1
|
Chen X, Zou T, Zeng Q, Chen Y, Zhang C, Jiang S, Ding G. Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries. J Dent 2024; 146:105059. [PMID: 38801939 DOI: 10.1016/j.jdent.2024.105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVES Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC. METHODS Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software. RESULTS 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome. CONCLUSIONS Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC. CLINICAL SIGNIFICANCE The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.
Collapse
Affiliation(s)
- Xin Chen
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China
| | - Ting Zou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China
| | - Qinglu Zeng
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Yubing Chen
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Chengfei Zhang
- Endodontology, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, PR China
| | - Shan Jiang
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China.
| | - Guicong Ding
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China.
| |
Collapse
|
2
|
Kashyap B, Kullaa A. Salivary Metabolites Produced by Oral Microbes in Oral Diseases and Oral Squamous Cell Carcinoma: A Review. Metabolites 2024; 14:277. [PMID: 38786754 PMCID: PMC11122927 DOI: 10.3390/metabo14050277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, salivary metabolome studies have provided new biological information and salivary biomarkers to diagnose different diseases at early stages. The saliva in the oral cavity is influenced by many factors that are reflected in the salivary metabolite profile. Oral microbes can alter the salivary metabolite profile and may express oral inflammation or oral diseases. The released microbial metabolites in the saliva represent the altered biochemical pathways in the oral cavity. This review highlights the oral microbial profile and microbial metabolites released in saliva and its use as a diagnostic biofluid for different oral diseases. The importance of salivary metabolites produced by oral microbes as risk factors for oral diseases and their possible relationship in oral carcinogenesis is discussed.
Collapse
Affiliation(s)
| | - Arja Kullaa
- Institute of Dentistry, University of Eastern Finland, 70211 Kuopio, Finland;
| |
Collapse
|
3
|
Kobakhidze S, Koulouris S, Kakabadze N, Kotetishvili M. Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus. BMC Microbiol 2024; 24:155. [PMID: 38704526 PMCID: PMC11069274 DOI: 10.1186/s12866-024-03312-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts. METHODS A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages. RESULTS The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins. CONCLUSIONS It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.
Collapse
Affiliation(s)
- Saba Kobakhidze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, 1 Ilia Chavchavadze Ave. 0179, Tbilisi, Georgia
| | - Stylianos Koulouris
- Directorate General for Health and Food Safety (DG-SANTE), European Commission, 1049, Bruxelles/Brussel, Belgium
| | - Nata Kakabadze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
| | - Mamuka Kotetishvili
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia.
- Scientific Research Institute, School of Science and Technology, the University of Georgia, 77a M. Kostava St., 0171, Tbilisi, Georgia.
| |
Collapse
|
4
|
Schwartz J, Capistrano KJ, Gluck J, Hezarkhani A, Naqvi AR. SARS-CoV-2, periodontal pathogens, and host factors: The trinity of oral post-acute sequelae of COVID-19. Rev Med Virol 2024; 34:e2543. [PMID: 38782605 DOI: 10.1002/rmv.2543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/04/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
COVID-19 as a pan-epidemic is waning but there it is imperative to understand virus interaction with oral tissues and oral inflammatory diseases. We review periodontal disease (PD), a common inflammatory oral disease, as a driver of COVID-19 and oral post-acute-sequelae conditions (PASC). Oral PASC identifies with PD, loss of teeth, dysgeusia, xerostomia, sialolitis-sialolith, and mucositis. We contend that PD-associated oral microbial dysbiosis involving higher burden of periodontopathic bacteria provide an optimal microenvironment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. These pathogens interact with oral epithelial cells activate molecular or biochemical pathways that promote viral adherence, entry, and persistence in the oral cavity. A repertoire of diverse molecules identifies this relationship including lipids, carbohydrates and enzymes. The S protein of SARS-CoV-2 binds to the ACE2 receptor and is activated by protease activity of host furin or TRMPSS2 that cleave S protein subunits to promote viral entry. However, PD pathogens provide additional enzymatic assistance mimicking furin and augment SARS-CoV-2 adherence by inducing viral entry receptors ACE2/TRMPSS, which are poorly expressed on oral epithelial cells. We discuss the mechanisms involving periodontopathogens and host factors that facilitate SARS-CoV-2 infection and immune resistance resulting in incomplete clearance and risk for 'long-haul' oral health issues characterising PASC. Finally, we suggest potential diagnostic markers and treatment avenues to mitigate oral PASC.
Collapse
Affiliation(s)
- Joel Schwartz
- Department of Oral Medicine and Diagnostic Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | | | - Joseph Gluck
- Department of Periodontics, University of Illinois Chicago, Chicago, Illinois, USA
| | - Armita Hezarkhani
- Department of Periodontics, University of Illinois Chicago, Chicago, Illinois, USA
| | - Afsar R Naqvi
- Department of Periodontics, University of Illinois Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| |
Collapse
|
5
|
Guo X, Wang X, Shi J, Ren J, Zeng J, Li J, Li Y. A review and new perspective on oral bacteriophages: manifestations in the ecology of oral diseases. J Oral Microbiol 2024; 16:2344272. [PMID: 38698893 PMCID: PMC11064738 DOI: 10.1080/20002297.2024.2344272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Objective To explore the manifestations of bacteriophages in different oral disease ecologies, including periodontal diseases, dental caries, endodontic infections, and oral cancer, as well as to propel phage therapy for safer and more effective clinical application in the field of dentistry. Methods In this literature review, we outlined interactions between bacteriophages, bacteria and even oral cells in the oral ecosystem, especially in disease states. We also analyzed the current status and future prospects of phage therapy in the perspective of different oral diseases. Results Various oral bacteriophages targeting at periodontal pathogens as Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola and Aggregatibacter actinomycetemcomitans, cariogenic pathogen Streptococcus mutans, endodontic pathogen Enterococcus faecalis were predicted or isolated, providing promising options for phage therapy. In the realm of oral cancer, aside from displaying tumor antigens or participating in tumor-targeted therapies, phage-like particle vaccines demonstrated the potential to prevent oral infections caused by human papillomaviruses (HPVs) associated with head-and-neck cancers. Conclusion Due to their intricate interactions with bacteria and oral cells, bacteriophages are closely linked to the progression and regression of diverse oral diseases. And there is an urgent need for research to explore additional possibilities of bacteriophages in the management of oral diseases.
