Bacteriophage infection--a possible mechanism for increased virulence of bacteria associated with rapidly destructive periodontitis

Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

BACKGROUND

Porphyromonas gingivalis (hereafter "Pg") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. One of the key forces often shaping strain-level diversity in microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg.

RESULTS

Here we systematically addressed the question of whether Pg are infected by phages-and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain-level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures.

CONCLUSION

This work definitively establishes that phages are a major unrecognized force shaping the ecology and intra-species strain-level diversity of the well-studied oral pathogen Pg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly. Video Abstract.

The human oral phageome

Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.

A novel phage from periodontal pockets associated with chronic periodontitis

Bacteriophages often constitute the majority of periodontal viral communities, but phages that infect oral bacteria remain uncharacterized. Here, we present the genetic analysis of the genome of a novel siphovirus, named Siphoviridae_29632, which was isolated from a patient with periodontitis using a viral metagenomics-based approach. Among 43 predicted open reading frames (ORFs) in the genome, the viral genes encoding structural proteins were distinct from the counterparts of other viruses, although a distant homology is shared among viral morphogenesis proteins. A total of 28 predicted coding sequences had significant homology to other known phage ORF sequences. In addition, the prevalence of Siphoviridae_29632 in a cohort of patients with chronic periodontitis was 41.67%, which was significantly higher than that in the healthy group (4.55%, P < 0.001), suggesting that this virus as well as its hosts may contribute to the ecological environment favored for chronic periodontitis.

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately reconstruct community assemblages. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated data sets with and without aDNA damage. Damage patterns had minimal impact on the taxonomic profiles produced by each program, while false-positive rates and biases were intrinsic to each program. Therefore, the most appropriate classification program is one that minimizes the biases related to the questions being addressed.

Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage characteristic of ancient samples (e.g., reduction in fragment size and cytosine deamination) may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT. In silico-generated data sets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha diversity, beta diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 reconstructed the most accurate community structure. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; false-positive rates were highest by CLARK-S and QIIME/UCLUST. Filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. The addition of ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern data sets for most programs. Overall, taxonomic profiling biases are program specific rather than damage dependent, and the choice of taxonomic classification program should be tailored to specific research questions.

IMPORTANCE Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately reconstruct community assemblages. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated data sets with and without aDNA damage. Damage patterns had minimal impact on the taxonomic profiles produced by each program, while false-positive rates and biases were intrinsic to each program. Therefore, the most appropriate classification program is one that minimizes the biases related to the questions being addressed.

Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2

Fusobacterium nucleatum is a strictly anaerobic, Gram negative bacterial species that has been associated with dental infections, pre-term labor, appendicitis, inflammatory bowel disease, and, more recently, colorectal cancer. The species is unusual in its phenotypic and genotypic heterogeneity, with some strains demonstrating a more virulent phenotype than others; however, as yet the genetic basis for these differences is not understood. Bacteriophage are known to contribute to the virulence phenotype of several bacterial species. In this work, we set out to characterize the bacteriophage associated with F. nucleatum subsp. animalis strain 7-1, a highly invasive isolate from the human gastrointestinal tract. As well, we used computational approaches to predict and compare bacteriophage signatures across available sequenced F. nucleatum genomes.

Bacteriophage and their potential roles in the human oral cavity

The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts.

Atomic force microscopy of bacteria from periodontal subgingival biofilm: Preliminary study results

Objective:

Atomic force microscope (AFM) is a technology that allows analysis of the nanoscale morphology of bacteria within biofilm and provides details that may be better useful for understanding the role of bacterial interactions in the periodontal disease.

Material and Methods:

Five patients with periodontal ≥5 mm pockets diagnosed as generalized periodontitis and five patients with slight gingivitis were selected for the investigation. Bacteria biofilms were collected and morphologically investigated by AFM application.

Results:

The investigation revealed how periodontitis bacteria are characterized by specific morphologic features of the cell wall. The major representative species of bacteria causing periodontal diseases have been reproduced by a three-dimensional reconstruction showing the bacteria surface details.

Conclusions:

The presence of complex glycocalyx structures, bacteriophage-like vesicles, spirochetes (classic and cystic morphology) and bacterial co-aggregation has been identified by the AFM analysis. The results suggest that AFM is a reliable technique for studying bacterial morphology and for examining microbial interactions in dental plaque.

Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans

The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans bacteriophage Aa Phi 23 was sequenced. Linear DNA contained in the phage particles is circularly permuted and terminally redundant. Therefore, the physical map of the phage genome is circular. Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%. Sixty-six potential open reading frames (ORFs) were identified, including an ORF resulting from a translational frameshift. A putative function could be assigned to 23 of them. Twenty-three other ORFs share homologies only with hypothetical proteins present in several bacteria or bacteriophages, and 20 ORFs seem to be specific for phage Aa Phi 23. The organization of the phage genome and several genetic functions share extensive similarities to that of the lambdoid phages. However, Aa Phi 23 encodes a DNA adenine methylase, and the DNA packaging strategy is more closely related to the P22 system. The attachment sites of Aa Phi 23 (attP) and several A. actinomycetemcomitans hosts (attB) are 49 bp long.

Presence of bacteriophage Aa phi 23 correlates with the population genetic structure of Actinobacillus actinomycetemcomitans

Several bacteriophages associated with the oral bacterium Actinobacillus actinomycetemcomitans have been identified. Lysogeny might affect the virulence of this bacterium, which has been implicated in the etiology of juvenile and adult periodontitis. We have determined the presence of bacteriophage Aa phi 23-related DNA sequences among 185 A. actinomycetemcomitans strains belonging to 2 well-characterized collections and have related the findings to the population genetic structure of the collections. 2 cloned Aa phi 23-specific DNA probes were used in Southern blot hybridization experiments to detect homologous sequences in whole-cell DNA of the strains. DNA from 65 (35%) of the 185 strains hybridized to either of the DNA probes. The majority (74%) of the hybridizing strains showed an identical hybridization pattern, indicating presence of phage Aa phi 23. Whole-cell DNA from the remaining hybridizing strains hybridized to the probes with different patterns, indicating that DNA sequences related to but different from phage Aa phi 23 occur in these strains. The majority (81%) of the strains which harbored phage Aa phi 23 were of serotype a, whereas serotype d strains appeared to be resistant to infection with this phage. There was a clear correlation between hybridization patterns and genetic subdivisions based on our previous population genetic analyses of A. actinomycetemcomitans. However, there was no significant correlation between occurrence of Aa phi 23 among A. actinomycetemcomitans strains and the periodontal status of the patients from whom the isolates were obtained, suggesting that this bacteriophage does not significantly influence the virulence of A. actinomycetemcomitans.

Occurrence of temperate bacteriophages in different Actinobacillus actinomycetemcomitans serotypes isolated from periodontally healthy individuals

The occurrence of temperate bacteriophages was studied in 34 isolates of Actinobacillus actinomycetemcomitans derived from 27 periodontally healthy Finnish individuals both by lysis/plaque assays and by DNA hybridizations. In addition the serotype, the ribotype and the arbitrarily primed polymerase chain reaction (AP-PCR) profile were determined for each A. actinomycetemcomitans strain. Fourteen isolates showed hybridization patterns very similar to that of a known lysogen when probed with the genome of the previously characterized temperate phage Aa phi 23. Only 6 of these 14 strains had produced lysis or single plaques on suitable indicator strains. Phage Aa phi 247 derived from one of these lysogens was indistinguishable from Aa phi 23 by electron microscopy, and the genomes showed highly related DNA hybridization patterns. The remaining 20 isolates exhibited hybridization patterns very different from that of Aa phi 23 DNA. Seven of these strains also gave lysis or single plaques, suggesting that 21 of the 34 strains were lysogenic. These data indicate that the prophages per se do not represent a virulence factor exclusively associated with periodontal disease. Presence of an Aa phi 23-related prophage correlated with serotype a and AP-PCR type 1 of the bacterial host. This may indicate that Aa phi 23 and related phages have a limited host range.

Periodontal inflammation and attachment loss: a critical problem for biological studies

BACKGROUND

In biological studies of periodontitis, there has been long-standing confusion between the ubiquitous phenomena of inflammation and the essential criterion of attachment loss. This is partly attributable to inadequate methods of clinical measurement, but seems also to be a consequence of an unproven and usually unstated assumption that the same biological processes underlie both inflammation and attachment loss. Developments in unidimensional clinical probing methods have helped in studies of periodontal treatment. However, such methods are intrinsically unsuitable in studies of periodontal diseases, and may have given them a false sense of security. the confusion has been compounded by inappropriate use of statistical techniques in an attempt to solve problems which do not arise from mathematical models but are intrinsic to measurement methods.

