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Zhang Y, Liu F, Mo D, Jiang Y, Lin T, Deng S, Lan J, Qiu R. Ethnicity-based analysis of supragingival plaque composition and dental health behaviours in healthy subjects without caries. Heliyon 2024; 10:e35238. [PMID: 39170429 PMCID: PMC11336456 DOI: 10.1016/j.heliyon.2024.e35238] [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: 10/11/2023] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Objective The primary objective of this study was to scrutinise the disparities in the diversity, structure, and function of the oral microbiome among caries-free children from the Zhuang and Han ethnic groups with a focus on the influence of ethnically distinct oral health behaviours on the composition of the oral microbiota. Methods A questionnaire survey was conducted to assess oral health behaviours and dental plaque samples were collected from 96 Zhuang and Han children aged 4-5 years living in Guangxi, southern China for high-throughput sequencing. PCR amplification was performed for sequencing of the V4 region of the 16S rDNA gene, and second-generation sequencing was performed using the Illumina MiSeq platform to compare and analyse the diversity, structure and function of the microbiota. Results Single-factor analysis revealed significant differences between the Zhuang and Han ethnic groups regarding juice consumption, the frequency of consuming sugar-sweetened food or beverages before bedtime, the age that individuals started toothbrushing, the frequency of toothbrushing and the frequency of parental assistance with toothbrushing (p < 0.001). The dominant phyla were Proteobacteria, Firmicutes, etc., and the dominant genera included Streptococcus and Neisseria. The dental plaques of the caries-free Zhuang and Han ethnic groups had similar core microbiomes, with no significant differences in the diversity and structure of the microbiota and no significant differences in the abundance of the dominant genera. In addition, no significant difference in metabolic function was observed between the Zhuang and Han ethnic groups. Conclusion The core oral microbiota was consistent in caries-free Zhuang and Han children. Despite differences in dietary habits and oral hygiene behaviours between the Zhuang and Han ethnic groups, with a high frequency of sugary food intake but better oral health behaviours in the Zhuang group, there were no significant differences in the diversity, structure and function of the oral microbiota of caries-free children in the Zhuang and Han ethnic groups.
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Affiliation(s)
| | | | - Dan Mo
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Yiling Jiang
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Tian Lin
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Sicheng Deng
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Jue Lan
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
| | - Rongmin Qiu
- College & Hospital of Stomatology, Guangxi Medical University, Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, Guangxi Clinical Research Center for Craniofacial Deformity, Guangxi Key Laboratory of Oral and Maxillofacial Surgery Disease Treatment, Guangxi Health Commission Key Laboratory of Prevention and Treatment for Oral Infectious Diseases, Key Laboratory of Research and Application of Stomatological Equipment, Education Department of Guangxi Zhuang Autonomous Region, No.10 Shuangyong Road, Nanning, Guangxi, 530021, China
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2
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Yadav S, Tripathi V, Saran V. Identification of habit specific bacteria in human saliva through Next-Generation Sequencing. Forensic Sci Int 2023; 353:111871. [PMID: 37939434 DOI: 10.1016/j.forsciint.2023.111871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Characterization of human saliva through Next-Generation Sequencing has emerged as a valuable tool for understanding the complex microbial communities residing in the oral cavity. This study aims to investigate the habit-based variations in the salivary microbiome using Next-Generation Sequencing technology. Saliva samples were collected from a diverse population representing different habits, including smoking, alcohol consumption, and vegan diet. The DNA from the samples was extracted, and the V3-V4 region of the 16 S rRNA gene was amplified for Next-Generation Sequencing analysis. The obtained sequences were processed and analysed using bioinformatics tools to determine the microbial composition and diversity. Preliminary results revealed distinct microbial profiles associated with different habits, indicating the potential influence of different habits on the salivary microbiome. Smokers exhibited a higher abundance of certain pathogenic bacteria, while alcohol consumers showed alterations in microbial diversity compared to non-consumers. Furthermore, individuals with vegan diet demonstrated an increased prevalence of specific bacteria. These findings highlight the significance of habit-based characterization of the salivary microbiome and its potential implications in the presence of certain bacteria. Understanding the relationship between habits and the salivary microbiome could contribute to developing personalized approaches for estimating and identifying any particular individual. Further research is warranted to explore additional factors and expand the scope of habit-based analysis in saliva-based microbial characterization through Next-Generation Sequencing.
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Affiliation(s)
- Shubham Yadav
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology And Sciences, Prayagraj, Uttar Pradesh, India.
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture, Technology And Sciences, Prayagraj, Uttar Pradesh, India; Department of Microbiology, Graphic Era Deemed to be University, Clement Town, Dehradun, U.K.-248002, India
| | - Vaibhav Saran
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology And Sciences, Prayagraj, Uttar Pradesh, India
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3
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Wu CM, Wheeler KM, Cárcamo-Oyarce G, Aoki K, McShane A, Datta SS, Mark Welch JL, Tiemeyer M, Griffen AL, Ribbeck K. Mucin glycans drive oral microbial community composition and function. NPJ Biofilms Microbiomes 2023; 9:11. [PMID: 36959210 PMCID: PMC10036478 DOI: 10.1038/s41522-023-00378-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/20/2023] [Indexed: 03/25/2023] Open
Abstract
Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.
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Affiliation(s)
- Chloe M Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey M Wheeler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Abigail McShane
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sujit S Datta
- Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Ann L Griffen
- Department of Dentistry, Nationwide Children's Hospital, Columbus, OH, USA
- Divisions of Biosciences and Pediatric Dentistry, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Bach L, Ram A, Ijaz UZ, Evans TJ, Haydon DT, Lindström J. The Effects of Smoking on Human Pharynx Microbiota Composition and Stability. Microbiol Spectr 2023; 11:e0216621. [PMID: 36786634 PMCID: PMC10101099 DOI: 10.1128/spectrum.02166-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
The oral microbiota is essential to the health of the host, yet little is known about how it responds to disturbances. We examined the oropharyngeal microbiota of 30 individuals over 40 weeks. As the oropharynx is an important gateway to pathogens, and as smoking is associated with increased incidence and severity of respiratory infections, we compared the microbiota of smokers and nonsmokers to shed light on its potential for facilitating infections. We hypothesized that decreased species diversity, decreased community stability, or increased differences in community structure could facilitate invading pathogens. We found that smoking is associated with reduced alpha diversity, greater differences in community structure, and increased environmental filtering. The effects of short-term perturbations (antibiotic use and participants exhibiting cold symptoms) were also investigated. Antibiotic use had a negative effect on alpha diversity, irrespective of smoking status, and both antibiotic use and cold symptoms were associated with highly unique bacterial communities. A stability analysis of models built from the data indicated that there were no differences in local or global stability in the microbial communities of smokers, compared to nonsmokers, and that their microbiota are equally resistant to species invasions. Results from these models suggest that smoker microbiota are perturbed but characterized by alternative stable states that are as stable and invasion-resistant as are the microbiota of nonsmokers. Smoking is unlikely to increase the risk of infectious disease through the altered composition and ecological function of the microbiota; this is more likely due to the effects of smoking on the local and systemic immune system. IMPORTANCE Smoking is associated with an increased risk of respiratory infections. Hypothetically, the altered community diversity of smokers' pharyngeal microbiota, together with changes in their ecological stability properties, could facilitate their invasion by pathogens. To address this question, we analyzed longitudinal microbiota data of baseline healthy individuals who were either smokers or nonsmokers. While the results indicate reduced biodiversity and increased species turnover in the smokers' pharyngeal microbiota, their ecological stability properties were not different from those of the microbiota of nonsmokers, implying, in ecological terms, that the smokers' microbial communities are not less resistant to invasions. Therefore, the study suggests that the increased propensity of respiratory infections that is seen in smokers is more likely associated with changes in the local and systemic immune system than with ecological changes in the microbial communities.
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Affiliation(s)
- Lydia Bach
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Asha Ram
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Science and Engineering, University of Glasgow, United Kingdom
| | - Thomas J. Evans
- School of Infection and Immunity, Glasgow Biomedical Research Centre, University of Glasgow, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Jan Lindström
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
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5
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Yamamoto A, Kambara Y, Fujiwara H. Impact of oral microbiota on pathophysiology of GVHD. Front Immunol 2023; 14:1132983. [PMID: 36969182 PMCID: PMC10033631 DOI: 10.3389/fimmu.2023.1132983] [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: 12/28/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Abstract
Allogeneic transplantation of hematopoietic cells is the only curative therapy for several hematopoietic disease in which patients receive cytotoxic conditioning regimens followed by infusion of hematopoietic stem cells. Although the outcomes have improved over the past decades, graft-versus-host-disease (GVHD), the most common life-threatening complication, remains a major cause of non-relapse morbidity and mortality. Pathophysiology of acute GVHD characterized by host antigen-presenting cells after tissue damage and donor T-cells is well studied, and additionally the importance of recipient microbiota in the intestine is elucidated in the GVHD setting. Oral microbiota is the second most abundant bacterial flora in the body after the intestinal tract, and it is related to chronic inflammation and carcinogenesis. Recently, composition of the oral microbiome in GVHD related to transplantation has been characterized and several common patterns, dysbiosis and enrichment of the specific bacterial groups, have been reported. This review focuses on the role of the oral microbiota in the context of GVHD.