Collapse
Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayi Ren
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Center for Archaeological Science, Sichuan University, Chengdu, China
| |
Collapse
|
6
|
Withatanung P, Janesomboon S, Vanaporn M, Muangsombut V, Charoensudjai S, Baker DJ, Wuthiekanun V, Galyov EE, Clokie MRJ, Gundogdu O, Korbsrisate S. Induced Burkholderia prophages detected from the hemoculture: a biomarker for Burkholderia pseudomallei infection. Front Microbiol 2024; 15:1361121. [PMID: 38633694 PMCID: PMC11022660 DOI: 10.3389/fmicb.2024.1361121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are found in abundance not only in the environment but also in the human body. The use of phages for the diagnosis of melioidosis, a tropical infectious disease caused by Burkholderia pseudomallei, is emerging as a promising novel approach, but our understanding of conditions under which Burkholderia prophages can be induced remains limited. Here, we first demonstrated the isolation of Burkholderia phages from the hemocultures of melioidosis patients. The B. pseudomallei-positive hemoculture bottles were filtered to remove bacteria, and then phages were isolated and purified by spot and double agar overlay plaque assays. Forty blood samples (hemoculture-confirmed melioidosis) were tested, and phages were found in 30% of the samples. Transmission electron microscopy and genome analysis of the isolated phages, vB_HM387 and vB_HM795, showed that both phages are Myoviruses. These two phages were stable at a pH of 5-7 and temperatures of 25-37°C, suggesting their ability to survive in human blood. The genome sizes of vB_HM387 and vB_HM795 are 36.3 and 44.0 kb, respectively. A phylogenetic analysis indicated that vB_HM387 has homologs, but vB_HM795 is a novel Myovirus, suggesting the heterogeneity of Burkholderia phages in melioidosis patients. The key finding that Burkholderia phages could be isolated from the blood of melioidosis patients highlights the potential application of phage-based assays by detecting phages in blood as a pathogen-derived biomarker of infection.
Collapse
Affiliation(s)
- Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sujintana Janesomboon
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Veerachat Muangsombut
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Dave J. Baker
- Science Operations, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Edouard E. Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
7
|
Xiong X, Gong J, Lu T, Yuan L, Lan Y, Tu X. Characteristics of intestinal bacteriophages and their relationship with Bacteria and serum metabolites during quail sexual maturity transition. BMC Vet Res 2024; 20:93. [PMID: 38459523 PMCID: PMC10921806 DOI: 10.1186/s12917-024-03945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Bacteriophages are prokaryotic viruses that rank among the most abundant microbes in the gut but remain among the least understood, especially in quails. In this study, we surveyed the gut bacteriophage communities in 22 quails at different ages (days 20 and 70) using shotgun metagenomic sequencing. We then systematically evaluated the relationships with gut bacteria and host serum metabolites. RESULTS We discovered that Myoviridae and Siphoviridae were the dominant bacteriophage families in quails. Through a random forest and LEfSe analysis, we identified 23 differential bacteriophages with overlapping presence. Of these, 21 bacteriophages (e.g., Enterococcus phage IME-EFm5 and Enterococcus phage IME-EFm1) showed higher abundances in the day 20 group, while two bacteriophages (Bacillus phage Silence and Bacillus virus WPh) were enriched in the day 70 group. These key bacteriophages can serve as biomarkers for quail sexual maturity. Additionally, the differential bacteriophages significantly correlated with specific bacterial species and shifts in the functional capacities of the gut microbiome. For example, Enterococcus phages (e.g., Enterococcus phage EFP01, Enterococcus phage IME-EFm5, and Enterococcus phage IME-EFm1) were significantly (P < 0.001, FDR) and positively correlated with Enterococcus faecalis. However, the relationships between the host serum metabolites and either bacteriophages or bacterial species varied. None of the bacteriophages significantly (P > 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. In contrast, some differential bacterial species (e.g., Christensenella massiliensis and Bacteroides neonati) significantly (P < 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. Furthermore, characteristic successional alterations in gut bacteriophages, bacteria, and host serum metabolites across different ages highlighted a sexual maturity transition coexpression network. CONCLUSION This study improves our understanding of the gut bacteriophage characteristics in quails and offers profound insights into the interactions among gut bacteriophages, bacteria, and host serum metabolites during the quail's sexual maturity transition.
Collapse
Affiliation(s)
- Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
| | - Jishang Gong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Tian Lu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Liuying Yuan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Yuehang Lan
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China
| | - Xutang Tu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang, Jiangxi, 330032, China.
| |
Collapse
|
8
|
Shanmugasundaram S, Nayak N, Puzhankara L, Kedlaya MN, Rajagopal A, Karmakar S. Bacteriophages: the dawn of a new era in periodontal microbiology? Crit Rev Microbiol 2024; 50:212-223. [PMID: 36883683 DOI: 10.1080/1040841x.2023.2182667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The oral microbiome, populated by a diverse range of species, plays a critical role in the initiation and progression of periodontal disease. The most dominant yet little-discussed players in the microbiome, the bacteriophages, influence the health and disease of the host in various ways. They, not only contribute to periodontal health by preventing the colonization of pathogens and disrupting biofilms but also play a role in periodontal disease by upregulating the virulence of periodontal pathogens through the transfer of antibiotic resistance and virulence factors. Since bacteriophages selectively infect only bacterial cells, they have an enormous scope to be used as a therapeutic strategy; recently, phage therapy has been successfully used to treat antibiotic-resistant systemic infections. Their ability to disrupt biofilms widens the scope against periodontal pathogens and dental plaque biofilms in periodontitis. Future research focussing on the oral phageome and phage therapy's effectiveness and safety could pave way for new avenues in periodontal therapy. This review explores our current understanding of bacteriophages, their interactions in the oral microbiome, and their therapeutic potential in periodontal disease.
Collapse
Affiliation(s)
- Shashikiran Shanmugasundaram
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Namratha Nayak
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lakshmi Puzhankara
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Madhurya N Kedlaya
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anjale Rajagopal
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shaswata Karmakar
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Banar M, Rokaya D, Azizian R, Khurshid Z, Banakar M. Oral bacteriophages: metagenomic clues to interpret microbiomes. PeerJ 2024; 12:e16947. [PMID: 38406289 PMCID: PMC10885796 DOI: 10.7717/peerj.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.
