Exploring the signature gut and oral microbiome in individuals of specific Ayurveda prakriti

Diagnosis and treatment of various diseases in Ayurveda, the Indian system of medicine, relies on 'prakriti' phenotyping of individuals into predominantly three constitutions, kapha, pitta and vata. Recent studies propose that microbiome play an integral role in precision medicine. A study of the relationship between prakriti - the basis of personalized medicine in Ayurveda and that of gut microbiome, and possible biomarker of an individual's health, would vastly improve precision therapy. Towards this, we analyzed bacterial metagenomes from buccal (oral microbiome) and fecal (gut microbiome) samples of 272 healthy individuals of various predominant prakritis. Major bacterial genera from gut microbiome included Prevotella, Bacteroides and Dialister while oral microbiome included Streptococcus, Neisseria, Veilonella, Haemophilus, Porphyromonas and Prevotella. Though the core microbiome was shared across all individuals, we found prakriti specific signatures such as preferential presence of Paraprevotella and Christensenellaceae in vata individuals. A comparison of core gut microbiome of each prakriti with a database of 'healthy' microbes identified microbes unique to each prakriti with functional roles similar to the physiological characteristics of various prakritis as described in Ayurveda. Our findings provide evidence to Ayurvedic interventions based on prakriti phenotyping and possible microbial biomarkers that can stratify the heterogenous population and aid in precision therapy.

Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species

The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota

The upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. Data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both veterinary and human medicine. Based on targeted next-generation sequencing of feces and samples collected at multiple levels of the airways from 16 healthy female dogs, we demonstrate that canine airways harbor a topographically continuous microbiota with increasing relative abundance of proteobacterial species from the upper to lower airways. The lung-associated microbiota, as assessed via bronchoalveolar lavage fluid (BALF), was the most consistent between dogs and was dominated by three distinct taxa, two of which were resolved to the species level and one to the level of family. The gene content of the nasal, oropharyngeal, and lung-associated microbiota, predicted using the Phylogenetic Investigations into Communities by Reconstruction of Unobserved States (PICRUSt) software, provided information regarding the glyoxylate and citrate cycle metabolic pathways utilized by these bacterial populations to colonize such nutrient-poor, low-throughput environments. These data generated in healthy subjects provide context for future analysis of diseased canine airways. Moreover, as dogs have similar respiratory anatomy, physiology, and immune systems as humans, are exposed to many of the same environmental stimuli, and spontaneously develop similar respiratory diseases, these data support the use of dogs as a model species for prospective studies of the airway microbiota, with findings translatable to the human condition.

[New Strains of an Aerobic Anoxygenic Phototrophic Bacterium Porphyrobacter donghaensis Isolated from a Siberian Thermal Spring and a Low-Mineralization Lake]

A strain of aerobic anoxygenic phototrophic bacteria (AAPB) isolated from the surface of a cyano- bacterial mat of an Eastern Siberian thermal spring (40 C) and designated Se 4 was identified as Porphyro- bacter donghaensis according to its 16S rRNA gene sequence. A DNA-DNA hybridization level of 95% was determined between strain Se-4 and the type strain of this species; SW-132@T. The isolate was an obligate aerobe,. forming orange round colonies on solid media, which turn red in the course of growth. The cells were motile rods capable of branching. The cells divided by uniform fission by constriction. Optimal growth was observed at pH 7.5 and NaCl concentrations from 0 to 1 g/L. The pigments present were carotenoids and bacteriochlorophyll a. Another Porphyrobacter donghaensis strain, Noj- 1, isolated from a purple mat developing on the surface of a coastal set-up in a steppe low-mineralization (1.5 g/L) soda lake Nozhii (Eastern Siberia) possessed similar characteristics. Thus, the AAPB species Porphyrobacter donghaensis was shown to-occur, apart from its known habitat, marine environments, in low-mineralization soda lakes and freshwater thermal springs. Description of the species Porphyrobacter donghaensis was amended.

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites

BACKGROUND

To investigate the microbial composition of biofilms at inflamed peri-implant and periodontal tissues in the same subject, using 16S rRNA sequencing.

METHODS

Supra- and submucosal, and supra- and subgingival plaque samples were collected from 7 subjects suffering from diseased peri-implant and periodontal tissues. Bacterial DNA was isolated and 16S rRNA genes were amplified, sequenced and aligned for the identification of bacterial genera.

RESULTS

43734 chimera-depleted, denoised sequences were identified, corresponding to 1 phylum, 8 classes, 10 orders, 44 families and 150 genera. The most abundant families or genera found in supramucosal or supragingival plaque were Streptoccocaceae, Rothia and Porphyromonas. In submucosal plaque, the most abundant family or genera found were Rothia, Streptococcaceae and Porphyromonas on implants. The most abundant subgingival bacteria on teeth were Prevotella, Streptococcaceae, and TG5. The number of sequences found for the genera Tannerella and Aggregatibacter on implants differed significantly between supra- and submucosal locations before multiple testing. The analyses demonstrated no significant differences between microbiomes on implants and teeth in supra- or submucosal and supra- or subgingival biofilms.

CONCLUSION

Diseased peri-implant and periodontal tissues in the same subject share similiar bacterial genera and based on the analysis of taxa on a genus level biofilm compositions may not account for the potentially distinct pathologies at implants or teeth.

Identification of Dipeptidyl-Peptidase (DPP)5 and DPP7 in Porphyromonas endodontalis, Distinct from Those in Porphyromonas gingivalis

Dipeptidyl peptidases (DPPs) that liberate dipeptides from the N-terminal end of oligopeptides are crucial for the growth of Porphyromonas species, anaerobic asaccharolytic gram negative rods that utilize amino acids as energy sources. Porphyromonas endodontalis is a causative agent of periapical lesions with acute symptoms and Asp/Glu-specific DPP11 has been solely characterized in this organism. In this study, we identified and characterized two P. endodontalis DPPs, DPP5 and DPP7. Cell-associated DPP activity toward Lys-Ala-4-methylcoumaryl-7-amide (MCA) was prominent in P. endodontalis ATCC 35406 as compared with the Porphyromonas gingivalis strains ATCC 33277, 16-1, HW24D1, ATCC 49417, W83, W50, and HNA99. The level of hydrolysis of Leu-Asp-MCA by DPP11, Gly-Pro-MCA by DPP4, and Met-Leu-MCA was also higher than in the P. gingivalis strains. MER236725 and MER278904 are P. endodontalis proteins belong to the S9- and S46-family peptidases, respectively. Recombinant MER236725 exhibited enzymatic properties including substrate specificity, and salt- and pH-dependence similar to P. gingivalis DPP5 belonging to the S9 family. However, the kcat/Km figure (194 µM-1·sec-1) for the most potent substrate (Lys-Ala-MCA) was 18.4-fold higher as compared to the P. gingivalis entity (10.5 µM-1·sec-1). In addition, P. endodontalis DPP5 mRNA and protein contents were increased several fold as compared with those in P. gingivalis. Recombinant MER278904 preferentially hydrolyzed Met-Leu-MCA and exhibited a substrate specificity similar to P. gingivalis DPP7 belonging to the S46 family. In accord with the deduced molecular mass of 818 amino acids, a 105-kDa band was immunologically detected, indicating that P. endodontalis DPP7 is an exceptionally large molecule in the DPP7/DPP11/S46 peptidase family. The enhancement of four DPP activities was conclusively demonstrated in P. endodontalis, and remarkable Lys-Ala-MCA-hydrolysis was achieved by qualitative and quantitative potentiation of the DPP5 molecule.

