Serum IgG titers against periodontal pathogens are associated with cerebral hemorrhage growth and 3-month outcome

To assess the influence of periodontal disease on cerebral hemorrhage and its clinical course, we examined the association of the serum IgG titer of periodontal pathogens with hemorrhage growth and 3-month outcome. We consecutively enrolled 115 patients with acute cerebral hemorrhage (44 females, aged 71.3 ± 13.1 years) and used ELISA to evaluate the serum IgG titers of 9 periodontal pathogens: Porphyromonas gingivalis, Aggregatibacter (A.) actinomycetemcomitans, Prevotella intermedia, Prevotella nigrescens, Fusobacterium (F.) nucleatum, Treponema denticola, Tannerella forsythensis, Campylobacter rectus, and Eikenella corrodens. Significant hematoma growth was defined as an increase in the volume of >33% or an absolute increase in the volume of >12.5 mL. A poor outcome was defined as a 3 or higher on the modified Rankin Scale. We observed hemorrhage growth in 13 patients (11.3%). Multivariate analysis revealed that increased IgG titers of A. actinomycetemcomitans independently predicted the elevated hemorrhage growth (odds ratio 5.26, 95% confidence interval 1.52-18.25, p = 0.01). Notably, augmented IgG titers of F. nucleatum but not A. actinomycetemcomitans led to a poorer 3-month outcome (odds ratio 7.86, 95% confidence interval 1.08-57.08, p = 0.04). Thus, we demonstrate that elevated serum IgG titers of A. actinomycetemcomitans are an independent factor for predicting cerebral hemorrhage growth and that high serum IgG titers of F. nucleatum may predict a poor outcome in patients with this disease. Together, these novel data reveal how systemic periodontal pathogens may affect stroke patients, and, should, therefore, be taken into consideration in the management and treatment of these individuals.

Establishing a mucosal gut microbial community in vitro using an artificial simulator

The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME^®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10–20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.

Extensive strain-level copy-number variation across human gut microbiome species

Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.

RNA-oligonucleotide quantification technique (ROQT) for the enumeration of uncultivated bacterial species in subgingival biofilms

Approximately 35% of the species present in subgingival biofilms are as yet uncultivated, so their role in periodontal pathogenesis is unknown. The aim of the present study was to develop a high throughput method to quantify a wide range of cultivated and uncultivated taxa in subgingival biofilm samples associated with periodontal disease or health. Oligonucleotides targeting the 16S ribosomal DNA gene were designed, synthesized and labeled with digoxigenin. These probes were hybridized with the total nucleic acids of pure cultures or subgingival biofilm samples. Target species included cultivated taxa associated with periodontal health and disease, as well as uncultivated species, such as TM7 sp. OT 346, Mitsuokella sp. OT 131 and Desulfobulbus sp. OT 041. Sensitivity and specificity of the probes were determined. A Universal probe was used to assess total bacterial load. Sequences complementary to the probes were used as standards for quantification. Chemiluminescent signals were visualized after film exposure or using a CCD camera. In a pilot clinical study, 266 subgingival plaque samples from eight periodontally healthy people and 11 patients with periodontitis were examined. Probes were specific and sensitivity reached 10(4) cells. Fusobacterium nucleatum ss. polymorphum and Actinomyces gerencseriae were the most abundant cultivated taxa in clinical samples. Among uncultivated/unrecognized species, Mitsuokella sp. OT 131 and Prevotella sp. OT 306 were the most numerous. Porphyromonas gingivalis and Desulfobulbus sp. OT 041 were only detected in patients with periodontitis. Direct hybridization of total nucleic acids using oligonucleotide probes permitted the quantification of multiple cultivated and uncultivated taxa in mixed species biofilm samples.

Genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; 'Acidaminococcaceae'; Megamonas

Megamonas hypermegale is the sole species of the genus Megamonas included in the List of Prokaryotic Names with Standing in Nomenclature and in the databases of DDBJ, EBI/EMBL and NCBI/GenBank it is placed in the lineage of Bacteroidetes; Bacteroidetes (class); 'Bacteroidales'; Bacteroidaceae; Megamonas. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this species clustered with species of the family 'Acidaminococcaceae' but not with those of the Bacteroidaceae. The genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; 'Acidaminococcaceae'; Megamonas.

Endosymbiotic Bacteroidales bacteria of the flagellated protist Pseudotrichonympha grassii in the gut of the termite Coptotermes formosanus

A unique lineage of bacteria belonging to the order Bacteroidales was identified as an intracellular endosymbiont of the protist Pseudotrichonympha grassii (Parabasalia, Hypermastigea) in the gut of the termite Coptotermes formosanus. We identified the 16S rRNA, gyrB, elongation factor Tu, and groEL gene sequences in the endosymbiont and detected a very low level of sequence divergence (<0.9% of the nucleotides) in the endosymbiont population within and among protist cells. The Bacteroidales endosymbiont sequence was affiliated with a cluster comprising only sequences from termite gut bacteria and was not closely related to sequences identified for members of the Bacteroidales attached to the cell surfaces of other gut protists. Transmission electron microscopy showed that there were numerous rod-shaped bacteria in the cytoplasm of the host protist, and we detected the endosymbiont by fluorescence in situ hybridization (FISH) with an oligonucleotide probe specific for the 16S rRNA gene identified. Quantification of the abundance of the Bacteroidales endosymbiont by sequence-specific cleavage of rRNA with RNase H and FISH cell counting revealed, surprisingly, that the endosymbiont accounted for 82% of the total bacterial rRNA and 71% of the total bacterial cells in the gut community. The genetically nearly homogeneous endosymbionts of Pseudotrichonympha were very abundant in the gut symbiotic community of the termite.