Collapse
Affiliation(s)
- Maryam Banar
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Dinesh Rokaya
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, Jordan
| | - Reza Azizian
- Biomedical Innovation and Start-up student association (Biomino), Tehran University of Medical Sciences, Tehran, Iran
- Pediatric Infectious Diseases Research Center (PIDRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Zohaib Khurshid
- Department of Prosthodontics and Implantology, College of Dentistry, King Faisal University, Al-Hofuf, Al Ahsa, Saudi Arabia
- Center of Excellence for Regenerative Dentistry, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Morteza Banakar
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
11
|
Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
Collapse
Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
12
|
Libertini G. Phenoptosis and the Various Types of Natural Selection. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:2007-2022. [PMID: 38462458 DOI: 10.1134/s0006297923120052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 03/12/2024]
Abstract
In the first description of evolution, the fundamental mechanism is the natural selection favoring the individuals best suited for survival and reproduction (selection at the individual level or classical Darwinian selection). However, this is a very reductive description of natural selection that does not consider or explain a long series of known phenomena, including those in which an individual sacrifices or jeopardizes his life on the basis of genetically determined mechanisms (i.e., phenoptosis). In fact, in addition to (i) selection at the individual level, it is essential to consider other types of natural selection such as those concerning: (ii) kin selection and some related forms of group selection; (iii) the interactions between the innumerable species that constitute a holobiont; (iv) the origin of the eukaryotic cell from prokaryotic organisms; (v) the origin of multicellular eukaryotic organisms from unicellular organisms; (vi) eusociality (e.g., in many species of ants, bees, termites); (vii) selection at the level of single genes, or groups of genes; (viii) the interactions between individuals (or more precisely their holobionts) of the innumerable species that make up an ecosystem. These forms of natural selection, which are all effects and not violations of the classical Darwinian selection, also show how concepts as life, species, individual, and phenoptosis are somewhat not entirely defined and somehow arbitrary. Furthermore, the idea of organisms selected on the basis of their survival and reproduction capabilities is intertwined with that of organisms also selected on the basis of their ability to cooperate and interact, even by losing their lives or their distinct identities.
Collapse
Affiliation(s)
- Giacinto Libertini
- Italian Society for Evolutionary Biology (ISEB), Asti, 14100, Italy.
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, 80131, Italy
| |
Collapse
|
13
|
Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
Collapse
Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
14
|
Bosco K, Lynch S, Sandaradura I, Khatami A. Therapeutic Phage Monitoring: A Review. Clin Infect Dis 2023; 77:S384-S394. [PMID: 37932121 DOI: 10.1093/cid/ciad497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
With the global rise in antimicrobial resistance, there has been a renewed interest in the application of therapeutic phages to treat bacterial infections. Therapeutic phage monitoring (TPM) is proposed as an essential element of phage therapy (PT) protocols to generate data and fill knowledge gaps regarding the in vivo efficacy of therapeutic phages, patients' immune responses to PT, and the wider ecological effects of PT. By monitoring phage concentrations in blood and tissues, together with immune responses and possible ecological changes during PT, TPM may enable the optimization of dosing and the implementation of precision medicine approaches. Furthermore, TPM can validate diagnostic surrogates of efficacy, direct research efforts, and establish quality assurance indicators for therapeutic phage products. Thus, TPM holds great potential for enhancing our understanding of the multidirectional phage-bacteria-host interactions and advancing "best practice" PT, ultimately improving patient care.
Collapse
Affiliation(s)
- Kiran Bosco
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Stephanie Lynch
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Indy Sandaradura
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ameneh Khatami
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| |
Collapse
|
15
|
Brookes Z, Teoh L, Cieplik F, Kumar P. Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced? Int Dent J 2023; 73 Suppl 2:S74-S81. [PMID: 37867065 PMCID: PMC10690560 DOI: 10.1016/j.identj.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023] Open
Abstract
This narrative review describes the oral microbiome, and its role in oral health and disease, before considering the impact of commonly used over-the-counter (OTC) mouthwashes on oral bacteria, viruses, bacteriophages, and fungi that make up these microbial communities in different niches of the mouth. Whilst certain mouthwashes have proven antimicrobial actions and clinical effectiveness supported by robust evidence, this review reports more recent metagenomics evidence, suggesting that mouthwashes such as chlorhexidine may cause "dysbiosis," whereby certain species of bacteria are killed, leaving others, sometimes unwanted, to predominate. There is little known about the effects of mouthwashes on fungi and viruses in the context of the oral microbiome (virome) in vivo, despite evidence that they "kill" certain viral pathogens ex vivo. Evidence for mouthwashes, much like antibiotics, is also emerging with regards to antimicrobial resistance, and this should further be considered in the context of their widespread use by clinicians and patients. Therefore, considering the potential of currently available OTC mouthwashes to alter the oral microbiome, this article finally proposes that the ideal mouthwash, whilst combatting oral disease, should "balance" antimicrobial communities, especially those associated with health. Which antimicrobial mouthwash best fits this ideal remains uncertain.
Collapse
Affiliation(s)
- Zoë Brookes
- Peninsula Dental School, Plymouth University, Plymouth, UK.
| | - Leanne Teoh
- Melbourne Dental School, The University of Melbourne, Carlton, Victoria, Australia
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Purnima Kumar
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, USA
| |
Collapse
|
16
|
Lopes AM, Abrantes J. On the virome's hidden diversity: lessons from RHDV. mBio 2023; 14:e0197123. [PMID: 37855614 PMCID: PMC10746256 DOI: 10.1128/mbio.01971-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Emerging infectious diseases are a major challenge to human and animal health. While predicting the emergence of pathogens is complex, the advent of high-throughput sequencing technologies has allowed the rapid identification of unknown microbiology diversity within organisms. Here, we discuss an example of a metatranscriptomics output to decipher viral evolution.
Collapse
Affiliation(s)
- Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR-Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
17
|
Bustos-Lobato L, Rus MJ, Saúco C, Simon-Soro A. Oral microbial biomap in the drought environment: Sjogren's syndrome. Mol Oral Microbiol 2023; 38:400-407. [PMID: 37767604 DOI: 10.1111/omi.12435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Sjogren's syndrome (SS) is an autoimmune disease that affects primarily the salivary glands, making perturbations in the oral ecosystem and potential factors of salivary flow that influence the onset and development of the disease. The oral cavity contains diverse microorganisms that inhabit various niches such as the oral microbial "biomap." It does not seem specific enough to establish a characteristic microbiome, given the diversity of clinical manifestations, variable rates of salivary secretion, and influential risk factors in patients with SS. This review discusses the biogeography of the oral microbiome in patients with SS such as saliva, tongue, tooth, mucosa, and gum. The microorganisms that were more abundant in the different oral niches were Gram-positive species, suggesting a higher survival of cell wall bacteria in this arid oral environment. Reduced salivary flow appears not to be linked to the cause of dysbiosis alone but influences host-associated risk factors. However, much work remains to be done to establish the role of the microbiome in the etiopathogenesis of autoimmune diseases such as SS. Future studies of the microbiome in autoimmunity will shed light on the role of specific microorganisms that have never been linked before with SS.