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Affiliation(s)
- Akira Yamamoto
- Department of Hematology and Oncology, Okayama University Hospital, Okayama, Japan
| | - Yui Kambara
- Department of Hematology and Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hideaki Fujiwara
- Department of Hematology and Oncology, Okayama University Hospital, Okayama, Japan
- *Correspondence: Hideaki Fujiwara,
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6
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Wang X, Li J, Zhang S, Zhou W, Zhang L, Huang X. pH-activated antibiofilm strategies for controlling dental caries. Front Cell Infect Microbiol 2023; 13:1130506. [PMID: 36949812 PMCID: PMC10025512 DOI: 10.3389/fcimb.2023.1130506] [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] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Dental biofilms are highly assembled microbial communities surrounded by an extracellular matrix, which protects the resident microbes. The microbes, including commensal bacteria and opportunistic pathogens, coexist with each other to maintain relative balance under healthy conditions. However, under hostile conditions such as sugar intake and poor oral care, biofilms can generate excessive acids. Prolonged low pH in biofilm increases proportions of acidogenic and aciduric microbes, which breaks the ecological equilibrium and finally causes dental caries. Given the complexity of oral microenvironment, controlling the acidic biofilms using antimicrobials that are activated at low pH could be a desirable approach to control dental caries. Therefore, recent researches have focused on designing novel kinds of pH-activated strategies, including pH-responsive antimicrobial agents and pH-sensitive drug delivery systems. These agents exert antibacterial properties only under low pH conditions, so they are able to disrupt acidic biofilms without breaking the neutral microenvironment and biodiversity in the mouth. The mechanisms of low pH activation are mainly based on protonation and deprotonation reactions, acids labile linkages, and H+-triggered reactive oxygen species production. This review summarized pH-activated antibiofilm strategies to control dental caries, concentrating on their effect, mechanisms of action, and biocompatibility, as well as the limitation of current research and the prospects for future study.
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Affiliation(s)
- Xiuqing Wang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Jingling Li
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Shujun Zhang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Wen Zhou
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Linglin Zhang
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaojing Huang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- *Correspondence: Xiaojing Huang,
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7
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Chen WD, Zhang X, Zhang MJ, Zhang YP, Shang ZQ, Xin YW, Zhang Y. Salivary Fusobacterium nucleatum serves as a potential diagnostic biomarker for gastric cancer. World J Gastroenterol 2022; 28:4120-4132. [PMID: 36157109 PMCID: PMC9403436 DOI: 10.3748/wjg.v28.i30.4120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 07/17/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As one of the most common tumors, gastric cancer (GC) has a high mortality rate, since current examination approaches cannot achieve early diagnosis. Fusobacterium nucleatum (Fn) primarily colonized in the oral cavity, has been reported to be involved in the development of gastrointestinal tumor. Until now, little is known about the relationship between salivary Fn and GC.
AIM To determine whether salivary Fn could be a biomarker to diagnose GC and explore the influence of Fn on GC cells.
METHODS The abundance of Fn in saliva was quantified by droplet digital polymerase chain reaction in 120 GC patients, 31 atrophic gastritis (AG) patients, 35 non-AG (NAG) patients, 26 gastric polyp (GP) patients, and 20 normal controls (NC) from Qilu Hospital of Shandong University from January 2019 to December 2020. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of Fn as well as traditional serum tumor markers, including carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 19-9, and CA72-4. Transwell assay and wound-healing assay were conducted to assess the influence of Fn infection on GC cells. The expression of epithelial-mesenchymal transition (EMT) markers was detected using western blot assay.
RESULTS We found that the level of salivary Fn in GC patients was significantly increased compared with those in AG, NAG, and GP patients and NC (P < 0.001). ROC curve analysis showed a favorable capability of Fn (73.33% sensitivity; 82.14% specificity; area under the curve: 0.813) in GC diagnosis, which was superior to that of CEA, CA19-9, CA72-4, ferritin, and sialic acid. The Fn level in saliva of GC patients was increased as the TNM stage increased. GC patients with lymph node metastasis had higher Fn levels than those without metastasis. Both transwell and wound-healing assays indicated that Fn infection promoted the migration and invasion of GC cells. Western blot analysis showed that Fn infection decreased the expression of E-cadherin and increased the expressions of N-cadherin, vimentin, and snail.
CONCLUSION Fn abundance in saliva could be used as a promising biomarker to diagnose GC, and Fn infection could promote GC metastasis by accelerating the EMT process.
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Affiliation(s)
- Wen-Dan Chen
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Meng-Jiao Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Ya-Ping Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Zi-Qi Shang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yi-Wei Xin
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
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8
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Vindenes HK, Lin H, Shigdel R, Ringel-Kulka T, Real FG, Svanes C, Peddada SD, Bertelsen RJ. Exposure to Antibacterial Chemicals Is Associated With Altered Composition of Oral Microbiome. Front Microbiol 2022; 13:790496. [PMID: 35572708 PMCID: PMC9096491 DOI: 10.3389/fmicb.2022.790496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, but whether they also interfere with human oral microbiome composition is largely unexplored. In this study, we explored whether the oral bacterial composition is affected by exposure to antibacterial and environmental chemicals. Gingival fluid, urine, and interview data were collected from 477 adults (18–47 years) from the RHINESSA study in Bergen, Norway. Urine biomarkers of triclosan, triclocarban, parabens, benzophenone-3, bisphenols, and 2,4- and 2,5-dichlorophenols (DCPs) were quantified (by mass spectrometry). Microbiome analysis was based on 16S amplicon sequencing. Diversity and differential abundance analyses were performed to identify how microbial communities may change when comparing groups of different chemical exposure. We identified that high urine levels (>75th percentile) of propyl parabens were associated with a lower abundance of bacteria genera TM7 [G-3], Helicobacter, Megasphaera, Mitsuokella, Tannerella, Propionibacteriaceae [G-2], and Dermabacter, as compared with low propylparaben levels (<25th percentile). High exposure to ethylparaben was associated with a higher abundance of Paracoccus. High urine levels of bisphenol A were associated with a lower abundance of Streptococcus and exposure to another environmental chemical, 2,4-DCP, was associated with a lower abundance of Treponema, Fretibacterium, and Bacteroidales [G-2]. High exposure to antibacterial and environmental chemicals was associated with an altered composition of gingiva bacteria; mostly commensal bacteria in the oral cavity. Our results highlight a need for a better understanding of how antimicrobial chemical exposure influences the human microbiome.
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Affiliation(s)
- Hilde Kristin Vindenes
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Huang Lin
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Tamar Ringel-Kulka
- Department of Maternal and Child Care, University of North Carolina, Chapel Hill, NC, United States
| | - Francisco Gomez Real
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Cecilie Svanes
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway.,Centre for International Health, University of Bergen, Bergen, Norway
| | - Shyamal D Peddada
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Randi J Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Oral Health Center of Expertise in Western Norway, Bergen, Norway
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9
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Negrini TDC, Carlos IZ, Duque C, Caiaffa KS, Arthur RA. Interplay Among the Oral Microbiome, Oral Cavity Conditions, the Host Immune Response, Diabetes Mellitus, and Its Associated-Risk Factors-An Overview. FRONTIERS IN ORAL HEALTH 2022; 2:697428. [PMID: 35048037 PMCID: PMC8757730 DOI: 10.3389/froh.2021.697428] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022] Open
Abstract
This comprehensive review of the literature aimed to investigate the interplay between the oral microbiome, oral cavity conditions, and host immune response in Diabetes mellitus (DM). Moreover, this review also aimed to investigate how DM related risk factors, such as advanced age, hyperglycemia, hyperlipidemia, obesity, hypertension and polycystic ovary syndrome (PCOS), act in promoting or modifying specific mechanisms that could potentially perpetuate both altered systemic and oral conditions. We found that poorly controlled glycemic index may exert a negative effect on the immune system of affected individuals, leading to a deficient immune response or to an exacerbation of the inflammatory response exacerbating DM-related complications. Hyperglycemia induces alterations in the oral microbiome since poor glycemic control is associated with increased levels and frequencies of periodontal pathogens in the subgingival biofilm of individuals with DM. A bidirectional relationship between periodontal diseases and DM has been suggested: DM patients may have an exaggerated inflammatory response, poor repair and bone resorption that aggravates periodontal disease whereas the increased levels of systemic pro-inflammatory mediators found in individuals affected with periodontal disease exacerbates insulin resistance. SARS-CoV-2 infection may represent an aggravating factor for individuals with DM. Individuals with DM tend to have low salivary flow and a high prevalence of xerostomia, but the association between prevalence/experience of dental caries and DM is still unclear. DM has also been associated to the development of lesions in the oral mucosa, especially potentially malignant ones and those associated with fungal infections. Obesity plays an important role in the induction and progression of DM. Co-affected obese and DM individuals tend to present worse oral health conditions. A decrease in HDL and, an increase in triglycerides bloodstream levels seem to be associated with an increase on the load of periodontopathogens on oral cavity. Moreover, DM may increase the likelihood of halitosis. Prevalence of impaired taste perception and impaired smell recognition tend to be greater in DM patients. An important interplay among oral cavity microbiome, DM, obesity and hypertension has been proposed as the reduction of nitrate into nitrite, in addition to contribute to lowering of blood pressure, reduces oxidative stress and increases insulin secretion, being these effects desirable for the control of obesity and DM. Women with PCOS tend to present a distinct oral microbial composition and an elevated systemic response to selective members of this microbial community, but the association between oral microbiome, PCOS are DM is still unknown. The results of the studies presented in this review suggest the interplay among the oral microbiome, oral cavity conditions, host immune response and DM and some of the DM associated risk factors exist. DM individuals need to be encouraged and motivated for an adequate oral health care. In addition, these results show the importance of adopting multidisciplinary management of DM and of strengthening physicians-dentists relationship focusing on both systemic and on oral cavity conditions of DM patients.
