Intravenous antibiotics in preterm infants have a negative effect upon microbiome development throughout preterm life

BACKGROUND

Intestinal dysbiosis is implicated in the origins of necrotising enterocolitis and late-onset sepsis in preterm babies. However, the effect of modulators of bacterial growth (e.g. antibiotics) upon the developing microbiome is not well-characterised. In this prospectively-recruited, retrospectively-classified, case-control study, high-throughput 16S rRNA gene sequencing was combined with contemporaneous clinical data collection, to assess the within-subject relationship between antibiotic administration and microbiome development, in comparison to preterm infants with minimal antibiotic exposure.

RESULTS

During courses of antibiotics, diversity progression fell in comparison to that seen outside periods of antibiotic use (-0.71units/week vs. + 0.63units/week, p < 0.01); Enterobacteriaceae relative abundance progression conversely rose (+ 10.6%/week vs. -8.9%/week, p < 0.01). After antibiotic cessation, diversity progression remained suppressed (+ 0.2units/week, p = 0.02).

CONCLUSIONS

Antibiotic use has an acute and longer-lasting impact on the developing preterm intestinal microbiome. This has clinical implications with regard to the contribution of antibiotic use to evolving dysbiosis, and affects the interpretation of existing microbiome studies where this effect modulator is rarely accounted for.

A systematic review of droplet and aerosol generation in dentistry

OBJECTIVES

This review aimed to identify which dental procedures generate droplets and aerosols with subsequent contamination, and for these, characterise their pattern, spread and settle.

DATA RESOURCES

Medline(OVID), Embase(OVID), Cochrane Central Register of Controlled Trials, Scopus, Web of Science and LILACS databases were searched for eligible studies from each database's inception to May 2020 (search updated 11/08/20). Studies investigating clinical dental activities that generate aerosol using duplicate independent screening. Data extraction by one reviewer and verified by another. Risk of bias assessed through contamination measurement tool sensitivity assessment.

STUDY SELECTION

A total eighty-three studies met the inclusion criteria and covered: ultrasonic scaling (USS, n = 44), highspeed air-rotor (HSAR, n = 31); oral surgery (n = 11), slow-speed handpiece (n = 4); air-water (triple) syringe (n = 4), air-polishing (n = 4), prophylaxis (n = 2) and hand-scaling (n = 2). Although no studies investigated respiratory viruses, those on bacteria, blood-splatter and aerosol showed activities using powered devices produced greatest contamination. Contamination was found for all activities, and at the furthest points studied. The operator's torso, operator's arm and patient's body were especially affected. Heterogeneity precluded inter-study comparisons but intra-study comparisons allowed construction of a proposed hierarchy of procedure contamination risk: higher (USS, HSAR, air-water syringe, air polishing, extractions using motorised handpieces); moderate (slow-speed handpieces, prophylaxis, extractions) and lower (air-water syringe [water only] and hand scaling).

CONCLUSION

Gaps in evidence, low sensitivity of measures and variable quality limit conclusions around contamination for procedures. A hierarchy of contamination from procedures is proposed for challenge/verification by future research which should consider standardised methodologies to facilitate research synthesis.

CLINICAL SIGNIFICANCE

This manuscript addresses uncertainty around aerosol generating procedures (AGPs) in dentistry. Findings indicate a continuum of procedure-related aerosol generation rather than the common binary AGP or non-AGP perspective. The findings inform discussion around AGPs and direct future research to support knowledge and decision making around COVID-19 and dental procedures.

Profiling of Oral Bacterial Communities

The profiling of bacterial communities by the sequencing of housekeeping genes such as that encoding the small subunit ribosomal RNA has revealed the extensive diversity of bacterial life on earth. Standard protocols have been developed and are widely used for this application, but individual habitats may require modification of methods. This review discusses the sequencing and analysis methods most appropriate for the study of the bacterial component of the human oral microbiota. If possible, DNA should be extracted from samples soon after collection. If samples have to be stored for practical reasons, precautions to avoid DNA degradation on freezing should be taken. A critical aspect of profiling oral bacterial communities is the choice of region of the 16S rRNA gene for sequencing. The V1-V2 region provides the best discrimination between species of the genus Streptococcus, the most common genus in the mouth and important in health and disease. The MiSeq platform is most commonly used for sequencing, but long-read technologies are now becoming available that should improve the resolution of analyses. There are a variety of well-established data analysis pipelines available, including mothur and QIIME, which identify sequence reads as phylotypes by comparing them to reference data sets or grouping them into operational taxonomic units. DADA2 has improved sequence error correction capabilities and resolves reads to unique variants. Two curated oral 16S rRNA databases are available: HOMD and CORE. Expert interpretation of community profiles is required, both to detect the presence of contaminating DNA, which is commonly present in the reagents used in analysis, and to differentiate oral and nonoral bacteria and determine the significance of findings. Despite advances in shotgun whole-genome metagenomic methods, oral bacterial community profiling via 16S rRNA sequence analysis remains a valuable technique for the characterization of oral bacterial populations.

Perinatal inflammation influences but does not arrest rapid immune development in preterm babies

Infection and infection-related complications are important causes of death and morbidity following preterm birth. Despite this risk, there is limited understanding of the development of the immune system in those born prematurely, and of how this development is influenced by perinatal factors. Here we prospectively and longitudinally follow a cohort of babies born before 32 weeks of gestation. We demonstrate that preterm babies, including those born extremely prematurely (<28 weeks), are capable of rapidly acquiring some adult levels of immune functionality, in which immune maturation occurs independently of the developing heterogeneous microbiome. By contrast, we observe a reduced percentage of CXCL8-producing T cells, but comparable levels of TNF-producing T cells, from babies exposed to in utero or postnatal infection, which precedes an unstable post-natal clinical course. These data show that rapid immune development is possible in preterm babies, but distinct identifiable differences in functionality may predict subsequent infection mediated outcomes.

