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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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2
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Zhou S, Bao Z, Ma S, Ou C, Hu H, Yang Y, Feng X, Pan Y, Gong S, Fan F, Chen P, Chu Q. A local dark tea - Liubao tea - extract exhibits remarkable performance in oral tissue regeneration, inflammation relief and oral microbiota reconstruction. Food Funct 2023; 14:7400-7412. [PMID: 37475617 DOI: 10.1039/d3fo02277c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The prevalence of oral health problems is ubiquitous in contemporary society, with particular emphasis placed on the central role of oral flora in mitigating this issue. Both ancient literature and modern research have highlighted the promising application of tea with substantial bioactive properties, particularly dark tea, in preserving and promoting oral health. Liubao tea, a widely consumed dark tea with increasing popularity in recent years, has been reported to possess abundant bioactive constituents, exhibit remarkable antioxidant and anti-inflammatory effects, modulate the flora structure and so on. It may be a promising candidate for addressing oral health problems. In this study, Liubao tea was meticulously extracted, purified and identified, followed by an investigation of its potential to modulate oral microecology by virtue of an acetic acid-induced oral disorder murine model. The results revealed that Liubao tea extract (LTE) application commendably reconstructed the oral mucosal barrier, promoted tissue regeneration and mitigated micro-inflammation. Furthermore, LTE treatment could also ameliorate the oral flora composition by decreasing the abundance of Proteobacteria and increasing the abundance of Firmicutes and Actinobacteria at the phylum level, as well as inhibiting pernicious bacteria such as Streptococcus and Delftia acidovorans. So, it could promote the generation of a beneficial microenvironment and regulate the immune process. Overall, LTE demonstrated remarkable potential in regulating the balance of oral microecology, suggesting that it may represent a promising therapeutic strategy for oral health concerns.
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Affiliation(s)
- Su Zhou
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhelu Bao
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Shicheng Ma
- Wuzhou Liubao Tea Research Association, Wuzhou, 543000, P. R. China
| | - Cansong Ou
- Wuzhou Tea Industry Development Service Center, Wuzhou, 543000, P. R. China
| | - Hao Hu
- College of Agriculture and Food Science, Zhejiang Agriculture & Forest University, Hangzhou 310058, P. R. China
| | - Yunyun Yang
- College of Standardization, China Jiliang University, Hangzhou 310018, P. R. China
| | - Xinyu Feng
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yani Pan
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Shuying Gong
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Fangyuan Fan
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Ping Chen
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
| | - Qiang Chu
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, P. R. China.
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3
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Kedlaya MN, Puzhankara L, Prasad R, Raj A. Periodontal Disease Pathogens, Pathogenesis, and Therapeutics: The CRISPR-Cas Effect. CRISPR J 2023; 6:90-98. [PMID: 36939849 DOI: 10.1089/crispr.2022.0094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Periodontal disease (PD) is an immune-inflammatory disease affecting the supporting structures of the teeth, which results in progressive destruction of the hard and soft tissues surrounding teeth, ultimately resulting in tooth loss. The primary etiological factor for this disease is the presence of pathogenic microorganisms. Pathogenic bacteria face antagonistic conditions and foreign DNA components during the infection stage and depend on defense mechanisms such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas to counter them. Virulence genes regulated by the CRISPR-Cas system are often expressed by bacteria as part of the stress response to the presence of stress conditions and foreign elements. There is ever-growing evidence regarding the role of CRISPR-Cas in virulence of periodontal pathogens. The same CRISPR-Cas system may also be targeted to reduce bacterial virulence and it may also be utilized to develop diagnostic and therapeutic strategies for prevention and control of PD progression. This review article describes the CRISPR-Cas systems in the periodontal dysbiotic microbial communities, their role in the virulence of periodontal pathogens, and their potential role in understanding the pathogenesis of periodontitis and treatment of PD.