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Affiliation(s)
- Thais de Cássia Negrini
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Iracilda Zeppone Carlos
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Cristiane Duque
- Department of Restorative and Preventive Dentistry, Araçatuba Dental School, São Paulo State University, Araçatuba, Brazil
| | - Karina Sampaio Caiaffa
- Department of Restorative and Preventive Dentistry, Araçatuba Dental School, São Paulo State University, Araçatuba, Brazil
| | - Rodrigo Alex Arthur
- Department of Preventive and Community Dentistry, Dental School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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10
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Benn AML, Heng NCK, Thomson WM, Sissons CH, Gellen LS, Gray AR, Broadbent JM. Associations of sex, oral hygiene and smoking with oral species in distinct habitats at age 32 years. Eur J Oral Sci 2021; 130:e12829. [PMID: 34874583 DOI: 10.1111/eos.12829] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
The oral microbiome is ecologically diverse, complex, dynamic, and little understood. We describe the microbiota of four oral habitats in a birth cohort at age 32 and examine differences by sex, oral hygiene, and current smoking status, dental caries, and periodontal health. Oral biofilm samples collected from anterior labial supragingival, posterior lingual supragingival, subgingival, and tongue sites of 841 Dunedin Multidisciplinary Health and Development Study members were analysed using checkerboard DNA-DNA hybridization; focusing on 30 ecologically important bacterial species. The four habitats exhibited distinct microbial profiles that differed by sex. Streptococcus gordonii was more dominant in supragingival and tongue biofilms of males; Porphyromonas gingivalis exhibited higher relative abundance in subgingival biofilm of females. Males had higher scores than females for periodontal pathogens at supragingival sites. The relative abundance of several putative caries and periodontal pathogens differed in smokers and non-smokers. With poor oral hygiene significantly higher proportions of Gram-negative facultative anaerobes were present in subgingival biofilm and there were higher scores for the principal components characterised by putative cariogenic and periodontal pathogens at each site. Distinctive microenvironments shape oral biofilms and systematic differences exist by sex, oral hygiene, and smoking status.
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Affiliation(s)
- Angela M L Benn
- Faculty of Dentistry, University of Otago, Sir John Walsh Research Institute, Dunedin, New Zealand.,Oral Health Services, Southern District Health Board, Dunedin, New Zealand
| | - Nicholas C K Heng
- Faculty of Dentistry, University of Otago, Sir John Walsh Research Institute, Dunedin, New Zealand
| | - W Murray Thomson
- Faculty of Dentistry, University of Otago, Sir John Walsh Research Institute, Dunedin, New Zealand
| | - Chris H Sissons
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Lisa S Gellen
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Andrew R Gray
- Biostatistics Centre, University of Otago, Dunedin, New Zealand
| | - Jonathan M Broadbent
- Faculty of Dentistry, University of Otago, Sir John Walsh Research Institute, Dunedin, New Zealand
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11
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Duran-Pinedo A, Solbiati J, Teles F, Teles R, Zang Y, Frias-Lopez J. Long-term dynamics of the human oral microbiome during clinical disease progression. BMC Biol 2021; 19:240. [PMID: 34742306 PMCID: PMC8572441 DOI: 10.1186/s12915-021-01169-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Oral microbiome dysbiosis is linked to overt inflammation of tooth-supporting tissues, leading to periodontitis, an oral condition that can cause tooth and bone loss. Microbiome dysbiosis has been described as a disruption in the symbiotic microbiota composition's stability that could adversely affect the host's health status. However, the precise microbiome dynamics that lead to dysbiosis and the progression of the disease are largely unknown. The objective of our study was to investigate the long-term dynamics of periodontitis progression and its connection to dysbiosis. RESULTS We studied three different teeth groups: sites that showed disease progression, sites that remained stable during the study, and sites that exhibited a cyclic deepening followed by spontaneous recovery. Time-series analysis revealed that communities followed a characteristic succession of bacteria clusters. Stable and fluctuating sites showed high asynchrony in the communities (i.e., different species responding dissimilarly through time) and a reordering of the communities where directional changes dominated (i.e., sample distance increases over time) in the stable sites but not in the fluctuating sites. Progressing sites exhibited low asynchrony and convergence (i.e., samples distance decreases over time). Moreover, new species were more likely to be recruited in stable samples if a close relative was not recruited previously. In contrast, progressing and fluctuating sites followed a neutral recruitment model, indicating that competition between closely related species is a significant component of species-species interactions in stable samples. Finally, periodontal treatment did not select similar communities but stabilized α-diversity, centered the abundance of different clusters to the mean, and increased community rearrangement. CONCLUSIONS Here, we show that ecological principles can define dysbiosis and explain the evolution and outcomes of specific microbial communities of the oral microbiome in periodontitis progression. All sites showed an ecological succession in community composition. Stable sites were characterized by high asynchrony, a reordering of the communities where directional changes dominated, and new species were more likely to be recruited if a close relative was not recruited previously. Progressing sites were characterized by low asynchrony, community convergence, and a neutral model of recruitment. Finally, fluctuating sites were characterized by high asynchrony, community convergence, and a neutral recruitment model.
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Affiliation(s)
- Ana Duran-Pinedo
- Department of Oral Biology, University of Florida, College of Dentistry, 1395 Center Drive, Gainesville, FL, 32610-0424, USA
| | - Jose Solbiati
- Department of Oral Biology, University of Florida, College of Dentistry, 1395 Center Drive, Gainesville, FL, 32610-0424, USA
| | - Flavia Teles
- Department of Basic & Translational Sciences, University of Pennsylvania, School of Dental Medicine, 240 South 40th Street, Philadelphia, PA, 19104-6030, USA
| | - Ricardo Teles
- Department of Periodontics, University of Pennsylvania, School of Dental Medicine, 240 South 40th Street, Philadelphia, PA, 19104-6030, USA
| | - Yanping Zang
- Gene Expression & Genotyping Core, Interdisciplinary Center for Biotechnology Research, University of Florida, 178 B CGRC, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Jorge Frias-Lopez
- Department of Oral Biology, University of Florida, College of Dentistry, 1395 Center Drive, Gainesville, FL, 32610-0424, USA.
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12
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Adjunctive dental therapies in caries-active children: Shifting the cariogenic salivary microbiome from dysbiosis towards non-cariogenic health. ACTA ACUST UNITED AC 2021; 18. [PMID: 34485763 PMCID: PMC8415465 DOI: 10.1016/j.humic.2020.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: The oral microbiome is a complex assembly of microbial species, whose constituents can tilt the balance towards progression of oral disease or sustained health. Recently we identified sex-specific differences in the salivary microbiome contained within caries-active and caries-free children. In this study, we sought to ascertain if adjunctive dental therapies, including povidone iodine and chlorhexidine, were effective in shifting the cariogenic microbiome from dysbiosis to non-cariogenic health. Design: We recruited young children (ages 2–12 years) to enter five enrollment groups, with each group (N = 9–30 participants/group) receiving caries restorative and/or adjunctive therapies, either singularly or in combination (OHSU IRB #6535). Saliva specimens were collected pre- and post-treatment (4–8 weeks) of caries preventive measures, and oral microbiota were identified using next generation sequencing (HOMINGS, Forsyth Institute, Cambridge, MA). Results: With the use of multi-dimensional scaling plots, support vector machine learning, odds ratio analysis, and other statistical methods, we have determined that treatment with povidone iodine can shift the composition of the salivary cariogenic microbiome to include higher proportions of aerobic microorganisms, such as Stentrophomonas maltophila, as well as non-cariogenic, anaerobic microorganisms including Poryphyromonas and Fusobacterium species. Conclusion: We have identified microorganisms that are associated with caries-active children and have determined that povidone iodine is an effective adjunctive therapy that has the potential to shift the composition of the cariogenic microbiome to one more closely aligned with non-cariogenic health.
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13
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Abstract
Measurement of saliva microbes is promoted as a way to detect oral and systemic disease, yet there is a multitude of factors that affect the oral microbiome. The salivary microbiome is influenced by biofilm of shedding (epithelial) and non-shedding (tooth) surfaces. Methods for study of the salivary microbiome are by no means standardized, and differences in sample collection, storage, and processing can all affect results to some degree. Here we describe one method of saliva collection that has been validated for reproducibility. Standard 16S rRNA gene analysis is done using the Human Oral Microbiome Database library which results in analysis that is straightforward. Everything about this procedure except the library synthesis and DNA sequencing itself can easily be done in-house. To gauge the ability of salivary microbial analytics to distinguish between edentulous and dentate oral conditions, differences in the saliva microbiome of subjects with and without teeth were examined. Fifty-two dentate and 49 edentulous subjects provided stimulated saliva samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analysis were done using several different analytical approaches to detect differences in the salivary microbiome between the two groups. Bacteria diversity was lower in the edentulous group. Remarkably, all 31 of the most significant differences in taxa were deficits that occurred in the edentulous group. As one might expect, many of these taxa are attributed to dental plaque and gingival sulcus-associated bacteria verifying that the measurement of 16S rRNA genes in the bacteria of the saliva can be used to reproducibly measure expected differences in the oral microbiome that occur with edentulism or other conditions and diseases.