Collapse
Affiliation(s)
- Laura Bustos-Lobato
- Facultad de Odontología, Departamento de Estomatología, Universidad de Sevilla, Sevilla, Spain
| | - Maria J Rus
- Facultad de Odontología, Departamento de Estomatología, Universidad de Sevilla, Sevilla, Spain
| | - Carlos Saúco
- Facultad de Odontología, Departamento de Estomatología, Universidad de Sevilla, Sevilla, Spain
| | - Aurea Simon-Soro
- Facultad de Odontología, Departamento de Estomatología, Universidad de Sevilla, Sevilla, Spain
| |
Collapse
|
18
|
Kan L, Barr JJ. A Mammalian Cell's Guide on How to Process a Bacteriophage. Annu Rev Virol 2023; 10:183-198. [PMID: 37774129 DOI: 10.1146/annurev-virology-111821-111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Bacteriophages are enigmatic entities that defy definition. Classically, they are specialist viruses that exclusively parasitize bacterial hosts. Yet this definition becomes limiting when we consider their ubiquity in the body coupled with their vast capacity to directly interact with the mammalian host. While phages certainly do not infect nor replicate within mammalian cells, they do interact with and gain unfettered access to the eukaryotic cell structure. With the growing appreciation for the human virome, coupled with our increased application of phages to patients within clinical settings, the potential impact of phage-mammalian interactions is progressively recognized. In this review, we provide a detailed mechanistic overview of how phages interact with the mammalian cell surface, the processes through which said phages are internalized by the cell, and the intracellular processing and fate of the phages. We then summarize the current state-of-the-field with respect to phage-mammalian interactions and their associations with health and disease states.
Collapse
Affiliation(s)
- Leo Kan
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia;
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia;
| |
Collapse
|
19
|
Paietta EN, Kraberger S, Custer JM, Vargas KL, Espy C, Ehmke E, Yoder AD, Varsani A. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Viruses 2023; 15:1821. [PMID: 37766228 PMCID: PMC10537320 DOI: 10.3390/v15091821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).
Collapse
Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Claudia Espy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Transient Positive SARS-CoV-2 PCR without Induction of Systemic Immune Responses. Vaccines (Basel) 2023; 11:vaccines11020482. [PMID: 36851359 PMCID: PMC9959254 DOI: 10.3390/vaccines11020482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
SARS-CoV-2 testing is dominated by PCR to guide treatment and individual as well as public health preventive measures. Among 1700 football (soccer) players and staff of the German Bundesliga and Bundesliga 2 who were regularly tested by PCR twice weekly, 98 individuals had a positive PCR (May 2020 to mid-January 2021). A subset of these were retested shortly after the initial positive result. Among those, 11 subjects were identified who only had a transient single positive PCR of low viral load. All individuals were asymptomatic and none developed long COVID. We tested SARS-CoV-2 IgG and IgA as well as SARS-CoV-2 specific CD4 und CD8 positive T cells, and showed that only one out of 11 individuals developed SARS-CoV-2 specific cellular and humoral immunity after the positive PCR, whereas a specific immunity was undetectable in all other individuals. Thus, a single positive PCR might indicate that transient colonization of the upper respiratory tract with SARS-CoV-2 may occur without systemic induction of specific adaptive immunity. Together with test artifacts as another potential reason for a transiently positive test, this finding may favor cautious interpretation of positive PCR results or retesting before initiating intervening treatment or infection control measures in some cases.
Collapse
|
22
|
When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages. Viruses 2023; 15:v15020420. [PMID: 36851634 PMCID: PMC9964552 DOI: 10.3390/v15020420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.
Collapse
|
23
|
Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 2023; 11:318. [PMID: 36838283 PMCID: PMC9962706 DOI: 10.3390/microorganisms11020318] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.
Collapse
Affiliation(s)
- Austin Gregory Morrison
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- 1717 Claflin Road, 136 Ackert Hall, Manhattan, KS 66506, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- 3901 Rainbow Blvd., 4031 Wahl Hall East, MS 3040, Kansas City, KS 66160, USA
| |
Collapse
|
24
|
Abstract
Oral commensal streptococci are primary colonizers of the oral cavity. These streptococci produce many adhesins, metabolites, and antimicrobials that modulate microbial succession and diversity within the oral cavity. Often, oral commensal streptococci antagonize cariogenic and periodontal pathogens such as Streptococcus mutans and Porphyromonas gingivalis, respectively. Mechanisms of antagonism are varied and range from the generation of hydrogen peroxide, competitive metabolite scavenging, the generation of reactive nitrogen intermediates, and bacteriocin production. Furthermore, several oral commensal streptococci have been shown to alter the host immune response at steady state and in response to oral pathogens. Collectively, these features highlight the remarkable ability of oral commensal streptococci to regulate the structure and function of the oral microbiome. In this review, we discuss mechanisms used by oral commensal streptococci to interact with diverse oral pathogens, both physically and through the production of antimicrobials. Finally, we conclude by exploring the critical roles of oral commensal streptococci in modulating the host immune response and maintaining health and homeostasis.
Collapse
|
25
|
Girija AS, Ganesh PS. Functional biomes beyond the bacteriome in the oral ecosystem. JAPANESE DENTAL SCIENCE REVIEW 2022; 58:217-226. [PMID: 35814739 PMCID: PMC9260289 DOI: 10.1016/j.jdsr.2022.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections.
Collapse
|
26
|
Akimbekov NS, Digel I, Yerezhepov AY, Shardarbek RS, Wu X, Zha J. Nutritional factors influencing microbiota-mediated colonization resistance of the oral cavity: A literature review. Front Nutr 2022; 9:1029324. [PMID: 36337619 PMCID: PMC9630914 DOI: 10.3389/fnut.2022.1029324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2023] Open
Abstract
The oral cavity is a key biocenosis for many distinct microbial communities that interact with both the external environment and internal body systems. The oral microbiota is a vital part of the human microbiome. It has been developed through mutual interactions among the environment, host physiological state, and microbial community composition. Indigenious microbiota of the oral cavity is one of the factors that prevent adhesion and invasion of pathogens on the mucous membrane, i.e., the development of the infectious process and thereby participating in the implementation of one of the mechanisms of local immunity-colonization resistance. The balance between bacterial symbiosis, microbial virulence, and host resistance ensures the integrity of the oral cavity. In this review we have tried to address how nutritional factors influence integrity of the oral indigenous microbiota and its involvement in colonization resistance.
Collapse
Affiliation(s)
- Nuraly S. Akimbekov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ilya Digel
- Institute for Bioengineering, FH Aachen University of Applied Sciences, Jülich, Germany
| | - Adil Y. Yerezhepov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Raiymbek S. Shardarbek
- Department of Internal Diseases, Kazakh National Medical University Named After S.D. Asfendiyarov, Almaty, Kazakhstan
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
| |
Collapse
|
27
|
Oral Microbiome and Dental Caries Development. Dent J (Basel) 2022; 10:dj10100184. [PMID: 36285994 PMCID: PMC9601200 DOI: 10.3390/dj10100184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods’ major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.