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Affiliation(s)
- Madhurya N Kedlaya
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, India; Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
| | - Lakshmi Puzhankara
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, India; Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
| | - Rohit Prasad
- Department of Periodontology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
| | - Akshatha Raj
- Department of Periodontology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
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4
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Isola G. Prospective Advances in Genome Editing Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:301-313. [DOI: 10.1007/978-981-19-5642-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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5
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Neves VCM, Pugh J, Savulescu J. Beyond oral hygiene, are capacity-altering, biologically based interventions within the moral domain of dentistry? Br Dent J 2021; 231:277-280. [PMID: 34508196 DOI: 10.1038/s41415-021-3335-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
Oral diseases such as dental caries (DC) and periodontitis are widely prevalent, and existing approaches to managing these conditions have only a limited effect. Accordingly, there is growing interest in the development of novel biological interventions (including, among others, CRISPR-Cas9) that might, in the future, be used to prevent the development of or cure these conditions. However, in addition to familiar concerns about using biological interventions in children who cannot provide valid consent, it is not clear whether the provision of these interventions would fall within the proper domain of dentistry. In this opinion paper, we defend the view that the provision of reasonably safe and effective novel biological interventions aimed at preventing DC and periodontitis should be understood to fall within the proper domain of dentistry. To do so, we first argue that their use would be consistent with existing practice in dentistry. We then argue that: i) they may substantially increase the recipient's wellbeing and future autonomy; and ii) that their use could constitute a form of indirect preventative medicine by addressing a threat to systemic health.
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Affiliation(s)
- Vitor C M Neves
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, UK.
| | - Jonathan Pugh
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, UK
| | - Julian Savulescu
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, UK
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6
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Barbour A, Glogauer J, Grinfeld L, Ostadsharif Memar R, Fine N, Tenenbaum H, Glogauer M. The role of CRISPR-Cas in advancing precision periodontics. J Periodontal Res 2021; 56:454-461. [PMID: 33452819 DOI: 10.1111/jre.12846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/23/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022]
Abstract
The significant advancement of molecular biology has revolutionized medicine and provided important technologies to further clinical research development. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are DNA sequences derived from bacteriophages which have previously infected the bacterial species. The CRISPR-Cas system plays a key role in bacterial defense by detecting and destroying DNA fragments during subsequent bacteriophage invasions. The Cas9 enzyme recognizes and cleaves new invading CRISPR-complementary DNA sequences. Researchers have taken advantage of this biological device to manipulate microbes' genes and develop novel therapeutics to tackle systemic disease. In this review, we discuss the potential of utilizing CRISPR-Cas systems in the periodontal field to develop personalized periodontal care. We summarize promising attempts to bring this technology to the clinical setting. Finally, we provide insights regarding future developments to best utilize the CRISPR-Cas systems to advance precision periodontics. Although further research is imperative to evaluate the safety and potential of using CRISPR-Cas to develop precision periodontics approaches, few studies showed promising data to support the investment into this important technology in the dental sector. CRISPR-Cas9 can be a useful tool to create knockouts in vitro and in vivo as a screening tool to identify cellular pathways involved in the pathogenesis of periodontitis. Alternative CRISPR systems such as CRISPRa, CRISPRi, and Cas13 can be used to modify the transcriptome and gene expression of genes involved in periodontitis progression. CRISPR systems such as Cas3 can be used to target the periodontal biofilm and to develop new strategies to reduce or eliminate periodontal pathogens. Currently, the utility of CRISPR-Cas applications in clinical settings is limited. Through this review, we hope to foster further discussion in the periodontal research and clinical communities with respect to the potential clinical application of novel, CRISPR-Cas based, therapeutics for periodontitis.