Horizontal and Vertical Transfer of Oral Microbial Dysbiosis and Periodontal Disease

One of the hallmark features of destructive periodontal disease, well documented over the last 50 y, is a change to the quantitative and qualitative composition of the associated microbiology. These alterations are now generally viewed as transformational shifts of the microbial populations associated with health leading to the emergence of bacterial species, which are only present in low abundance in health and a proportionate decrease in the abundance of others. The role of this dysbiosis of the health associated microbiota in the development of disease remains controversial: is this altered microbiology the driving agent of disease or merely a consequence of the altered environmental conditions that invariably accompany destructive disease? In this work, we aimed to address this controversy through controlled transmission experiments in the mouse in which a dysbiotic oral microbiome was transferred either horizontally or vertically into healthy recipient mice. The results of these murine studies demonstrate conclusively that natural transfer of the dysbiotic oral microbiome from a periodontally diseased individual into a healthy individual will lead to establishment of the dysbiotic community in the recipient and concomitant transmission of the disease phenotype. The inherent resilience of the dysbiotic microbial community structure in diseased animals was further demonstrated by analysis of the effects of antibiotic therapy on periodontally diseased mice. Although antibiotic treatment led to a reversal of dysbiosis of the oral microbiome, in terms of both microbial load and community structure, dysbiosis of the microbiome was reestablished following cessation of therapy. Collectively, these data suggest that an oral dysbiotic microbial community structure is stable to transfer and can act in a similar manner to a conventional transmissible infectious disease agent with concomitant effects on pathology. These findings have implications to our understanding of the role of microbial dysbiosis in the development and progression of human periodontal disease.

Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double-blind, placebo-controlled trial with microbiome analysis

Objective

To determine the effects on the vaginal microbiota of an oral probiotic preparation administered from early pregnancy.

Design

Randomised, double blind, placebo‐controlled trial.

Setting

Four maternity units in the UK.

Population

Women aged 16 years or older recruited at 9–14 weeks' gestation.

Methods

Participants were randomly allocated to receive oral capsules of probiotic containing Lactobacillus rhamnosus GR‐1 and Lactobacillus reuteri RC‐14 each at 2.5 × 10⁹ colony‐forming units (CFUs) or placebo once daily from recruitment until the end of pregnancy.

Main outcome measure

Rates of bacterial vaginosis (BV, defined as Nugent score ≥7) at 18–20 weeks' gestation compared by logistic regression adjusted for possible confounders.

Results

The primary analysis included 78% (238/304) of participants who initially consented (probiotic group 123, placebo group 115). Of these participants, 95% (227/238) reported an intake of 93% or more of the required number of capsules. The rates of BV did not differ between groups at 18–20 weeks' gestation (15% (19/123) in the probiotic group vs. 9% (10/115) in the placebo group, adjusted odds ratio 1.82, 95% confidence interval 0.64–5.19). There were also no differences between the groups in the proportion of women colonised with the probiotic strains, Escherichia coli, group B streptococci or other vaginal microbiota. There were no differences in the alpha diversity or composition of the bacterial communities between or within the probiotic and placebo groups at 9–14 and 18–20 weeks’ gestation.

Conclusions

Oral probiotics taken from early pregnancy did not modify the vaginal microbiota.

Tweetable abstract

The oral probiotic preparation used in this study does not prevent BV in pregnant women.

The oral probiotic preparation used in this study does not prevent BV in pregnant women.

First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063)

Despite significant advances in recent years in culture-independent molecular microbiology methods, the detailed study of individual bacterial species still relies on having pure cultures in the laboratory. Yet, more than a third of the approximately 700 bacterial taxa found in the human oral cavity are as yet uncultivated in vitro. One such taxon, Tannerella sp. HOT-286 (phylotype BU063), is the focus of much interest since it is associated with periodontal health, while Tannerella forsythia, its closest phylogenetic neighbor, is strongly associated with periodontal disease. HOT-286, however, has remained uncultivated despite the efforts of several research groups, spanning over a decade. The aim of this study was to cultivate Tannerella sp. HOT-286. A heavily diluted sample of subgingival plaque was inoculated onto culture plates supplemented with siderophores (pyoverdines-Fe complex or desferricoprogen) or a neat plaque suspension. After 8 d of anaerobic incubation, microcolonies and colonies showing satellitism were passaged onto fresh culture plates cross-streaked with potential helper strains or onto cellulose-acetate membranes placed over lawn cultures of helper strains. Subcultured colonies were identified by 16S rRNA gene sequencing, and purity was confirmed by sequencing 20 clones per library prepared from a single colony. Three colonies of interest (derived from pyoverdines- and plaque-supplemented plates) were identified as Tannerella sp. HOT-286. The isolates were found to be incapable of independent growth, requiring helpers such as Propionibacterium acnes and Prevotella intermedia for stimulation, with best growth on membranes over "helper" lawns. A representative isolate was subjected to phenotypic characterization and found to produce a range of glycosidic and proteolytic enzymes. Further comparison of this novel "periodontal health-associated" taxon with T. forsythia will be valuable in investigating virulence factors of the latter and possible health benefits of the former.