Collapse
|
28
|
Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
Collapse
|
29
|
Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection. J Virol 2022; 96:e0106322. [PMID: 36000841 PMCID: PMC9472602 DOI: 10.1128/jvi.01063-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.
Collapse
|
30
|
Esposito AM, Esposito MM, Ptashnik A. Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses. Microorganisms 2022; 10:microorganisms10091815. [PMID: 36144417 PMCID: PMC9506515 DOI: 10.3390/microorganisms10091815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans—from the oral cavity, to the gut, to fecal excretions—have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.
Collapse
Affiliation(s)
| | - Michelle Marie Esposito
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, NY 10016, USA
- Correspondence:
| | - Albert Ptashnik
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, NY 10016, USA
- DDS Program, NYU College of Dentistry, New York, NY 10010, USA
| |
Collapse
|
31
|
Sundberg LR, Rantanen N, de Freitas Almeida GM. Mucosal Environment Induces Phage Susceptibility in Streptococcus mutans. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:128-135. [PMID: 36793554 PMCID: PMC9917281 DOI: 10.1089/phage.2022.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pathogenic bacteria are attracted toward mucosa, as it is their way of entry into the body. However, we know surprisingly little about the phage-bacterium interactions in the mucosal environment. Here, we explored the effect of the mucosal environment on growth characteristics and phage-bacterium interactions in Streptococcus mutans, a causative agent of dental caries. We found that although mucin supplementation increased bacterial growth and survival, it decreased S. mutans biofilm formation. More importantly, the presence of mucin had a significant effect on S. mutans phage susceptibility. In two experiments done in Brain Heart Infusion Broth, phage M102 replication was detected only with 0.2% mucin supplementation. In 0.1 × Tryptic Soy Broth, 0.5% mucin supplementation led to a 4-log increase in phage titers compared with the control. These results suggest that the mucosal environment can have a major role in the growth, phage sensitivity, and phage resistance of S. mutans, and underline the importance of understanding the effect of mucosal environment on phage-bacterium interactions.
Collapse
Affiliation(s)
- Lotta-Riina Sundberg
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Noora Rantanen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Gabriel Magno de Freitas Almeida
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
32
|
Li S, Guo R, Zhang Y, Li P, Chen F, Wang X, Li J, Jie Z, Lv Q, Jin H, Wang G, Yan Q. A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome. iScience 2022; 25:104418. [PMID: 35663034 PMCID: PMC9160773 DOI: 10.1016/j.isci.2022.104418] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/26/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies. The Oral Virus Database comprises 48,425 viral genomes from 2,792 oral metagenomes Novel Saccharibacteria phages and jumbo viruses are ubiquitously distributed Oral virome shows a high degree of spatial variability Salivary virome exhibits a characteristic age-dependent pattern
Collapse
Affiliation(s)
- Shenghui Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.,Puensum Genetech Institute, Wuhan 430076, China.,Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Peng Li
- Puensum Genetech Institute, Wuhan 430076, China
| | - Fang Chen
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.,Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing 100044, China
| | - Zhuye Jie
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China.,College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| |
Collapse
|
33
|
Porto BN. Insights Into the Role of the Lung Virome During Respiratory Viral Infections. Front Immunol 2022; 13:885341. [PMID: 35572506 PMCID: PMC9091589 DOI: 10.3389/fimmu.2022.885341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.
Collapse
Affiliation(s)
- Bárbara N Porto
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Biology of Breathing Group, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
34
|
Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol 2022; 13:895537. [PMID: 35572634 PMCID: PMC9100676 DOI: 10.3389/fmicb.2022.895537] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
The human oral cavity provides a habitat for oral microbial communities. The complexity of its anatomical structure, its connectivity to the outside, and its moist environment contribute to the complexity and ecological site specificity of the microbiome colonized therein. Complex endogenous and exogenous factors affect the occurrence and development of the oral microbiota, and maintain it in a dynamic balance. The dysbiotic state, in which the microbial composition is altered and the microecological balance between host and microorganisms is disturbed, can lead to oral and even systemic diseases. In this review, we discuss the current research on the composition of the oral microbiota, the factors influencing it, and its relationships with common oral diseases. We focus on the specificity of the microbiota at different niches in the oral cavity, the communities of the oral microbiome, the mycobiome, and the virome within oral biofilms, and interventions targeting oral pathogens associated with disease. With these data, we aim to extend our understanding of oral microorganisms and provide new ideas for the clinical management of infectious oral diseases.
Collapse
Affiliation(s)
- Xinyi Li
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Yanmei Liu
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xingyou Yang
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Chengwen Li
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- *Correspondence: Chengwen Li,
| | - Zhangyong Song
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- Zhangyong Song,
| |
Collapse
|
35
|
Issrani R, Reddy J, Dabah THEM, Prabhu N. Role of Oral Microbiota in Carcinogenesis: A Short Review. J Cancer Prev 2022; 27:16-21. [PMID: 35419305 PMCID: PMC8984651 DOI: 10.15430/jcp.2022.27.1.16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
A strong and healthy microbiome is responsible for homeostasis between the host and microbiota which is necessary to achieve the normal functioning of the body. Dysbiosis provokes prevalence of pathogenic microbes, leading to alterations in gene expression profiles and metabolic processes. This in turn results in anomalous immune responses of the host. Dysbiosis may be associated with a wide variety of diseases like irritable bowel syndrome, coeliac disease, allergic conditions, bronchitis, asthma, heart diseases and oncogenesis. Presently, the links between oral microbial consortia and their functions, not only in the preservation of homeostasis but also pathogenesis of several malignancies have gained much awareness from the scientific community. The primary intent of this review is to highlight the dynamic role of oral microbiome in oncogenesis and its progression through various mechanisms. A literature search was conducted using multiple databases comprising of PubMed, Scopus, Google Scholar, and Cochrane electronic databases with keywords including microbiome, microbiota, carcinogenesis, tumorigenesis, and immunosuppression. Current and the past literature has pointed out the role of microorganisms in oncogenesis. It may be put forth that both the commensal and pathogenic strains of oral microbiome play an undeniably conspicuous role in carcinogenesis at different body sites.