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14
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Karadayı S, Arasoglu T, Akmayan İ, Karadayı B. Assessment of the exclusion potential of suspects by using microbial signature in sexual assault cases: A scenario-based experimental study. Forensic Sci Int 2021; 325:110886. [PMID: 34192646 DOI: 10.1016/j.forsciint.2021.110886] [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: 04/19/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023]
Abstract
Sexual assault offences are one of the most serious crimes committed against a person, typically rank only second to homicide, and represent one of the major challenges in forensic sciences. In some cases of sexual assault, there may be more than one suspect and the analysis of the biological evidence with currently available methods such as human DNA analysis may not yield results. In this study using the designed experimental model (with different experimental scenarios that can be designed), it was aimed to investigate the effectiveness of the microbiome profile for the identification of the offender by comparing the microbiome structures of the suspects' saliva samples with the mixed samples on the victim (saliva transmitted on breast skin) within the first 48 h after a sexual assault. For this purpose, a total of 44 samples was collected from four healthy females and four healthy males aged 20-50 years. Microbiome profiles of 44 samples in four groups containing saliva, breast skin and mixed samples were determined with the IIlumina HiSeq platform. Differentiation between samples were calculated by beta-diversity analysis methods by using QIIME software (v1.80). To compare the differentiation among samples and groups, unweighted UniFrac distance values were applied. Eight dominant microbial genera accounted for 86.15% of the total bacterial population in male saliva samples and were composed of Fusobacterium, Haemophilus, Neisseria, Porphyromonas, Prevotella, Rothia, Streptococcus and Veillonella. These genera constituted 76.72% of the bacterial population in mixed samples, whereas they constituted 34.40% of the bacterial population in the breast skin samples. Results of this study show that bacterial DNA in saliva can be recovered from saliva transmitted breast skin within at least 48 h. In conclusion, it has been found that examination of the microbiota of the saliva transmitted to breast skin of a sexual assault victim as a forensic tool may have the potential to determine the offender of the incident among the suspects or to reduce the number of suspects. Supporting the results of this study with further studies using parameters such as different case models, different body regions, larger time periods and a higher number of participants will be beneficial to draw accurate conclusion of the judicial case.
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Affiliation(s)
- Sukriye Karadayı
- Vocational School of Health Services, Altınbaş University, Istanbul, Turkey.
| | - Tulin Arasoglu
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, İstanbul, Turkey.
| | - İlkgül Akmayan
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, İstanbul, Turkey.
| | - Beytullah Karadayı
- Department of Forensic Sciences, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
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15
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Chen Q, Shao Z, Liu K, Zhou X, Wang L, Jiang E, Luo T, Shang Z. Salivary Porphyromonas gingivalis predicts outcome in oral squamous cell carcinomas: a cohort study. BMC Oral Health 2021; 21:228. [PMID: 33941164 PMCID: PMC8091688 DOI: 10.1186/s12903-021-01580-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/21/2021] [Indexed: 01/11/2023] Open
Abstract
Background Studies suggest Porphyromonas gingivalis (Pg) increased the incidence of oral squamous cell carcinoma (OSCC). However, fimA genotypes distribution of Pg, the origination of Pg in tissue, and its prognostic value are inconclusive. We aimed to investigate the frequency of fimA genotypes in OSCC patients, study the association between Pg and OSCC, and explore the prognostic value of Pg. Methods The abundance of Pg in saliva from the OSCC group and the OSCC-free group was analysed by qPCR. The presence of Pg was explored in OSCC tissue and para-cancerous tissue by in situ hybridization. The frequency of fimA genotypes in saliva and OSCC tissue was determined by PCR, then PCR products were sequenced and compared. Clinical data were extracted, and patients followed up for a median period of 23 months. Clinicopathological variables were compared with the abundance of Pg using Pearson Chi-square test or Fisher’s exact test. The disease-free survival (DFS) rate was calculated by Kaplan–Meier method with log-rank tests. Results Comparing the OSCC-free group, 95 patients with OSCC showed a high abundance of Pg in saliva (P = 0.033), and OSCC tissue showed strong in situ expression of Pg compared with paired normal tissue. Patients with OSCC showed a dominant distribution of Pg with genotype I + Ib (21.1%), II (31.6%), and IV (21.1%). FimA genotypes detected in saliva were in accordance with those in OSCC tissue, there was, moreover, a significant similarity in amplified Pg fragments. Of the 94 responsive OSCC patients, the recurrence rate was 26.6% (25/94). Overabundance of Pg in saliva showed advanced pathologic staging (P = 0.008), longer disease-free time (P = 0.029) and lower recurrence rate (P = 0.033). The overabundance of Pg in saliva was associated with improved disease-free survival (P = 0.049). Conclusions This study indicated that Pg might involve in the pathogenesis of OSCC, Pg carrying fimA I, Ib, II, and IV were prevalent genotypes in patients with OSCC, the provenance of Pg in OSCC tissue might be from the salivary microbial reservoir, and the abundance of Pg in saliva might consider as a favorable potential prognostic indicator in OSCC.
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Affiliation(s)
- Qingli Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China
| | - Zhe Shao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China.,Department of Oral and Maxillofacial-Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Ke Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China.,Department of Oral and Maxillofacial-Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Xiaocheng Zhou
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China
| | - Lin Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China
| | - Erhui Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China.,Department of Oral and Maxillofacial-Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Tingting Luo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China
| | - Zhengjun Shang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospita1 of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, People's Republic of China. .,Department of Oral and Maxillofacial-Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China.
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16
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Manipulation of Saliva-Derived Microcosm Biofilms To Resemble Dysbiotic Subgingival Microbiota. Appl Environ Microbiol 2021; 87:AEM.02371-20. [PMID: 33158898 PMCID: PMC7848911 DOI: 10.1128/aem.02371-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and reestablish a health-associated microbiota, a high-throughput in vitro multispecies biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rRNA gene amplicon sequencing as well as measurement of dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principal-component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis to saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder a microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies. IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in a dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large-scale evaluation of strategies that can potentially modulate microbial ecology.
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17
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Abstract
Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density1 and rich diversity2 of species in environmental microbiomes and the limitations of optical imaging technology3–6. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence in situ Hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging, and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli isolates, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and single-cell image analysis, reveals the disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH reveals the diverse ribosome organization strategies of human oral microbial taxa. HiPR-FISH provides a framework for analyzing the spatial ecology of environmental microbial communities at single-cell resolution.
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18
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D’Angiolella G, Tozzo P, Gino S, Caenazzo L. Trick or Treating in Forensics-The Challenge of the Saliva Microbiome: A Narrative Review. Microorganisms 2020; 8:E1501. [PMID: 33003446 PMCID: PMC7599466 DOI: 10.3390/microorganisms8101501] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
The oral microbiome harbours microbial community signatures that differ among individuals, highlighting that it could be highly individualizing and potentially unique to each individual. Therefore, the oral microbial traces collected in crime scenes could produce investigative leads. This narrative review will describe the current state-of-the-art of how the salivary microbiome could be exploited as a genetic signature to make inferences in the forensic field. This review has been performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Guidelines. Even if further studies are needed to relate the variation in the oral microbiome to specific factors, in order to understand how the salivary microbiome is influenced by an individual's lifestyle, by reviewing the studies published so far, it is clear that the oral microbial analysis could become a useful forensic tool. Even if promising, caution is required in interpreting the results and an effort to direct research towards studies that fill the current knowledge gaps is certainly useful.
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Affiliation(s)
- Gabriella D’Angiolella
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy;
| | - Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, Via Falloppio 50, 35121 Padova, Italy;
| | - Sarah Gino
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, Via Falloppio 50, 35121 Padova, Italy;
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19
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Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M, Al Khodor S. Profiling the Salivary microbiome of the Qatari population. J Transl Med 2020; 18:127. [PMID: 32169076 PMCID: PMC7071716 DOI: 10.1186/s12967-020-02291-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions. MATERIALS AND METHODS We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene. RESULTS In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers. CONCLUSION This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.
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Affiliation(s)
| | | | - Parul Singh
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
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Hickey NA, Shalamanova L, Whitehead KA, Dempsey-Hibbert N, van der Gast C, Taylor RL. Exploring the putative interactions between chronic kidney disease and chronic periodontitis. Crit Rev Microbiol 2020; 46:61-77. [PMID: 32046541 DOI: 10.1080/1040841x.2020.1724872] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chronic kidney disease (CKD) and chronic periodontitis (CP) are both common diseases, which are found disproportionately comorbid with each other and have been reported to have a detrimental effect on the progression of each respective disease. They have an overlap in risk factors and both are a source of systemic inflammation along with a wide selection of immunological and non-specific effects that can affect the body over the lifespan of the conditions. Previous studies have investigated the directionality of the relationship between these two diseases; however, there is a lack of literature that has examined how these diseases may be interacting at the localized and systemic level. This review discusses how oral microorganisms have the ability to translocate and have distal effects and provides evidence for microbial involvement in a systemic disease. Furthermore, it summarizes the reported local and systemic effects of CKD and CP and discusses how the interaction of these effects may be responsible for directionality associations reported.
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Affiliation(s)
- Niall A Hickey
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Liliana Shalamanova
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Kathryn A Whitehead
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Nina Dempsey-Hibbert
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Christopher van der Gast
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rebecca L Taylor
- Centre for Bioscience, Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
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21
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Karabudak S, Ari O, Durmaz B, Dal T, Basyigit T, Kalcioglu MT, Durmaz R. Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology. J Med Microbiol 2019; 68:1148-1158. [PMID: 31199220 DOI: 10.1099/jmm.0.001003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURPOSE This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. METHODOLOGY Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. RESULTS Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. CONCLUSION The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.