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.

A rapid DNA probe test compared to culture methods for identification of subgingival plaque bacteria

There has been a significant amount of interest in developing a more rapid and cost-effective test to identify bacterial pathogens in plaque. DNA probe technology may meet both these objectives, it is more rapid and cost-effective when compared to culture methods. The purpose of this study was to compare an automated DNA probe test with classical culture methods for identifying Bacteroides forsythus and Porphyromonas gingivalis in subgingival plaque of patients with adult periodontitis. Subgingival plaque samples were collected from sites with moderate to severe periodontitis and divided into two aliquots for analysis by either DNA probe or culture methods. When the DNA probe method was compared with the culture method (gold standard), the sensitivity and specificity for B. forsythus were 92.0% (SE = 3.4%) and 50.5% (SE = 7.8%), respectively; for P. gingivalis they were 52.2% (SE = 8.7%) and 74.7% (SE = 5.9%), respectively. Detection of B. forsythus and P. gingivalis by DNA probe correlated with probing depth (P = 0.01 for B. forsythus and P = 0.03 for P. gingivalis). It was concluded the DNA probe test was comparable to culture methods in detecting B. forsythus. In addition, when compared to the culture method, a better correlation was obtained with DNA probe detection of B. forsythus or P. gingivalis and clinical parameters.

Roles of mucosal bacteria and succinic acid in colitis caused by dextran sulfate sodium in mice

Intestines of mice with colitis caused by dextran sulfate sodium (DSS) contain more Bacteroidaceae cells than untreated controls. We investigated the roles of intestinal bacteria and succinic acid, a by-product of Bacteroidaceae metabolism, in this model of colitis. CBA/J mice were given 3% DSS in water for 14 days. After mice were anesthetized and killed, concentrations of organic acids in stools from the cecum and colon were measured. The resected rectum and colon were washed with sterile saline; some specimens were incubated with imipenem in saline for 1 h to kill bacteria on the surfaces and others were not. Their homogenates were cultured anaerobically and aerobically. Separately, 1 mL of 20 mM succinic acid was infused into the rectum of mice, whose anal verge was glued. Animals were anesthetized and killed the next day. The rectum and colon were examined histologically. Concentrations of succinate were higher everywhere in the colon of mice with colitis than in controls. Mice with colitis had more Bacteroidaceae cells, especially B. caccae, than controls. Mice given succinate enemas had focal erosions of the mucosa and edema of the submucosa. Succinic acid, produced abundantly by members of the family Bacteroidaceae, especially B. caccae, may be the ulcerogenic agent in DSS colitis.

Phylogenetic analysis of genus Marinilabilia and related bacteria based on the amino acid sequences of gyrB and emended description of Marinilabilia salmonicolor with Marinilabilia agarovorans as its subjective synonym

The detailed phylogenetic relationships for genus Marinilabilia and related taxa were analysed by using DNA gyrase B subunit gene (gyrB) sequences. Anaerobic bacteria in the Cytophaga-Flavobacterium-Bacteroides phylum, namely genera Marinilabilia, Bacteroides, Rikenella, Prevotella and Porphyromonas and Cytophaga fermentans, were clustered in the same branch and the facultative anaerobes Marinilabilia and Cytophaga fermentans formed a subcluster in the branch of the anaerobic bacteria. Phylogenetic analysis using 16S rDNA sequences gave a similar result but with a lower bootstrap value for each cluster. The gyrB sequences of Marinilabilia salmonicolor and Marinilabilia agarovorans were the same, and the relatedness of their chromosomal DNA, as determined by DNA-DNA hybridization, was greater than 70%. These genetic aspects led to the conclusion that M. salmonicolor IFO 15948T and M. agarovorans IFO 14957T belong to a single species. Since M. salmonicolor was described first, as Cytophaga salmonicolor, M. salmonicolor is a senior subjective synonym of M. agarovorans. Therefore, the name M. salmonicolor should be retained and strain IFO 14957T should be reclassified as M. salmonicolor. However, the agar-degrading ability of strain IFO 14957T is a prominent biochemical characteristic. It is therefore proposed that strain IFO 14957T should be renamed M. salmonicolor biovar agarovorans.