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Affiliation(s)
| | - Judah Glogauer
- Michael G. DeGroote School of Medicine, McMaster University, Toronto, ON, Canada
| | - Lis Grinfeld
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | | | - Noah Fine
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - Howard Tenenbaum
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada.,Department of Dentistry, Centre for Advanced Dental Research and Care, Mount Sinai Hospital, Toronto, ON, Canada
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, ON, Canada.,Department of Dental Oncology, Maxillofacial and Ocular Prosthetics, Princess Margaret Cancer Centre, Toronto, ON, Canada
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7
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Filamentation initiated by Cas2 and its association with the acquisition process in cells. Int J Oral Sci 2019; 11:29. [PMID: 31578319 PMCID: PMC6802651 DOI: 10.1038/s41368-019-0063-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/18/2019] [Accepted: 07/07/2019] [Indexed: 12/15/2022] Open
Abstract
Cas1-and-Cas2-mediated new spacer acquisition is an essential process for bacterial adaptive immunity. The process is critical for the ecology of the oral microflora and oral health. Although molecular mechanisms for spacer acquisition are known, it has never been established if this process is associated with the morphological changes of bacteria. In this study, we demonstrated a novel Cas2-induced filamentation phenotype in E. coli that was regulated by co-expression of the Cas1 protein. A 30 amino acid motif at the carboxyl terminus of Cas2 is necessary for this function. By imaging analysis, we provided evidence to argue that Cas-induced filamentation is a step coupled with new spacer acquisition during which filaments are characterised by polyploidy with asymmetric cell division. This work may open new opportunities to investigate the adaptive immune response and microbial balance for oral health.
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8
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Zaffino M, Dubar M, Debourgogne A, Bisson C, Machouart M. Development of a new TaqMan PCR assay for the detection of both Entamoeba gingivalis genotypes. Diagn Microbiol Infect Dis 2019; 95:114886. [PMID: 31522801 DOI: 10.1016/j.diagmicrobio.2019.114886] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 07/06/2019] [Accepted: 08/07/2019] [Indexed: 11/15/2022]
Abstract
Entamoeba gingivalis is a parasitic protozoan found in the mouth of patients suffering from periodontitis, a widespread oral disease with an underestimated prevalence and major consequences on health. We present the development of the first TaqMan PCR assay targeting both E. gingivalis subtypes. This method has been evaluated on 50 samples from patients diagnosed with periodontitis in comparison with 2 different conventional PCRs, and a real-time SYBR Green PCR. Fifty percent of the samples were found positive for the E. gingivalis ST1 subtype with this new PCR, the SYBR Green PCR and one of the conventional PCRs. Among the 25 remaining samples, 12 (24%) were found positive for the E. gingivalis ST2 kamaktlii variant. This new TaqMan PCR could be used before and after periodontitis treatment to follow its efficacy and measure the parasite load in order to better understand the role of these parasites in oral diseases.
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Affiliation(s)
- Marie Zaffino
- Stress, Immunity, Pathogens Laboratory, EA7300 Lorraine University, Faculty of Medicine, 9 Avenue de la forêt de Haye, F-54500 Vandoeuvre-lès-Nancy, France
| | - Marie Dubar
- Stress, Immunity, Pathogens Laboratory, EA7300 Lorraine University, Faculty of Medicine, 9 Avenue de la forêt de Haye, F-54500 Vandoeuvre-lès-Nancy, France; Department of Periodontology, Lille University, Place de Verdun, 59000 Lille, France
| | - Anne Debourgogne
- Stress, Immunity, Pathogens Laboratory, EA7300 Lorraine University, Faculty of Medicine, 9 Avenue de la forêt de Haye, F-54500 Vandoeuvre-lès-Nancy, France; Parasitology-Mycology Laboratory, CHU Nancy-Brabois, 11 allée du Morvan, 54511 Vandoeuvre-les -Nancy, France
| | - Catherine Bisson
- Stress, Immunity, Pathogens Laboratory, EA7300 Lorraine University, Faculty of Medicine, 9 Avenue de la forêt de Haye, F-54500 Vandoeuvre-lès-Nancy, France; Department of Periodontology, Lorraine University, Rue du Dr Heydenreich, 54000 Nancy, France
| | - Marie Machouart
- Stress, Immunity, Pathogens Laboratory, EA7300 Lorraine University, Faculty of Medicine, 9 Avenue de la forêt de Haye, F-54500 Vandoeuvre-lès-Nancy, France; Parasitology-Mycology Laboratory, CHU Nancy-Brabois, 11 allée du Morvan, 54511 Vandoeuvre-les -Nancy, France.