Cultivation of a Synergistetes strain representing a previously uncultivated lineage

Subgingival plaque samples obtained from human subjects with periodontitis, shown to include previously uncultivable members of the phylum Synergistetes, were used to inoculate Cooked Meat Medium (CMM). The presence of Cluster A (uncultivable) Synergistetes was monitored by fluorescent in situ hybridization (FISH) and quantitative PCR (Q-PCR). Cluster A Synergistetes were found to grow in CMM in co-culture with other plaque bacteria and growth was stimulated by the addition of mucin and serum. Plaque samples were also used to inoculate Blood Agar (BA) plates and growth of Cluster A Synergistetes was revealed after anaerobic incubation, by colony hybridization with specific probes. Surface growth on the plates in regions identified by colony hybridization was harvested and used to inoculate fresh plates, thus enriching for Cluster A Synergistetes. Cross-streaks of other plaque bacteria were also used to stimulate Synergistetes growth. In the early passages, no discrete Synergistetes colonies were seen, but after eight passages and the use of cross-streaks of other bacteria present in the enriched community, colonies arose, which consisted solely of Cluster A Synergistetes cells, as determined by 16S rRNA gene PCR and cloning. This is the first report of the successful culture of a member of the uncultivable branch of this phylum.

Periodontal Disease: Production of volatile sulphur compounds in diseased periodontal pockets is significantly increased in smokers

OBJECTIVE

This study was undertaken in order to test the hypothesis that the consequences of tobacco smoking may include increased synthesis of toxic volatile sulphur compounds in diseased periodontal pockets.

DESIGN

A cross-sectional, parallel study comparing groups of smokers and non-smokers with periodontitis and the level of volatile sulphur compounds in the gingival sulci of these subjects.

PATIENTS AND METHODS

Levels of volatile sulphur compounds were measured in diseased periodontal sites of 12 smokers and 11 non-smokers using a portable sulphide monitor. Anaerobic and aerobic counts of the total cultivable subgingival microflora of both groups were also determined.

RESULTS

The percentage of sites per subject with high levels of sulphides (> or = 10 units) detected in moderate (4-6 mm) and deep (> or = 7 mm) periodontal pockets was found to be significantly higher in smokers, compared to non-smokers (P = 0.040 and P = 0.005, respectively). No significant difference in the microbiological parameters tested were observed between the two groups.

CONCLUSIONS

Increased production of volatile sulphur compounds may represent a further mechanism of increased susceptibility to periodontitis in smokers and also help to explain the reported association between smoking and halitosis.

Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets

INTRODUCTION

Molecular ecological analysis based on 16S rRNA gene sequence analysis is well established for the characterisation of complex bacterial communities. However, 'universal' PCR primers can introduce biases into the analysis of the species composition of clone libraries because of mismatches between the primer and target organism sequences. In this study, three universal primer sets were compared for the analysis of the microflora in subgingival plaque.

METHODS

Three subgingival plaque samples were collected from two subjects with localised severe chronic periodontitis. Half of each sample was cultured while DNA was extracted from the remaining half and 16S rDNA amplified with universal primer pairs 27F, 1525R (A); 27F, 1492R (B) and 530F, 1525R (C). Amplified genes were cloned, sequenced and identified by comparison with 16S rRNA databases.

RESULTS

137 taxa were identified among 177 isolates and 417 clones sequenced. Of these, 86 were detected only by the molecular technique whereas 26 were found only by culture. Sequences from 81 taxa did not correspond to those of named species and of these, 38 were not represented in the nucleotide databases. 16S RNA genes for these 38 taxa were sequenced and deposited with GenBank.

CONCLUSION

The use of three sets of universal primers allowed the identification of 38 novel bacterial phylotypes. There were marked differences in the composition of the libraries generated by the different primer sets. A combination of molecular and cultural techniques is recommended to maximise the coverage of detection of bacterial taxa in oral samples.

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.

Molecular analysis of the microflora associated with dental caries

Molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. The aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. Samples were collected with a hand excavator from five teeth with carious lesions involving dentine. Samples were cultured on blood agar and Rogosa agar incubated in air plus 5% CO(2) and on fastidious anaerobe agar anaerobically. DNA was also extracted directly from the samples and 16S rRNA genes were amplified by PCR with universal primers. PCR products were singularized by cloning, and the cloned inserts and cultured isolates were identified by 16S rRNA gene sequence analysis. We identified 95 taxa among the 496 isolates and 1,577 clones sequenced; 44 taxa were detected by the molecular method alone; 31 taxa were previously undescribed. Only three taxa, Streptococcus mutans, Rothia dentocariosa, and an unnamed Propionibacterium sp., were found in all five samples. The predominant taxa by anaerobic cultivation were the novel Propionibacterium sp. (18%), Olsenella profusa (14%), and Lactobacillus rhamnosus (8%). The predominant taxa in the molecular analysis were Streptococcus mutans (16%), Lactobacillus gasseri/johnsonii (13%), and Lactobacillus rhamnosus (8%). There was no significant difference between the compositions of the microflora in the middle and advancing front samples (P < 0.05, Wilcoxon matched pairs, signed ranks test). In conclusion, combined cultural and molecular analyses have shown that a diverse bacterial community is found in dentinal caries and that numerous novel taxa are present.