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Affiliation(s)
- Sema Karabudak
- Ankara Yildirim Beyazit University, Central Research and Application Center, Ankara, Turkey
| | - Oguz Ari
- Ankara Yildirim Beyazit University, Central Research and Application Center, Ankara, Turkey
| | - Bengul Durmaz
- Yuksek Ihtisas University, Faculty of Medicine, Department of Clinical Microbiology, Ankara, Turkey
| | - Tuba Dal
- Ankara Yildirim Beyazit University, Faculty of Medicine, Department of Clinical Microbiology, Ankara, Turkey
| | - Tugcan Basyigit
- Ankara Yildirim Beyazit University, Faculty of Medicine, Department of Clinical Microbiology, Ankara, Turkey
| | - Mahmut Tayyar Kalcioglu
- Istanbul Medeniyet University, Faculty of Medicine, Department of Otolaryngology, Istanbul, Turkey
| | - Riza Durmaz
- Ankara Yildirim Beyazit University, Faculty of Medicine, Department of Clinical Microbiology, Ankara, Turkey.,Ankara Yildirim Beyazit University, Central Research and Application Center, Ankara, Turkey
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22
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Guven DC, Dizdar O, Alp A, Akdoğan Kittana FN, Karakoc D, Hamaloglu E, Lacin S, Karakas Y, Kilickap S, Hayran M, Yalcin S. Analysis of Fusobacterium nucleatum and Streptococcus gallolyticus in saliva of colorectal cancer patients. Biomark Med 2019; 13:725-735. [PMID: 31157977 DOI: 10.2217/bmm-2019-0020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: The aim of the study was to examine the prevalence and amount of Fusobacterium nucleatum (Fn), Porphyromonas gingivalis (Pg) and Streptococcus gallolyticus (Sg) in the saliva of colorectal cancer (CRC) patients and controls. Methods: PCR analyses performed in 71 CRC patients and 77 controls. Results: Saliva samples of patients had higher amounts of Fn (p = 0.001) and Sg (p < 0.001) compared with controls. Amount of Fn and Sg were lower in the microsatellite instability (+) group. Evaluation of salivary Sg amount by receiver operating characteristics analysis found to have diagnostic value for CRC (AUC: 0.84, 95% CI: 0.72-0.96). Conclusion: We found higher amounts of Fn and Sg in the saliva of CRC patients. Salivary Sg could helpful in distinction of CRC.
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Affiliation(s)
- Deniz Can Guven
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Omer Dizdar
- Department of Preventive Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Alpaslan Alp
- Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara 06230, Turkey
| | | | - Derya Karakoc
- Department of General Surgery, Hacettepe University Faculty of Medicine, Ankara 06230, Turkey
| | - Erhan Hamaloglu
- Department of General Surgery, Hacettepe University Faculty of Medicine, Ankara 06230, Turkey
| | - Sahin Lacin
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Yusuf Karakas
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Saadettin Kilickap
- Department of Preventive Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Mutlu Hayran
- Department of Preventive Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
| | - Suayib Yalcin
- Department of Medical Oncology, Hacettepe University Cancer Institute, Ankara 06230, Turkey
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23
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Gazdeck RK, Fruscione SR, Adami GR, Zhou Y, Cooper LF, Schwartz JL. Diversity of the oral microbiome between dentate and edentulous individuals. Oral Dis 2019; 25:911-918. [DOI: 10.1111/odi.13039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/20/2018] [Accepted: 12/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- R. Kyle Gazdeck
- Department of Prosthodontics and Implant Innovation University of Illinois at Chicago College of Dentistry Chicago Illinois
| | - Sarah R. Fruscione
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Guy R. Adami
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Yalu Zhou
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Lyndon F. Cooper
- Department of Oral Biology, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Joel L. Schwartz
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
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24
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Differences in carbon source usage by dental plaque in children with and without early childhood caries. Int J Oral Sci 2017; 9:e6. [PMID: 32987969 PMCID: PMC5750455 DOI: 10.1038/ijos.2017.47] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 01/24/2023] Open
Abstract
Early childhood caries (ECC) is a considerable pediatric and public health problem worldwide. Preceding studies have focused primarily on bacterial diversity at the taxonomic level. Although these studies have provided significant information regarding the connection between dental caries and oral microbiomes, further comprehension of this microbial community’s ecological relevance is limited. This study identified the carbon source metabolic differences in dental plaque between children with and without ECC. We compared the microbial community functional diversity in 18 caries-free subjects with 18 severe ECC patients based on sole carbon source usage using a Biolog assay. The anaerobic microbial community in the ECC patients displayed greater metabolic activity than that of the control group. Specific carbon source metabolism differed significantly between the two groups. Subjects from the two groups were well distinguished by cluster and principal component analyses based on discriminative carbon sources. Our results implied that the microbial functional diversity between the ECC patients and healthy subjects differed significantly. In addition, the Biolog assay furthered our understanding of oral microbiomes as a composite of functional abilities, thus enabling us to identify the ecologically relevant functional differences among oral microbial communities.
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25
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Rosier BT, Marsh PD, Mira A. Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis. J Dent Res 2017; 97:371-380. [PMID: 29195050 DOI: 10.1177/0022034517742139] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Dental diseases are now viewed as a consequence of a deleterious shift in the balance of the normally stable resident oral microbiome. It is known that frequent carbohydrate consumption or reduced saliva flow can lead to caries, and excessive plaque accumulation increases the risk of periodontal diseases. However, when these "disease drivers" are present, while some individuals appear to be susceptible, others are more tolerant or resilient to suffering from undesirable changes in their oral microbiome. Health-maintaining mechanisms that limit the effect of disease drivers include the complex set of metabolic and functional interrelationships that develop within dental biofilms and between biofilms and the host. In contrast, "positive feedback loops" can develop within these microbial communities that disrupt resilience and provoke a large and abrupt change in function and structure of the ecosystem (a microbial "regime shift"), which promotes dysbiosis and oral disease. For instance, acidification due to carbohydrate fermentation or inflammation in response to accumulated plaque select for a cariogenic or periopathogenic microbiota, respectively, in a chain of self-reinforcing events. Conversely, in tolerant individuals, health-maintaining mechanisms, including negative feedback to the drivers, can maintain resilience and promote resistance to and recovery from disease drivers. Recently studied health-maintaining mechanisms include ammonia production, limiting a drop in pH that can lead to caries, and denitrification, which could inhibit several stages of disease-associated positive feedback loops. Omics studies comparing the microbiome of, and its interaction with, susceptible and tolerant hosts can detect markers of resilience. The neutralization or inhibition of disease drivers, together with the identification and promotion of health-promoting species and functions, for example, by pre- and probiotics, could enhance microbiome resilience and lead to new strategies to prevent disease.
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Affiliation(s)
- B T Rosier
- 1 Department of Genomics and Health, FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
| | - P D Marsh
- 2 Department of Oral Biology, School of Dentistry, University of Leeds, UK
| | - A Mira
- 1 Department of Genomics and Health, FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
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26
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Dilhari A, Sampath A, Gunasekara C, Fernando N, Weerasekara D, Sissons C, McBain A, Weerasekera M. Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method. AMB Express 2017; 7:179. [PMID: 28929383 PMCID: PMC5605482 DOI: 10.1186/s13568-017-0477-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/05/2017] [Indexed: 12/25/2022] Open
Abstract
Infected chronic wounds are polymicrobial in nature which include a diverse group of aerobic and anaerobic microorganisms. Majority of these communal microorganisms are difficult to grow in vitro. DNA fingerprinting methods such as polymerase chain reaction-denaturation gradient gel electrophoresis (PCR-DGGE) facilitate the microbial profiling of complex ecosystems including infected chronic wounds. Six different DNA extraction methods were compared for profiling of the microbial community associated with chronic wound infections using PCR-DGGE. Tissue debris obtained from chronic wound ulcers of ten patients were used for DNA extraction. Total nucleic acid was extracted from each specimen using six DNA extraction methods. The yield, purity and quality of DNA was measured and used for PCR amplification targeting V2–V3 region of eubacterial 16S rRNA gene. QIAGEN DNeasy Blood and Tissue Kit (K method) produced good quality genomic DNA compared to the other five DNA extraction methods and gave a broad diversity of bacterial communities in chronic wounds. Among the five conventional methods, bead beater/phenol–chloroform based DNA extraction method with STES buffer (BP1 method) gave a yield of DNA with a high purity and resulted in a higher DGGE band diversity. Although DNA extraction using heat and NaOH had the lowest purity, DGGE revealed a higher bacterial diversity. The findings suggest that the quality and the yield of genomic DNA are influenced by the DNA extraction protocol, thus a method should be carefully selected in profiling a complex microbial community.
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27
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Chen H, Peng S, Dai L, Zou Q, Yi B, Yang X, Ma Z(S. Oral microbial community assembly under the influence of periodontitis. PLoS One 2017; 12:e0182259. [PMID: 28813450 PMCID: PMC5558961 DOI: 10.1371/journal.pone.0182259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/14/2017] [Indexed: 11/24/2022] Open
Abstract
Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.