Porphyromonas gingivalis prevalence related to other micro-organisms in adult refractory periodontitis

Forty-six adult periodontal patients, selected on the basis of clinical examination, and 46 adult healthy subjects were examined. The subgingival plaque samples from one inflammatory and one non-inflammatory site of each periodontal patient were studied to determine Porphyromonas gingivalis prevalence related to other periodontal micro-organisms and to periodontal tissue destruction. The results showed Porphyromonas gingivalis as the main pathogenic micro-organism isolated in the inflammatory sites together with Bacteroides forsythus. Peptostreptococcus sp., Actinomyces sp. and Prevotella sp. were found as a normal oral flora in the healthy subjects. Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus and Eikenella corrodens were detected both in inflammatory and in non-inflammatory sites of periodontal patients as well as in the healthy subjects.

Subgingival microflora associated with nifedipine-induced gingival overgrowth

The purpose of this study was to examine the composition of subgingival plaque of 140 periodontal lesions in 35 patients with cardiovascular disorders who were administered nifedipine and manifested nifedipine-induced gingival overgrowth (GO). Age was inversely associated with the GO. Plaque index and bleeding index showed a significant association with GO, while nifedipine dosage and duration of nifedipine therapy were not found to be significant predictors of GO. The gingival inflammation as expressed in the logistic regression model by the interaction term color x tone was found to be significantly associated with the GO. Statistically significant differences between the groups of comparable probing depth and different degrees of GO were detected for Propionibacterium acnes, Capnocytophaga gingivalis, Capnocytophaga ochracea, Capnocytophaga sputigena, Bacteroides gracilis, Fusobacterium mortiferum, Fusobacterium nucleatum, Fusobacterium varium and Selenomonas sputigena in deep and enlarged lesions. Significantly more frequently isolated were the bacterial species Eubacterium alactolyticum, Campylobacter concisus, C. gingivalis, C. ochracea, C. sputigena, F. mortiferum, F. nucleatum, and F. varium from the more enlarged lesions (GO >3).

Subgingival microbiota in healthy, well-maintained elder and periodontitis subjects

This investigation compared the site prevalence of 40 subgingival species in 30 periodontally healthy (mean age 36+/-9 years), 35 elders with a well-maintained periodontium (mean age 77+/-5) and 138 adult periodontitis subjects (mean age 46+/-11). Subgingival plaque samples were taken from the mesial aspect of each tooth (up to 28 samples) in the 203 subjects at baseline. The presence and levels of 40 subgingival taxa were determined in 5003 plaque samples using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments including dichotomous measures of gingival redness, bleeding on probing, plaque accumulation and suppuration, as well as duplicate measures of pocket depth and attachment level, were made at 6 sites per tooth. The % of sites colonized by each species (prevalence) was computed for each subject. Differences in prevalence and levels among groups were sought using the Kruskal-Wallis test. Commonly detected species, such as Actinomyces naeslundii genospecies 2, Streptococcus sanguis and Streptococcus oralis did not differ significantly among subject groups. After adjusting for multiple comparisons, 4 species were significantly elevated and at greater prevalence in the periodontitis group. Mean % of sites (+/-SEM) colonized by Bacteroides forsythus was 10+/-3, 12+/-2 and 40+/-2 (p<0.001) for healthy, elder and periodontitis groups respectively. The odds ratio was 14.4:1 that a subject had periodontitis when B. forsythus was detected at > or = 5% of sampled sites. Mean prevalence for Porphyromonas gingivalis in healthy, elder and periodontitis subjects was 4+/-2, 5+/-2 and 23+/-2 respectively (p<0.001); for Treponema denticola 12+/-4, 10+/-3 and 30+/-2 (p<0.001) and for Selenomonas noxia 6+/-2, 7+/-2 and 19+/-2 (p<0.01). Similar differences among subject groups were observed when only sites with PD 0-4 mm were analyzed. The data suggest an etiologic role for B. forsythus, P. gingivalis, T. denticola and S. noxia in adult periodontitis.

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.

Phylogenetic placement of Dialister pneumosintes (formerly Bacteroides pneumosintes) within the Sporomusa subbranch of the Clostridium subphylum of the gram-positive bacteria

The nucleotide sequence of the 16S rRNA gene of the type strain of Dialister pneumosintes was determined. Phylogenetic analysis revealed that this species belongs to the Sporomusa branch of the Clostridium subphylum of the gram-positive bacteria and should therefore be excluded from the family Bacteroidaceae. Within this branch, which encompasses several other gram-negative taxa, such as Acidaminococcus, Pectinatus, Phascolarcobacterium, Quinella, Selenomonas, and Zymophilus, Dialister showed a specific, albeit distant, affinity with the genera Megasphaera and Veillonella.