Isolation and identification of Porphyromonas spp. and other putative pathogens from cats with periodontal disease

The purpose of this study was to evaluate the subgingival microbiota and determine the most prevalent periodontal pathogens implicated in feline periodontal disease and to correlate these findings with the clinical periodontal status. Subgingival microbiological samples were taken under sedation from 50 cats with clinical signs of periodontal disease. Pooled paper point samples from 4 selected subgingival sites were cultured on blood agar and on Dentaid-1 medium. Suspected pathogens were identified, subcultured, and preserved. The association between the microbiological findings and the clinical status was studied using correlation coefficients (CC). In addition, cats were stratified in subgroups according to presence of putative pathogens, and comparisons were carried out using unpaired t-test. Three bacterial species were frequently detected including Porphyromonas gulae (86%), Porphyromonas circumdentaria (70%) and Fusobacterium nucleatum (90%). The mean proportion of total flora was high for P. gulae (32.54%), moderate for P. circundentaria (8.82%), and low for F. nucleatum (3.96%). Among the clinical variables, tooth mobility was correlated (CC > 0.50, p < 0.001) with recession, pocket depth, attachment level, gingival index, and calculus index (CC = 0.29, p = 0.04) as well as with total bacterial counts (CC = 0.38, p = 0.006). Cats with more than 10% of P. gulae showed significantly more mobility (p = 0.014) and recession (p = 0.038), and a tendency for deeper probing pocket depths (p = 0.084) and attachment loss (p = 0.087). The results from this cross-sectional study confirmed that P. gulae is the most relevant pathogen in periodontal disease in cats.

Porphyromonas somerae sp. nov., a pathogen isolated from humans and distinct from porphyromonas levii

Porphyromonas levii is an anaerobic, pigmented gram-negative bacillus originally isolated from bovine rumen. We describe 58 human clinical strains of P. levii-like organisms, isolated from various human clinical specimens that are phenotypically similar to the type strain of P. levii, a rumen isolate (ATCC 29147). Our biochemical, comparative 16S rRNA sequence analyses, and DNAlpha-DNA relatedness studies indicate that the human P. levii-like organisms are similar to each other but genetically different from the P. levii type strain isolated from bovine rumen. We therefore propose the name Porphyromonas somerae to encompass the human P. levii-like organisms. P. somerae was predominantly isolated from patients with chronic skin and soft tissue or bone infections, especially in the lower extremities.

16S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas

The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260(T) divided the sequences into two clusters, of which one was alpha-fucosidase-positive (like the type strain) while the other was alpha-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of 'Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called 'Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of alpha-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

Culture-independent identification of periodontitis-associated Porphyromonas and Tannerella populations by targeted molecular analysis

Periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. About half of the oral microflora is unculturable; and 16S rRNA PCR, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. In the present study, a PCR primer set specific for the genera Porphyromonas and Tannerella was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep sites in subjects with periodontitis and shallow sites in age- and sex-matched controls. A total of 308 clones were sequenced and found to belong to one of six Porphyromonas or Tannerella species or phylotypes, one of which, Porphyromonas P3, was novel. Tannerella forsythensis was found in significantly higher proportions in patients than in controls. Porphyromonas catoniae and Tannerella phylotype BU063 appeared to be associated with shallow sites. Targeted culture-independent molecular ecology studies have a valuable role to play in the identification of bacterial targets for further investigations of the pathogenesis of bacterial infections.

Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis

Three Porphyromonas species (Porphyromonas asaccharolytica, P. endodontalis, and the novel species that is the subject of the present report, P. uenonis) are very much alike in terms of biochemical characteristics, such as enzyme profiles and cellular fatty acid contents. P. asaccharolytica is distinguished from the other two species by virtue of production of alpha-fucosidase and glyoxylic acid positivity. The novel species is difficult to differentiate from P. endodontalis phenotypically and was designated a P. endodontalis-like organism for some time. However, P. endodontalis is recovered almost exclusively from oral sources and also grows poorly on Biolog Universal Agar, both characteristics that are in contrast to those of the other two organisms. Furthermore, P. uenonis is glycerol positive in the Biolog AN Microplate system. Both P. asaccharolytica and P. uenonis are positive by 13 other tests in the Biolog system, whereas P. endodontalis is negative by all of these tests. P. asaccharolytica grew well in both solid and liquid media without supplementation with 5% horse serum, whereas the other two species grew poorly without supplementation. Sequencing of 16S rRNA revealed about 10% divergence between the novel species and P. endodontalis but less than 2% sequence difference between the novel species and P. asaccharolytica. Subsequent DNA-DNA hybridization studies documented that the novel organism was indeed distinct from P. asaccharolytica. We propose the name Porphyromonas uenonis for the novel species. We have recovered P. uenonis from four clinical infections in adults, all likely of intestinal origin, and from the feces of six children.

Degradation of cross-linked and non-cross-linked arabinoxylans by the intestinal microbiota in children

In humans, nonstarch polysaccharides (NSP), such as arabinoxylans (AX), are not digested in the upper gut and provide fermentable carbon sources for bacteria growing in the large bowel. Despite the ubiquity of AX in nature, the microbiologic and physiologic consequences of AX digestion in the gut are poorly understood. In this study, we investigated the breakdown of ferulic acid-cross-linked AX (AXF) and non-cross-linked AX in children's intestinal microbiotas, using starch as a readily fermentable polysaccharide for comparative purposes. The experiments were performed using pH-controlled fermentation vessels under anaerobic conditions. The results demonstrated that there was variation in the metabolism of these polysaccharides by colonic microbiotas. AX was always degraded more slowly than starch, while ferulic acid cross-linking reduced the rate of AX fermentation, as shown by fermentation product measurements. Starch digestion was associated with significant acetate and butyrate production, whereas AX breakdown resulted in increased propionate formation. In general, the presence of fermentable carbohydrate significantly increased the total anaerobe counts and eubacterial rRNA concentrations (P < 0.01), while non-cross-linked AX digestion was principally associated with increased viable counts of Bacteroides fragilis group organisms, which was supported by increases in Bacteroides-Porphyromonas-Prevotella group rRNA (P < 0.01). Starch was considerably more bifidogenic than AX in these fermentations. In conclusion, in this study we found that the effects of AX and AXF on the microbial ecology and metabolism of intestinal microbiotas are similar in children and adults.