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Affiliation(s)
- Hongju Chen
- College of Mathematics, Honghe University, Mengzi, Yunnan Province, China
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shuting Peng
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Faculty of Science, Kunming University of Science and Technology, Kunming, China
| | - Lin Dai
- Faculty of Science, Kunming University of Science and Technology, Kunming, China
| | - Quan Zou
- Department of Computer Science, Tianjin University, Tianjin China
| | - Bin Yi
- College of Mathematics, Honghe University, Mengzi, Yunnan Province, China
| | - Xianghong Yang
- Oral Medicine Department, Yan’an Hospital of Kunming City, Kunming, Yunnan, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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28
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Wang Y, Fan Y, Zhou Z, Tu H, Ren Q, Wang X, Ding L, Zhou X, Zhang L. De novo synthetic short antimicrobial peptides against cariogenic bacteria. Arch Oral Biol 2017; 80:41-50. [DOI: 10.1016/j.archoralbio.2017.03.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/17/2017] [Accepted: 03/23/2017] [Indexed: 01/10/2023]
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29
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Dental Biofilm and Laboratory Microbial Culture Models for Cariology Research. Dent J (Basel) 2017; 5:dj5020021. [PMID: 29563427 PMCID: PMC5806974 DOI: 10.3390/dj5020021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/24/2017] [Accepted: 06/15/2017] [Indexed: 01/03/2023] Open
Abstract
Dental caries form through a complex interaction over time among dental plaque, fermentable carbohydrate, and host factors (including teeth and saliva). As a key factor, dental plaque or biofilm substantially influence the characteristic of the carious lesions. Laboratory microbial culture models are often used because they provide a controllable and constant environment for cariology research. Moreover, they do not have ethical problems associated with clinical studies. The design of the microbial culture model varies from simple to sophisticated according to the purpose of the investigation. Each model is a compromise between the reality of the oral cavity and the simplification of the model. Researchers, however, can still obtain meaningful and useful results from the models they select. Laboratory microbial culture models can be categorized into a closed system and an open system. Models in the closed system have a finite supply of nutrients, and are also simple and cost-effective. Models in the open system enabled the supply of a fresh culture medium and the removal of metabolites and spent culture liquid simultaneously. They provide better regulation of the biofilm growth rate than the models in the closed system. This review paper gives an overview of the dental plaque biofilm and laboratory microbial culture models used for cariology research.
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30
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Beerens MW, ten Cate JM, van der Veen MH. Microbial profile of dental plaque associated to white spot lesions in orthodontic patients immediately after the bracket removal. Arch Oral Biol 2017; 78:88-93. [DOI: 10.1016/j.archoralbio.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/13/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
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31
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M Weerasekera M, H Sissons C, Wong L, A Anderson S, R Holmes A, D Cannon R. Denaturing gradient gel electrophoresis profiles of bacteria from the saliva of twenty four different individuals form clusters that showed no relationship to the yeasts present. Arch Oral Biol 2017; 82:6-10. [PMID: 28577425 DOI: 10.1016/j.archoralbio.2017.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 04/25/2017] [Accepted: 05/20/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The aim was to investigate the relationship between groups of bacteria identified by cluster analysis of the DGGE fingerprints and the amounts and diversity of yeast present. METHODS Bacterial and yeast populations in saliva samples from 24 adults were analysed using denaturing gradient gel electrophoresis (DGGE) of the bacteria present and by yeast culture. RESULTS Eubacterial DGGE banding patterns showed considerable variation between individuals. Seventy one different amplicon bands were detected, the band number per saliva sample ranged from 21 to 39 (mean±SD=29.3±4.9). Cluster and principal component analysis of the bacterial DGGE patterns yielded three major clusters containing 20 of the samples. Seventeen of the 24 (71%) saliva samples were yeast positive with concentrations up to 103cfu/mL. Candida albicans was the predominant species in saliva samples although six other yeast species, including Candida dubliniensis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida rugosa and Saccharomyces cerevisiae, were identified. The presence, concentration, and species of yeast in samples showed no clear relationship to the bacterial clusters. CONCLUSION Despite indications of in vitro bacteria-yeast interactions, there was a lack of association between the presence, identity and diversity of yeasts and the bacterial DGGE fingerprint clusters in saliva. This suggests significant ecological individual-specificity of these associations in highly complex in vivo oral biofilm systems under normal oral conditions.
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Affiliation(s)
- Manjula M Weerasekera
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Department of Microbiology, Faculty of Medical Sciences,University of Sri Jayewardenepura, Sri Lanka.
| | - Chris H Sissons
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Lisa Wong
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Sally A Anderson
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Ann R Holmes
- Sir John Walsh Research Institute and Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Richard D Cannon
- Sir John Walsh Research Institute and Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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32
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Majchrzak K, Mierzwinska-Nastalska E, Chmura A, Kwiatkowski A, Paczek L, Mlynarczyk G, Szymanek-Majchrzak K. Comparison of Staphylococcal Flora in Denture Plaque and the Surface of the Pharyngeal Mucous Membrane in Kidney Transplant Recipients. Transplant Proc 2017; 48:1590-7. [PMID: 27496452 DOI: 10.1016/j.transproceed.2016.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/24/2016] [Accepted: 03/08/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Biofilm occurring on removable prostheses is a reservoir of bacterial flora, consisting of both physiological and pathogenic multidrug-resistant microorganisms. Patients undergoing dialysis and organ transplantation are particularly prone to bacterial infections, which can have its source in denture plaque. This study was a comparison of the composition of staphylococcal flora within the surface of the pharyngeal mucous membrane as well as denture plaque in kidney transplant recipients. METHODS The study included 44 subjects with removable prostheses who reported for a kidney transplant procedure. Swab samples were collected from prostheses and the pharyngeal wall. Isolated strains were identified and investigated for drug resistance. RESULTS A total of 72 strains of Staphylococcus were isolated from the denture plaque and 53 from the pharynx. In the pharynx, the following species prevailed: Staphylococcus epidermidis, Staphylococcus warneri, and Staphylococcus aureus. The following species prevailed in denture plaque: S epidermidis, S aureus, and Staphylococcus haemolyticus. Among the pharyngeal strains, antibiotic resistance most commonly referred to natural penicillin (77%), constitutive macrolide-lincosamide-streptogramin B resistance (28%), and tetracycline (26.4%). In case of denture plaque, the highest percentage of strains demonstrated resistance to natural penicillin (60%), fosfomycin (32%), and cefoxitin (25%). In 10 subjects (48%), Staphylococcus-induced infections occurred in the first year after transplantation, 5 of which had the same bacterial strain as cultured previously from dentures. CONCLUSIONS The denture biofilm and surface of the pharynx differ in terms of bacterial composition and bacterial drug resistance profiles. Denture plaque constitutes a considerable reservoir of staphylococcal flora, which can be a potential source of infection in organ transplant recipients.
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Affiliation(s)
- K Majchrzak
- Department of Prosthetic Dentistry, Warsaw Medical University, Warsaw, Poland
| | | | - A Chmura
- Department of General and Transplant Surgery, Warsaw Medical University, Warsaw, Poland
| | - A Kwiatkowski
- Department of General and Transplant Surgery, Warsaw Medical University, Warsaw, Poland
| | - L Paczek
- Department of Immunology, Transplant Medicine, and Internal Diseases, Warsaw Medical University, Warsaw, Poland
| | - G Mlynarczyk
- Department of Medical Microbiology, Warsaw Medical University, Warsaw, Poland
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33
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Exploration of bacterial species associated with the salivary microbiome of individuals with a low susceptibility to dental caries. Clin Oral Investig 2016; 21:2399-2406. [DOI: 10.1007/s00784-016-2035-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/12/2016] [Indexed: 11/26/2022]
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34
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Weerasekera MM, Wijesinghe GK, Jayarathna TA, Gunasekara CP, Fernando N, Kottegoda N, Samaranayake LP. Culture media profoundly affect Candida albicans and Candida tropicalis growth, adhesion and biofilm development. Mem Inst Oswaldo Cruz 2016; 111:697-702. [PMID: 27706381 PMCID: PMC5125054 DOI: 10.1590/0074-02760160294] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 07/25/2016] [Indexed: 01/09/2023] Open
Abstract
As there are sparse data on the impact of growth media on the phenomenon of biofilm
development for Candida we evaluated the efficacy of three culture
media on growth, adhesion and biofilm formation of two pathogenic yeasts,
Candida albicans and Candida tropicalis. The
planktonic phase yeast growth, either as monocultures or mixed cultures, in sabouraud
dextrose broth (SDB), yeast nitrogen base (YNB), and RPMI 1640 was compared, and
adhesion as well as biofilm formation were monitored using MTT and crystal violet
(CV) assays and scanning electron microscopy. Planktonic cells of C.
albicans, C. tropicalis and their 1:1 co-culture showed
maximal growth in SDB. C. albicans/C. tropicalis adhesion was
significantly facilitated in RPMI 1640 although the YNB elicited the maximum growth
for C. tropicalis. Similarly, the biofilm growth was uniformly
higher for both species in RPMI 1640, and C. tropicalis was the
slower biofilm former in all three media. Scanning electron microscopy images tended
to confirm the results of MTT and CV assay. Taken together, our data indicate that
researchers should pay heed to the choice of laboratory culture media when comparing
relative planktonic/biofilm growth of Candida. There is also a need
for standardisation of biofilm development media so as to facilitate cross
comparisons between laboratories.
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Affiliation(s)
- Manjula M Weerasekera
- University of Sri Jayewardenepura, Faculty of Medical Sciences, Department of Microbiology, Nugegoda, Gangodawila, Sri Lanka.,University of Sri Jayewardenepura, Center for Advanced Material Research, Nugegoda, Sri Lanka
| | - Gayan K Wijesinghe
- University of Sri Jayewardenepura, Faculty of Medical Sciences, Department of Microbiology, Nugegoda, Gangodawila, Sri Lanka
| | - Thilini A Jayarathna
- University of Sri Jayewardenepura, Faculty of Medical Sciences, Department of Microbiology, Nugegoda, Gangodawila, Sri Lanka
| | - Chinthika P Gunasekara
- University of Sri Jayewardenepura, Faculty of Medical Sciences, Department of Microbiology, Nugegoda, Gangodawila, Sri Lanka
| | - Neluka Fernando
- University of Sri Jayewardenepura, Faculty of Medical Sciences, Department of Microbiology, Nugegoda, Gangodawila, Sri Lanka
| | - Nilwala Kottegoda
- University of Sri Jayewardenepura, Faculty of Applied Sciences, Department of Chemistry, Nugegoda, Sri Lanka.,Sri Lanka Institute of Nanotechnology, Nanoscience and Technology Park, Pitipana, Homagama, Sri Lanka.,University of Sri Jayewardenepura, Center for Advanced Material Research, Nugegoda, Sri Lanka
| | - Lakshman P Samaranayake
- University of Queensland, Department of Oral Microbiomics and Infection, Brisbane, Australia
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35
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Madhwani T, McBain AJ. The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins. PLoS One 2016; 11:e0158288. [PMID: 27483159 PMCID: PMC4970730 DOI: 10.1371/journal.pone.0158288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/13/2016] [Indexed: 11/19/2022] Open
Abstract
The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of "self" and "non-self" origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota.