Gram-positive anaerobic bacilli in human periodontal disease

OBJECTIVE

The uncertain taxonomy of oral anaerobic gram-positive bacilli and their generally slow growing nature has limited the understanding of their role in periodontal disease. The current objective was to design and use species-specific oligonucleotide probes to investigate the relationship of selected gram-positive anaerobic bacilli to periodontal disease.

METHODS

Plaque and clinical measurements were collected from 40 patients with periodontitis and from 40 matched controls. Oligonucleotide probes were designed for Bulleidia extructa, Eubacterium nodatum, Mogibacterium timidum and Slackia exigua and used to probe nucleic acids extracted from the samples with a chemiluminescent detection method. Species were quantified as absent or present at low (approximately 10(3)-10(4) cells), medium (approximately 10(4)-10(5) cells) or high levels (approximately 10(5)-10(6) cells).

RESULTS

M. timidum and B. extructa were detected in only three and four samples, respectively. The level of both E. nodatum and S. exigua was significantly higher in deep than shallow pockets (Wilcoxon, p < 0.001). The level of E. nodatum, but not S. exigua, was higher in patients than matched controls (Mann-Whitney U, p < 0.03). Using an ordered logistic regression model, the probing depth of the sampled sites had the greatest influence on the level of both species and significant variations occurred between individuals. Bleeding also influenced the levels of both species, with supragingival plaque influencing S. exigua.

CONCLUSION

Both E. nodatum and S. exigua were associated with clinical indicators of periodontal disease.

Dialister invisus sp. nov., isolated from the human oral cavity

Six strains of anaerobic, Gram-negative coccobacilli isolated from the root canals of patients with endodontic infections (five strains) and from a deep periodontal pocket (one strain) were subjected to a comprehensive range of phenotypic and genetic tests and were found to comprise a homogeneous group. Following 16S rRNA gene sequence analysis, they were found to be most closely related to Dialister pneumosintes, with 93 % sequence similarity between the two taxa. A novel species, Dialister invisus sp. nov., is proposed. Biochemically, the species is largely unreactive and is asaccharolytic, with only traces of acetate and propionate detected as metabolic end-products. The G+C content of the DNA of D. invisus strains is 45-46 mol%. The type strain is E7.25(T) (=CCUG 47026(T)=DSM 15470(T)).

Molecular and cultural analysis of the microflora associated with endodontic infections

Cultural studies have indicated that a subset of the oral microflora is responsible for endodontic infections. Approximately 50% of oral bacteria are unculturable, so it is likely that currently unknown bacteria are present in such infections. In this study, cultural and molecular analyses were performed on the microflora in aspirate samples collected from 5 infected root canals. 16S rDNA sequences from 261 isolates and 624 clones were identified by comparison with database sequences. Sixty-five taxa were identified, of which 26 were found by the molecular method alone. A mean of 20.2 taxa was found in each sample. A new species of Dialister was the only organism present in all 5 samples. Twenty-seven novel taxa were detected, 18 of which belonged to the phylum Firmicutes and 8 to Bacteroidetes. Culture-independent, molecular analysis has revealed a more diverse microflora associated with endodontic infections than that revealed by cultural methods alone.

Adjunctive effects to non-surgical periodontal therapy of systemic metronidazole and amoxycillin alone and combined. A placebo controlled study

BACKGROUND AND AIM

Several studies have reported adjunctive benefits to scaling and root planing (SRP) of systemic amoxycillin and metronidazole in the treatment of periodontal diseases. To date no comparisons have been made of these antimicrobials alone or in combination. The aim of this study was to compare the adjunctive benefits to SRP of amoxycillin and metronidazole alone and combined.

METHODS

66 subjects <46 years of age with advanced chronic periodontal disease participated in this randomised, double blind, 4 parallel treatment group designed study. All subjects received quadrant SRP and then were prescribed amoxycillin capsules (250 mg) and metronidazole tablets (200 mg) (AM) or lactate capsules and metronidazole (PM) or amoxycillin and calcium lactate tablets (AP) or lactate and calcium lactate (PP). All medication was 3 of each per day for 7 days. Subgingival plaque samples were obtained and probing depth (PD), loss of attachment (LOA), bleeding on probing (BOP), suppuration (SUPP) and plaque (DEP) were recorded pre-treatment, 1, 3 and 6 months post-treatment.

RESULTS

Final group sizes were: AM=15, PM=16, AP=16 and PP=15. PD improved in all groups. Treatment effects were highly significantly different and always greatest in the AM and least in the PP groups. Benefits of PM and AP over PP were also noted. LOA improved in all groups and showed the same highly significant treatment differences, again favouring AM. BOP improved in all groups, particularly in AM compared to the other groups. SUPP improved in all groups and was virtually eradicated in AM with differences among treatments highly significant. DEP changed little in any group and there were no significant differences among groups. Microbiological data showed significant differences in favour of AM compared to PP and PM for total aerobes and anaerobes at 1 month. P. intermedia counts were always lower in active groups compared to PP and reached significance for AM and AP at 1 month and AM and PM at 3 months.

CONCLUSION

The significant differences among treatment groups and the overall trend in the data, in line with other studies, support the considerable adjunctive benefits to SRP of amoxycillin and metronidazole combined in the treatment of advanced chronic periodontal disease.