Human root caries: microbiota in plaque covering sound, carious and arrested carious root surfaces

The plaque microbiota covering sound or carious root surfaces were studied and compared with that covering arrested root caries lesions. From each of these categories five extracted teeth were examined. The experimental design of the study allowed us to relate the qualitative and quantitative microbial composition to the degree of integrity of the root surface. Plaque was sampled by a newly developed 'mowing' technique. Plaque samples were cultured anaerobically on nonselective Columbia blood agar plates supplemented with 5% hemolyzed human blood and on media selective for Lactobacillus spp. and streptococci of the mutans group. The cultivable microbiota were quantitatively speciated using Rapid ID 32A, Rapid ID 32 Strep, API 20 Strep, API ZYM, and API 50 CH tests and SDS-PAG electrophoresis. Regardless of the state of mineralization, the microbiota on all surfaces resembled marginal plaque associated with gingivitis. In addition to the gram-positive predominant facultative anaerobic genera Streptococcus, Staphylococcus, Lactobacillus and Actinomyces, gram-negative anaerobes, predominantly Bacteroides, Prevotella, Selenomonas, Fusobacterium, Leptotrichia, and Capnocytophaga, showed the highest isolation frequencies. On all surfaces Actinomyces spp. predominated, with streptococci and lactobacilli forming a minor part of the microbiota. With respect to the detected proportions of anaerobes, microaerophiles, Actinomyces naeslundii, Prevotella buccae and Selenomonas dianae, significant differences were observed between the three categories of root surfaces. The total CFU's on both caries-free and caries-active surfaces were significantly higher than on arrested lesions. In general, the results support a polymicrobial etiology for caries initiation on root surfaces, with A. naeslundii, Capnocytophaga spp., and Prevotella spp. making specific contributions to the processes of cementum and dentin breakdown.

A rapid method for preparation of rough and smooth lipopolysaccharide from Bacteroides, Porphyromonas and Prevotella

We describe a new method for lipopolysaccharide (LPS) preparation by water extraction at 100 degrees C and subsequent digestion with proteinase K. The crude LPS could be reliably used for immunoblotting since it retained a high level of antigenicity, and was free of SDS and proteinase K, both of which can cause problems. Two monoclonal antibodies which failed to react with LPS prepared by two conventional methods reacted well with our preparation. We used the new method to prepare LPS from 44 strains of bacteria formerly classified as Bacteroides, some of which have been reclassified as Porphyromonas or Prevotella. In general, yields were good, and electrophoretic profiles obtained with SDS-PAGE and silver staining enabled strains to be rated rough, semi-rough, or smooth.

Porphyromonas-like gram-negative rods in naturally occurring periodontitis in dogs

A total of 259 Gram-negative Porphyromonas-like rods isolated from subgingival plaque samples of 16 family-owned dogs with naturally occurring periodontitis were characterized phenotypically by biochemical reactions, metabolic end products and enzymatic activities (API-ZYMTM, RoscoTM). Four distinct groups were found. Group A isolates (63) were asaccharolytic, lipase negative, trypsin positive and produced phenylacetic acid (PAA) from peptone-yeast extract glucose broth. Unlike P. gingivalis strains they were catalase positive. Group B isolates (42) differed from those of group A by a positive lipase reaction and from those of group D by failing to ferment sugars. Group C isolates (88) were asaccharolytic and did not produce PAA. They were alpha-fucosidase, N-acetyl-beta-glucosaminidase (beta-NAG) and trypsin negative, resembling P. endodontalis, but unlike human isolates, they were catalase positive. Subgroup C.1 isolates (6) differed from those of parent group C by producing minor amounts of PAA, and subgroup C.2 isolates (12) were beta-NAG positive. Group D isolates (46) were weakly fermentative, lipase, catalase and trypsin positive, and produced PAA. They resembled the B (P.) salivosus type strain which, in our hands, fermented weakly glucose, lactose and mannose. Two isolates could not be assigned to any of the previous groups.

Non-radioactively labelled DNA probes for the detection of periodontopathogenic Prevotella and Porphyromonas species

Digoxigenin-labelled synthetic DNA probes directed against the 16S rRNA were used for the direct detection of the periodontopathogenic bacteria Prevotella intermedia and Porphyromonas gingivalis in subgingival plaque by applying a DNA-RNA dot-blot hybridization procedure. The test was evaluated with 134 plaque samples from 26 patients with adult periodontitis or rapidly progressive periodontitis. The lower limit of detection was 10(4)-10(5) bacteria/specimen. A semiquantitative assessment of the two species in each sample and in the corresponding periodontal site was achieved by this technique. It is possible to examine 80-90 samples within two days with low material costs.

Fluorescence in situ hybridization for direct visualization of gram-negative anaerobes in subgingival plaque samples

Fluorescent oligonucleotide probes complementary to variable regions of Porphyromonas gingivalis and Bacteroides forsythus 16S ribosomal RNA were used to identify these organisms in smears of formaldehyde-fixed subgingival plaque samples from patients suffering from periodontitis. Fluorescence in situ hybridization represents a useful method for assessing the microbial ecology of the periodontal flora.

Classification and typing methods of black-pigmented gram-negative anaerobes

Until recently, black-pigmented Gram-negative anaerobes were classified as 'black-pigmented Bacteroides'. At present, 11 distinct species are recognized in this group. Because of major differences with Bacteroides fragilis, the type species of the genus Bacteroides, new genera have been proposed: Porphyromonas for three asaccharolytic species, and Prevotella for the saccharolytic species. Typing methods have been developed for some species of black-pigmented Gram-negative anaerobes. These include biotyping and serotyping, but relatively few types can be distinguished with these methods. Recently, DNA restriction endonuclease analysis has been used for typing of P. gingivalis, Pr. intermedia and P. endodontalis strains. Great heterogeneity was observed within all three species. This typing method can be useful for epidemiological studies.