Coaggregation of Streptococcus salivarius with periodontopathogens: evidence for involvement of fimbriae in the interaction with Prevotella intermedia

Streptococcus salivarius is divided into two serological subgroups that carry either fibrils or fimbriae. Although fimbriae have been observed on up to 50% of S. salivarius strains in the human oral cavity, no function has yet been assigned to them. To determine whether S. salivarius fimbriae have a role in adhesion, we examined the ability of S. salivarius to coaggregate with selected microorganisms involved in periodontal diseases. Our results show that S. salivarius coaggregated with Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia. However, only fimbriated S. salivarius cells were able to coaggregate with P. intermedia, suggesting a specific role for these structures in the interaction. Heat treatment, sensitivity to sugars, amino acids, and EDTA, as well as protease treatment were also used to further characterize coaggregation between S. salivarius and periodontopathogens.

Sensitivity of genera Porphyromonas and Prevotella to the bactericidal action of C-terminal domain of human CAP18 and its analogues

This paper reports the effect of the synthesized 27-amino acid sequence in the C-terminal domain of human CAP18 (hCAP18), a human cationic antibacterial protein or cathelicidin, on certain strains belonging to the genera Porophyromonas and Prevotella. The domain binds lipopolysaccharides (LPS) from Porophyromonas gingivalis and Porophyromonas circumdentaria as well as enterobacterial LPS. Two analogues of hCAP18, designated LL/CAP18 and FF/CAP18, were also tested to determine whether additional activity was obtained. The analogue peptides replaced with hydrophobic and cationic amino acid residues showed more potent bactericidal and LPS-binding activities than the original one.

PCR methodology as a valuable tool for identification of endodontic pathogens

OBJECTIVES

This paper reviews the principles of polymerase chain reaction (PCR) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.

DATA SOURCES

Studies published in the medical, dental and biological literature.

STUDY SELECTION

Evaluation of published epidemiological studies examining the endodontic microbiota through PCR methodology.

CONCLUSIONS

PCR technology has enabled the detection of bacterial species that are difficult or even impossible to culture as well as cultivable bacterial strains showing a phenotypically divergent or convergent behaviour. Moreover, PCR is more rapid, much more sensitive, and more accurate when compared with culture. Its use in endodontics to investigate the microbiota associated with infected root canals has expanded the knowledge on the bacteria involved in the pathogenesis of periradicular diseases. For instance, Tannerella forsythensis (formerly Bacteroides forsythus), Treponema denticola, other Treponema species, Dialister pneumosintes, and Prevotella tannerae were detected in infected root canals for the first time and in high prevalence when using PCR analysis. The diversity of endodontic microbiota has been demonstrated by studies using PCR amplification, cloning and sequencing of the PCR products. Moreover, other fastidious bacterial species, such as Porphyromonas endodontalis, Porphyromonas gingivalis and some Eubacterium spp., have been reported in endodontic infections at a higher prevalence than those reported by culture procedures.

Periodontal microbiota and clinical periodontal status in a rural sample in southern Thailand

We sought to determine (i) the association of subgingival bacterial profiles to clinical periodontal status in a population with limited access to dental care in Thailand, and (ii) the external validity of our earlier findings from a similar study in rural China. We examined 356 subjects, 30-39 yr old and 50-59 yr old, with respect to clinical periodontal status and subgingival plaque at maximally 14 sites per subject. Checkerboard hybridizations were used to analyse a total of 4343 samples. The prevalence of the 27 species investigated ranged between 87.2% and 100%. Discriminant analysis based on microbial profiles classified correctly 67.5% of all deep (> or = 5 mm) and 64.2% of all shallow sites, and 67.4% of all subjects with and 69.3% of all subjects without > or = 3 deep pockets. High colonization by 'red complex' bacteria was four times as likely (95% Confidence Limits (CL) 2.5-6.6) in subjects with > or = 10 sites with attachment loss of > or = 5 mm, and 4.3 times as likely (95% CL 2.6-7.1) in subjects with > or = 30 such sites. The data confirmed (i) the ubiquitous prevalence of the bacteria investigated in subjects with no regular access to dental care; and (ii) the high odds for periodontal pathology conferred by increased levels of specific periodontal bacteria.

Recent taxonomic changes and terminology update of clinically significant anaerobic gram-negative bacteria (excluding spirochetes)

Because of access to 16S rDNA sequencing, changes in the taxonomy and nomenclature of anaerobic gram-negative bacteria have occurred lately. New genera and species have been described, and existing taxa have been reclassified. The present article compiles a list of clinically relevant anaerobes and provides synonyms as well as the old nomenclature used for these bacteria. Although names and classifications of anaerobic bacteria are changing quickly, it is important to keep track of new bacterial names to work toward better description and recognition of bacterium-disease associations.

Invasion of vascular cells in vitro by Porphyromonas endodontalis

AIM

The objective of this study was to determine whether laboratory strains and clinical isolates of microorganisms associated with root canal infections can invade primary cultures of cardiovascular cells.

METHODOLOGY

Quantitative levels of bacterial invasion of human coronary artery endothelial cells (HCAEC) and coronary artery smooth muscle cells (CASMC) were measured using a standard antibiotic protection assay. Transmission electron microscopy was used to confirm and visualize internalization within the vascular cells.

RESULTS

Of the laboratory and clinical strains tested, only P. endodontalis ATCC 35406 was invasive in an antibiotic protection assay using HCAEC and CASMC. Invasion of P. endodontalis ATCC 35406 was confirmed by transmission electron microscopy.

DISCUSSION

Certain microorganisms associated with endodontic infections are invasive. If bacterial invasion of the vasculature contributes to the pathogenesis of cardiovascular disease, then microorganisms in the pulp chamber represent potential pathogens.