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9
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Chen T, Olsen I. Porphyromonas gingivalis and its CRISPR-Cas system. J Oral Microbiol 2019; 11:1638196. [PMID: 31303969 PMCID: PMC6609313 DOI: 10.1080/20002297.2019.1638196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/12/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) are immune systems in prokaryotes present in most Bacteria and Archaea. They provide adaptive immunity against foreign elements such as bacteriophages/viruses, plasmids and transposons. During immunization a small sequence of foreign DNA, a so-called spacer is integrated into the CRISPR locus in the host cell. Spacers are then transcribed into small RNA guides that direct cleavage of foreign DNA by Cas nucleases. Immunization through spacer acquisition is transferred vertically to the progeny. It is possible that this genetic immune system of bacteria participates in modulating the microbiome of ‘chronic’ periodontitis, in which Porphyromonas gingivalis has been identified as a keystone pathogen causing microbial dysbiosis. An in-depth review of our current knowledge on the CRISPR-Cas systems in P. gingivalis is given in this paper with the attempt to understand how this anaerobic bacterium may protect itself in the periodontal pocket where bacteriophages are abundant and even out-number bacteria.
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Affiliation(s)
- 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
| | - Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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10
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Yu N, Yang J, Mishina Y, Giannobile WV. Genome Editing: A New Horizon for Oral and Craniofacial Research. J Dent Res 2018; 98:36-45. [PMID: 30354846 DOI: 10.1177/0022034518805978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Precise and efficient genetic manipulations have enabled researchers to understand gene functions in disease and development, providing a platform to search for molecular cures. Over the past decade, the unprecedented advancement of genome editing techniques has revolutionized the biological research fields. Early genome editing strategies involved many naturally occurring nucleases, including meganucleases, zinc finger nucleases, and transcription activator-like effector-based nucleases. More recently, the clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated nucleases (CRISPR/Cas) system has greatly enriched genetic manipulation methods in conducting research. Those nucleases generate double-strand breaks in the target gene sequences and then utilize DNA repair mechanisms to permit precise yet versatile genetic manipulations. The oral and craniofacial field harbors a plethora of diseases and developmental defects that require genetic models that can exploit these genome editing techniques. This review provides an overview of the genome editing techniques, particularly the CRISPR/Cas9 technique, for the oral and craniofacial research community. We also discuss the details about the emerging applications of genome editing in oral and craniofacial biology.
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Affiliation(s)
- N Yu
- 1 Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - J Yang
- 2 Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.,3 The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Y Mishina
- 2 Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - W V Giannobile
- 1 Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.,4 Department of Biomedical Engineering, College of Engineering, University of Michigan, Ann Arbor, MI, USA
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11
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Zhang Y, Zhen M, Zhan Y, Song Y, Zhang Q, Wang J. Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease. Front Cell Infect Microbiol 2017; 7:409. [PMID: 28983469 PMCID: PMC5613308 DOI: 10.3389/fcimb.2017.00409] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences. The results showed that both P. intermedia and P. nigrescens have highly dynamic genomes and can take up various exogenous factors through horizontal gene transfer. The major differences between disease-derived and health-derived samples of P. intermedia and P. nigrescens were factors related to genome modification and recombination, indicating that the Prevotella isolates from disease sites may be more capable of genomic reconstruction. We also identified genetic elements specific to each sample, and found that disease groups had more unique virulence factors related to capsule and lipopolysaccharide synthesis, secretion systems, proteinases, and toxins, suggesting that strains from disease sites may have more specific virulence, particularly for P. intermedia. The differentially represented pathways between samples from disease and health were related to energy metabolism, carbohydrate and lipid metabolism, and amino acid metabolism, consistent with data from the whole subgingival microbiome in periodontal disease and health. Disease-derived samples had gained or lost several metabolic genes compared to healthy-derived samples, which could be linked with the difference in virulence performance between diseased and healthy sample groups. Our findings suggest that P. intermedia and P. nigrescens may serve as “crucial substances” in subgingival plaque, which may reflect changes in microbial and environmental dynamics in subgingival microbial ecosystems. This provides insight into the potential of P. intermedia and P. nigrescens as new predictive biomarkers and targets for effective interventions in periodontal disease.
