Clonal analysis by ribotyping of Fusobacterium nucleatum isolates obtained from healthy young adults with optimal plaque control

Clonal Persistence of Oral Fusobacterium nucleatum in Infancy

Once established, early-colonizing bacterial species tend to persist in the mouth. To obtain detailed information on the population dynamics of early-colonizing oral anaerobes, we examined the clonal diversity and persistence of clones among oral Fusobacterium nucleatum populations during the first 2 yrs of life. Consecutive salivary samples from 12 infants, collected at 2, 6, 12, 18, and 24 mos of age, yielded a total of 546 F. nucleatum isolates for clonal typing with arbitrarily primed PCR (AP-PCR). Up to 7 AP-PCR types were simultaneously detected in each sample. In 11 out of the 12 infants examined, AP-PCR types persisted for up to 1 yr. Strain turnover rate was high during the first year of life, but then the occurrence of persistent clones increased. This study indicates a wide genetic diversity within the species and provides evidence for the increasing persistence of F. nucleatum clones in the oral cavity with age.

Fusobacterium nucleatum: an emerging gut pathogen?

The Gram-negative, non-sporulating, obligately anaerobic species, Fusobacterium nucleatum, is rapidly gaining notoriety as a pathogen with a surprising number of associated diseases. Recently, we have found that F. nucleatum is a more common resident of the GI tract than originally thought, and thus, through several studies, we have attempted to determine its gut-relevant potential for virulence. We have found that F. nucleatum possesses a number of pathogenic traits with relevance to gut diseases such as inflammatory bowel disease (IBD), however, we have also documented strain-associated differences in virulence. An intriguing picture emerges that paints F. nucleatum as both conferring beneficial as well as detrimental effects on host cells; and we suggest that the ultimate effects of F. nucleatum infection in the gut are a consequence of the microbes with which this species aggregates.

Phenotypic and genotypic analyses of clinical Fusobacterium nucleatum and Fusobacterium periodonticum isolates from the human gut

Fusobacterium nucleatum is a Gram-negative anaerobic rod that is part of the normal human microflora, and has also been associated with various infections. Bacterial strains belonging to the species are typically heterogeneous in both phenotype and genotype, which can hinder their identification in a clinical setting. The majority of F. nucleatum isolates originate from oral sites, however the species is also a resident of the human gastrointestinal tract. The aim of this study was to compare F. nucleatum isolates from human intestinal biopsy samples to try and determine whether isolates from this site are divergent from oral isolates. We used a variety of phenotypic and genotypic markers to compare 21 F. nucleatum and Fusobacterium periodonticum isolates from the GI tract to oral isolates and recognized type strains in order to study heterogeneity within this set. 16S rDNA and rpoB gene sequence analysis allowed us to build phylogenetic trees that consistently placed isolates into distinct clusters. 16S rDNA copy number analyses using Denaturing Gradient Gel Electrophoresis (DGGE) demonstrated potential for use as a method to examine clonality amongst species. Phenotypic analyses gave variable results that were generally unhelpful in distinguishing between phylogenetic clusters. Our results suggest that a) F. periodonticum isolates are not restricted to the oral niche; b) phenotypic classification is not sufficient to subspeciate isolates; c) heterogeneity within the species is extensive but constrained; and d) F. nucleatum isolates from the gut tend to identify with the animalis subspecies.

Genotypic and phenotypic characterization of fusobacteria from Chinese and European patients with inflammatory periodontal diseases

