A. C. R. Tanner

The Human Oral Microbiome

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

Photodynamic treatment of endodontic polymicrobial infection in vitro

We investigated the photodynamic effects of methylene blue on multispecies root canal biofilms comprising Actinomyces israelii, Fusobacterium nucleatum subspecies nucleatum, Porphyromonas gingivalis, and Prevotella intermedia in experimentally infected root canals of extracted human teeth in vitro. The 4 test microorganisms were detected in root canals by using DNA probes. Scanning electron microscopy showed the presence of biofilms in root canals before therapy. Root canal systems were incubated with methylene blue (25 microg/mL) for 10 minutes followed by exposure to red light at 665 nm with an energy fluence of 30 J/cm(2). Light was delivered from a diode laser via a 250-microm diameter polymethyl methacrylate optical fiber that uniformly distributed light over 360 degrees. Photodynamic therapy (PDT) achieved up to 80% reduction of colony-forming unit counts. We concluded that PDT can be an effective adjunct to standard endodontic antimicrobial treatment when the PDT parameters are optimized.

The Microbiota of Young Children from Tooth and Tongue Samples

This study determined the frequency with which 38 microbial species were detected in 171 randomly selected children from 6 to 36 months of age. Children were sampled and dental caries measured. Oral samples were assayed by means of a checkerboard DNA probe assay. The detection frequencies from tongue samples in children under 18 mos were: S. mutans 70%, S. sobrinus 72%, P. gingivalis 23%, B. forsythus 11%, and A. actinomycetemcomitans 30%, with similar detection frequencies in children over 18 mos. Thus, S. mutans and the periodontal pathogens, P. gingivalis and B. forsythus, were detected even in the youngest subjects. Species associated with caries included S. mutans (children ages 18-36 mos) and A. israelii (children ages < 18 mos), the latter species possibly reflecting increased plaque in children with caries. Species detection from tooth and tongue samples was highly associated, with most species detected more frequently from tongue than from tooth samples in children under 18 mos, suggesting that the tongue was a potential microbial reservoir.

Nanoparticle-based endodontic antimicrobial photodynamic therapy

OBJECTIVE To study the in vitro effects of poly(lactic-co-glycolic acid) (PLGA) nanoparticles loaded with the photosensitizer methylene blue (MB) and light against Enterococcus faecalis (ATCC 29212). MATERIALS AND METHODS The uptake and distribution of nanoparticles in E. faecalis in suspension was investigated by transmission electron microscopy (TEM) after incubation with PLGA complexed with colloidal gold particles for 2.5, 5, and 10 minutes. E. faecalis species were sensitized in planktonic phase and in experimentally infected root canals of human extracted teeth with MB-loaded nanoparticles for 10 minutes followed by exposure to red light at 665 nm. RESULTS The nanoparticles were found to be concentrated mainly on the cell walls of microorganisms at all three time points. The synergism of light and MB-loaded nanoparticles led to approximately 2 and 1 log10 reduction of colony-forming units (CFUs) in planktonic phase and root canals, respectively. In both cases, mean log10 CFU levels were significantly lower than controls and MB-loaded nanoparticles without light. CONCLUSION The utilization of PLGA nanoparticles encapsulated with photoactive drugs may be a promising adjunct in antimicrobial endodontic treatment.

Cultivable Anaerobic Microbiota of Severe Early Childhood Caries

ABSTRACT Severe early childhood caries (ECC), while strongly associated with Streptococcus mutans using selective detection (culture, PCR), has also been associated with a widely diverse microbiota using molecular cloning approaches. The aim of this study was to evaluate the microbiota of severe ECC using anaerobic culture. The microbial composition of dental plaque from 42 severe ECC children was compared with that of 40 caries-free children. Bacterial samples were cultured anaerobically on blood and acid (pH 5) agars. Isolates were purified, and partial sequences for the 16S rRNA gene were obtained from 5,608 isolates. Sequence-based analysis of the 16S rRNA isolate libraries from blood and acid agars of severe ECC and caries-free children had >90% population coverage, with greater diversity occurring in the blood isolate library. Isolate sequences were compared with taxon sequences in the Human Oral Microbiome Database (HOMD), and 198 HOMD taxa were identified, including 45 previously uncultivated taxa, 29 extended HOMD taxa, and 45 potential novel groups. The major species associated with severe ECC included Streptococcus mutans, Scardovia wiggsiae, Veillonella parvula, Streptococcus cristatus, and Actinomyces gerensceriae. S. wiggsiae was significantly associated with severe ECC children in the presence and absence of S. mutans detection. We conclude that anaerobic culture detected as wide a diversity of species in ECC as that observed using cloning approaches. Culture coupled with 16S rRNA identification identified over 74 isolates for human oral taxa without previously cultivated representatives. The major caries-associated species were S. mutans and S. wiggsiae, the latter of which is a candidate as a newly recognized caries pathogen.

Bacteroides forsythus sp. nov., a Slow-Growing, Fusiform Bacteroides sp. from the Human Oral Cavity

The characteristics of a group of slow-growing, fusiform, fastidious anaerobes isolated from advanced periodontal lesions in human oral cavities were examined. Our results indicated that 12 fusiform Bacteroides strains belong to a new species in the genus Bacteroides. The name Bacteroides forsythus is proposed for these isolates. The type strain is strain ATCC 43037.