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Affiliation(s)
- Yifei Zhang
- Central Laboratory, Peking University School and Hospital of StomatologyBeijing, China
| | - Min Zhen
- Department of Periodontology, Peking University School and Hospital of StomatologyBeijing, China
| | - Yalin Zhan
- Department of Periodontology, Peking University School and Hospital of StomatologyBeijing, China
| | - Yeqing Song
- Central Laboratory, Peking University School and Hospital of StomatologyBeijing, China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of StomatologyBeijing, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of SciencesBeijing, China
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12
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Abstract
Periodontitis is an extremely prevalent disease worldwide and is driven by complex dysbiotic microbiota. Here we analyzed the transcriptional activity of the periodontal pocket microbiota from all domains of life as well as the human host in health and chronic periodontitis. Bacteria showed strong enrichment of 18 KEGG functional modules in chronic periodontitis, including bacterial chemotaxis, flagellar assembly, type III secretion system, type III CRISPR-Cas system, and two component system proteins. Upregulation of these functions was driven by the red-complex pathogens and candidate pathogens, e.g. Filifactor alocis, Prevotella intermedia, Fretibacterium fastidiosum and Selenomonas sputigena. Nine virulence factors were strongly up-regulated, among them the arginine deiminase arcA from Porphyromonas gingivalis and Mycoplasma arginini. Viruses and archaea accounted for about 0.1% and 0.22% of total putative mRNA reads, respectively, and a protozoan, Entamoeba gingivalis, was highly enriched in periodontitis. Fourteen human transcripts were enriched in periodontitis, including a gene for a ferric iron binding protein, indicating competition with the microbiota for iron, and genes associated with cancer, namely nucleolar phosphoprotein B23, ankyrin-repeat domain 30B-like protein and beta-enolase. The data provide evidence on the level of gene expression in vivo for the potentially severe impact of the dysbiotic microbiota on human health.
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13
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Ji P, Zhang Y, Wang J, Zhao F. MetaSort untangles metagenome assembly by reducing microbial community complexity. Nat Commun 2017; 8:14306. [PMID: 28112173 PMCID: PMC5264255 DOI: 10.1038/ncomms14306] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/14/2016] [Indexed: 12/31/2022] Open
Abstract
Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.
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Affiliation(s)
- Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanming Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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14
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Szafrański SP, Winkel A, Stiesch M. The use of bacteriophages to biocontrol oral biofilms. J Biotechnol 2017; 250:29-44. [PMID: 28108235 DOI: 10.1016/j.jbiotec.2017.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/15/2022]
Abstract
Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.
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Affiliation(s)
- Szymon P Szafrański
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
| | - Andreas Winkel
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Meike Stiesch
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
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Ecology of the Oral Microbiome: Beyond Bacteria. Trends Microbiol 2017; 25:362-374. [PMID: 28089325 DOI: 10.1016/j.tim.2016.12.012] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 01/08/2023]
Abstract
Although great strides have been made in understanding the complex bacterial community inhabiting the human oral cavity, for a variety of (mainly technical) reasons the ecological contributions of oral fungi, viruses, phages, and the candidate phyla radiation (CPR) group of ultrasmall bacteria have remained understudied. Several recent reports have illustrated the diversity and importance of these organisms in the oral cavity, while TM7x and Candida albicans have served as crucial paradigms for CPR species and oral fungi, respectively. A comprehensive understanding of the oral microbiota and its influence on host health and disease will require a holistic view that emphasizes interactions among different residents within the oral community, as well as their interaction with the host.
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