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Abstract
Sessile forms of bacteria remain as an aggregation on biotic and abiotic surfaces, known as biofilm, that protects them from various environmental stress, like antibiotic and host immune response. The oral cavity is enriched with microbial biofilm, formed on dental surface, gingival plaques, and associated tissue. Several pathogenic viruses enter the oral cavity and form biofilms either on pre-existing biofilms or on cell surfaces. They achieved persistence and the ability to prompt dissemination in the biofilm. Dental biofilms of COVID-19 patients are found to harbor SARS-CoV-2 RNA and may act as a budding reservoir, which also promotes COVID-19 transmission. On the other hand, most of the prokaryotic viruses or bacteriophages essentially kill the host bacteria and thereby destroy the biofilm. Bacteria try to evade from phage attack by concealing in biofilm, whereas the eukaryotic virus often utilize bacterial biofilm to escape host's immune response and to achieve an easy way of dissemination. The opposite action of viruses as an inducer and eradicator of biofilm has made the oral biofilm a unique ecosystem.
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Affiliation(s)
- Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, India
- Department of Biotechnology and Bioinformatics, Sambalpur University, FVHM+9QP, Jyoti Vihar, Burla, Odisha, 768019, India
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2
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Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The oral microbiome: diversity, biogeography and human health. Nat Rev Microbiol 2024; 22:89-104. [PMID: 37700024 PMCID: PMC11084736 DOI: 10.1038/s41579-023-00963-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/14/2023]
Abstract
The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.
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Affiliation(s)
- Jonathon L Baker
- Oregon Health & Science University, Portland, OR, USA
- J. Craig Venter Institute, La Jolla, CA, USA
- UC San Diego School of Medicine, La Jolla, CA, USA
| | - Jessica L Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Xuesong He
- The Forsyth Institute, Cambridge, MA, USA.
- Harvard School of Dental Medicine, Boston, MA, USA.
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3
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Matrishin CB, Haase EM, Dewhirst FE, Mark Welch JL, Miranda-Sanchez F, Chen T, MacFarland DC, Kauffman KM. Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis. MICROBIOME 2023; 11:161. [PMID: 37491415 PMCID: PMC10367356 DOI: 10.1186/s40168-023-01607-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/22/2023] [Indexed: 07/27/2023]
Abstract
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.
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Affiliation(s)
- Cole B Matrishin
- Department of Oral Biology, School of Dental Medicine, The University at Buffalo, Buffalo, NY, USA
| | - Elaine M Haase
- Department of Oral Biology, School of Dental Medicine, The University at Buffalo, Buffalo, NY, USA
| | - Floyd E Dewhirst
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | | | | | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Donald C MacFarland
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine, The University at Buffalo, Buffalo, NY, USA
| | - Kathryn M Kauffman
- Department of Oral Biology, School of Dental Medicine, The University at Buffalo, Buffalo, NY, USA.
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4
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Abstract
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.
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Affiliation(s)
- Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jørgen Slots
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, California, USA
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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Szafrański SP, Winkel A, Stiesch M. The use of bacteriophages to biocontrol oral biofilms. J Biotechnol 2017; 250:29-44. [PMID: 28108235 DOI: 10.1016/j.jbiotec.2017.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/15/2022]
Abstract
Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.
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Affiliation(s)
- Szymon P Szafrański
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
| | - Andreas Winkel
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Meike Stiesch
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
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6
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Abstract
Three phages ofStreptococcus mutans were obtained and partially characterized. The three phages, designated M102, e10, and f1, were found to be strictly lytic, with host ranges restricted to only serotype c, e, and f strains of this species, respectively. Phage sensitivity was not correlated with the presence of plasmids, at least in host strains of serotypes c and e. Each phage produced clear plaques in a number of standard media, even in the presence of sucrose, indicating that the extracellular glucan polysaccharides (mutan) produced by the hosts from this substrate do not prevent phage adsorption and growth. The phages were similar in size and morphology, having icosahedral heads and long (283-287 nm), flexible, noncontractile tails. The genome of each phage was found to consist of linear, double-stranded DNA, 31-35 kb in length, with a base composition of 37-38% G+C. Restricting phage DNAs with four enzymes produced fragment patterns unique to each phage, but common bands between M102 and e10 and between e10 and f1 were produced byBamHI. Labeled e10 and M102 DNAs hybridized strongly with all three phage DNAs, indicating that they share some common sequences. The three phages appear to be more similar than expected and probably evolved from a common ancestor.