OBJECTIVE

This paper is a clinician's attempt to state the current difficulties and suggest some ways forward, including the development of three-dimensional measurement, non-invasive probing, and several objectives for biochemical, microbiological and immunological research.

Temperate bacteriophages are common among Actinobacillus actinomycetemcomitans isolates from periodontal pockets

Actinobacillus actinomycetemcomitans is a suspected etiologic agent in destructive periodontal diseases. The detection of bacteriophages in A. actinomycetemcomitans in the subgingival plaque of patients with rapidly destructive forms of periodontitis led to the hypothesis that bacteriophage infection might increase the virulence of this bacterium (19). A. actinomycetemcomitans was isolated from 68 subjects from the Netherlands and Switzerland with localized juvenile periodontitis, rapidly progressing periodontitis, or adult periodontitis, and was tested for the presence of temperate bacteriophage with the overlay plate technique. More than half of the A. actinomycetemcomitans strains were found to release bacteriophage which formed individual plaques on indicator strains. Electron microscopy of preparations from 7 strains revealed virions with an icosahedral head and a contractile tail typical for double-stranded DNA bacteriophages. The presence of A. actinomycetemcomitans carrying temperate bacteriophage was not correlated with the composition of the subgingival microflora nor with the clinical form of periodontal disease. Destructive periodontal disease of subjects with phage-carrying A. actinomycetemcomitans was not more severe than of subjects with phage-free A. actinomycetemcomitans as determined by several clinical parameters. In contrast, the pocket depth and the attachment loss were significantly lower for adult periodontitis subjects with phage-carrying A. actinomycetemcomitans. It seems unlikely that the frequently occurring temperate bacteriophages increase significantly the virulence of A. actinomycetemcomitans.

Inducible bacteriophages of Actinobacillus actinomycetemcomitans

Doses of 0.1 to 1.0 micrograms/ml of mitomycin C induced cell lysis of six of eight strains of Actinobacillus actinomycetemcomitans tested. Infectious phages were induced from ATCC strains 43717, 29524, 33384, and 43719; non-plaque-forming, possibly defective phages were induced from ATCC strains 29522 and 29523. No phages were detected in strain FDC 651 or ATCC strain 43718. No correlation between lysogeny and leukotoxin production or serotype of the strains could be established. Gel electrophoresis of phage DNAs indicated that the induced phages were of three types, based on size. By electron microscopy, the phages were found to belong to either morphotype A1 or morphotype B1; no other morphotypes were observed. Curing experiments led to the isolation of nonlysogenic derivatives of two strains, which supported plaque formation by the phages they originally carried. On the basis of our results, lysogeny appears to be widespread in A. actinomycetemcomitans.

Electron microscopy of phages in serotypes of Actinobacillus actinomycetemcomitans

Actinobacillus actinomycetemcomitans, Actinobacillus ureae, Haemophilus aphrophilus, Haemophilus paraphrophilus, Haemophilus influenzae, Haemophilus parainfluenzae, Pasteurella haemolytica and Pasteurella multocida strains were examined by transmission electron microscopy for the presence of bacteriophages. Phages were detected in serotype a (SUNY 75) and e (UOH 1705) and in the fresh clinical isolates UOH Q1243 and UOH Q1247 of A. actinomycetemcomitans. Phages were not found in serotype b, c and d strains of A. actinomycetemcomitans, in the fresh clinical isolate UOH Q1244 of this species or in old strains (including reference strains) of related species from the Actinobacillus-Haemophilus-Pasteurella group.

A possible late onset variation of Papillon-Lefèvre syndrome: report of 3 cases

Three unusual cases of Papillon-Lefèvre syndrome with late onset of features and relatively mild periodontal disease are presented. These examples confirm some of the late onset of features and mild periodontal presentation of a previous case report. Bacteriologic associations, polymorphonuclear leukocyte chemotactic, phagocytic, and bactericidal activity, and therapeutics with regard to this syndrome are discussed.