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Affiliation(s)
- Tejal Madhwani
- Manchester Pharmacy School, The University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Andrew J. McBain
- Manchester Pharmacy School, The University of Manchester, Manchester, M13 9PT, United Kingdom
- * E-mail:
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Effect of mouthwashes on the composition and metabolic activity of oral biofilms grown in vitro. Clin Oral Investig 2016; 21:1221-1230. [PMID: 27337976 PMCID: PMC5399055 DOI: 10.1007/s00784-016-1876-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 06/06/2016] [Indexed: 11/26/2022]
Abstract
Objective The aim of this study was to determine the effect of an oxygenating mouthwash compared to two other established mouthwash products on bacterial composition and metabolic activity of oral biofilms in vitro. Material and methods Twelve healthy subjects participated as donors. Plaque-saliva mixture inoculated biofilms were grown and treated with 3 different chemotherapeutic mouthwashes [amine fluoride/stannous fluoride (MD), oxygenating agent (AX), chlorhexidine 0.12 % (PA), and water (W)]. Effects of treatments were assessed on biofilm composition (16S rRNA gene amplicon sequencing), production of organic acids (formate, acetate, lactate, propionate, butyrate using capillary electrophoresis), and viability of the remaining biofilm (CFUs). Results Microbial profiles of biofilms clustered per inoculum donor and were dominated by the genera Veillonella, Streptococcus, and Prevotella. Microbial diversity was only reduced after PA treatment. Significant changes in composition occurred after treatment with AX, resulting in lower proportions of Veillonella and higher proportions of non-mutans streptococci. Production of all organic acids after PA and lactate after MD was significantly lower as compared to W. AX resulted in reduction of acetate, butyrate, and propionate and increase in lactate production (p < 0.05). Viable counts were significantly lower after PA and AX treatments compared to W, while no significant reduction was observed after MD. Conclusions All studied mouthwashes affected the in vitro biofilms differently. The effects of the AX treatment were the most prominent which resulted in changes of the bacterial composition and metabolism. Clinical implications Awareness by the dental team that mouthwashes can change the bacterial composition and metabolism is important when advising its use.
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Hao W, Xu H, Chen X, Zhou Q, Zhang P, Chen F, Qin M. Changes in dental plaque microbial richness and oral behavioral habits during caries development in young Chinese children. Caries Res 2016; 49:116-23. [PMID: 25591545 DOI: 10.1159/000366505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 08/07/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To detect changes in the microbial richness of dental plaque and oral behaviors during caries development in young Chinese children. METHODS Supragingival plaque samples and a survey of oral behaviors of 130 children aged 3 at baseline were analyzed at 6 months and 12 months. Total DNA was isolated from all samples and PCR-denaturing gradient gel electrophoresis analysis was conducted. RESULTS In the follow-up, 44 children had caries or cavity fillings at 6 months, a further 28 children had caries or cavity fillings at 12 months. The other 58 children remained caries-free at 12 months. According to the changes in caries status at the 12-month follow-up, all participants were divided into three groups: caries-free, caries at 6 months and caries at 12 months. The changes in oral behaviors during the 12-month follow-up were not significantly different in the three groups. The frequency of eating sweets and eating sweets before sleeping was significantly different among the three groups at baseline. At baseline, the average detectable bands of caries in the 12-month caries group were similar to those of the caries-free group; both of them were higher than that of the 6-month caries group. At 6 months, the average detectable bands of the 12-month caries group were significantly lower than that of the caries-free group although the children of the 12-month caries group were caries-free at that time. CONCLUSIONS For young Chinese children, the high frequency of eating sweets and eating sweets before sleeping are risk factors of caries onset, and the decrease in microbial richness could occur 6 months before the onset of caries.
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Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG, Henderson WA. The microbiome of the oral mucosa in irritable bowel syndrome. Gut Microbes 2016; 7:286-301. [PMID: 26963804 PMCID: PMC4988452 DOI: 10.1080/19490976.2016.1162363] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. The severity of visceral pain was assessed by orally administering a gastrointestinal test solution. Participants self-reported their induced visceral pain. Pain severity was highest in IBS participants (P = 0.0002), particularly IBS-overweight participants (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008). Analysis of β-diversity found significant separation of the IBS-overweight group (P < 0.05). Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes, was the most important factor in describing the severity of visceral pain and variation in the microbiome. Pain severity was strongly correlated to the abundance of many taxa, suggesting the potential of the oral microbiome in diagnosis and patient phenotyping. The oral microbiome has potential as a source of microbial information in IBS.
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Affiliation(s)
- Nicolaas H. Fourie
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Dan Wang
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Sarah K. Abey
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - LeeAnne B. Sherwin
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Paule V. Joseph
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Bridgett Rahim-Williams
- National Institute on Minority Health and Health Disparities, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Eric G. Ferguson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Wendy A. Henderson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
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Chen M, Wu BL, Chen T, Liu Z, Deng ZL, Peng L. The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis. J Dent Sci 2016; 11:54-58. [PMID: 30894946 PMCID: PMC6395153 DOI: 10.1016/j.jds.2015.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/06/2015] [Indexed: 11/11/2022] Open
Abstract
Background/purpose Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), as a conventional molecular technique, was utilized to analyze the diversity of oral microbiota. However, studies found that the results of PCR-DGGE were affected by the DNA isolation method. This study compared QIAamp DNA Micro Kit extraction method with the phenol and chloroform extraction method for DNA isolation of saliva of healthy youths and analyzed PCR-DGGE fingerprints. Materials and methods In the first stage, samples were divided into two after collection from eight health youths. Two methods were used to isolate the DNA for PCR-DGGE analysis. In the second stage, another 16 samples were collected from 14 youths. The better method, QIAamp DNA Micro Kit, was used to isolate the DNA for PCR-DGGE analysis. The cluster analysis was performed with unweighted pair-group method with arithmetic means. Results The results in the first stage showed that the QIAamp DNA Micro Kit extraction method was more suitable for DNA extraction of saliva than the phenol-chloroform extraction method. In the second stage, the bands were changed into numbers “0”, “1”, and “2” to analyze the similarity of samples according to the bands' lightness. The similarity indices of different periods from the same individual showed that the microbiological composition was very similar (>0.95), while those from different individuals varied greatly (<0.90). Conclusion PCR-DGGE was more accurate in assessing oral microbial diversity by QIAamp DNA Micro Kit. Different individuals had large differences in oral microbial diversity but also had some common microbial dominant communities.
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Affiliation(s)
- Ming Chen
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Bu-Ling Wu
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhao Liu
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zi-Long Deng
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Peng
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study. Sci Rep 2016; 6:22164. [PMID: 26907866 PMCID: PMC4764907 DOI: 10.1038/srep22164] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/09/2016] [Indexed: 12/25/2022] Open
Abstract
This population-based study determined the salivary microbiota composition of 2,343 adult residents of Hisayama town, Japan, using 16S rRNA gene next-generation high-throughput sequencing. Of 550 identified species-level operational taxonomic units (OTUs), 72 were common, in ≥75% of all individuals, as well as in ≥75% of the individuals in the lowest quintile of phylogenetic diversity (PD). These “core” OTUs constituted 90.9 ± 6.1% of each microbiome. The relative abundance profiles of 22 of the core OTUs with mean relative abundances ≥1% were stratified into community type I and community type II by partitioning around medoids clustering. Multiple regression analysis revealed that a lower PD was associated with better conditions for oral health, including a lower plaque index, absence of decayed teeth, less gingival bleeding, shallower periodontal pockets and not smoking, and was also associated with tooth loss. By contrast, multiple Poisson regression analysis demonstrated that community type II, as characterized by a higher ratio of the nine dominant core OTUs, including Neisseria flavescens, was implicated in younger age, lower body mass index, fewer teeth with caries experience, and not smoking. Our large-scale data analyses reveal variation in the salivary microbiome among Japanese adults and oral health-related conditions associated with the salivary microbiome.
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Belstrøm D, Holmstrup P, Bardow A, Kokaras A, Fiehn NE, Paster BJ. Temporal Stability of the Salivary Microbiota in Oral Health. PLoS One 2016; 11:e0147472. [PMID: 26799067 PMCID: PMC4723053 DOI: 10.1371/journal.pone.0147472] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/04/2016] [Indexed: 11/23/2022] Open
Abstract
Objectives Saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. For such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal variation. The purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling. Design Stimulated saliva samples were collected from 5 orally healthy individuals in 4 h intervals for 24 h, and collection was repeated 7 days later (number of samples per person, n = 12, total number of samples, n = 60). Salivary microbiota was analyzed using the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using the Kruskal-Wallis test with Benjamini-Hochberg’s correction for multiple comparisons, cluster analysis, principal component analysis and correspondence analysis. Results From a total of 60 saliva samples, 477 probe targets were collectively identified with a mean number of probes per sample of 207 (range: 153–307). Little or no variation in microbial profiles within subjects was observed over time. Conclusions Although there was considerable variation between subjects, microbial profiles within subjects were stable throughout a 24 hour period and after 1 week. Since there is little or no evidence of diurnal variation of the salivary microbiome, time of sampling of saliva is not critical for perturbation or other microbial studies.
