbial flagellins were the dominant cluster of antigens identified. About half of the sera from patients with Crohn's disease have IgG antibodies to these flagellins.

Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions

Psoriasis, a common cutaneous disease of unknown etiology, may be triggered by infections, including those due to fungi. Since the fungal community of human skin is poorly characterized, we aimed to analyze the mycological microbiota in healthy skin and psoriatic lesions. Twenty-five skin samples from five healthy subjects (flexor forearm) and three patients with psoriasis were analyzed using broad-range 18S ribosomal DNA (rDNA) and 5.8S rDNA/internal transcribed spacer 2 (ITS2) Malassezia-specific PCR primers. Broad-range PCR analysis indicated that most organisms resembled Malassezia. Malassezia-specific 5.8S/ITS2 analysis of 1,374 clones identified five species and four unknown phylotypes, potentially representing new species. The species distribution appears largely host specific and conserved in different sites of healthy skin. In three subjects, the Malassezia microbiota composition appeared relatively stable over time. Samples of Malassezia microbiota from healthy skin and psoriatic lesions were similar in one patient but substantially different in two others. These data indicate the predominance of Malassezia organisms in healthy human skin, host-specific variation, stability over time, and as yet, no consistent patterns differentiating psoriatic skin from healthy skin.

Genetic profiling of the oral microbiota associated with severe early-childhood caries

The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (n = 12) (42 +/- 3.7) than in the S-ECC children (n = 8) (35 +/- 4.3); the difference was statistically significant (P = 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (P = 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.