A possible mechanism of maxillofacial abscess formation: involvement of Porphyromonas endodontalis lipopolysaccharide via the expression of inflammatory cytokines

In a previous study, we developed a specific monoclonal antibody against Porphyromonas endodontalis lipopolysaccharide, and demonstrated that this lipopolysaccharide was detected in bacterially infected root canal fluid. We suggest here that P. endodontalis lipopolysaccharide in the infectious materials plays a stimulatory role in maxillofacial abscess formation via the expression of inflammatory cytokines. Our epidemiological study showed that this lipopolysaccharide was detected in significant levels the infectious material of patients with periapical periodontitis and odontogenic abscesses. Interestingly, infectious material-induced expression of tumor necrosis factor-alpha, interleukin-1beta, or neutrophil chemoattractant KC genes in mouse macrophages, was significantly neutralized by monoclonal antibody against the lipopolysaccharide. In addition, we also detected a significant amount of tumor necrosis factor-alpha in the infectious material. These results suggest that P. endodontalis lipopolysaccharide plays an important role in the pathogenic mechanism of maxillofacial abscess formation via the expression of inflammatory cytokines.

The purification and characterization of an 88-kDa Porphyromonas endodontalis 35406 protease

A Porphyromonas endodontalis ATCC 35406 protease was purified from Triton X-114 cell extracts by preparative SDS-PAGE followed by electroelution. The purified enzyme exhibits a molecular size of 88 kDa and was dissociated into two polypeptides of 43 and 41 kDa upon heating in the presence of sodium dodecyl sulfate with or without a reducing agent. The protease (pH optimum 7.5-8.0) degraded the extracellular matrix proteins fibrinogen and fibronectin. Collagen IV was also degraded at 37 degrees C but not at 28 degrees C. The protease also cleaved the bioactive peptide angiotensin at amino acid residue phenylalanine-8 and tyrosine-4 but failed to hydrolyze bradykinin, vasopressin and synthetic chromogenic substrates with phenylalanine or tyrosine at the P1 position. In addition, two peptidases were detected in P. endodontalis cells: a proline aminopeptidase that remained associated with the cell pellet after detergent extraction and peptidase/s that partitioned into the Triton X-114 phase after phase separation and degraded the bioactive peptides bradykinin and vasopressin. These P. endodontalis peptidases and proteases may play an important role in both the nutrition and pathogenicity of these assacharolytic microorganisms. The inactivation of bioactive peptides and degradation of extracellular matrix proteins by bacterial enzymes may contribute to the damage of host tissues accompanied with endodontic infections.

Porphyromonas gulae sp. nov., an anaerobic, gram-negative coccobacillus from the gingival sulcus of various animal hosts

A new species, Porphyromonas gulae sp. nov., is proposed to include strains isolated from the gingival sulcus of various animal hosts which are distinct from related strains of Porphyromonas gingivalis of human origin. This bacterium exhibits the following characteristics: black-pigmented colonies; asaccharolytic, obligate anaerobic growth; and Gram-negative, non-motile and non-spore-forming, rod-shaped cells. Colonies do not fluoresce under UV light. Vitamin K1 and haemin are required for growth. Cells haemagglutinate sheep erythrocytes. Major fatty acid end products are butyric acid, isovaleric acid, succinic acid and phenylacetic acid. Strains are catalase-positive and indole is produced. Alkaline phosphatase, trypsin-like and N-acetyl-beta-glucosaminidase activities are strong. A beta-galactosidase and a glutamylglutamic acid arylamidase are also present. The G+C content of the chromosomal DNA is 51 mol%. DNA-DNA homology data and 16S rRNA gene sequence analysis provide strong evidence that strains from the animal biotype of P. gingivalis represent a Porphyromonas species that is distinct from P. gingivalis. The type strain of P. gulae is Loup 1T (= ATCC 51700T = NCTC 13180T).

Isolation and genotyping of black-pigmented anaerobes from periodontal sites of HIV-positive and non-infected subjects in Thailand

BACKGROUND, AIMS

The aims of this study were to investigate the prevalence of periodontitis, the prevalence of black-pigmented anaerobes and the genotypes of Porphyromonas gingivalis and Prevotella intermedia present in HIV-infected and control subjects in a heterosexual Thai population.

METHOD

50 AIDS patients and 50 control subjects were included in the study. Their periodontal condition was examined by assessment of bleeding on probing, attachment loss and probing depth, and presence of erythema around 6 teeth (16, 21, 24, 36, 41, 44). Subgingival plaque was collected from the mesiobuccal sites of these teeth and was cultured anaerobically for black-pigmented bacteria. Species were characterised using biochemical profiles and total protein profiles. Genotyping of each isolate was performed using PCR techniques.

RESULTS

There was little clinical evidence of HIV-associated periodontitis in the HIV-positive subjects and no difference was found in the prevalence or genotype distribution of black-pigmented anaerobes between HIV-infected and control subjects.

CONCLUSIONS

These data suggest lack of severe periodontal destruction due to HIV-infection in Thailand and that these subjects are not colonised by more numerous or characteristic clones of certain putative periodontal pathogens.

Detection of putative oral pathogens in acute periradicular abscesses by 16S rDNA-directed polymerase chain reaction

A 16S rDNA-directed polymerase chain reaction method was used to assess the occurrence of four black-pigmented anaerobic rods, Treponema denticola, and Actinobacillus actinomycetemcomitans in acute periradicular abscesses. Pus was collected by aspiration from 10 cases diagnosed as acute abscesses of endodontic origin. DNA was extracted from the samples and analyzed using a polymerase chain reaction-based identification assay. The method allowed detecting black-pigmented anaerobes in 80% of the examined abscesses. Porphyromonas endodontalis was found in 70%, T. denticola in 50%, Porphyromonas gingivalis in 40%, and Prevotella intermedia in 10% of the cases. P. gingivalis was always found associated with P. endodontalis. Prevotella nigrescens and A. actinomycetemcomitans were not found in any pus sample. The high prevalence of P. endodontalis, T. denticola, and P. gingivalis suggests that they can play an important role in the etiology of acute periradicular abscesses.

