Bacterial diversity within the human subgingival crevice

Effects of sequential infections of Caenorhabditis elegans with Staphylococcus aureus and Proteus mirabilis

Caenorhabditis elegans can be used to study the dynamics of polymicrobial infections, specifically those between Gram-positive and Gram-negative bacteria. With C. elegans, Proteus mirabilis acts as an opportunistic pathogen and does not kill this host. Hence, in the present study, C. elegans was immunochallenged by pre-infecting it with the pathogen Staphylococcus aureus in order to study the subsequent effect of P. mirabilis on the host. It was found that 12 hrs of S. aureus and 80 hrs of subsequent P. mirabilis infection significantly reduced the life span of exposed C. elegans by 80%. However, preinfection with S. aureus for 8 and 4 hrs reduced the life span of C. elegans by only 60 and 30%, respectively. Further, there was greater production of reactive oxygen species in the sequentially infected samples than in the S. aureus and P. mirabilis controls. Real time PCR analysis indicated regulation of candidate immune regulatory genes, lysozyme (lys-7), CUB-like proteins (F08G5.6), neuropeptide-like factors (nlp-29), transcription factors of mitogen-activated protein kinase (ATF-7) and daf-2-daf-16 (daf-16), insulin-like signaling pathways and C-type lectin (clec-60 and clec-87) family members during S. aureus and subsequent P. mirabilis-mediated infections, indicating possible roles of, and contributions by, the above factors during host immune responses against these sequential infections. The present findings demonstrate that S. aureus infections increase the vulnerability of the C. elegans host by subverting its immune system, which then permits the opportunistic pathogen P. mirabilis to be pathogenic to this host.

Wound biofilms: lessons learned from oral biofilms

Biofilms play an important role in the development and pathogenesis of many chronic infections. Oral biofilms, more commonly known as dental plaque, are a primary cause of oral diseases including caries, gingivitis, and periodontitis. Oral biofilms are commonly studied as model biofilm systems as they are easily accessible; thus, biofilm research in oral diseases is advanced with details of biofilm formation and bacterial interactions being well elucidated. In contrast, wound research has relatively recently directed attention to the role biofilms have in chronic wounds. This review discusses the biofilms in periodontal disease and chronic wounds with comparisons focusing on biofilm detection, biofilm formation, the immune response to biofilms, bacterial interaction, and quorum sensing. Current treatment modalities used by both fields and future therapies are also discussed.

Evaluation of a nonthermal plasma needle to eliminate ex vivo biofilms in root canals of extracted human teeth

AIM

To evaluate the efficacy of a nonthermal plasma (NTP) at atmospheric pressure on ex vivo biofilm in root canals of extracted teeth.

METHODOLOGY

Intracanal contents from three teeth with root canal infections were collected, pooled and grown in thirty-five microCT-mapped root canals of extracted and instrumented human teeth. One group of teeth was treated with NTP, another with 6% NaOCl and one set was left untreated. The intracanal contents from twenty-seven teeth (nine teeth in each group) were plated on agar and colony forming units were determined. Parametric test of one-way analysis of variance (anova) was used to analyse statistical significance. The remaining teeth were cut open, stained with LIVE/DEAD(®) and examined with confocal laser scanning microscopy.

RESULTS

The untreated root canals were covered with biofilm of varying thickness. Treatment with nonthermal plasma decreased the number of viable bacteria in biofilms by one order of magnitude, whilst the NaOCl control achieved a reduction of more than four magnitudes. Both the NTP and the NaOCl treatment results were significantly different from the negative control (P < 0.05).

CONCLUSION

The nonthermal plasma displayed antimicrobial activity against endodontic biofilms in root canals, but was not as effective as the use of 6% NaOCl.

Organo-selenium-containing dental sealant inhibits bacterial biofilm

Oral bacteria, including Streptococcus mutans and Streptococcus salivarius, contribute to tooth decay and plaque formation; therefore, it is essential to develop strategies to prevent dental caries and plaque formation. We recently showed that organo-selenium compounds covalently attached to different biomaterials inhibited bacterial biofilms. Our current study investigates the efficacy of an organo-selenium dental sealant (SeLECT-Defense(TM) sealant) in inhibiting S. mutans and S. salivarius biofilm formation in vitro. The organo-selenium was synthesized and covalently attached to dental sealant material via standard polymer chemistry. By colony-forming unit (CFU) assay and confocal microscopy, SeLECT-Defense(TM) sealant was found to completely inhibit the development of S. mutans and S. salivarius biofilms. To assess the durability of the anti-biofilm effect, we soaked the SeLECT-Defense(TM) sealant in PBS for 2 mos at 37°C and found that the biofilm-inhibitory effect was not diminished after soaking. To determine if organo-selenium inhibits bacterial growth under the sealant, we placed SeLECT-Defense sealant over a lawn of S. mutans. In contrast to a control sealant, SeLECT-Defense(TM) sealant completely inhibited the growth of S. mutans. These results suggest that the inhibitory effect of SeLECT-Defense(TM) sealant against S. mutans and S. salivarius biofilms is very effective and durable.

Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study

This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/ phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

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

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

The Human Microbiome Project: a community resource for the healthy human microbiome

This manuscript describes the NIH Human Microbiome Project, including a brief review of human microbiome research, a history of the project, and a comprehensive overview of the consortium's recent collection of publications analyzing the human microbiome.

Hydroxy decenoic acid down regulates gtfB and gtfC expression and prevents Streptococcus mutans adherence to the cell surfaces

BACKGROUND

10-Hydroxy-2-decenoic acid, an unsaturated fatty acid is the most active and unique component to the royal jelly that has antimicrobial properties. Streptococcus mutans is associated with pathogenesis of oral cavity, gingivoperiodontal diseases and bacteremia following dental manipulations. In the oral cavity, S. mutans colonize the soft tissues including tongue, palate, and buccal mucosa. When considering the role of supragingival dental plaque in caries, the proportion of acid producing bacteria (particularly S. mutans), has direct relevance to the pathogenicity of the plaque. The genes that encode glucosyltransferases (gtfs) especially gtfB and gtfC are important in S. mutans colonization and pathogenesis. This study investigated the hydroxy-decenoic acid (HDA) effects on gtfB and gtfC expression and S. mutans adherence to cells surfaces.

METHODS

Streptococcus mutans was treated by different concentrations of HPLC purified HDA supplied by Iran Beekeeping and Veterinary Association. Real time RT-PCR and western blot assays were conducted to evaluate gtfB and gtfC genes transcription and translation before and after HDA treatment. The bacterial attachment to the cell surfaces was evaluated microscopically.

RESULTS

500 μg ml-1 of HDA inhibited gtfB and gtfC mRNA transcription and its expression. The same concentration of HDA decreased 60% the adherence of S. mutans to the surface of P19 cells.

CONCLUSION

Hydroxy-decenoic acid prevents gtfB and gtfC expression efficiently in the bactericide sub-concentrations and it could effectively reduce S. mutans adherence to the cell surfaces. In the future, therapeutic approaches to affecting S. mutans could be selective and it's not necessary to put down the oral flora completely.

Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma

BACKGROUND

Bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. We investigated the association of oral bacteria in oral squamous cell carcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). By using culture-independent 16S rRNA approaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples.

RESULTS

DGGE fingerprints showed variations in the band intensity profiles within non-tumor and tumor tissues of the same patient and among the two groups. The clonal analysis indicated that from a total of 1200 sequences characterized, 80 bacterial species/phylotypes were detected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library, 12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species, Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius, Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignava and Streptococcus parasanguinis I were highly associated with tumor site where as Granulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius was present in 70% of both non-tumor and tumor sites.

CONCLUSIONS

The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumor and tumor sites of OSCC subjects indicated a shift in bacterial colonization. These most prevalent or unique bacterial species/phylotypes present in tumor tissues may be associated with OSCC and needs to be further investigated with a larger sample size.

Using high throughput sequencing to explore the biodiversity in oral bacterial communities

High throughput sequencing of 16S ribosomal RNA gene amplicons is a cost-effective method for characterization of oral bacterial communities. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then characterized the bacterial communities in saliva and buccal mucosa of five healthy subjects to investigate the power of high throughput sequencing in revealing their diversity and biogeography patterns. Mock community analysis showed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities found a total of 455 OTUs (0.3% dissimilarity) with only 78 of these present in all subjects. We demonstrate that this variability was partly the result of incomplete richness coverage even at great sequencing depths, and so comparing communities by their structure was more effective than comparisons based solely on membership. With respect to oral biogeography, we found inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident at very low sequencing depths and were mostly caused by the abundance of Streptococcus mitis and Gemella haemolysans in mucosa. In summary, we present an experimental and data analysis framework that will facilitate design and interpretation of pyrosequencing-based studies. Despite challenges associated with this technique, we demonstrate its power for evaluation of oral diversity and biogeography patterns.