Collapse
Affiliation(s)
- Rakhi Issrani
- Department of Preventive Dentistry, College of Dentistry, Jouf University, Sakaka, Kingdom of Saudi Arabia
- Department of Oral Medicine & Radiology, Indira Gandhi Institute of Dental Sciences, SBV University, Pondicherry, India
| | - Jagat Reddy
- Department of Oral Medicine & Radiology, Indira Gandhi Institute of Dental Sciences, SBV University, Pondicherry, India
| | - Tarek H. El-Metwally Dabah
- Medical Biochemistry Division, Department of Pathology, College of Medicine, Jouf University, Sakaka, Kingdom of Saudi Arabia
| | - Namdeo Prabhu
- Department of Oral & Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jouf University, Sakaka, Kingdom of Saudi Arabia
| |
Collapse
|
36
|
Spencer L, Olawuni B, Singh P. Gut Virome: Role and Distribution in Health and Gastrointestinal Diseases. Front Cell Infect Microbiol 2022; 12:836706. [PMID: 35360104 PMCID: PMC8960297 DOI: 10.3389/fcimb.2022.836706] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 12/11/2022] Open
Abstract
The study of the intestinal microbiome is an evolving field of research that includes comprehensive analysis of the vast array of microbes – bacterial, archaeal, fungal, and viral. Various gastrointestinal (GI) diseases, such as Crohn’s disease and ulcerative colitis, have been associated with instability of the gut microbiota. Many studies have focused on importance of bacterial communities with relation to health and disease in humans. The role of viruses, specifically bacteriophages, have recently begin to emerge and have profound impact on the host. Here, we comprehensively review the importance of viruses in GI diseases and summarize their influence in the complex intestinal environment, including their biochemical and genetic activities. We also discuss the distribution of the gut virome as it relates with treatment and immunological advantages. In conclusion, we suggest the need for further studies on this critical component of the intestinal microbiome to decipher the role of the gut virome in human health and disease.
Collapse
|
37
|
Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
Collapse
Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| |
Collapse
|
38
|
Tadmor AD, Phillips R. MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study. Bioinformatics 2022; 38:631-647. [PMID: 34636854 PMCID: PMC10060711 DOI: 10.1093/bioinformatics/btab703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. RESULTS To address this problem, we developed a novel clustering approach called 'metagenomic clustering by reference library' (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed 'signatures', are iteratively clustered in a greedy fashion, retaining at each step the reference genes yielding the lowest E values, and terminating when signatures of remaining reference genes have a minimal overlap. The outcome of this computation is a non-redundant list of reference genes homologous to minimally overlapping sets of contigs, representing potential candidates for gene families present in the metagenome. Unlike metagenomic clustering methods, there is no need for contigs to overlap to be associated with a cluster, enabling MCRL to draw on more information encoded in the metagenome when computing tentative gene families. We demonstrate how MCRL can be used to extract candidate viral gene families from an oral metagenome and an oral virome that otherwise could not be determined using standard approaches. We evaluate the sensitivity, accuracy and robustness of our proposed method for the viral case study and compare it with existing analysis approaches. AVAILABILITY AND IMPLEMENTATION https://github.com/a-tadmor/MCRL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Arbel D Tadmor
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
39
|
Xu HM, Xu WM, Zhang L. Current Status of Phage Therapy against Infectious Diseases and Potential Application beyond Infectious Diseases. Int J Clin Pract 2022; 2022:4913146. [PMID: 36263241 PMCID: PMC9550513 DOI: 10.1155/2022/4913146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/19/2022] [Indexed: 12/02/2022] Open
Abstract
Intestinal microbiota plays a key role in regulating the pathogenesis of human disease and maintaining health. Many diseases, mainly induced by bacteria, are on the rise due to the emergence of antibiotic-resistant strains. Intestinal microorganisms include organisms such as bacteria, viruses, and fungi. They play an important role in maintaining human health. Among these microorganisms, phages are the main members of intestinal viromes. In particular, the viral fraction, composed essentially of phages, affects homeostasis by exerting selective pressure on bacterial communities living in the intestinal tract. In recent years, with the widespread use and even abuse of antibacterial drugs, more and more drug-resistant bacteria have been found, and they show a trend of high drug resistance and multidrug resistance. Therefore, it has also become increasingly difficult to treat serious bacterial infections. Phages, a natural antibacterial agent with strong specificity and rapid proliferation, have come back to the field of vision of clinicians and scholars. In this study, the current state of research on intestinal phages was discussed, with an exploration of the impact of phage therapy against infectious diseases, as well as potential application beyond infectious diseases.
Collapse
Affiliation(s)
- Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Wen-Min Xu
- Department of Endoscopy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510091, China
| | - Long Zhang
- Department of Endoscopy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510091, China
| |
Collapse
|
40
|
Retnakumar R, Nath AN, Nair GB, Chattopadhyay S. Gastrointestinal microbiome in the context of Helicobacter pylori infection in stomach and gastroduodenal diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:53-95. [DOI: 10.1016/bs.pmbts.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
41
|
Guo Y, Huang X, Sun X, Yu Y, Wang Y, Zhang B, Cao J, Wen S, Li Y, Wang X, Cai S, Xia W, Wei F, Duan J, Dong H, Guo S, Zhang F, Zheng D, Sun Z. The Underrated Salivary Virome of Men Who Have Sex With Men Infected With HIV. Front Immunol 2021; 12:759253. [PMID: 34925329 PMCID: PMC8674211 DOI: 10.3389/fimmu.2021.759253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Salivary virome is important for oral ecosystem, but there are few reports on people living with HIV. We performed metagenomic sequencing to compare composition and functional genes of salivary virobiota between one HIV-negative and four HIV-positive groups in which participants were all men who have sex with men (MSM) with different immunosuppression statuses (five samples per group) to find the evidence that salivary virobiota plays a role in the pathogenesis of oral disease. Acute-stage subjects achieved a positive result of HIV RNA, but HIV antibody negative or indeterminate, whereas individuals with mild, moderate, and severe immunosuppression exhibited CD4+ T-lymphocyte counts of at least 500, 200–499, and less than 200 cells/μL or opportunistic infection, respectively. The results showed the composition of salivary virus genera in subjects with mild immunosuppression was the most similar to that in healthy people, followed by that in the acute stage; under severe immunosuppression, virus genera were suppressed and more similar to that under moderate immunosuppression. Furthermore, abnormally high abundance of Lymphocryptovirus was particularly obvious in MSM with HIV infection. Analysis of KEGG Pathway revealed that Caulobacter cell cycle, which affects cell duplication, became shorter in HIV-positive subjects. It is worth noting that in acute-stage participants, protein digestion and absorption related to the anti-HIV-1 activity of secretory leukocyte protease inhibitor was increased. Moreover, in the severely immunosuppressed subjects, glutathione metabolism, which is associated with the activation of lymphocytes, was enhanced. Nevertheless, the ecological dysbiosis in HIV-positive salivary virobiota possibly depended on the changes in blood viral load, and salivary dysfunction of MSM infected with HIV may be related to CD4 counts. Ribonucleoside diphosphate reductase subunit M1 in purine metabolism was negatively correlated, though weakly, to CD4 counts, which may be related to the promotion of HIV-1 DNA synthesis in peripheral blood lymphocytes. 7-Cyano-7-deazaguanine synthase in folate biosynthesis was weakly positively correlated with HIV viral load, suggesting that this compound was produced excessively to correct oral dysfunction for maintaining normal cell development. Despite the limited number of samples, the present study provided insight into the potential role of salivary virome in the oral function of HIV infected MSM.