Classification of black-pigmented anaerobes by pyrolysis mass spectrometry (PMS) and conventional tests (CTs)

Clinical (66: dental 53; vaginal 4; wound 9) and reference (5*) strains of pigmented Gram-negative anaerobic bacilli were examined in pyrolysis mass spectrometry (PMS) and conventional tests (CTs). The strains were identified in CTs as: Prevotella intermedia (48*); Pr. melaninogenica (1); Pr. corporis (7); Porphyromonas asaccharolytica (12*); P. endodontalis (1*) and P. gingivalis (2*). Numerical classification based on CTs resolved five clusters comprising strains identified as (I) Pr. corporis, (II) Pr. melaninogenica, (III) Pr. intermedia, (IV) P. gingivalis and (V) P. asaccharolytica and P. endodontalis. Numerical classification based on PMS showed a similar division, with decreasing homogeneity in the order Pr. intermedia, Pr. corporis, P. asaccharolytica, in agreement with the ordering of homogeneity for these species in CTs. PMS clusters corresponding the Porphyromonas spp. were clearly distinct from those of Prevotella spp. PMS and CT classifications disagreed on cluster membership for only six of the strains. PMS identification from blind challenge sets agreed with conventional identification for 64 of 67 strains.

The importance of black-pigmented gram-negative anaerobes in human infections

Black-pigmented Gram-negative anaerobic rods are found on mucosal surfaces as indigenous flora. With mucosal damage due to disease, trauma or surgery, these organisms may invade tissues and set up infection. Other important factors determining whether or not infection results include 'inoculum' size, synergy with other organisms and production of virulence factors that include capsules, lipopolysaccharide, attachment factors, proteases, collagenase, neuraminidase, and phospholipase A; also, they may have fibrinolytic and anti-phagocytic activity and may degrade complement and IgG and IgM. Pigmented anaerobes are found in all types of infections including such serious infections as bacteraemia, endocarditis, intracranial abscess, necrotizing pneumonia and necrotizing fasciitis, generally as part of a mixed infecting flora, and they play a key role in experimental mixed infections. They dominate or are prominent in infections involving organisms originating in the oropharynx, such as central nervous system, head and neck, dental and pleuropulmonary infections. Therapy of infections involving pigmented anaerobes includes surgery plus antimicrobial agents; a significant percentage of strains produce beta-lactamase. Much remains to be done to determine the relative importance of the various taxa of black-pigmented Gram-negative anaerobes and of the different virulence factors produced by them.

DNA base composition, aerotolerance and enzyme patterns of Leptotrichia buccalis

The guanine plus cytosine content of the DNA of Leptotrichia buccalis varied from 28.4 to 29.5 mol% (three strains). Eleven strains examined grew well under anaerobic and microaerobic conditions, but slowly in air in the presence of CO2. When examined for preformed enzymes in the APIZYM Complete Research Kit, positive reactions were obtained for several glucosidases and carboxylic ester hydrolases, and for a few peptidases.

Identification of Selenomonas species by whole-genomic DNA probes, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, biochemical tests and cellular fatty acid analysis

Nonisotopic, whole-genomic DNA probes, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), biochemical tests in microtiter trays and cellular fatty acid (CFA) analysis were compared for the identification of 5 oral Selenomonas species. DNA probes were prepared by biotin-labeling DNA extracted from the type strains of Selenomonas noxia, Selenomonas flueggei, Selenomonas artemidis, Selenomonas infelix and Selenomonas sputigena. The probes were hybridized with DNA from 21 reference strains, 18 fresh isolates of Selenomonas species, and 21 strains of other oral gram-negative species. Target DNAs were obtained by in situ extraction of colonies blotted onto filter paper. Streptavidin-linked alkaline phosphatase was used to detect homologous reactions of probe and target DNA. Each Selenomonas species DNA probe reacted with reference strains of only that species. All Selenomonas strains that reacted with the DNA probe for a particular species gave similar biochemical test results, SDS-PAGE protein profiles, and CFA profiles to those of the type strain of the corresponding species. All the methods tested were useful for identifying the species, and all yielded similar identifications of the fresh isolates. The DNA probes, however, had the potential for identifying Selenomonas species directly from primary isolation plates or plaque samples.

Use of chemotaxonomy as an aid to differentiate among Capnocytophaga species, CDC group DF-3, and aerotolerant strains of Leptotrichia buccalis

Four strains of fastidious gram-negative rods, thought to be Capnocytophaga species (formerly CDC group DF-1 or Bacteroides ochraceus) or CDC group DF-3 on the basis of conventional phenotypic criteria, were also analyzed for cellular fatty acid (CFA) composition. It was found that the CFA compositions of these strains were qualitatively incorrect for those taxa. Subsequently, it was determined that all four bacteria were in fact aerotolerant strains of Leptotrichia buccalis, based on biochemical reactions, CFA composition, and lactic acid as the major end product of glucose fermentation. It is recommended that, in addition to conventional cultural and biochemical criteria, all strains of Capnocytophaga or CDC group DF-3 should also be tested for metabolic end products of fermentation and CFA composition as essential adjuncts for identification.