Bioadhesion: a review of concepts and applications

Bioadhesion refers to the phenomenon where natural and synthetic materials adhere to biological surfaces. An understanding of the fundamental mechanisms that govern bioadhesion is of great interest for various researchers who aim to develop new biomaterials, therapies and technological applications such as biosensors. This review paper will first describe various examples of the manifestation of bioadhesion along with the underlying mechanisms. This will be followed by a discussion of some of the methods for the optimization of bioadhesion. Finally, nanoscale and macroscale characterization techniques for the efficacy of bioadhesion and the analysis of failure surfaces are described.

Quantification of subgingival bacterial pathogens at different stages of periodontal diseases

Anaerobic gram-negative oral bacteria such as Treponema denticola, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Campylobacter rectus, and Fusobacterium nucleatum are closely associated with periodontal diseases. We measured the relative population (bacterial levels) of these oral pathogens in subgingival tissues of patients at different stages of Korean chronic periodontal diseases. We divided the individuals into those with chronic gingivitis (G), moderate periodontitis (P1), severe periodontitis (P2), and normal individuals (N) (n = 20 for each group) and subgingival tissue samples were collected. We used real-time PCR with TaqMan probes to evaluate the change of periodontal pathogens among different stages of periodontitis. Bacterial levels of A. actinomycetemcomitans and C. rectus are significantly increased in individuals with chronic gingivitis and moderate periodontitis, but unchanged in severe periodontitis patients. These results suggest that analyzing certain bacterial levels among total oral pathogens may facilitate understanding of the role of periodontal bacteria in the early stages of periodontitis.

Microbial profiles in saliva from children with and without caries in mixed dentition

OBJECTIVE

The purpose of this study was to determine the bacterial profiles in saliva of the isolated children for studying caries etiology.

MATERIALS AND METHODS

  Samples were collected from isolated children from 6 to 8years old including 20 caries-free (dmfs=0) (healthy) and 30 caries-active individuals (dmfs>8) (patients). 16S rRNA genes were amplified by PCR from bacterial DNA of saliva sample and labeled via incorporation of Cy3-dCTP in second nested PCR. After hybridization of labeled amplicons on HOMIM, the microarray slides were scanned and original data acquired from professional software.

RESULTS

Collectively, 94 bacterial species or clusters representing six bacterial phyla and 30 genera were detected. A higher bacterial diversity was observed in patients than in healthy samples. Statistical analyses revealed eight species or clusters were detected more frequently in diseased patients than in healthy samples, while six different species were detected more frequently in healthy as compared to diseased patients.

CONCLUSION

The diversity of microbe within saliva derived from isolated population increased in caries-active status, and there are some bacteria in salivary flora can be as candidate biomarkers for caries prognosis in mixed dentition. The imbalances in the resident microflora may be the ultimate mechanism of dental caries.

Extravaginal reservoirs of vaginal bacteria as risk factors for incident bacterial vaginosis

BACKGROUND

Bacterial vaginosis (BV) represents shifts in microbiota from Lactobacillus spp. to diverse anaerobes. Although antibiotics relieve symptoms and temporarily eradicate BV-associated bacteria (BVAB), BV usually recurs. We investigated the role of extravaginal BVAB reservoirs in recurrence.

METHODS

Risks for BV acquisition over the course of 1 year were defined. DNA in vaginal, anal, and oral swab samples from enrollment was subjected to quantitative polymerase chain reaction assays targeting 16S ribosomal RNA genes of Gardnerella vaginalis, Lactobacillus crispatus, BVAB1, BVAB2, BVAB3, Megasphaera spp., Lactobacillus jensenii, and Leptotrichia/Sneathia spp. A case-control approach analyzed BVAB detection at enrollment for case patients (BV acquisition) versus controls (none).

RESULTS

Of 239 women enrolled without BV, 199 were seen in follow-up, and 40 experienced BV; 15 had all samples for analysis. Detection of G. vaginalis in oral cavity or anal samples and Leptotrichia/Sneathia spp. in anal samples was more common at enrollment among case patients, who also had higher concentrations of these bacteria and Megasphaera relative to 30 controls at each site. In contrast, L. crispatus was detected more frequently in anal samples among controls.

CONCLUSIONS

Women who acquire BV are more likely have previous colonization of extravaginal reservoirs with some BVAB, and less likely to have L. crispatus, suggesting that BVAB may be acquired vaginally from extravaginal reservoirs.