The clinical and microbiological effects of a novel acidified sodium chlorite mouthrinse on oral bacterial mucosal infections

Acidified sodium chlorite mouthrinses have been shown to have equivalent anti-plaque activity to those containing chlorhexidine, the current 'gold standard'. In this study, sodium chlorite mouthrinses (ASC) acidified with either malic or gluconic acids were compared to each other and with a chlorhexidine rinse and sterile water for their effect on salivary bacterial counts. Sixteen subjects participated in the study, which had a cross-over Latin square design. In a second study, a sodium chlorite/gluconic acid rinse was compared with chlorhexidine for its clinical and microbiological effects in 36 patients with oral mucosal infections. The sodium chlorite rinses acidified with malic and gluconic acids and the chlorhexidine rinse caused significant reductions in salivary bacterial counts up to 7 h after a single rinse compared with water. There were no significant differences between the three active treatments. In the mucosal infection study, there was a significant reduction in erythema in the chlorhexidine group compared with the ASC group. Patients who received the ASC rinse reported significantly less discomfort following treatment than those receiving the chlorhexidine rinse. Staphylococcus aureus counts were significantly reduced in the group who received the sodium chlorite rinse. There were no other significant differences between the treatments. ASC appears to be an effective alternative to chlorhexidine mouthrinse.

Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov

The diversity of organisms present in the subgingival pockets of patients with periodontitis and acute necrotizing ulcerative gingivitis (ANUG) were examined previously. The 16S rRNA genes of subgingival plaque bacteria were amplified using PCR with a universal forward primer and a spirochaete-selective reverse primer. The amplified DNA was cloned into Escherichia coli. In one subject with ANUG, 70 clones were sequenced. Seventy-five per cent of the clones were spirochaetal, as expected. Twelve of the remaining clones fell into two clusters that represent novel phylotypes in the family Coriobacteriaceae. The first novel phylotype was most closely related to Atopobium rimae (98% similarity). The phylotype probably represents a novel Atopobium species, but will not be named until cultivable strains are obtained. The second novel phylotype was only 91% similar to described Atopobium species and 84% similar to Coriobacterium glomerans. The 16S rRNA sequences of the type strain of Lactobacillus uli and a strain representing the Moores' Eubacterium group D52 were determined as part of on ongoing sequence analysis of oral bacteria. The sequence for L. uli was more than 99.8% similar to sequences for the second clone phylotype. It therefore appears that the second clone phylotype and L. uli represent the same species. The sequence for the Eubacterium D52 strain was 95.6% similar to that of L. uli. The G+C content of the DNA of L. uli and Eubacterium D52 is 63-64 mol %. These organisms are thus distinct from the neighbouring genus Atopobium, which has a DNA G+C content of 35-46 mol%. A new genus, Olsenella gen. nov., is proposed for these two species on the basis of phenotypic characteristics and 16S rRNA sequence analysis to include Olsenella uli comb. nov. and Olsenella profusa sp. nov.

Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity

Five strains of anaerobic non-sporing Gram-positive bacilli isolated from advanced periodontitis (four strains) and a dentoalveolar abscess (one strain) that did not correspond to existing species were subjected to phenotypic and genetic characterization. Following 16S rDNA sequence analysis, they were found to constitute a novel branch of the low G+C Gram-positive division of the phylogenetic tree related to Erysipelothrix rhusiopathiae and Holdemania filiformis. A new genus Bulleidia, and the species Bulleidia extructa, are proposed. Growth of B. extructa in broth media was poor but was enhanced by the addition of fructose, glucose or maltose together with Tween 80. Glucose and maltose were fermented and arginine was hydrolysed. Acetate, lactate and trace amounts of succinate were the end products of glucose fermentation. The G+C content of the DNA of the type strain is 38 mol%. The type strain of Bulleidia extructa is DSM 13220T.

Eubacterium minutum is an earlier synonym of Eubacterium tardum and has priority

The recently proposed species Eubacterium minutum and Eubacterium tardum appeared to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of strains of both species to clarify their taxonomic position. The type strains of E. minutum and E. tardum exhibited identical biochemical and protein profiles and their 16S rRNA gene sequences displayed 99.9% similarity. The G + C content of the DNA of both strains was estimated at 45 mol%. It is concluded that E. minutum and E. tardum are synonyms; E. minutum has priority. An emended description of E. minutum is given.

Detection of unculturable bacteria in periodontal health and disease by PCR

Recently developed molecular methods have made it possible to characterize mixed microflora in their entirety, including the substantial numbers of bacteria which do not grow on artificial culture media. In a previous study, molecular analysis of the microflora associated with acute oral infections resulted in the identification of three phylotypes, PUS3.42, PUS9.170, and PUS9.180, representing as-yet-uncultured organisms. The aim of this study was to design and validate specific PCR primers for these phylotypes and to determine their incidences in samples collected from healthy and diseased periodontal tissues. Two specific reverse primers were devised for each phylotype, and these were used in duplex PCRs with universal forward and reverse primers. All three phylotypes were detected in periodontal sites; PUS9.170, related to oral asaccharolytic Eubacterium spp., was significantly associated with disease. This study demonstrates the possibility of using unculturable, and therefore uncharacterized, organisms as markers of disease.

The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov

16S rRNA gene sequences were determined for Eubacterium exiguum and Peptostreptococcus heliotrinreducens. These species were found to be closely related and, together with Eubacterium lentum, to constitute a branch of the Coriobacteriaceae. Two new genera are proposed on the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons: Slackia to include the bile-sensitive species Eubacterium exiguum and P. heliotrinreducens, and Eggerthella to include the bile-resistant Eubacterium lentum. It is proposed that Eubacterium exiguum and Peptostreptococcus heliotrinreducens are transferred to the genus Slackia gen. nov. as Slackia exigua gen. nov., comb. nov. (type strain ATCC 700122T) and Slackia heliotrinireducens gen. nov., comb. nov. (type strain NTCC 11029T), respectively, and Eubacterium lentum is transferred to the genus Eggerthella gen. nov. as Eggerthella lenta gen. nov., comb. nov. with Eggerthella lenta as the type species.