Atypical structure of the 23S ribosomal RNA molecule in certain oral bacteria

Ribosomal RNA (rRNA) isolated from Wolinella recta and seven related bacteria was examined by agarose gel electrophoresis. The 23S rRNA molecule could not be detected in W. recta, Wolinella curva, Bacteroides gracilis, or Bacteroides ureolyticus. In place of the 23S molecule, there were three smaller molecules of approximately 1700, 650, and 600 bases designated 23S alpha, 23S beta, and 23S delta, respectively. An intact 23S rRNA molecule could be isolated from Wolinella succinogenes, Campylobacter concisus, and Campylobacter sputorum. The cleavage sites of the W. recta 23S rRNA molecule were located by direct RNA sequence analysis and were found to be in similar locations, nucleotides 546 and 1180, as cleavage sites described in other prokaryotes. The presence or absence of the 23S rRNA molecule may be a useful marker for these micro-organisms.

Propionigenium modestum: a separate line of descent within the eubacteria

The complete nucleotide sequence of 16S rRNA from Propionigenium modestum was determined and compared with 380 16S rRNA sequences from representatives of all eu- and archaebacterial phyla known so far. The phylogenetic analysis of this data set indicated P. modestum to represent a new separated line of descent within the radiation of eubacterial phyla moderately related to cyanobacteria and Gram-positive bacteria with low DNA GC content.

Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov

Hybridization experiments were carried out between DNAs from more than 70 strains of Campylobacter spp. and related taxa and either 3H-labeled 23S rRNAs from reference strains belonging to Campylobacter fetus, Campylobacter concisus, Campylobacter sputorum, Campylobacter coli, and Campylobacter nitrofigilis, an unnamed Campylobacter sp. strain, and a Wolinella succinogenes strain or 3H- or 14C-labeled 23S rRNAs from 13 gram-negative reference strains. An immunotyping analysis of 130 antigens versus 34 antisera of campylobacters and related taxa was also performed. We found that all of the named campylobacters and related taxa belong to the same phylogenetic group, which we name rRNA superfamily VI and which is far removed from the gram-negative bacteria allocated to the five rRNA superfamilies sensu De Ley. There is a high degree of heterogeneity within this rRNA superfamily. Organisms belonging to rRNA superfamily VI should be reclassified in several genera. We propose that the emended genus Campylobacter should be limited to Campylobacter fetus, Campylobacter hyointestinalis, Campylobacter concisus, Campylobacter mucosalis, Campylobacter sputorum, Campylobacter jejuni, Campylobacter coli, Campylobacter lari, and "Campylobacter upsaliensis." Wolinella curva and Wolinella recta are transferred to the genus Campylobacter as Campylobacter curvus comb. nov. and Campylobacter rectus comb. nov., respectively. Bacteroides gracilis and Bacteroides ureolyticus are generically misnamed and are closely related to the genus Campylobacter. Campylobacter nitrofigilis, Campylobacter cryaerophila, and an unnamed Campylobacter sp. strain constitute a new genus, for which the name Arcobacter is proposed; this genus contains two species, Arcobacter nitrofigilis comb. nov. (type species) and Arcobacter cryaerophilus comb. nov. Wolinella succinogenes so far is the only species of the genus Wolinella. The genus Helicobacter is also emended; Campylobacter cinaedi and Campylobacter fennelliae are included in this genus as Helicobacter cinaedi comb. nov. and Helicobacter fennelliae comb. nov., respectively. The genus "Flexispira," with "Flexispira rappini" as the only species, is closely related to the genus Helicobacter. The free-living, sulfur-reducing campylobacters do not belong to any of these genera; they probably constitute a distinct genus within rRNA superfamily VI.

Assignment of Clostridium bryantii to Syntrophospora bryantii gen. nov., comb. nov. on the basis of a 16S rRNA sequence analysis of its crotonate-grown pure culture

The Clostridium bryantii-Methanospirillum hungatei syntrophic coculture, grown on caproate, was adapted to grow on crotonate. Then, C. bryantii was isolated in pure culture from crotonate bottle plates. A 16S rRNA sequence analysis of the pure subculture revealed that, as a member of the gram-positive phylum, it was not closely related to any of the Clostridium species with which it was compared or to any of the other clusters in the gram-positive phylum with which it was compared. However, it was closely related to another syntrophic fatty acid-degrading bacterium, Syntrophomonas wolfei. On the basis of its phylogeny, physiology, and cell wall ultrastructure, we propose assignment of C. bryantii to Syntrophospora bryantii gen. nov., nov. comb.