Changes in the cultivable flora in deep carious lesions following a stepwise excavation procedure

This study examined the cultivable microflora before and after stepwise excavation procedures in deep carious lesions in 9 permanent teeth, categorized according to degrees of proximal surface destruction. The final excavation was performed 4-6 months after the initial treatment, which included peripheral dentine excavation and removal of the central cariogenic biomass and the superficial necrotic dentine. Dentine colour and consistency were assessed by means of standardized scales before the application of a Ca(OH)(2) compound and temporary sealing. Reassessments were performed before and after the final excavation. Microbiological samples of the central demineralized dentine were obtained with a sterile bur before and after the first excavation, as well as before and after the final excavation. After anaerobic cultivation on enriched non-selective tryptic soy agar, 30 colonies from a representative area were identified by standardized biochemical and physiological tests. Before temporary restoration, a yellowish and light brown demineralized soft dentine was typically observed, and gram-positive rods accounted for 70% and lactobacilli for 50% of the total colony-forming units. Lactobacillus casei subsp. rhamnosus and Actinomyces naeslundii dominated the lactobacilli and the other gram-positive rods, respectively. Gram-negative rods were the next most frequent isolates, followed by streptococci, each group accounting for about 20% of the colony-forming units in positive samples. Before the final excavation, which did not cause exposure of the pulp in any of the cases, the retained demineralized dentine had changed into a darker and harder tissue, and the total colony-forming units, as well as the frequency and proportions of lactobacilli were substantially reduced. Gram-negative rods also declined, and the flora was dominated by A. naeslundii and various streptococci. In conclusion, the cultivable flora detected following the treatment interval had declined substantially, and the distribution of bacterial species did not represent a typical cariogenic microbiota of deep lesions, confirming the clinical findings of arrested caries progression.

Assessment of periradicular microbiota by DNA-DNA hybridization

In the present study the "checkerboard" DNA-DNA hybridization technique was used to identify bacteria in periapical endodontic lesions of asymptomatic teeth. Thirty-four patients with root-filled teeth and apical periodontitis were divided into two groups, each containing 17 patients. In Group 1, a marginal incision was performed during surgery to expose the lesion, and in Group 2, a submarginal incision was applied. The gingiva and mucosa were swabbed with an 0.2% chlorhexidine gluconate solution prior to surgery. Bacterial DNA was identified in all samples from the two groups using 40 different whole genomic probes. The mean number (+/- SD) of species detected was 33.7 +/- 3.3 in Group 1 and 21.3 +/- 6.3 in Group 2 (P < 0.001). The majority of the probe-detected bacteria were present in more lesions from Group 1 than from Group 2. The differences were most notable for Campylobacter gracilis, Porphyromonas endodontalis, Propionibacterium acnes, Capnocytophaga gingivalis, Fusobacterium nucleatum ssp. nucleatum, Fusobacterium nucleatum ssp. polymorphum, Prevotella intermedia, Treponema denticola, Streptococcus constellatus and Actinomyces naeslundii I. Bacterial species such as Actinobacillus actinomycetemcomitans and Bacteroides forsythus were detected in more than 60% of the lesions from both groups. Also, P. endodontalis was abundant in periapical tissue. The data supported the idea that following a marginal incision, bacteria from the periodontal pocket might reach the underlying tissues by surgeon-released bacteremia. The study provided solid evidence that bacteria invade the periapical tissue of asymptomatic teeth with apical periodontitis. The detection of much more bacteria with the "checkerboard" DNA-DNA hybridization method than has previously been recovered by anaerobic culture indicated that the endodontic (and periodontal) microfloras should be redefined using molecular methods.

"Checkerboard" assessments of periodontal microbiota and serum antibody responses: a case-control study

BACKGROUND

We explored the association between subgingival microbial profiles and serum IgG responses to periodontal microbiota in relation to clinical periodontal status.

METHODS

One hundred thirty-one (131) periodontitis patients aged 29 to 74 years (mean 51.8) were age- and gender-matched with 74 periodontally intact controls (range 26 to 77, mean 49.3). Smoking habits and health history were recorded and assessments of plaque, bleeding on probing, probing depth, and attachment level were performed at 6 sites per tooth on all present teeth, excluding third molars. Subgingival plaque samples were obtained from each tooth in one upper and one lower quadrant (maximum 14 samples/subject; 2,440 samples total) and analyzed with respect to 19 species by means of whole genomic DNA probes. Serum IgG antibodies against the same 19 species were assessed by an immunoassay.

RESULTS

Cases displayed an average of 22.7 teeth, 20.3 sites with probing depth > or =6 mm, and 18.9 sites with attachment loss > or =6 mm. Corresponding figures for controls were 27.1, 0.1, and 1.0, respectively. Heavy smoking was 3 times more frequent among cases than controls (32.1% versus 9.6%). Higher levels of Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia, Prevotella nigrescens, Prevotella melaninogenica, Bacteroides forsythus, Fusobacterium nucleatum, Treponema denticola, Eubacterium nodatum, Peptostreptococcus micros, and Campylobacter rectus were found in cases and higher levels of Eikenella corrodens, Veillonella parvula, and Actinomyces naeslundii in controls. Cases displayed higher IgG levels against P. gingivalis and Actinobacillus actinomycetemcomitans, while controls displayed higher levels against F. nucleatum, T. denticola, E. nodatum, and Capnocytophaga ochracea. Positive correlations between bacterial colonization and antibody responses were identified for 9 species in controls. In cases, however, statistically significant correlations were observed for only 3 species out of which only one was positive (V. parvula). Both bacterial levels and antibody responses declined in ages over 55 years. A logistic regression employing selected elements of bacterial colonization and antibody responses as independent variables resulted in 81.1% correct diagnosis, with sensitivity of 83.1%, specificity of 77.8%, positive predictability of 86%, and negative predictability of 73.7%. Smoking did not reach statistical significance in this model.

CONCLUSION

A combined microbial colonization/antibody response profile can effectively discriminate between periodontitis patients and periodontally intact controls.

Whole genomic DNA probe for detection of Porphyromonas endodontalis

The purpose of the present study was to develop a DNA probe for Porphyromonas endodontalis. Pure cultures of P. endodontalis were grown in TYP medium, in an anaerobic chamber. DNA was extracted from the P. endodontalis and labeled using the Genius System by Boehringer Mannheim. The labeled P. endodontalis DNA was used in dot-blot hybridization reactions with homologous (P. endodontalis) and unrelated bacterial samples. To determine specificity, strains of 40 other oral bacterial species (e.g. Porphyromonas gingivalis, Porphyromonas asaccharolytica, and Prevotella intermedia) were spotted and reacted with the P. endodontalis DNA probe. None of the panel of 40 oral bacteria hybridized with the P. endodontalis probe, whereas the blot of the homologous organism showed a strong positive reaction. To determine the sensitivity of the probe, dilutions of a P. endodontalis suspension of known concentration were blotted onto a nylon membrane and reacted with the probe. The results of our investigation indicate that the DNA probe that we have prepared specifically detects only P. endodontalis and can detect at least 3 x 10(4) cells.