Phospholipid analogue distribution in Capnocytophaga

Polar lipids of nineteen previously characterised culture collection strains of Capnocytophaga were analysed using fast atom bombardment mass spectrometry (FAB MS) in negative mode. All strains examined had a major peak at m/z 241, consistent with the expected presence of the pentadecanoate anion. The most intense higher mass anions, consistent with expected presence of phospholipid molecular species, were as follows: m/z 574, 588, 618 and 662 which are consistent with presence of PE(24:2), PE(25:2), PE(27:1) and PE(30:0) respectively. Other anions putatively identified as phospholipid anions were: m/z 572, 578, 592, 602, 604, 616 and 720 consistent with presence of PE(24:3), PE(24:0), PE(25:0), PE(26:2), PE(26:1), PE(27:2) and OH-PE(33:0). Capnocytophaga isolates share a distinctive phospholipid fingerprint which appears to lack the somewhat higher mass phospholipid analogues observed in related oral bacteria. Within the genus, the profiles obtained showed only quantitative differences which did not correlate with previous studies.

Diversity of oral asaccharolytic Eubacterium species in periodontitis--identification of novel phylotypes representing uncultivated taxa

Oral asaccharolytic Eubacterium species are associated with periodontal disease and other oral infections. The aim of this study was to use a culture-independent molecular technique to determine the diversity of asaccharolytic Eubacterium species in subgingival plaque in periodontitis. An oligonucleotide PCR primer designed to amplify 16S rRNA genes of the oral asaccharolytic Eubacterium branch of the phylogenetic tree was constructed. This primer was used together with a universal primer in PCRs to amplify gene sequences directly from a single subgingival plaque sample. Fifty PCR products were purified by cloning, fully sequenced and subjected to molecular phylogenetic analysis. The sequences were assigned to four groups within a single lineage of the low G + C gram-positive bacteria. Group I (58% of the cloned sequences) was assigned to a branch that included Eubacterium nodatum, and Group II (22%) to a branch including Eubacterium infirmum. Group III (8%) was distinct from but related to E. infirmum at the species level, and Group IV (12%) was another novel taxon more distantly related to E. infirmum and E. nodatum.

The deconvolution of pyrolysis mass spectra using genetic programming: application to the identification of some Eubacterium species

Pyrolysis mass spectrometry was used to produce complex biochemical fingerprints of Eubacterium exiguum, E. infirmum, E. tardum and E. timidum. To examine the relationship between these organisms the spectra were clustered by canonical variates analysis, and four clusters, one for each species, were observed. In an earlier study we trained artificial neural networks to identify these clinical isolates successfully; however, the information used by the neural network was not accessible from this so-called 'black box' technique. To allow the deconvolution of such complex spectra (in terms of which masses were important for discrimination) it was necessary to develop a system that itself produces 'rules' that are readily comprehensible. We here exploit the evolutionary computational technique of genetic programming; this rapidly and automatically produced simple mathematical functions that were also able to classify organisms to each of the four bacterial groups correctly and unambiguously. Since the rules used only a very limited set of masses, from a search space some 50 orders of magnitude greater than the dimensionality actually necessary, visual discrimination of the organisms on the basis of these spectral masses alone was also then possible.

Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA

We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.

The comparative effect of acidified sodium chlorite and chlorhexidine mouthrinses on plaque regrowth and salivary bacterial counts

Acidified sodium chlorite (ASC) is recognised as a highly potent, broad spectrum antimicrobial system that has been successfully developed for uses in veterinary, food processing and medical device fields. The current studies aimed to investigate the persistence of antimicrobial action and plaque inhibitory properties of 3 ASC mouthrinses by comparison with positive control, chlorhexidine 0.12%, and placebo control, water, rinses. Both studies were randomised, double-blind, cross-over 5-cell designs balanced for carryover. The 1st study involved 15 healthy subjects who immediately before and at 30, 60, 180, 300 and 420 min after rinsing provided 2 ml saliva samples. The samples were immediately processed for total anaerobic bacterial counts recorded after 96 h incubation. Washout periods were a minimum of 3 days. The second study involved 20 healthy subjects who on day 1 of each study were rendered plaque free, suspended normal oral hygiene methods and commenced rinsing twice daily with the allocated rinse. On day 5, plaque was scored by index and area after disclosing with erythrosin. Washout periods were 2 1/2 days. The 3 ASC and chlorhexidine rinses produced similar reductions in salivary bacterial counts which remained significantly below the placebo control to 7 h. There were no significant differences between ASC and chlorhexidine rinses except at 30 and 60 min when significantly greater reductions were produced by 2 ASC rinses compared to the chlorhexidine rinse. Plaque indices and areas were considerably and significantly lower with the ASC and chlorhexidine rinses compared to the placebo rinse. There were no significant differences between plaque scores for the 3 ASC rinses and the chlorhexidine rinse, although for 2 ASC rinses plaque scores were lower than for the chlorhexidine rinse. The results indicate that the 3 ASC rinses have equivalent plaque inhibitory action to chlorhexidine as a rinse. Similar to chlorhexidine, the plaque inhibitory action of the rinses appears to be derived from a persistence of antimicrobial action in the mouth.