Collapse
Affiliation(s)
- Ying Guo
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaojie Huang
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xintong Sun
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yixi Yu
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Baojin Zhang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jie Cao
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shuo Wen
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yuchen Li
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xin Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Siyu Cai
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junyi Duan
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Haozhi Dong
- Department of Stomatology, Beijing Daxing District Hospital of Integrated Chinese and Western Medicine, Beijing, China
| | - Shan Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Fengqiu Zhang
- Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Dongxiang Zheng
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zheng Sun
- Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
42
|
Sedghi LM, Bacino M, Kapila YL. Periodontal Disease: The Good, The Bad, and The Unknown. Front Cell Infect Microbiol 2021; 11:766944. [PMID: 34950607 PMCID: PMC8688827 DOI: 10.3389/fcimb.2021.766944] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
Periodontal disease is classically characterized by progressive destruction of the soft and hard tissues of the periodontal complex, mediated by an interplay between dysbiotic microbial communities and aberrant immune responses within gingival and periodontal tissues. Putative periodontal pathogens are enriched as the resident oral microbiota becomes dysbiotic and inflammatory responses evoke tissue destruction, thus inducing an unremitting positive feedback loop of proteolysis, inflammation, and enrichment for periodontal pathogens. Keystone microbial pathogens and sustained gingival inflammation are critical to periodontal disease progression. However, recent studies have revealed the importance of previously unidentified microbes involved in disease progression, including various viruses, phages and bacterial species. Moreover, newly identified immunological and genetic mechanisms, as well as environmental host factors, including diet and lifestyle, have been discerned in recent years as further contributory factors in periodontitis. These factors have collectively expanded the established narrative of periodontal disease progression. In line with this, new ideologies related to maintaining periodontal health and treating existing disease have been explored, such as the application of oral probiotics, to limit and attenuate disease progression. The role of systemic host pathologies, such as autoimmune disorders and diabetes, in periodontal disease pathogenesis has been well noted. Recent studies have additionally identified the reciprocated importance of periodontal disease in potentiating systemic disease states at distal sites, such as in Alzheimer's disease, inflammatory bowel diseases, and oral cancer, further highlighting the importance of the oral cavity in systemic health. Here we review long-standing knowledge of periodontal disease progression while integrating novel research concepts that have broadened our understanding of periodontal health and disease. Further, we delve into innovative hypotheses that may evolve to address significant gaps in the foundational knowledge of periodontal disease.
Collapse
Affiliation(s)
- Lea M. Sedghi
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Margot Bacino
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Yvonne Lorraine Kapila
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Periodontology, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
43
|
Salabura A, Łuniewski A, Kucharska M, Myszak D, Dołęgowska B, Ciechanowski K, Kędzierska-Kapuza K, Wojciuk B. Urinary Tract Virome as an Urgent Target for Metagenomics. Life (Basel) 2021; 11:life11111264. [PMID: 34833140 PMCID: PMC8618529 DOI: 10.3390/life11111264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
Virome—a part of a microbiome—is a term used to describe all viruses found in the specific organism or system. Recently, as new technologies emerged, it has been confirmed that kidneys and the lower urinary tract are colonized not only by the previously described viruses, but also completely novel species. Viruses can be both pathogenic and protective, as they often carry important virulence factors, while at the same time represent anti-inflammatory functions. This paper aims to show and compare the viral species detected in various, specific clinical conditions. Because of the unique characteristics of viruses, new sequencing techniques and databases had to be developed to conduct research on the urinary virome. The dynamic development of research on the human microbiome suggests that the detailed studies on the urinary system virome will provide answers to many questions about the risk factors for civilization, cancer, and autoimmune diseases.
Collapse
Affiliation(s)
- Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
- Correspondence: ; Tel.: +48-664-477-450
| | - Aleksander Łuniewski
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Maria Kucharska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Denis Myszak
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Barbara Dołęgowska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
| | - Karolina Kędzierska-Kapuza
- Center of Postgraduate Medical Education in Warsaw, Department of Gastroenterological Surgery and Transplantology, 137 Wołoska St., 02-507 Warsaw, Poland;
| | - Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| |
Collapse
|
44
|
Abstract
Mediators of the initiation, development, and recurrence of periodontitis include the oral microbiome embedded in subgingival plaque and the host immune response to a dysbiosis within this dynamic and complex microbial community. Although mediators have been studied extensively, researchers in the field have been unable to fully ascribe certain clinical presentations of periodontitis to their nature. Emergence of high-throughput sequencing technologies has resulted in better characterization of the microbial oral dysbiosis that extends beyond the extensively studied putative bacterial periodontopathogens to a shift in the oral virome composition during disease conditions. Although the biological dark matter inserted by retroviruses was once believed to be nonfunctional, research has revealed that it encodes historical viral-eukaryotic interactions and influences host development. The objective of this review is to evaluate the proposed association of herpesviruses to the etiology and pathogenesis of periodontal disease and survey the highly abundant prokaryotic viruses to delineate their potential roles in biofilm dynamics, as well as their interactions with putative bacterial periodontopathogens and eukaryotic cells. The findings suggest that potential novel periodontal therapies targeting or utilizing the oral virome can alleviate certain clinical presentations of periodontitis. Perhaps it is time to embrace the viral dark matter within the periodontal environment to fully comprehend the pathogenesis and systemic implications of periodontitis.