Phylogenetic and antigenic studies were performed on 48 human oral Fusobacterium strains from Chinese patients with either necrotizing ulcerative gingivitis (NUG) or gingivitis and on 23 Fusobacterium nucleatum or Fusobacterium periodonticum strains from European periodontitis patients. Alignment of partial 16S rRNA gene sequences resulted in a phylogenetic tree that corresponded well with the current classification of oral fusobacteria into F. periodonticum and several subspecies of F. nucleatum, in spite of much minor genetic variability. F. periodonticum, F. nucleatum subsp. animalis and a previously undescribed phylogenetic cluster (C4), that may represent an additional F. nucleatum subspecies, constituted discrete clusters distinct from the remainder of F. nucleatum with high bootstrap values. Chinese and European strains differed markedly with regard to their respective classification patterns, suggesting a predominance of F. peridonticum and F. nucleatum susp. animalis over F. nucleatum subsp. nucleatum and F. nucleatum subsp. fusiforme/vincentii in samples from China. Antigenic typing enabled the association of many previously described serovars with distinct phylogenetic clusters and when applied directly to uncultured clinical samples confirmed the differential distribution of oral Fusobacterium taxa in Chinese and European samples. Bacteria from cluster C4 and F. nucleatum subsp. animalis were significantly more prevalent and accounted for higher cell numbers in NUG than in gingivitis samples, suggesting a possible association of these rarely observed taxa with NUG in Chinese patients.

Clonal diversity and stability of subgingival Eikenella corrodens

Eikenella corrodens is a commensal subgingival bacterium commonly found in both periodontally nondiseased and diseased subjects. The present study examined the clonal diversity and stability of subgingival E. corrodens over time. Ninety-five subjects were enrolled at the baseline examination, including 44 periodontally nondiseased subjects and 51 subjects with aggressive periodontitis. Twenty-two nondiseased subjects and 11 subjects with aggressive periodontitis were subsequently reexamined after an average interval of 14 months. Two subgingival plaque samples were obtained from each subject to determine the total cultivable bacteria. In addition, multiple E. corrodens isolates from each sample were recovered for clonal analysis by arbitrarily primed PCR. The mean numbers of distinct E. corrodens clones harbored by nondiseased subjects and subjects with aggressive periodontitis were 1.3 and 3.0, respectively. Thirty-nine percent of the nondiseased subjects and 63% of the subjects with aggressive periodontitis harbored multiple clones of E. corrodens. The numbers of distinct E. corrodens clones increased significantly (Mann-Whitney ranking test, P < 0.05) in sites from patients with aggressive periodontitis, in sites with pocket depths of 4 mm or greater, in sites with a clinical attachment loss of 2 mm or greater, and in sites coinfected with Porphyromonas gingivalis. Comparison of E. corrodens clones recovered at the baseline and those recovered at the follow-up examination showed that E. corrodens colonization was not stable. Thirty-eight of the 66 follow-up samples (58%) showed a complete change (including de novo colonization of the sites or complete elimination of the organism from the sites) of the subgingival E. corrodens clonal types between the baseline and the follow-up examinations. Our results suggest a complexity of subgingival microbiota not seen previously.

Clonality of Fusobacterium nucleatum in root canal infections

Fusobacterium nucleatum is a gram-negative non-spore-forming, non-motile, obligate anaerobic rod that is normally isolated from the oral cavity. Several studies have reported a significant heterogeneity within the F. nucleatum species. The aim of the present study was to analyze the clonal diversity of F. nucleatum strains isolated from intracanal infections and to evaluate the presence of Enterobacterial Repetitive Intergenic Consensus (ERIC)-like sequences in the genome of F. nucleatum. Samples were collected from 13 single-root teeth from adult patients, all having carious lesions, necrotic pulps and radiographic evidence of periradicular bone loss. F. nucleatum was isolated from two different patients (subjects 5 and 7) by culture. Amplification of 19 colonies from subject 5 and 15 colonies from subject 7 using ERIC primers resulted in four clonal types, two per subject. An intense amplicon of approximately 700 bp was generated by ERIC-PCR for all F. nucleatum isolates and F. nucleatum ssp. polymorphum ATCC 10953. The amplification reaction using primer 1254 confirmed the results obtained with the ERIC primer. Our findings indicate that DNA fingerprints provided by ERIC- and Arbitrarily Primed (AP)-PCR may constitute a powerful tool for investigating F. nucleatum clonal diversity.

Saliva and dental plaque

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