The problem of the taxonomy of the fusiform bacillus of acute necrotizing ulcerative gingivitis (Vincent's gingivitis)

The characteristic microscopic appearance of the fusospirochaetal complex in smears from patients with acute necrotizing ulcerative gingivitis has long been regarded as virtually pathognomonic of the disease. Unfortunately there is considerable confusion surrounding the taxonomy of the fusiform organism in the fusospirochaetal complex. The conflicting views appear to be irreconcilable and a re-evaluation of the taxonomy of oral fusiforms is urgently required.

Differentiation of ruminal bacterial species by enzyme-linked immunosorbent assay using egg yolk antibodies from immunized chicken hens

Cross-reactivity among four species of ruminal bacteria was examined by using egg yolk antibodies from immunized Leghorn laying hens and an enzyme-linked-immunosorbent assay. The effects of the four species on the hens were compared on various days postimmunization. Hens injected with the same bacterial species had similar apparent antibody levels over the entire postimmunization period, but only Bacteroides ruminicola B1(4) and Selenomonas ruminantium D antigens elicited early increases in apparent antibody levels during weeks 2 and 3. Antibody cross-reactivity was greatly reduced by week 2, except for antibodies against Streptococcus bovis JB1.

Characterization of Wolinella spp., Campylobacter concisus, Bacteroides gracilis, and Eikenella corrodens by polyacrylamide gel electrophoresis

The small asaccharolytic, nonpigmenting gram-negative rods of the human oral cavity are difficult to differentiate from each other. Protein profiles of sonicated cells of Wolinella species, Campylobacter concisus, Bacteroides gracilis, and Eikenella corrodens were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and visualized with a silver stain. The gels were scanned with a laser densitometer, and the similarity of strains was computed by determining correlation coefficients of normalized densities along the gels. The strains were grouped by cluster analysis of the correlation coefficients. All species were distinct from each other. Several groups were found within E. corrodens. A colored silver stain was found to highlight species differences and appears to be useful in the rapid identification of fresh isolates.

API ZYM and API An-Ident reactions of fastidious oral gram-negative species

API ZYM and API An-Ident enzymatic substrate tests were done on six oral species which are difficult to characterize with conventional biochemical tests. "Bacteroides forsythus, the "fusiform" Bacteroides species (A. C. R. Tanner, M. A. Listgarten, M. N. Strzempko, and J. L. Ebersole, manuscript in preparation), is difficult to cultivate in broth media, yet it gave 15 positive tests in these series. The tests were able to separate this new species from species of Capnocytophaga and Fusobacterium. "B. forsythus" reactions were similar but not identical to those of reference Bacteroides species. Positive reactions for alpha-glucosidase, beta-glucosidase, alpha-fucosidase, and alpha-glucuronidase suggest that "B. forsythus" may be saccharolytic. It was the only species tested which was trypsin positive. Wolinella species, Campylobacter concisus, B. gracilis, and Eikenella corrodens are asaccharolytic, and characterization relies heavily on sensitivities to inhibitory agents. These species reacted weakly in the API ZYM and API An-Ident enzymatic substrate tests, and the reactions were not useful for separating these species. The enzyme reactions differentiated Wolinella recta and C. concisus from Selenomonas sputigena, another oral motile but saccharolytic organism.

Identification of fusobacteria in a routine diagnostic laboratory

A scheme for differentiating Fusobacterium spp. and Leptotrichia spp. from Bacteroides spp. was devised after examining 114 strains of fusobacteria and asaccharolytic bacteroides (17 reference strains and 97 clinical isolates). Sensitivity to a 300 micrograms/ml plate of phosphomycin and an acid reaction on a lysine plate were found to be reliable for differentiating Fusobacterium spp. and L. buccalis from Bacteroides. Using a short set of simple cultural and biochemical tests, isolates could be identified as F. necrophorum, F. necrogenes, F. nucleatum, F. varium or L. buccalis. These tests were: indole, lecithinase, phosphatase, DNase and gas production, aesculin and casein hydrolysis, greening of casein/methylene blue agar, nitrite reduction, bile tolerance and haemolysis on horse blood agar.

Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract

This report describes a new group of anaerobic bacteria that degrade oxalic acid. The new genus and species, Oxalobacter formigenes, are inhabitants of the rumen and also of the large bowel of man and other animals where their actions in destruction of oxalic acid may be of considerable importance to the host. Isolates from the rumen of a sheep, the cecum of a pig, and from human feces were all similar Gram-negative, obligately anaerobic rods, but differences between isolates in cellular fatty acid composition and in serologic reaction were noted. Measurements made with type strain OxB indicated that 1 mol of protons was consumed per mol of oxalate degraded to produce approximately 1 mol of CO2 and 0.9 mol of formate. Substances that replaced oxalate as a growth substrate were not found.

Fatty acid composition of oral isolates of Selenomonas

Fatty acids of 16 strains of Selenomonas isolated from the human oral cavity were examined by gas-liquid chromatography. The strains showed similar patterns, characterized by the presence of straight-chain fatty acids in the range C11 to C18. Fatty acids of odd-numbered carbon atoms dominated and the major acids were n-pentadecanoate and 3-hydroxytridecanoate. The general fatty acid pattern of Selenomonas differed distinctly from those of other previously analysed anaerobic or microaerophilic Gram-negative bacilli.