Phylogeny of oral asaccharolytic Eubacterium species determined by 16S ribosomal DNA sequence comparison and proposal of Eubacterium infirmum sp. nov. and Eubacterium tardum sp. nov

16S rRNA gene sequences of Eubacterium brachy, Eubacterium nodatum, Eubacterium saphenum, Eubacterium timidum, and two previously unnamed taxa were determined. The results of a phylogenetic analysis indicated that all of the strains sequenced belonged to a deep branch of the low-G+C-content gram-positive group. The levels of 16S ribosomal DNA sequence similarity between species were low, suggesting that a number of genera may be represented in this group. The representatives of the two unnamed taxa, which were isolated from patients with periodontitis, were clearly distinct from the previously described species, and, therefore, the following two new species are proposed: Eubacterium infirmum (type strain, NCTC 12940) and Eubacterium tardum (type strain, NCTC 12941).

Molecular analysis of microflora associated with dentoalveolar abscesses

The microflora associated with three dentoalveolar abscesses was determined by cultural and molecular methods. 16S rRNA genes were randomly amplified by means of conserved eubacterial primers and cloned. Restriction fragment length polymorphism analysis of the clones and amplified genes encoding 16S rRNA from the cultured bacteria was used to detect putative unculturable bacteria. Clones representative of five predominant groups of uncultured organisms were sequenced. Two were identified as Porphyromonas gingivalis and Prevotella oris, and one was found to be closely related to Peptostreptococcus micros. The remaining two clones did not correspond to known, previously sequenced organisms. One was related to Zoogloea ramigera, a species of aerobic waterborne organisms, while the other was distantly related to the genus Prevotella. This study has demonstrated the possibility of the characterization of microflora associated with human infection by molecular methods without the inherent biases of culture.

Identification and discrimination of oral asaccharolytic Eubacterium spp. by pyrolysis mass spectrometry and artificial neural networks

Curie-point pyrolysis mass spectra were obtained from 29 oral asaccharolytic Eubacterium strains and 6 abscess isolates previously identified as Peptostreptococcus heliotrinreducens. Pyrolysis mass spectrometry (PyMS) with cluster analysis was able to clarify the taxonomic position of this group of organisms. Artificial neural networks (ANNS) were then trained by supervised learning (with the back-propagation algorithm) to recognize the strains from their pyrolysis mass spectra; all Eubacterium strains were correctly identified, and the abscess isolates were identified as un-named Eubacterium taxon C2 and were distinct from the type strain of P. heliotrinreducens. These results demonstrate that the combination of PyMS and ANNs provides a rapid and accurate identification technique.

Rapid differentiation of Prevotella intermedia and P. nigrescens by 16S rDNA PCR-RFLP

Prevotella intermedia and the newly described P. nigrescens cannot be reliably distinguished by phenotypic tests. In this study, restriction endonuclease digestion of amplified 16S rDNA (16S rDNA PCR-RFLP) was used to generate restriction profiles of the type strains of P. intermedia and P. nigrescens and 43 fresh isolates identified as belonging to one of the two species. Whole-cell protein profiles were obtained by SDS-PAGE for comparative purposes. The type strains of P. intermedia and P. nigrescens were easily distinguished by 16S rDNA PCR-RFLP and the fresh isolates were assigned to either species on the basis of their restriction profiles. The identifications obtained were identical to those obtained by protein profiles. 16S rDNA PCR-RFLP is a rapid and reliable method for the differentiation of P. intermedia and P. nigrescens.

A 6-month home-usage trial of 0.1% and 0.2% delmopinol mouthwashes (II). Effects on the plaque microflora

The effects of 0.1% and 0.2% delmopinol mouthwashes on supragingival plaque flora were investigated in a 6-month home-use study. 141 subjects were studied from whom plaque was collected at baseline, 12, 24, and 36 weeks. Overall, there were no consistent effects on microscopic or total counts. However, there was a significant reduction in the proportion of dextran-producing streptococci in the active groups compared to the control group throughout treatment. There was no colonisation by Candida or Gram-negative aerobic bacilli in the active groups nor was there any decrease in susceptibility to delmopinol. Delmopinol appears to mediate its anti-plaque effect without causing a major shift in bacterial populations, although dextran-producing bacteria appear to be affected, which may have relevance to this agent's mode of action.

Analysis of cultivable Porphyromonas gingivalis with trypsin-like protease enzyme activity and serum antibodies in chronic adult periodontitis

OBJECTIVE

Trypsin-like protease (TLPase) enzyme produced by Porphyromonas gingivalis has been implicated as a virulence factor in the pathogenesis of periodontal disease. The aims of this study were to investigate the relationship between cultivable P. gingivalis, TLPase enzyme activity (BANA hydrolysis) and serum antibody levels against cell sonicate and a purified TLPase antigen from P. gingivalis W50.

MATERIALS AND METHODS

Sub-gingival plaque samples were cultured for levels of P. gingivalis together with a chairside analysis of TLPase enzyme activity (Perioscan) from periodontitis and gingivitis sites of adult periodontitis patients. A TLPase from P. gingivalis was purified by gel filtration and ion exchange chromatography from the vesicle fraction for use as a test antigen.