Identifying clinically important gram-negative anaerobes from the oral cavity

Gram-negative oral anaerobes have frequently been associated with periodontal disease, some species more frequently than others. The confusing classification of these organisms has often obscured the association with disease of particular species within this group of organisms. This investigation aimed to compare different identification methods that could be applied in clinical research. Clinical isolates were collected and identified by three different methods: screening with phenotypic tests, commercial identification kits, and a 16S rRNA-based polymerase chain reaction (PCR) method. Forty-three reference strains of 19 Prevotella and Porphyromonas species were also included in the investigation. The phenotypic screen easily differentiated Porph. gingivalis from the other pigmented species. The screen also gave a good indication of separation of the lactose-fermenting species from the lactose non-fermenting species, although diversity can be seen in beta-galactosidase activity. Commercial identification kits did not add much to identification achieved with the phenotypic screen, only 20% of Porph. gingivalis isolates could be identified to species level with the kits. Neither the kits nor the phenotypic screen could differentiate Pr. intermedia and Pr. nigrescens. With the PCR method, Pr. intermedia and Pr. nigrescens were easily separated, and Porph. gingivalis was readily identified. Because of 16S rRNA gene sequence similarity, Pr. melaninogenica and Pr. veroralis could not be separated by the PCR method.

Ecology of genus Porphyromonas in canine periodontal disease

Asaccharolytic pigmented Porphyromonas species, including P. endodontalis, P. gingivalis, P. circumdentaria and unclassified species, were isolated from the plaque of adult dogs, but not from any oral sites of puppies and adolescent dogs. With age-dependency, the proportion of Porphyromonas species in the flora of plaque increased. Isolation of the genus Porphyromonas was clearly associated with the progress of periodontol disease. We suggested that Porphyromonas is the exogenous organism and obligate pathogen for canine periodontal diseases.

Survey for collagenase gene prtC in Porphyromonas gingivalis and Porphyromonas endodontalis isolated from endodontic infections

Collagenase is a potential virulence factor shown to be expressed by Porphyromonas gingivalis associated with periodontal disease. The purpose of this study was to use the polymerase chain reaction (PCR) to detect the presence of the collagenase gene (prtC) in 21 strains of Porphyromonas species isolated from endodontic infections. Type strains for P. gingivalis (ATCC 33277), P. endodontalis (ATCC 35406), Prevotella intermedia (ATCC 25611), and Prevotella nigrescens (ATCC 33563) were used as controls. When PCR primers specific for the 16S ribosomal RNA gene of P. gingivalis or P. endodontalis were used, 16 of the strains were identified as P. gingivalis, and five strains were identified as P. endodontalis. The presence of the prtC gene for collagenase was detected using PCR. Amplicons were analyzed by agarose gel electrophoresis, with an 815 bp amplicon representing the presence of the collagenase gene. Type strain ATCC 33277 and all 16 clinical isolates of P. gingivalis produced the collagenase gene amplicon. Neither type strain ATCC 35406 nor the five strains from clinical isolates of P. endodontalis produced the collagenase gene amplicon. These results indicate that P. gingivalis from endodontic infections possesses the prtC gene. P. endodontalis does not seem to exhibit prtC. The virulence of P. gingivalis may be related to its production of collagenase.

Associations amongst three feline Porphyromonas species from the gingival margin of cats during periodontal health and disease

Digoxigenin labelled whole chromosomal DNA probes directed against three feline members of the genus Porphyromonas (P. gingivalis VPB 3492, P. circumdentaria NCTC 12469T and P. salivosa VPB 3313) were used to identify and quantify organisms in samples taken from the gingival margins of 40 domestic cats with different grades of periodontal disease. At the right upper canine tooth, the grade of periodontal disease ranged from 0 to 5 and the cfu of facultative/obligate anaerobes ranged from 5.5 x 10(4) to 2.0 x 10(6)). In 38 of the 40 cats, at least one of the three Porphyromonas species was isolated and regression analysis showed that the cfu of total Porphyromonas sp. was a highly significant indicator of the grade of periodontal disease (p < 0.001, R2 0.510). Feline P. gingivalis was isolated from 37 of the 40 cats and regression analysis showed that it was a highly significant predictor of the grade of periodontal disease (p < 0.001, R2 0.561). The cfu of P. salivosa was a significant predictor of the grade of periodontal disease (p < 0.001, R2 0.286) and regression analysis showed that there was a significant positive relationship between cfu of P. circumdentaria and grade of periodontal disease (p = 0.018, R2 0.116). The periodontal grades at the right upper third premolar tooth ranged from 0 to 6. The cfu of facultative/obligate anaerobes isolated ranged from 1.2 x 10(5) to 7.9 x 10(6), and regression analysis showed that cfu was a significant predictor of periodontal grade (p < 0.001, R2 0.378). The cfu of total Porphyromonas species ranged from 1.2 x 10(4) to 1.7 x 10(6) and regression analysis of the cfu against the grade of periodontal disease showed a highly significant association (p < 0.001, R2 0.633). The cfu of P. gingivalis ranged from 0 to 1.1 x 10(6) and regression analysis of the cfu of P. gingivalis against the grade of periodontal disease showed a highly significant association (p < 0.001, R2 0.439). The cfu of P. salivosa was a significant predictor of the grade of periodontal disease (p < 0.001, R2 0.479) and the same association was found between cfu of P. circumdentaria and grade of periodontal disease (p = 0.002, R2 0.204). This study has established Porphyromonas as anumerically significant and highly prevalent genus in feline periodontal disease.

The isolation and enumeration of three feline oral Porphyromonas species from subcutaneous abscesses in cats

Samples were examined from 15 subcutaneous fight wound abscesses from 15 cats. All abscesses were closed at the time of sampling and cats had received no prior treatment. Samples were processed within 20 min and quantitative assessment made of total facultative and obligately anaerobic flora isolated. Digoxigenin labelled whole chromosomal DNA probes directed against three feline members of the genus Porphyromonas (P. gingivalis VPB 3492, P. circumdentaria NCTC 12469T and P. salivosa VPB 3313) were used to identify members of this genus and quantification of these species was made from each cat using colony lifts and southern hybridisation from nitrocellulose membranes taken from replicate plates from each abscess sample. Twelve of the 15 abscesses yielded a variety of facultative and obligately anaerobic (FOA) bacterial species and members of the genus Porphyromounas were enumerated from each of these 12 abscesses. Of the 12 abscesses in which Porphyromonas species were detected, seven contained one species only (five contained only P. gingivalis and two contained only P. salivosa) three abscesses contained two species (both P. gingivalis and P. circumdentaria) and two abscesses contained all three species of Porphyromonas. These results show that members of the genus Porphyromonas are likely to be significant contributors to the purulent disease process in subcutaneous abscesses in cats.