Effects of nicotine on the growth and protein expression of Porphyromonas gingivalis

Tobacco smoking is considered one of the most significant environmental risk factors for destructive periodontal disease. The effect of smoking on periodontopathic microbiota has not yet been elucidated, as previous studies failed to identify a concrete relationship between periodontopathic microorganisms and smoking. However, it is likely that smoking, as an environmental stress factor, may affect the behavior of dental plaque microorganisms, ultimately leading to alteration of the host-parasite interaction. The goal of this study was to examine the effect of nicotine, a major component of tobacco, on the growth and protein expression of the crucial periodontal pathogen Porphyromonas gingivalis. The growth of P. gingivalis 381 was measured after bacterial cells were cultivated in liquid broth containing various nicotine concentrations. First, P. gingivalis cells were allowed to grow in the presence of a single dose of nicotine (the single exposure protocol) at 0, 1, 2, 4, and 8 mg/L, respectively. Second, P. gingivalis cells were exposed to five consecutive doses of nicotine (the multiple exposure protocol) at 0, 1, 2, and 4 mg/L, respectively. Bacterial growth was measured by optical density and protein expression was analyzed by SDS-PAGE and 2-D gel electrophoresis. In the single nicotine exposure protocol, it was observed that the growth of P. gingivalis 381 was inhibited by nicotine in a dose-dependent manner. In the multiple nicotine exposure protocol, the growth rate of P. gingivalis increased with each subsequent nicotine exposure, even though bacterial growth was also inhibited in a dose dependent fashion. SDS-PAGE and 2-D gel electrophoresis analyses revealed a minor change in the pattern of protein expression, showing differences in proteins with low molecular weights (around 20 kDa) on exposure to nicotine. The results of this study suggest that nicotine exerts an inhibitory effect on the growth of P. gingivalis, and has a potential to modulate protein expression in P. gingivalis.

Optimizing culture methods for diagnosis of prosthetic joint infections: a summary of modifications and improvements reported since 1995

Improving diagnosis of prosthetic joint infections (PJIs) has become an increasing challenge due to a steadily rising number of patients with prosthetic implants. Based on a systematic literature search we have ascertained the evidence base for improvement of culture diagnosis. We searched PubMed/MEDLINE using the medical subject heading (MeSH) 'prosthesis-related infections' 1995 through 2010 without further restrictions. An analogous search was conducted for ISI Web of Knowledge. A total of 1409 reports were screened for original results, obtained by methods described in sufficient detail to make replication possible. We gave priority to methods for sample preparation, culture media, culture methods and incubation time. Clinical sensitivity and specificity were calculated where possible. We found evidence to support superiority of cultures obtained from the diluent after sonication of prosthetic implants in comparison with culturing tissue biopsies. Sonication parameters and accessory steps have been studied extensively, and thresholds for significant growth have been defined. Conversely, methods for processing of soft tissue biopsies have been studied to a limited extent. Culture of synovial fluid in blood culture vials has been shown to be more sensitive (90-92 %) than intraoperative swab cultures (68-76 %) and tissue cultures (77-82 %). Formal evaluation of agar media for culturing PJI specimens seemed to be lacking. The polymicrobial nature of PJIs supports the routine use of an assortment of media suitable for recovery of fastidious, slow-growing, anaerobic and sublethally damaged bacteria. A number of studies supported an incubation period for up to 14 days. Although we identified evidence-based improvements of culture methods, there is a need for more studies especially with regard to tissue biopsies. Culturing remains an important means to identify and characterize pathogenic micro-organisms and supplements the increasing number of culture-independent assays.

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

BACKGROUND

Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing.

METHODS

Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR.

RESULTS

The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results.

CONCLUSIONS

This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis.

New approaches for isolation of previously uncultivated oral bacteria

A significant number of microorganisms from the human oral cavity remain uncultivated. This is a major impediment to the study of human health since some of the uncultivated species may be involved in a variety of systemic diseases. We used a range of innovations previously developed to cultivate microorganisms from the human oral cavity, focusing on anaerobic species. These innovations include (i) in vivo cultivation to specifically enrich for species actively growing in the oral cavity (the "minitrap" method), (ii) single-cell long-term cultivation to minimize the effect of fast-growing microorganisms, and (iii) modifications of conventional enrichment techniques, using media that did not contain sugar, including glucose. To enable cultivation of obligate anaerobes, we maintained strict anaerobic conditions in most of our cultivation experiments. We report that, on a per cell basis, the most successful recovery was achieved using minitrap enrichment (11%), followed by single-cell cultivation (3%) and conventional plating (1%). Taxonomically, the richest collection was obtained using the single-cell cultivation method, followed by minitrap and conventional enrichment, comprising representatives of 13, 9, and 4 genera, respectively. Interestingly, no single species was isolated by all three methods, indicating method complementarity. An important result is the isolation and maintenance in pure culture of 10 strains previously only known by their molecular signatures, as well as representatives of what are likely to be three new microbial genera. We conclude that the ensemble of new methods we introduced will likely help close the gap between cultivated and uncultivated species from the human oral cavity.