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Affiliation(s)
- A L Delisle
- Department of Microbiology, School of Dentistry, University of Maryland at Baltimore, 21201, Baltimore, Maryland, USA
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Delisle AL, Donkersloot JA. Relationships amongActinomyces naeslundii (A. viscosus)Bacteriophages Isolated from Sewage and the Oral Cavity. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.3109/08910609509140089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Allan L. Delisle
- Department of Microbiology, School of Dentistry, University of Maryland at Baltimore, Baltimore, MD, 21201, USA
| | - Jacob A. Donkersloot
- Laboratory of Microbial Ecology, National Institute of Dental Research, National Institutes of Health, Bethesda, MD, 20892, USA
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Kolenbrander PE. Surface recognition among oral bacteria: multigeneric coaggregations and their mediators. Crit Rev Microbiol 1989; 17:137-59. [PMID: 2692602 DOI: 10.3109/10408418909105746] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Delisle AL, Donkersloot JA, Kolenbrander PE, Tylenda CA. Use of lytic bacteriophage for Actinomyces viscosus T14V as a probe for cell surface components mediating intergeneric coaggregation. Infect Immun 1988; 56:54-9. [PMID: 3335409 PMCID: PMC259233 DOI: 10.1128/iai.56.1.54-59.1988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A lytic bacteriophage for Actinomyces viscosus T14V (the reference strain for actinomyces coaggregation group A) was isolated from raw sewage. This phage, designated BF307, also lysed the T14V-derived nonfimbriated mutant PK455-2 as well as A. viscosus MG-1 and T14AV but not the other serotype 2 or serotype 1 strains of this species that were tested or any of nine Actinomyces naeslundii isolates. Phages BF307 belonged to Bradley morphological group C and was similar in appearance to the A. viscosus MG-1 phages Av-1 and Av-3, which do not productively infect A. viscosus T14V. A. viscosus MG-1 mutants selected for resistance to phage BF307, Av-3, or CT7 (a human dental plaque isolate with the same host range as BF307) were coresistant to the other two phages but sensitive to Av-1. These results indicate that the receptors on A. viscosus MG-1 for phages BF307, Av-3, and CT7 are identical or share a common precursor and that the receptor for phage Av-1 is distinct. Comparison of the genomes of BF307, Av-3, and CT7 revealed that their DNAs were similar in size but distinguishable by restriction analysis. Two altered coaggregation phenotypes were identified among the phage BF307-resistant mutants of strains MG-1, T14V, T14AV, and PK455-2. Class I mutants had lost the ability to interact with coaggregation group 1 streptococci, and class II mutants did not coaggregate with either group 1 or group 2 streptococci. These results are consistent with the proposal that the phage BF307 receptor on these A. viscosus strains is related to one of the structures that mediates coaggregation with oral streptococci. A model to delineate the various coaggregation mediators on the surface of actinomyces coaggregation group A cells is presented, and the use of these phages to probe surface components of human oral actinomyces strains is discussed.
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Affiliation(s)
- A L Delisle
- Department of Microbiology, School of Dentistry, University of Maryland, Baltimore 21201
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Kolenbrander PE, Andersen RN. Multigeneric aggregations among oral bacteria: a network of independent cell-to-cell interactions. J Bacteriol 1986; 168:851-9. [PMID: 3782029 PMCID: PMC213563 DOI: 10.1128/jb.168.2.851-859.1986] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A radioactivity-based assay was developed to define the participation of radioactively labeled cell types within the milieu of unlabeled partners in multigeneric aggregates. The cell types in these multigeneric aggregations consisted of various combinations of 21 strains representing five genera of human oral bacteria. The coaggregation properties of each cell type, when paired individually with various strains, were delineated and were unchanged when the microbes took part in the more complex multigeneric aggregations. Competition between homologous labeled and unlabeled cells for binding to a partner cell type was achieved only when the homologous cells were mixed together before the addition of their partner cells. Attempts to displace a labeled cell type from an aggregate by subsequent addition of a large excess of the same unlabeled cell type were unsuccessful, which suggested that the forces that bound different cell types together were very strong and the cell-to-cell interactions were stable. However, a cell type that exhibited only lactose-reversible coaggregations with partners was easily and selectively released by the addition of lactose to multigeneric aggregates otherwise consisting solely of lactose-nonreversible cell-to-cell interactions. This not only indicates the independent nature of individual coaggregations but also suggests the involvement of lectinlike adhesins in these sugar-inhibitable coaggregations. Although the molecular mechanisms responsible for multigeneric aggregations are unknown, the principle of a common partner cell type serving as a bridge between two otherwise noncoaggregating cell types was firmly established by the observation of sequential addition of one cell type to another. Thus, competition, bridging, coaggregate stability, independent nature of interactions, and partner specificity are the key principles of adherence that form the framework for continued studies of multigeneric aggregates. While the human oral cavity is a prime example of a complex microbial community, collectively the community appears to consist of simple and testable individual interactions.
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Tylenda CA, Calvert C, Kolenbrander PE, Tylenda A. Isolation of Actinomyces bacteriophage from human dental plaque. Infect Immun 1985; 49:1-6. [PMID: 4008044 PMCID: PMC262048 DOI: 10.1128/iai.49.1.1-6.1985] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human dental plaque samples were screened for the presence of bacteriophage for Actinomyces viscosus and Streptococcus sanguis. None of the 336 samples yielded phage for S. sanguis, but 10 contained virulent actinomyces phage. A high host cell specificity was observed in that one phage isolate infected only A. viscosus T14V, eight phage isolates infected only A. viscosus MG-1, and one infected both strains. None was capable of productively infecting various other actinomyces strains that represented the six actinomyces coaggregation groups. Because phage-containing samples occurred randomly in this survey, no correlation between the individual collecting the samples, dental clinic, or type of patient and the presence of phage in the sample was noted. Examination of one of the samples that yielded phage for the presence of a natural host strain for that particular phage resulted in the isolation of two strains which were identified as A. viscosus serotype II and Actinomyces naeslundii serotype I. This is the first report of an A. naeslundii host strain and actinomyces bacteriophage of human dental plaque origin. The finding of both phage and host strains in the same dental plaque sample along with the observation of high host cell specificity by these phage provide indicators that support an active role for actinomyces bacteriophage in oral microbial ecology. The use of these freshly isolated phage as probes to study actinomyces coaggregation properties is discussed.
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