Endopeptidase activities of selected Porphyromonas spp., Prevotella spp. and Fusobacterium spp. of oral and non-oral origin

The ability of three Porphyromonas spp., seven Prevotella spp., seven Fusobacterium spp. and two related Bacteroides spp. (B. levii and B. macacae) to degrade an extensive range of synthetic endo-, amino- and diamino peptidase substrates linked to the fluorescent leaving group 7-amido-4-methylcoumarin (NHMec) was investigated. Many more species than was previously recognized exhibited peptidase activities, albeit at lower levels than those already described for Porphyromonas gingivalis. Detection of chymotrypsin-like activity was dependent on which of three NHMec-linked substrates was used, but all species exhibited degradative activity with at least one of these substrates. Elastase-like activity was detected in all species though not all species reacted with each of the elastase substrates. Glycylprolyl peptidase activity was detected in all of the species tested with the exception of F. mortiferum, F. gonidiaformans, F. naviforme and F. necrophorum. While the detection of peptidase activities does not appear to be useful for the differentiation of species within the genera Bacteroides and Prevotella, its ability to differentiate species of the genus Porphyromonas or Fusobacterium warrants further investigation.

Isolation and characterization of a nonpigmented variant of Porphyromonas endodontalis

Porphyromonas endodontalis forms dark colonies on media containing blood. We isolated, from an infected root canal, a non-black-pigmented P. endodontalis variant, KSEW01, which forms beige colonies on blood agar media. To characterize this variant, we compared its properties with those of two black-pigmented P. endodontalis strains, ATCC35406 and KSE105. Strain KSEW01 had a gelatinase activity comparable to that of the pigmented strains. Cell lysates of these three strains resolved by SDS-PAGE electrophoresis showed similar protein patterns. Quantitative DNA-DNA hybridization experiments indicated high homology between the nonpigmented strain KSEW01 and the two dark-pigmented strains. From these results, we identified strain KSEW01 as a P. endodontalis nonpigmented variant. DNA restriction endonuclease analysis indicated that the variant was closely related to a pigmented strain, KSE105. In contrast to the pigmented strains, strain KSEW01 did not degrade hemoglobin and formed no vesicles when cultured in the presence of blood. The susceptibilities of these three strains to 22 antibiotics were similar except for vancomycin. The nonpigmented variant was the most resistant to vancomycin (MIC: ATCC35406, 6.25 micrograms/ml; KSE105,12.5 micrograms/ml; KSEW01, 100 micrograms/ml). Overall, a relationship may exist between the presence of black-pigmentation and outer membrane systems of P. endodontalis.

Taxonomy and identification of periodontopathogenic bacteria and related species

The tumultuous evolution of oral and periodontal microbiology has focussed the attention of many researchers on the necessity to clarify the taxonomic position and identification criteria of putative periodontopathogens, in order to elucidate the role played by each species in the pathogenesis of periodontal disease. Many of the most important periodontopathogens recently underwent a radical reclassification process that may create some confusion and certainly deserves an accurate analysis aimed at focussing the actual situation of these bacteria. The taxonomic evolution and identification criteria of species of the genera Bacteroides, Prevotella, Porphyromonas and Actinobacillus is here analyzed in detail to clarify this recent evolutive taxonomic process, and to explain the importance of molecular studies for both taxonomic and identification purposes in this field.

Reclassification of Oribaculum catoniae (Moore and Moore 1994) as Porphyromonas catoniae comb. nov. and emendation of the genus Porphyromonas

A partial 16S rRNA gene sequence of the type strain of Oribaculum catoniae was determined by using PCR direct sequencing. A comparative sequence analysis demonstrated that this species, although saccharolytic, is phylogenetically a member of the genus Porphyromonas. On the basis of the phylogenetic and phenotypic distinctiveness of O. catoniae, we formally propose that this species should be reclassified in the genus Porphyromonas catoniae comb. nov. An emended description of the genus Porphyromonas is presented.

Update on the taxonomy and the clinical and laboratory characteristics of pigmented anaerobic gram-negative rods

Pigmented anaerobic gram-negative rods are currently categorized as 17 species distributed in three genera: Prevotella, Porphyromonas, and Bacteroides. These organisms are often encountered in clinical specimens but are also found as part of the indigenous flora on various mucosal surfaces. Several studies are presently assessing the association of individual species with health and disease. For example, Porphyromonas gingivalis and Porphyromonas endodontalis are key putative pathogens in adult periodontitis and root canal infections, respectively. Porphyromonas asaccharolytica is prevalent in extraoral infections. The Porphyromonas species of animal origin have been isolated from infected bite wounds in humans. Isolates closely resembling Bacteroides levii have been recovered from various types of human infections. According to preliminary reports, Prevotella intermedia tends to be associated more often with periodontal disease than with a healthy oral cavity. In the laboratory, enzyme profiling facilitates the identification of these pigmented rods. Beta-Lactamase production is more common among prevotella species (30%-50%) than among Porphyromonas species (< 10%).

Chemotaxonomy of Bacteroides: a review

The loose definition of Bacteroides, some species of which are important etiologic agents of oral diseases, has enabled isolates with only marginal similarities to be reposited in this genus. Many attempts have been made over the years to improve the taxonomy of this heterogeneous group of bacteria. The present article reviews major chemotaxonomic characters and techniques that have been used for this purpose: pigmentation, metabolites, whole-cell fatty acids, phospholipids, isoprenoid quinones, carbohydrates of lipopolysaccharide, whole-cell proteins, peptidoglycans, enzymes, pyrolysis mass spectrometry, DNA composition, restriction fragment length polymorphisms of DNA and ribosomal (r) RNA, homology of DNA and RNA, DNA-rRNA hybridization, and 16S and 5S rRNA oligonucleotide cataloging and sequencing. Despite improvements in their taxonomy, some bacteroides are still misclassified. Suggestions for further improvements in the taxonomy of bacteroides are made.

Phylogenetic analysis of members of the genus Porphyromonas and description of Porphyromonas cangingivalis sp. nov. and Porphyromonas cansulci sp. nov

The partial 16S rRNA gene sequences of representative strains of two groups of anaerobic, gram-negative, pigmented, asaccharolytic, rod-shaped bacteria isolated from subgingival plaque of dogs with naturally occurring periodontal disease were determined. A comparative analysis of the rRNA sequence data revealed that the two groups of organisms represent previously unknown lines of descent within the genus Porphyromonas. On the basis of our phylogenetic findings and the phenotypic distinctiveness of the organisms, two new species, Porphyromonas cangingivalis and Porphyromonas cansulci, are proposed.