Clonal analysis of the microbiota of severe early childhood caries.

Background/Aims: Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the microbiota of severe early childhood caries. Methods: Dental plaque samples from 2- to 6-year-old children were analyzed using 16S rRNA gene cloning and sequencing, and by specific PCR amplification for Streptococcus mutans and Bifidobacteriaceae species. Results: Children with severe caries (n = 39) had more dental plaque and gingival inflammation than caries-free children (n = 41). Analysis of phylotypes from operational taxonomic unit analysis of 16S rRNA clonal metalibraries from severe caries and caries-free children indicated that while libraries differed significantly (p < 0.0001), there was increased diversity than detected in this clonal analysis. Using the Human Oral Microbiome Database, 139 different taxa were identified. Within the limits of this study, caries-associated taxa included Granulicatella elegans (p < 0.01) and Veillonella sp. HOT-780 (p < 0.01). The species associated with caries-free children included Capnocytophaga gingivalis (p < 0.01), Abiotrophia defectiva (p < 0.01), Lachnospiraceae sp. HOT-100 (p < 0.05), Streptococcus sanguinis (p < 0.05) and Streptococcus cristatus (p < 0.05). By specific PCR, S. mutans (p < 0.005) and Bifidobacteriaceae spp. (p < 0.0001) were significantly associated with severe caries. Conclusion: Clonal analysis of 80 children identified a diverse microbiota that differed between severe caries and caries-free children, but the association of S. mutans with caries was from specific PCR analysis, not from clonal analysis, of samples.

The antibacterial effect of photodynamic therapy in dental plaque‐derived biofilms

BACKGROUND AND OBJECTIVE Photodynamic therapy has been advocated as an alternative to antimicrobial agents to suppress subgingival species and to treat periodontitis. Bacteria located within dense biofilms, such as those encountered in dental plaque, have been found to be relatively resistant to antimicrobial therapy. In the present study, we investigated the ability of photodynamic therapy to reduce the number of bacteria in biofilms by comparing the photodynamic effects of methylene blue on human dental plaque microorganisms in the planktonic phase and in biofilms. MATERIAL AND METHODS Dental plaque samples were obtained from 10 subjects with chronic periodontitis. Suspensions of plaque microorganisms from five subjects were sensitized with methylene blue (25 microg/mL) for 5 min then exposed to red light. Multispecies microbial biofilms developed from the same plaque samples were also exposed to methylene blue (25 microg/mL) and the same light conditions as their planktonic counterparts. In a second set of experiments, biofilms were developed with plaque bacteria from five subjects, sensitized with 25 or 50 microg/mL of methylene blue and then exposed to red light. After photodynamic therapy, survival fractions were calculated by counting the number of colony-forming units. RESULTS Photodynamic therapy killed approximately 63% of bacteria present in suspension. By contrast, in biofilms, photodynamic therapy had much less of an effect on the viability of bacteria (32% maximal killing). CONCLUSION Oral bacteria in biofilms are affected less by photodynamic therapy than bacteria in the planktonic phase. The antibacterial effect of photodynamic therapy is reduced in biofilm bacteria but not to the same degree as has been reported for treatment with antibiotics under similar conditions.

Diet and Caries-associated Bacteria in Severe Early Childhood Caries

Frequent consumption of cariogenic foods and bacterial infection are risk factors for early childhood caries (ECC). This study hypothesized that a short diet survey focused on frequency of foods, categorized by putative cariogenicity, would differentiate severe ECC (S-ECC) from caries-free children. Children’s diets were obtained by survey and plaque bacteria detected by PCR from 72 S-ECC and 38 caries-free children. S-ECC children had higher scores for between-meal juice (p < 0.01), solid-retentive foods (p < 0.001), eating frequency (p < 0.005), and estimated food cariogenicity (p < 0.0001) than caries-free children. S-ECC children with lesion recurrence ate fewer putative caries-protective foods than children without new lesions. Streptococcus mutans (p < 0.005), Streptococcus sobrinus (p < 0.005), and Bifidobacteria (p < 0.0001) were associated with S-ECC, and S. mutans with S. sobrinus was associated with lesion recurrence (p < 0.05). S. mutans-positive children had higher food cariogenicity scores. Food frequency, putative cariogenicity, and S. mutans were associated with S-ECC individually and in combination.

Capnocytophaga: new genus of gram-negative gliding bacteria. III. Physiological characterization.

Sixty-eight strains of capnophilic fusiform Gram-negative rods from the human oral cavity were subjected to extensive physiologic characterization, tested for susceptibility to various antibiotics, and the mol-percent guanine plus cytosine of each isolate determined. The characteristics of the isolates were compared with 10 fresh and 2 stock isolates of Fusobacterium nucleatum. The isolates clearly differed from the Fusobacterium species on the basis of molpercent guanine plus cytosine, end products, growth in a capnophilic environment and fermentation of carbohydrates.All of the gliding isolates required CO2 and formed acetate and succinate, but not H2S, indole or acetylmethylcarbinol. All fermented glucose, sucrose, maltose and mannose. The organisms may be differentiated on the basis of fermentation of additional carbohydrates, hydrolysis of polymers and reduction of nitrate. Three species are proposed: Capnocytophaga ochracea, Capnocytophaga sputigena and Capnocytophaga gingivalis. Ten isolates did not fit into the proposed species.