Chemical composition, ultrastructure and some serological properties of lipopolysaccharides from Leptotrichia buccalis

Lipopolysaccharide (LPS) was extracted with aqueous phenol from Leptotrichia buccalis strains L 11, ATCC 14201 and ATCC 19616. Virtually all the LPS was found in the water phase. LPS could also be extracted with phenol/chloroform/petroleum ether, but not with cold trichloroacetic acid. All LPS preparations contained D-glycero-D-manno-heptose, galactose, glucose, glucosamin, n-dodecanoate, 3-hydroxy-n-tetradecanoate and phosphorus. In addition LPS from L11 contained 2-keto-3-deoxyoctonate and an unidentified aldose. LPS from L11 was serologically distinct from LPS of ATCC 14201 and ATCC 19616. LPS from the two latter strains crossreacted.

Feasibility of automated head-space gas chromatography in identification of anaerobic bacteria

Neutral and acidic metabolites of some anaerobic bacteria cultured in a liquid growth medium were analysed by gas chromatography. Studies on the head-space vapours above heated broth cultures, using a gas chromatograph equipped with a fused silica capillary column and a unit for automatic head-space injection, enabled volatile alcohols and fatty acids to be readily detected. By contrast, when studying ether extracts of the same cultures, using a packed column, alcohols were only rarely registered, being more or less "hidden" under the solvent peak. Head-space gas chromatography was thus found to provide more diagnostic information on anaerobes, as exemplified by the registration of volatile alcohols produced by Clostridium sporogenes. Being suited for automation, this technique should be considered as an alternative to the study of solvent extracts of broth cultures in gas chromatographic identification of anaerobic bacteria.

Neuraminidase production by Bacteroidaceae

The production of neuraminidase (EC 3.2.1.18) by 77 strains of Bacteroidaceae was investigated by techniques previously used to study neuraminidase production by clostridia. Conditions for culture and assay of Bacteroides fragilis neuraminidase were characterised. The enzyme is predominantly cell associated; it is not calcium dependent and the pH optimum for its production is c. 4.5. Most neuraminidase-positive Bacteroides strains produced the enzyme well in the test media but a few strains failed to produce it consistently in one or other of the media. Because of these occasional variations, strains were grown and tested in at least two media before being defined as neuraminidase negative. Within the B. fragilis group of species, B. fragilis, B. vulgatus, B. distasonis, B. ovatus, B. thetaiotaomicron and B. variabilis were neuraminidase positive while B. eggerthii, B. uniformis and B. splanchnicus were negative. Two subspecies of B. melaninogenicus (ss. melaninogenicus and ss. levii) were positive but the other (ss. intermedius) was negative. Strains of B. oralis and B. bivius produced the enzyme while B. ruminicola, B. disiens, B. asaccharolyticus and B. corrodens did not. The microaerophilic B. ochraceus were also positive. None of the Fusobacterium or Leptotrichia species tested produced neuraminidase. Our results for neuraminidase production are consistent for all strains of each species examined and we suggest that tests for neuraminidase production would be a valuable addition to biochemical tests currently used in taxonomic studies of the Bacteroidaceae.

A scheme for the identification of clinical isolates of Gram-negative anaerobic bacilli by conventional bacteriological tests

More than 1000 strains of gram-negative anaerobic bacilli, including reference strains, clinical isolates, and members of the normal flora of the mouth, lower gastro-intestinal tract and vagina of healthy human subjects, were studied by conventional bacteriological methods and by gas-liquid chromatographic analysis of metabolic products in a series of investigations. A short combined set of tests with particular discriminant value was selected, and a scheme for the identification of the species and subspecies encountered in the diagnostic bacteriological laboratory was based upon our composite results. The tests are: antibiotic-disk resistance tests with neomycin 1000 micrograms, kanamycin 1000 micrograms, penicillin 2 units and rifampicin 15 micrograms per disk; tolerance tests with sodium taurocholate, Victoria blue 4R and gentian violet; and tests for pigment production, indole production, aesculin hydrolysis and the fermentation of glucose, lactose, sucrose, rhamnose, trehalose, mannitol and xylose. Gram-negative anaerobic bacilli are divided into four groups: (1) the fragilis group with nine species, which include the five subgroups previously classified as subspecies of B. fragilis; (2) the melaninogenicus-oralis group, which includes the three saccharolytic subspecies (ss.) of B. melaninogenicus--ss. melaninogenicus, ss. intermedius and ss. levii--and four non-pigmented species; (3) the asaccharolytic group, which comprises B. asaccharolyticus (formerly B. melaninogenicus ss. asaccharolyticus), B. corrodens and other non-pigmented non-saccharolytic strains, and (4) the fusobacteria.

Serological properties of Bacteroidaceae

A review of immunological experiments with Sphaerophorus species and anaerobes of the Bacteroides fragilis group is presented.