Hydrolytic enzymes and lectin-binding activity of black-pigmented anaerobic rods

Recent taxonomic studies on black-pigmented anaerobic rods, a group of bacteria found on mucosal surfaces of humans and animals, led to the subdivision of existing species and to the creation of new species. The aim of this study was to characterize all 11 currently recognized species of black-pigmented bacteria (55 strains) for their ability to hydrolyse a variety of natural and synthetic substrates and for their lectin reactivity. Although most of the strains demonstrated some activity against proteinaceous substrates, Porphyromonas gingivalis was the only species able to hydrolyse type I collagen. Most strains possessed glycylprolyl protease activity, elastase-like activity and phospholipase C activity, whereas trypsin-like activity was restricted to P. gingivalis, Porphyromonas salivosa and Bacteroides macacae. beta-Lactamase activity was demonstrated in five strains belonging to the saccharolytic group. The lectin reactivity of the bacteria was determined by a dot-blot procedure using horseradish-peroxidase-conjugated lectins. Three lectins, LOTUS A, RCA-I and ConA, failed to react with any of the bacteria tested. WGA reacted strongly with the cell surface of human biotypes of asaccharolytic black-pigmented bacteria (P. gingivalis, Porphyromonas asaccharolytica and Porphyromonas endodontalis) and Prevotella intermedia. The animal biotype strains of P. gingivalis showed a higher affinity for SBA and PNA than for WGA.

Porphyromonas canoris sp. nov., an asaccharolytic, black-pigmented species from the gingival sulcus of dogs

A new species, Porphyromonas canoris, is proposed for black-pigmented asaccharolytic strains isolated from subgingival plaque samples from dogs with naturally occurring periodontal disease. This bacterium is an obligately anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organism. On laked rabbit blood or sheep blood agar plates, colonies are light brown to greenish brown after 2 to 4 days of incubation and dark brown after 14 days of incubation. Colonies on egg yolk agar and on nonhemolyzed sheep blood agar are orange. The cells do not grow in the presence of 20% bile and have a guanine-plus-cytosine content of 49 to 51 mol%. The type strain is VPB 4878 (= NCTC 12835). The average levels of DNA-DNA hybridization between P. canoris strains and other members of the genus Porphyromonas are as follows: Porphyromonas gingivalis ATCC 33277T (T = type strain), 6.5%; Porphyromonas gingivalis cat strain VPB 3492, 5%; Porphyromonas endodontalis ATCC 35406T, 1%; Porphyromonas salivosa NCTC 11362T, 5%; and Porphyromonas circumdentaria NCTC 12469T, 6%. The level of hybridization between P. canoris NCTC 12835T DNA and Porphyromonas asaccharolytica ATCC 25260T DNA is 3%. P. canoris cells produce major amounts of acetic, propionic, isovaleric, and succinic acids and minor amounts of isobutyric and butyric acids as end products of metabolism in cooked meat medium. The major cellular fatty acid is 13-methyltetradecanoic acid (iso-C15:0). Glutamate and malate dehydrogenases are present, as are glucose-6-phosphate dehydrogenase activity (65.7 nmol mg of protein-1 min-1) and 6-phosphogluconate dehydrogenase activity (63.0 nmol mg of protein-1 min-1).(ABSTRACT TRUNCATED AT 250 WORDS)

Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria

The phylogenetic structure of the bacteroides subgroup of the cytophaga-flavobacter-bacteroides (CFB) phylum was examined by 16S rRNA sequence comparative analysis. Approximately 95% of the 16S rRNA sequence was determined for 36 representative strains of species of Prevotella, Bacteroides, and Porphyromonas and related species by a modified Sanger sequencing method. A phylogenetic tree was constructed from a corrected distance matrix by the neighbor-joining method, and the reliability of tree branching was established by bootstrap analysis. The bacteroides subgroup was divided primarily into three major phylogenetic clusters which contained most of the species examined. The first cluster, termed the prevotella cluster, was composed of 16 species of Prevotella, including P. melaninogenica, P. intermedia, P. nigrescens, and the ruminal species P. ruminicola. Two oral species, P. zoogleoformans and P. heparinolytica, which had been recently placed in the genus Prevotella, did not fall within the prevotella cluster. These two species and six species of Bacteroides, including the type species B. fragilis, formed the second cluster, termed the bacteroides cluster. The third cluster, termed the porphyromonas cluster, was divided into two subclusters. The first contained Porphyromonas gingivalis, P. endodontalis, P. asaccharolytica, P. circumdentaria, P. salivosa, [Bacteroides] levii (the brackets around genus are used to indicate that the species does not belong to the genus by the sensu stricto definition), and [Bacteroides] macacae, and the second subcluster contained [Bacteroides] forsythus and [Bacteroides] distasonis. [Bacteroides] splanchnicus fell just outside the three major clusters but still belonged within the bacteroides subgroup. With few exceptions, the 16 S rRNA data were in overall agreement with previously proposed reclassifications of species of Bacteroides, Prevotella, and Porphyromonas. Suggestions are made to accommodate those species which do not fit previous reclassification schemes.

Porphyromonas endodontalis: prevalence and distribution of restriction enzyme patterns in families

In this study we determined the prevalence and distribution of Porphyromonas endodontalis in 26 families consisting of 107 subjects. P. endodontalis was present in 24% of the investigated subjects and was recovered most often from the dorsum of the tongue (50%). Isolation was also possible from the tonsils, the buccal mucosa, the saliva and the periodontal pocket. The usefulness of restriction endonuclease analysis as a typing method for this particular species was investigated by typing 19 isolates from unrelated individuals. All these isolates had unique restriction endonuclease patterns. The observed heterogeneity indicates that restriction endonuclease analysis is a sensitive measure of genetic dissimilarity between P. endodontalis isolates and is able to characterize individual isolates. Application of restriction endonuclease analysis to the obtained clinical isolates in this study shows the possibility of the presence of multiple clonal types within one subject. The DNA patterns of all P. endodontalis isolates from unrelated individuals were found to be distinct. In 3 families the DNA patterns of isolates from the mother and her child were indistinguishable. These data indicate the possibility of intrafamilial transmission of P. endodontalis.

Porphyromonas (Bacteroides) endodontalis: its role in endodontal infections

Porphyromonas endodontalis (formerly Bacteroides endodontalis) is a black-pigmented anaerobic Gram-negative rod which is associated with endodontal infections. It has been isolated from infected dental root canals and submucous abscesses of endodontal origin. The presence of P. endodontalis in infected dental root canals has been correlated with symptoms of an acute infection. It is occasionally found on oral mucous membranes and periodontal pockets. P. endodontalis has shown relatively low virulence in experimental monoinfections. In anaerobic mixed infections it can play an essential role. Differences in virulence between strains have been related to capsular material. On the basis of different types of capsules, three serotypes have been described. P. endodontalis is sensitive to a wide range of antibiotics, including the penicillins, the tetracyclines, and metronidazole.