Associations between six DNA probe-detected periodontal bacteria and alveolar bone loss and other clinical signs of periodontitis

The purpose of the present study was to assess the associations between the presence and amounts of Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, B. intermedius, Eikenella corrodens, Wolinella recta, and Fusobacterium nucleatum in the periodontal pocket and the degree of alveolar bone loss and other clinical signs of periodonitis, such as probing pocket depth, attachment level, and presence of bleeding on probing at the same site. The study material comprised 16 subjects with or without approximal sites showing longitudinal alveolar bone loss who were selected from a group of 142 subjects monitored radiographically over the past 4 years. In this group 105 sites were examined, of which 58 showed recent alveolar bone loss greater than or equal to 1 mm. Subgingival plaque was collected with absorbent paper points and hybridized with 32P-labeled DNA probes specific for the above-mentioned bacteria. The amount of each bacterial species was correlated with the degree of bone loss over time and the three clinical measurements by means of Spearman rank correlation. A. actinomycetemcomitans showed poor correlations with all three clinical signs of periodontal inflammation, whereas B. gingivalis and W. recta demonstrated significant positive correlations with the three clinical measurements and with attachment level and pocket depth, respectively. In addition, the amount of A. actinomycetemcomitans, B. gingivalis and W. recta showed significant positive correlation with the extent of alveolar bone loss at the site. In contrast, the amounts of B. intermedius, E. corrodens, and F. nucleatum showed negative correlations with all four measurements.(ABSTRACT TRUNCATED AT 250 WORDS)

Changes in periodontal disease indicators in 35-year-old Oslo citizens from 1973 to 1984

Periodontal disease indicators were evaluated according to the periodontal treatment need system (PTNS) in random samples of 35-year-old citizens of Oslo in 1973 and 1984. The study indicated that although periodontal disease was a common finding in both samples, there was a significant reduction in score C (indicating need for complex periodontal treatment) in 1984 compared to 1973. Whereas 37.9% of the subjects showed inflamed pockets deeper than 5 mm (score C) in 1973, only 22.9% scored C in 1984 (non-Caucasians excluded). This reduction was most pronounced in females. The mean number of C-quadrants in subjects needing complex periodontal treatment was also reduced from 2.0 in 1973 to 1.7 in 1984. Further analyses of the 1984 sample showed that the mean number of C-quadrants was significantly lower in subjects with low OHI-S scores and in regular dental visitors, whereas sex, years at school, toothbrushing frequency, interdental cleaning habits, previous periodontal therapy, self-experienced need for treatment, health attitude or smoking habits, did not seem to influence the prevalence of score C.

Nucleic acid probes as potential tools in oral microbial epidemiology

The present review deals with genetic tools in the microbial diagnostic laboratory, types of nucleic acid probes, their construction and cloning, hybridization reactions, their sensitivity and specificity, and their advantages and limitations. The nucleic acid probes seem to possess a number of advantages over traditional diagnostic methods. DNA, RNA, and oligonucleotide probes are expected to have increased impact on our understanding of the pathogenesis and the treatment of infectious inflammatory periodontal diseases. In addition, these probes have potential application in epidemiological studies of oral microorganisms. However, the limitations of the probes must be kept in mind, and newly developed probes must be controlled with respect to the critical issues of sensitivity and specificity.

Treatment of rapidly destructive periodontitis in Papillon-Lefèvre syndrome. Laboratory and clinical observations

This paper reports the successful treatment of the periodontal component of the Papillon-Lefèvre syndrome in 2 siblings. Treatment consisted of extractions of periodontally-involved teeth under antibiotic therapy. The exogenous source of the suspected pathogenic A. actinomycetemcomitans in this family, identified as a pet dog, was also treated with antibiotics. Assessments of monocyte function and levels of serum antibodies against A. actinomycetemcomitans were performed prior to an immediately after treatment. Microbiological screening of subgingival dental plaque of the PLS patients as well as the rest of the household members, including the dog, was performed every month during the study period. Remission of the rapidly destructive periodontitis, as well as an earlier-described monocyte dysfunction in these two PLS patients occurred concomitantly with the eradication of A. actinomycetemcomitans from the family. 15 months after this treatment, the children still had no signs of periodontitis or of A. actinomycetemcomitans infection. The legitimacy with which PLS is defined as a disease entity is discussed and questioned.

The presence of phage-infected Actinobacillus actinomycetemcomitans in localized juvenile periodontitis patients

Electron microscopy revealed 2 different types of bacteriophages isolated from Actinobacillus actinomycetemcomitans colonizing exclusively diseased sites in 4 patients with localized juvenile periodontitis (LJP). All sites infected with phage were undergoing periodontal destruction, as judged from consecutive routine radiographs. The phages isolated had a wide host range as assessed from their ability to infect a series of reference strains of A. actinomycetemcomitans. A 5th patient harboured non-infected A. actinomycetemcomitans in a surgically treated site which had undergone no bone destruction during the last 12 months. The present findings suggested that the pathogenic potential of A. actinomycetemcomitans in LJP may increase due to phage infection.