RESULTS

Elevated levels of P. gingivalis were found at periodontitis sites, however, there was no correlation with sub-gingival plaque TLPase enzyme activity. Adult periodontitis patients had higher levels of IgG and IgA against cell sonicate and TLPase antigens than did controls. Those patients who were P. gingivalis culture-positive demonstrated an elevated immune response against both cell sonicate and TLPase when compared to P. gingivalis culture-negative patients. Treatment resulted in an improvement of clinical indices and no cultivable P. gingivalis could be recovered from the treated sites and there was a concomitant decrease in IgG levels against the TLPase. There was no significant difference in BANA hydrolysis at gingivitis sites or periodontitis sites after treatment.

CONCLUSIONS

Further longitudinal studies are suggested to investigate the role of the TLPase in the response to treatment of chronic adult periodontitis patients.

Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of human Capnocytophaga

The confusion in the taxonomic status of the genus Capnocytophaga has made identification of strains and studies on the role of this genus in infectious diseases equivocal. In this study 33 strains of Capnocytophaga including reference strains and various clinical isolates, were studied using RFLP analysis of 16S ribosomal RNA genes. The 16S ribosomal RNA (rRNA) gene sequences from whole cell suspensions and isolated genomic DNA samples were amplified by the polymerase chain reaction (PCR) using eubacterial specific primers. PCR products were purified and characterized by single digestions with 12 restriction endonucleases. Five of these, BanI, CfoI, HaeIII, HphI and RsaII were found to discriminate reproducibly between strains, and restriction patterns (ribotypes) produced by these were analysed to clarify the classification of Capnocytophaga strains. Dendrograms inferring similarities were derived from these data by the UPGMA method. This analysis produced three major clusters of strains, each of which was associated with a previously proposed species type strain: C. gingivalis, C. sputigena and C. ochracea. The results support the division of Capnocytophaga into three species and demonstrate that, despite the heterogeneity of this genus, the modified ribotyping method provides a simple, rapid and reproducible way to identify Capnocytophaga strains.

Antimicrobial properties of delmopinol against oral bacteria

Antimicrobial properties of the morpholine derivative delmopinol hydrochloride were investigated in vitro. Minimum inhibitory concentrations were measured for a range of oral bacteria by broth and agar dilution techniques and minimum bactericidal concentrations were measured in broth. The rate of kill was investigated by determination and analysis of kill curves. The results indicated that delmopinol is a relatively weak antimicrobial in comparison with chlorhexidine. However, it may selectively affect certain species of oral bacteria which are of importance in plaque formation.

The antibacterial and anti-staining properties of the novel anti-adherent agent M239, 144 alone and in combination with chlorhexidine

The anti-adherent agent M239,144 has been shown to reduce the adhesion of S. sanguis strains to saliva-coated hydroxyapatite by 27-94%. The purpose of this study was to determine any antibacterial properties of M239,144 which might inhibit replication of the organisms which do adhere and to determine whether M239,144 interferes with the antibacterial properties of the antiseptic agent chlorhexidine. Maximum inhibitory dilutions (MIDs) were calculated using both broth and agar methods. 0.1% M239,144 displayed no antibacterial activity against S. oralis NCTC 7864 or S. sanguis NCTC 7863 using the broth dilution method and had no antibacterial activity against a range of plaque-forming organisms using the agar dilution method. The anti-bacterial activity of chlorhexidine against four of five oral plaque-forming species was reduced by 0.1% M239,144. The effect of a novel anti-adherent agent, MK239,144, on chlorhexidine staining was assessed in an in vitro model. 1% M239,144 completely prevented chlorhexidine staining at concentrations from 0.0002% to 0.2%. M239,144/chlorhexidine formulations show potential for a non-staining anti-plaque mouthwash.

An unclassified Eubacterium taxon in acute dento-alveolar abscess

The microflora of pus samples aspirated from 50 acute dento-alveolar abscesses was examined. A total of 143 bacterial strains was isolated, consisting predominantly of Prevotella spp., alpha-haemolytic Streptococcus spp., Peptostreptococcus spp. and Eubacterium spp. An unclassified asaccharolytic Eubacterium taxon was encountered in 17 (34%) of the abscesses. This taxon was found to have a positive association with Fusobacterium spp. and a negative association with alpha-haemolytic Streptococcus spp.

Does gingivitis lead to periodontitis in young adults?

It has been assumed that poor oral hygiene predisposes to gingivitis with progression to periodontitis and tooth loss. However, a high prevalence of gingivitis occurs in some populations in which severe periodontitis is rare. To assess whether gingivitis is a reliable predictor of periodontitis, we compared the periodontal health of tea pickers and university students aged between 18 and 30 in Indonesia. Oral hygiene and gingival health was significantly better in students than in tea pickers. However, the prevalence and the severity of chronic periodontitis were similar in the two groups. Our findings suggest that gingivitis is a poor predictor of periodontitis in subjects younger than 30 years. Attempts to prevent periodontitis in young adults through antigingivitis measures such as plaque control may be unsuccessful.

A 6-month home usage trial of a 1% chlorhexidine toothpaste (II). Effects on the oral microflora

The effects of 1% chlorhexidine and 1% chlorhexidine/fluoride dentifrices on supragingival plaque flora were investigated in a 6-month home-usage study. 146 subjects were studied from whom plaque around 6 teeth was collected at baseline, 6 weeks and 24 weeks. Total anaerobic counts were reduced at 6 and 24 weeks in both active groups compared to control. No differences were seen in any other bacterial parameters. There was a significant decrease in the susceptibility to chlorhexidine of bacteria recovered from the subjects on the active treatments compared to control but, since the magnitude of effect was less than one dilution, this was not thought to be of any clinical significance.