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Affiliation(s)
- Daniel Belstrøm
- Section for Periodontology, Microbiology, and Community Dentistry, School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Palle Holmstrup
- Section for Periodontology, Microbiology, and Community Dentistry, School of Dentistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Bardow
- Department of Oral Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Alexis Kokaras
- The Forsyth Institute, Department of Microbiology, Cambridge, Massachusetts, United States of America
| | - Nils-Erik Fiehn
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Bruce J. Paster
- The Forsyth Institute, Department of Microbiology, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
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Barroso E, Martín V, Martínez-Cuesta MC, Peláez C, Requena T. Stability of saliva microbiota during moderate consumption of red wine. Arch Oral Biol 2015; 60:1763-8. [DOI: 10.1016/j.archoralbio.2015.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/29/2015] [Accepted: 09/20/2015] [Indexed: 12/21/2022]
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Zhang M, Wang R, Liao Y, Buijs MJ, Li J. Profiling of Oral and Nasal Microbiome in Children With Cleft Palate. Cleft Palate Craniofac J 2015; 53:332-8. [PMID: 26068382 DOI: 10.1597/14-162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To identify the oral and nasal microbial profile of cleft palate children and control children and to reveal interrelationships between the microbiome and the high prevalence of infectious diseases. DESIGN Saliva and nasal samples of 10 cleft palate children and 10 age-matched control children were analyzed. Total microbial genomic DNA was isolated, polymerase chain reaction-denaturing gradient gel electrophoresis was applied to obtain fingerprints, and selected bands on fingerprints were sequenced. RESULTS The results revealed a significantly lower saliva microbial diversity in cleft children and a different microbial component in both saliva and nares in children with cleft palate. A higher component similarity between the oral and nasal samples was found in the cleft group than in the control group. Lautropia species and Bacillus species were significantly less present among the saliva samples of cleft group. Dolosigranulum species and Bacillus species were significantly fewer in the nasal cavity of cleft group. Streptococcus species became much more predominant in the nasal cavity of the cleft group than in that of the control group. CONCLUSIONS A disturbed ecological ecosystem is found in oral and nasal microbiome of children with cleft palate as a consequence of the abnormal communication between the two cavities. Further studies are needed to explore the relationship between the disturbed microbiome and diseases.
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Kumar PS, Mason MR. Mouthguards: does the indigenous microbiome play a role in maintaining oral health? Front Cell Infect Microbiol 2015; 5:35. [PMID: 26000251 PMCID: PMC4422079 DOI: 10.3389/fcimb.2015.00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 03/25/2015] [Indexed: 01/23/2023] Open
Abstract
The existence of symbiotic relationships between bacteria and their hosts in various ecosystems have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities. Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function, and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.
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Affiliation(s)
- Purnima S. Kumar
- Division of Periodontology, College of Dentistry, The Ohio State UniversityColumbus, OH, USA
| | - Matthew R. Mason
- Division of Biosciences, College of Dentistry, The Ohio State UniversityColumbus, OH, USA
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Salli KM, Ouwehand AC. The use of in vitro model systems to study dental biofilms associated with caries: a short review. J Oral Microbiol 2015; 7:26149. [PMID: 25740099 PMCID: PMC4349908 DOI: 10.3402/jom.v7.26149] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 11/14/2022] Open
Abstract
A dental biofilm forms a distinct environment where microorganisms live in a matrix of extracellular polysaccharides. The biofilm favors certain bacteria and creates a habitat that functions differently compared to planktonic bacteria. Reproducible model systems which help to address various questions related to biofilm formation, the process of caries development, and its prevention are needed and are continuously developed. Recent research using both batch culture, continuous culture and flow cells in caries biofilm formation is presented. The development of new techniques and equipment has led to a deeper understanding of how caries biofilms function. Biofilm models have also been used in the development of materials inhibiting secondary caries. This short review summarizes available models to study these questions.
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Affiliation(s)
- Krista M Salli
- DuPont Nutrition and Health, Kantvik Active Nutrition, Kirkkonummi, Finland;
| | - Arthur C Ouwehand
- DuPont Nutrition and Health, Kantvik Active Nutrition, Kirkkonummi, Finland
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46
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Distribution of 8 periodontal microorganisms in family members of Chinese patients with aggressive periodontitis. Arch Oral Biol 2015; 60:400-7. [DOI: 10.1016/j.archoralbio.2014.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 11/20/2014] [Accepted: 11/23/2014] [Indexed: 01/01/2023]
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Abstract
PURPOSE OF REVIEW Oral mucositis is one of the most prevalent toxicities after hematopoietic stem cell transplantation. Mucositis is initiated by the chemotherapy or radiotherapy preceding the transplantation. It is commonly accepted that microorganisms play a role in the process of oral mucositis. Despite the upcoming techniques to determine the whole oral bacterial ecosystem, the exact role of the microflora in mucositis is not yet understood. This article provides an overview of the state-of-the-art research on the oral microflora and mucositis. RECENT FINDINGS A shift in microflora, in both the intestine and the oral cavity, can be found after chemotherapy or radiation therapy. The presence of oral ulcerative mucositis coincides with the presence of periodontitis-associated bacteria, in particular Porphyromonas gingivalis. Moreover, this bacterium can inhibit wound healing processes in an in-vitro model. SUMMARY We come to realize that some diseases are associated with a shift in the microflora. The role of the microflora in oral and intestinal mucositis is gaining more attention in recent literature. In the oral cavity, periodontitis-associated bacteria may influence the healing of ulcerations and the role they play in mucositis may be more subtle and complicated than was previously thought.
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Zaura E, Nicu EA, Krom BP, Keijser BJF. Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Microbiol 2014; 4:85. [PMID: 25019064 PMCID: PMC4071637 DOI: 10.3389/fcimb.2014.00085] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/08/2014] [Indexed: 12/15/2022] Open
Abstract
The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift toward a disease, e.g., periodontitis or caries. Although processes that underlie oral diseases have been studied extensively, processes involved in maintaining of a normal, healthy microbiome are poorly understood. In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained. We introduce our view on the prenatal development of tolerance for the normal oral microbiome: we propose that development of fetal tolerance toward the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome. We describe the processes that influence the establishment of such microbiome, followed by our perspective on the process of sustaining a healthy oral microbiome. We divide microbiome-maintenance factors into host-derived and microbe-derived, while focusing on the host. Finally, we highlight the need and directions for future research.
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Affiliation(s)
- Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Elena A Nicu
- Department of Periodontology, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Bart J F Keijser
- Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences Zeist, Netherlands ; Top Institute Food and Nutrition Wageningen, Netherlands
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Wang S, Guo L, Seneviratne CJ, Huang B, Han J, Peng L, Liu X, Zhang C. Biofilm formation of salivary microbiota on dental restorative materials analyzed by denaturing gradient gel electrophoresis and sequencing. Dent Mater J 2014; 33:325-31. [PMID: 24598237 DOI: 10.4012/dmj.2013-152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The microbial diversity of biofilms formed on the surfaces of amalgam, glass-ionomer cement, and resin composite was analyzed by denaturing gradient gel electrophoresis (DGGE). The V2-V3 region of salivary microbial 16S rDNA gene sequences of planktonic and biofilm bacteria, after 1 day and 1 week of incubation, was amplified by polymerase chain reaction (PCR) and analyzed by DGGE. The amounts of strongly adherent phylotypes after 1 day and 1 week on the three dental restorative materials were more than those on hydroxyapatite. Streptococcus salivarius was detected in both loosely adherent and strong adherent groups of all 1-day samples. At 1 week, the amounts of loosely adherent and strongly adherent phylotypes present on the three restorative materials ranked in this ascending order: glass-ionomer cement < resin composite < amalgam. Results of DGGE analysis suggested that glass-ionomer cement was the best material of choice in terms of suppressing bacterial phylotypes in biofilms.
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Affiliation(s)
- Shuai Wang
- Comprehensive Dental Care (Endodontics), Faculty of Dentistry, The University of Hong Kong
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Langfeldt D, Neulinger SC, Heuer W, Staufenbiel I, Künzel S, Baines JF, Eberhard J, Schmitz RA. Composition of microbial oral biofilms during maturation in young healthy adults. PLoS One 2014; 9:e87449. [PMID: 24503584 PMCID: PMC3913613 DOI: 10.1371/journal.pone.0087449] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/26/2013] [Indexed: 11/18/2022] Open
Abstract
In the present study we aimed to analyze the bacterial community structure of oral biofilms at different maturation stages in young healthy adults. Oral biofilms established on membrane filters were collected from 32 human subjects after 5 different maturation intervals (1, 3, 5, 9 and 14 days) and the respective phylogenetic diversity was analyzed by 16S rDNA amplicon sequencing. Our analyses revealed highly diverse entire colonization profiles, spread into 8 phyla/candidate divisions and in 15 different bacterial classes. A large inter-individual difference in the subjects' microbiota was observed, comprising 35% of the total variance, but lacking conspicuous general temporal trends in both alpha and beta diversity. We further obtained strong evidence that subjects can be categorized into three clusters based on three differently occurring and mutually exclusive species clusters.
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Affiliation(s)
- Daniela Langfeldt
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Sven C. Neulinger
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Wieland Heuer
- Department of Prosthetic Dentistry and Biomaterials Science, Hannover Medical School, Hannover, Germany
| | - Ingmar Staufenbiel
- Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany
| | - Sven Künzel
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - John F. Baines
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Jörg Eberhard
- Department of Prosthetic Dentistry and Biomaterials Science, Hannover Medical School, Hannover, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
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