Contribution of host genotype to the composition of health-associated supragingival and subgingival microbiomes

AIM

Periodontitis and caries are two of the most prevalent diseases to affect humans, however; the individual susceptibility to these diseases varies significantly in the population. The aim of this investigation, therefore, was to examine the influence of host genotype on the composition of health-associated supragingival and subgingival microbiomes.

MATERIALS AND METHODS

Subgingival and supragingival plaque was collected from orally and systemically healthy adult monozygotic and dizygotic twin pairs. Zygosity was determined by multiplexed PCR amplification of 13 short tandem repeats. Terminal restriction fragment length polymorphism was used for bacterial community profiling. The number of species shared by the twin pairs as well as the similarity of the microbial communities between the twins was computed and compared using two-sample t-test

RESULTS

There was no difference in the number of species shared by the twin pairs as well as the similarity of the microbial communities between the twin dyads. Age was not a modifier of genetic influence on these microbial parameters. There was no difference between monozygotic and dizygotic twin pairs in the correlation between supragingival and subgingival community similarity.

CONCLUSION

The contributory role of host genotype, if any, is not apparent on an established, health-associated oral microbial community.

Characterization of antibiotic resistance determinants in oral biofilms

Oral biofilms contain numerous antibiotic resistance determinants that can be transferred within or outside of the oral cavity. The aim of this study was to evaluate the prevalence and the relative level of antibiotic resistance determinants from oral biofilms. Oral biofilm samples that were collected from healthy subjects and periodontitis patients were subjected to qualitative and quantitative analyses for selected antibiotic resistance determinants using PCR. The prevalence of tet(Q), tet(M), cfxA, and bla ( TEM ) was very high both in the patient and the healthy subject group, with a tendency toward higher values in the patient group, with the exception of erm(F), which was more prevalent in the healthy group. The two extended spectrum β-lactam (ESBL) resistance determinants bla ( SHV ) and bla ( TEM ) showed a dramatic difference, as bla ( TEM ) was present in all of the samples and bla ( SHV ) was not found at all. The aacA-aphD, vanA, and mecA genes were rarely detected, suggesting that they are not common in oral bacteria. A quantitative PCR analysis showed that the relative amount of resistance determinants present in oral biofilms of the patient group was much greater than that of the healthy group, exhibiting 17-, 13-, 145-, and 3-fold increases for tet(Q), tet(M), erm(F), and cfxA, respectively. The results of this study suggest that the oral antibiotic resistome is more diverse and abundant in periodontitis patients than in healthy subjects, suggesting that there is a difference in the diversity and distribution of antibiotic resistance in oral biofilms associated with health and disease.

Novel sensitive real-time PCR for quantification of bacterial 16S rRNA genes in plasma of HIV-infected patients as a marker for microbial translocation

We developed a real-time PCR to quantify 16S rRNA gene levels in plasma from HIV-infected patients as a marker of microbial translocation. The assay uses shrimp nuclease (SNuc) to eliminate DNA contamination, giving high sensitivity and low variability. The 16S rRNA gene levels measured in plasma from HIV patients correlated significantly with lipopolysaccharide levels.

Bacterial diversity of subgingival plaque in 6 healthy Chinese individuals

The subgingival microbial ecology is complex, and little is known regarding its bacteria species composition in healthy Chinese individuals. This study aimed to identify the subgingival microbiota from 6 healthy Chinese subjects. Subgingival samples from 6 volunteers were collected, the 16S rRNA gene was amplified using broad-range bacterial primers, and clone libraries were constructed. For the initial 2,439 sequences analyzed, 383 species-level operational taxonomic units (SLOTUs) belonging to seven phyla were identified, estimated as 51% [95% confidence interval (CI) 44-55] of the SLOTUs in this ecosystem. Most (85%) of the bacterial sequences, falling into 228 types of species, corresponded to known and cultivated species. However, 146 (6%) sequences, comprising 104 phylotypes, had <97% similarity to prior database sequences. Ten bacterial genera were conserved among all 6 individuals, comprising 2,000 (82%) of the 2,439 clones analyzed. Ten species were noted in all of the 6 subjects, comprising 1,435 (58.8%) of the 2,439 clones. Streptococcus infantis was the species most frequently cloned. Furthermore, certain species which may participate in the pathogenesis of periodontal disease were present in the 6 subjects. Although the initial subgingival plaque community of each subject was unique in terms of diversity and composition, 10 common key species were found in the 6 Chinese individuals. These ten species of bacteria in the human subgingival plaque in the 6 healthy individuals may be key species which, to some extent, affect periodontal health. Destruction of these key species in subgingival bacteria may break the microbiota balance and may easily lead to over-breeding conditions resulting in pathogenic oral disease.

Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing

Pyrosequencing of 16S rRNA genes allows for in-depth characterization of complex microbial communities. Although it is known that primer selection can influence the profile of a community generated by sequencing, the extent and severity of this bias on deep-sequencing methodologies is not well elucidated. We tested the hypothesis that the hypervariable region targeted for sequencing and primer degeneracy play important roles in influencing the composition of 16S pyrotag communities. Subgingival plaque from deep sites of current smokers with chronic periodontitis was analyzed using Sanger sequencing and pyrosequencing using 4 primer pairs. Greater numbers of species were detected by pyrosequencing than by Sanger sequencing. Rare taxa constituted nearly 6% of each pyrotag community and less than 1% of the Sanger sequencing community. However, the different target regions selected for pyrosequencing did not demonstrate a significant difference in the number of rare and abundant taxa detected. The genera Prevotella, Fusobacterium, Streptococcus, Granulicatella, Bacteroides, Porphyromonas and Treponema were abundant when the V1–V3 region was targeted, while Streptococcus, Treponema, Prevotella, Eubacterium, Porphyromonas, Campylobacer and Enterococcus predominated in the community generated by V4–V6 primers, and the most numerous genera in the V7–V9 community were Veillonella, Streptococcus, Eubacterium, Enterococcus, Treponema, Catonella and Selenomonas. Targeting the V4–V6 region failed to detect the genus Fusobacterium, while the taxa Selenomonas, TM7 and Mycoplasma were not detected by the V7–V9 primer pairs. The communities generated by degenerate and non-degenerate primers did not demonstrate significant differences. Averaging the community fingerprints generated by V1–V3 and V7–V9 primers providesd results similar to Sanger sequencing, while allowing a significantly greater depth of coverage than is possible with Sanger sequencing. It is therefore important to use primers targeted to these two regions of the 16S rRNA gene in all deep-sequencing efforts to obtain representational characterization of complex microbial communities.

Does routine analysis of subgingival microbiota in periodontitis contribute to patient benefit?

In clinical periodontology it is common practice to sample subgingival plaque from periodontitis patients and to search for the presence of alleged periodontal pathogens using routine laboratory techniques such as culture, DNA-DNA hybridization or real-time PCR. Usually, special attention is given to the recognition of 'red complex' microorganisms and to Aggregatibacter actinomycetemcomitans. Recently, molecular open-ended techniques have been introduced which are distinct from the more 'classical' approaches in that they do not preselect for certain species. In this study, we investigated to what extent the outcome of these techniques has changed our insight into the composition of the subgingival microbiota and whether this has consequences on clinical decision making. The open-ended approaches showed that the composition of subgingival plaque is much more complex than previously thought. Next to the 'classical' putative periodontal pathogens, several non-culturable and fastidious species are now recognized as being associated with periodontitis, thus enlarging the group of suspected periodontal pathogens. We conclude that routine analyses of subgingival plaque in the clinic are not necessarily of benefit to the patient.

Comparison of microbial diversity of edible flowers and basil grown with organic versus conventional methods

The consumption and use of edible flowers as food is growing; however, no study has been conducted to evaluate their role in the cause of food-borne illness or in food safety. Recent food-borne outbreaks traced to fresh herbs have raised concern about their processing and handling. Basil, one of the most commonly used fresh herbs, has been identified as a source of food-borne illness. Baseline assessments of microflora were performed, and the microbial diversity between growing methods (organic vs. conventional) was compared. DNA sequencing was used to identify the microbial flora present on fresh edible flower and basil samples. The most predominant species identified were Enterobacter hormaechei (10%), Acinetobacter calcoaceticus (10%), Enterobacter ludwigii (10%), Enterobacter asburiae (6%), and Enterobacter cowanii (6%). Pseudomonas aeruginosa (6%), Salmonella enterica (6%), and Bacillus amyloliquefaciens (2%) were also isolated. Phylogenetic analysis showed that most species of isolated bacteria belonged to the phyla Gammaproteobacteria (81.2%) and Firmicutes (18.8%). Statistical analysis, diversity index for species richness, and lineage-per-time plots showed that for basil, organically grown samples had a higher microbial diversity than conventionally grown samples. Edible flowers and basil are often grown using organic methods and are commonly consumed raw without any washing or cooking, to preserve aesthetic value, but these practices may pose a potential risk for food-borne illness. The baseline assessment, together with phylogenetic and statistical analyses, indicated possible microbial contamination in edible flowers and basil. The use of statistical estimation of molecular diversity based on the 16S rRNA sequences and lineage-per-time plots with phylogenetic analysis well served as a means for comparing microbial diversity in food samples between the growing methods (organic vs. conventional).

Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing

Human dental plaque is a complex microbial community containing an estimated 700 to 19,000 species/phylotypes. Despite numerous studies analysing species richness in healthy and diseased human subjects, the true genomic composition of the human dental plaque microbiota remains unknown. Here we report a metagenomic analysis of a healthy human plaque sample using a combination of second-generation sequencing platforms. A total of 860 million base pairs of non-human sequences were generated. Various analysis tools revealed the presence of 12 well-characterized phyla, members of the TM-7 and BRC1 clade, and sequences that could not be classified. Both pathogens and opportunistic pathogens were identified, supporting the ecological plaque hypothesis for oral diseases. Mapping the metagenomic reads to sequenced reference genomes demonstrated that 4% of the reads could be assigned to the sequenced species. Preliminary annotation identified genes belonging to all known functional categories. Interestingly, although 73% of the total assembled contig sequences were predicted to code for proteins, only 51% of them could be assigned a functional role. Furthermore, ~2.8% of the total predicted genes coded for proteins involved in resistance to antibiotics and toxic compounds, suggesting that the oral cavity is an important reservoir for antimicrobial resistance.

Oral infections and antibiotic therapy

Oral infections commonly originate from an odontogenic source in adults and from tonsil and lymphatic sources in children. Odontogenic infections arise from advanced dental caries or periodontal disease. Oral trauma, radiation injury, chemotherapy mucositis, salivary gland infection, lymph node abscess, and postoperative infection are potential nonodontogenic sources of infections that could potentially be life threatening. This article reviews the serious nature and potential danger that exists from oral infection and the antibiotics available to treat them are reviewed. Successful treatment requires an understanding of the microflora, the regional anatomy, the disease process, the treatment methods available, and interdisciplinary team collaboration.

Oral multispecies biofilm development and the key role of cell-cell distance

Growth of oral bacteria in situ requires adhesion to a surface because the constant flow of host secretions thwarts the ability of planktonic cells to grow before they are swallowed. Therefore, oral bacteria evolved to form biofilms on hard tooth surfaces and on soft epithelial tissues, which often contain multiple bacterial species. Because these biofilms are easy to study, they have become the paradigm of multispecies biofilms. In this Review we describe the factors involved in the formation of these biofilms, including the initial adherence to the oral tissues and teeth, cooperation between bacterial species in the biofilm, signalling between the bacteria and its role in pathogenesis, and the transfer of DNA between bacteria. In all these aspects distance between cells of different species is integral for oral biofilm growth.

Inhibition of Streptococcus mutans biofilm formation by Streptococcus salivarius FruA

The oral microbial flora consists of many beneficial species of bacteria that are associated with a healthy condition and control the progression of oral disease. Cooperative interactions between oral streptococci and the pathogens play important roles in the development of dental biofilms in the oral cavity. To determine the roles of oral streptococci in multispecies biofilm development and the effects of the streptococci in biofilm formation, the active substances inhibiting Streptococcus mutans biofilm formation were purified from Streptococcus salivarius ATCC 9759 and HT9R culture supernatants using ion exchange and gel filtration chromatography. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry analysis was performed, and the results were compared to databases. The S. salivarius HT9R genome sequence was determined and used to indentify candidate proteins for inhibition. The candidates inhibiting biofilms were identified as S. salivarius fructosyltransferase (FTF) and exo-beta-d-fructosidase (FruA). The activity of the inhibitors was elevated in the presence of sucrose, and the inhibitory effects were dependent on the sucrose concentration in the biofilm formation assay medium. Purified and commercial FruA from Aspergillus niger (31.6% identity and 59.6% similarity to the amino acid sequence of FruA from S. salivarius HT9R) completely inhibited S. mutans GS-5 biofilm formation on saliva-coated polystyrene and hydroxyapatite surfaces. Inhibition was induced by decreasing polysaccharide production, which is dependent on sucrose digestion rather than fructan digestion. The data indicate that S. salivarius produces large quantities of FruA and that FruA alone may play an important role in multispecies microbial interactions for sucrose-dependent biofilm formation in the oral cavity.