Collapse
Affiliation(s)
- April Martínez
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ryutaro Kuraji
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Life Science DentistryThe Nippon Dental UniversityTokyoJapan
- Department of PeriodontologyThe Nippon Dental University School of Life Dentistry at TokyoTokyoJapan
| | - Yvonne L. Kapila
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| |
Collapse
|
45
|
Brookes ZLS, Belfield LA, Ashworth A, Casas-Agustench P, Raja M, Pollard AJ, Bescos R. Effects of chlorhexidine mouthwash on the oral microbiome. J Dent 2021; 113:103768. [PMID: 34418463 DOI: 10.1016/j.jdent.2021.103768] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/11/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION/OBJECTIVES Chlorhexidine (CHX) is a commonly used mouthwash with potent anti-microbial effects useful for the management of oral disease. However, we are moving away from the view of simply 'killing' bacteria, towards managing oral microbial ecosystems (oral microbiome), as an integrated system, to promote oral and systemic health. Here, we aimed to review the effects of CHX mouthwash on the balance of microbial communities in the mouth in vivo in oral health and disease. SOURCES AND STUDY SECTION The hierarchy of evidence was applied, with systematic reviews and randomised controlled trials consulted where available and case controlled studies being described thereafter. Search terms for each subject category were entered into MEDLINE, PubMed, Google Scholar and the Cochrane database. Focussing on metagenomics studies provides unique overview of the oral microbiome as an integrated system. DATA Evidence was limited, but several next generation sequencing case-controlled studies suggested that in an integrated system, CHX may cause a shift towards lower bacterial diversity and abundance, in particular nitrate-reducing bacteria in vivo. CHX also appeared to alter salivary pH, lactate, nitrate and nitrite concentrations in saliva. Evidence regarding the effects of CHX on the oral microbiome during oral disease is still emerging. CONCLUSIONS CHX alters the composition the oral microbiome. However, as CHX use remains widespread in dentistry to manage oral disease, urgent research using metagenomics studies of microbial communities in vivo are still needed to determine CHX mouthwash is 'good', 'bad' or otherwise for bacteria, in the context of oral and systemic health.
Collapse
Affiliation(s)
- Zoë L S Brookes
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom.
| | - Louise A Belfield
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom
| | - Ann Ashworth
- Institute of Health & Community, University of Plymouth, Plymouth, PL4 8AA, United Kingdom
| | - Patricia Casas-Agustench
- School of Health Professions, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom; Department of Health Sciences, Open University of Catalonia, Barcelona, Spain
| | | | - Alexander J Pollard
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom; Bristol Dental School, University of Bristol, Bristol BS1 2LY, United Kingdom
| | - Raul Bescos
- School of Health Professions, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom.
| |
Collapse
|
46
|
Hussein H. Oral Sampling Techniques. Methods Mol Biol 2021; 2327:17-29. [PMID: 34410637 DOI: 10.1007/978-1-0716-1518-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The human oral cavity is a major point of entry for microorganisms, many of which live and multiply in the mouth. In addition, it provides an accessible site for sampling compared to other parts of the body; however, caution should be taken during oral sampling as many factors contribute to the microbial diversity in a site-dependent manner. The accessibility of the oral cavity and its microbial diversity emphasize the crucial need to avoid cross-contamination during the sampling procedure. In this chapter, we describe various detailed oral sampling procedures. These methods include supragingival dental plaque sampling, subgingival dental plaque sampling, oral mucosal sampling, and endodontic sampling methods for extracted teeth or in the patient's mouth. The proposed protocols provide tips to avoid contamination between different oral sources of bacteria and possible alternatives to the tools used.
Collapse
Affiliation(s)
- Heba Hussein
- Oral Medicine, Diagnosis, and Periodontology Department, Faculty of Dentistry, Cairo University, Cairo, Egypt. .,Department of Oral Medicine and Diagnostic Sciences, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA.
| |
Collapse
|
47
|
Progress in Oral Microbiome Related to Oral and Systemic Diseases: An Update. Diagnostics (Basel) 2021; 11:diagnostics11071283. [PMID: 34359364 PMCID: PMC8306157 DOI: 10.3390/diagnostics11071283] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
The human oral microbiome refers to an ecological community of symbiotic and pathogenic microorganisms found in the oral cavity. The oral cavity is an environment that provides various biological niches, such as the teeth, tongue, and oral mucosa. The oral cavity is the gateway between the external environment and the human body, maintaining oral homeostasis, protecting the mouth, and preventing disease. On the flip side, the oral microbiome also plays an important role in the triggering, development, and progression of oral and systemic diseases. In recent years, disease diagnosis through the analysis of the human oral microbiome has been realized with the recent development of innovative detection technology and is overwhelmingly promising compared to the previous era. It has been found that patients with oral and systemic diseases have variations in their oral microbiome compared to normal subjects. This narrative review provides insight into the pathophysiological role that the oral microbiome plays in influencing oral and systemic diseases and furthers the knowledge related to the oral microbiome produced over the past 30 years. A wide range of updates were provided with the latest knowledge of the oral microbiome to help researchers and clinicians in both academic and clinical aspects. The microbial community information can be utilized in non-invasive diagnosis and can help to develop a new paradigm in precision medicine, which will benefit human health in the era of post-metagenomics.
Collapse
|
48
|
El-Sayed A, Aleya L, Kamel M. Microbiota's role in health and diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:36967-36983. [PMID: 34043164 PMCID: PMC8155182 DOI: 10.1007/s11356-021-14593-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/24/2021] [Indexed: 05/06/2023]
Abstract
The microbiome is a term that usually refers to the community of various microorganisms that inhabit/live inside human/animal bodies or on their skin. It forms a complex ecosystem that includes trillions of commensals, symbiotics, and even pathogenic microorganisms. The external environment, diet, and lifestyle are the major determinants influencing the microbiome's composition and vitality. Recent studies have indicated the tremendous influence of the microbiome on health and disease. Their number, constitution, variation, and viability are dynamic. All these elements are responsible for the induction, development, and treatment of many health disorders. Serious diseases such as cancer, metabolic disorders, cardiovascular diseases, and even psychological disorders such as schizophrenia are influenced directly or indirectly by microbiota. In addition, in the last few weeks, accumulating data about the link between COVID-19 and the microbiota were published. In the present work, the role of the microbiome in health and disease is discussed. A deep understanding of the exact role of microbiota in disease induction enables the prevention of diseases and the development of new therapeutic concepts for most diseases through the correction of diet and lifestyle. The present review brings together evidence from the most recent works and discusses suggested nutraceutical approaches for the management of COVID-19 pandemic.
Collapse
Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| |
Collapse
|
49
|
Gabashvili E, Kobakhidze S, Koulouris S, Robinson T, Kotetishvili M. Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:179-202. [PMID: 33484405 DOI: 10.1007/s12560-021-09460-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
Collapse
Affiliation(s)
- Ekaterine Gabashvili
- School of Natural Sciences and Medicine, Ilia State University, 1 Giorgi Tsereteli exit, 0162, Tbilisi, Georgia
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Stylianos Koulouris
- Engagement and Cooperation Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Tobin Robinson
- Scientific Committee, and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Mamuka Kotetishvili
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia.
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitation, 78 D. Uznadze St., 0102, Tbilisi, Georgia.
| |
Collapse
|
50
|
Sommers P, Chatterjee A, Varsani A, Trubl G. Integrating Viral Metagenomics into an Ecological Framework. Annu Rev Virol 2021; 8:133-158. [PMID: 34033501 DOI: 10.1146/annurev-virology-010421-053015] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. An ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Anushila Chatterjee
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA.,These authors contributed equally to this article
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA; .,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| |
Collapse
|