The Human Lung Microbiome

The human lower respiratory tract is considered sterile in normal healthy individuals (Flanagan et al., 2007; Speert, 2006) despite the fact that every day we breathe in multiple microorganisms present in the air and aspirate thousands of organisms from the mouth and nasopharynx. This apparent sterility is maintained by numerous interrelated components of the lung physical structures such as the mucociliary elevator and components of the innate and adaptive immune systems (discussed below) (reviewed in (Diamond et al., 2000; Gerritsen, 2000)). However, it is possible that the observed sterility might be a result of the laboratory practices applied to study the flora of the lungs. Historically, researchers faced with a set of diseases characterized by a changing and largely cryptic lung microbiome have lacked tools to study lung ecology as a whole and have concentrated on familiar, cultivatable candidate pathogens.

The bacterial microbiota in the oral mucosa of rural Amerindians

The oral microbiota plays an important role in buccal health and in diseases such as periodontitis and meningitis. The study of the human oral bacteria has so far focused on subjects from Western societies, while little is known about subjects from isolated communities. This work determined the composition of the oral mucosa microbiota from six Amazon Amerindians, and tested a sample preservation alternative to freezing. Paired oral swabs were taken from six adults of Guahibo ethnicity living in the community of Platanillal, Amazonas State, Venezuela. Replicate swabs were preserved in liquid nitrogen and in Aware Messenger fluid (Calypte). Buccal DNA was extracted, and the V2 region of the 16S rRNA gene was amplified and pyrosequenced. A total of 17 214 oral bacterial sequences were obtained from the six subjects; these were binned into 1034 OTUs from 10 phyla, 30 families and 51 genera. The oral mucosa was highly dominated by four phyla: Firmicutes (mostly the genera Streptococcus and Veillonella), Proteobacteria (mostly Neisseria), Bacterioidetes (Prevotella) and Actinobacteria (Micrococcineae). Although the microbiota were similar at the phylum level, the Amerindians shared only 62 % of the families and 23 % of the genera with non-Amerindians from previous studies, and had a lower richness of genera (51 vs 177 reported in non-Amerindians). The Amerindians carried unidentified members of the phyla Bacteroidetes, Firmicutes and Proteobacteria and their microbiota included soil bacteria Gp1 (Acidobacteriaceae) and Xylanibacter (Prevotellaceae), and the rare genus Phocoenobacter (Pasteurellaceae). Preserving buccal swabs in the Aware Messenger oral fluid collection device substantially altered the bacterial composition in comparison to freezing, and therefore this method cannot be used to preserve samples for the study of microbial communities.

Bacterial 16S sequence analysis of severe caries in young permanent teeth

Previous studies have confirmed the association of the acid producers Streptococcus mutans and Lactobacillus spp. with childhood caries, but they also suggested these microorganisms are not sufficient to explain all cases of caries. In addition, health-associated bacterial community profiles are not well understood, including the importance of base production and acid catabolism in pH homeostasis. The bacterial community composition in health and in severe caries of the young permanent dentition was compared using Sanger sequencing of the ribosomal 16S rRNA genes. Lactobacillus species were dominant in severe caries, and levels rose significantly as caries progressed from initial to deep lesions. S. mutans was often observed at high levels in the early stages of caries but also in some healthy subjects and was not statistically significantly associated with caries progression in the overall model. Lactobacillus or S. mutans was found either at low levels or not present in several samples. Other potential acid producers observed at high levels in these subjects included strains of Selenomonas, Neisseria, and Streptococcus mitis. Propionibacterium FMA5 was significantly associated with caries progression but was not found at high levels. An overall loss of community diversity occurred as caries progressed, and species that significantly decreased included the Streptococcus mitis-S. pneumoniae-S. infantis group, Corynebacterium matruchotii, Streptococcus gordonii, Streptococcus cristatus, Capnocytophaga gingivalis, Eubacterium IR009, Campylobacter rectus, and Lachnospiraceae sp. C1. The relationship of acid-base metabolism to 16S rRNA gene-based species assignments appears to be complex, and metagenomic approaches that would allow functional profiling of entire genomes will be helpful in elucidating the microbial pathogenesis of caries.