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Bhardwaj RG, Khalaf ME, Karched M. Secretome analysis and virulence assessment in Abiotrophia defectiva. J Oral Microbiol 2024; 16:2307067. [PMID: 38352067 PMCID: PMC10863525 DOI: 10.1080/20002297.2024.2307067] [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] [Received: 08/13/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Background Abiotrophia defectiva, although infrequently occurring, is a notable cause of culture-negative infective endocarditis with limited research on its virulence. Associated with oral infections such as dental caries, exploring its secretome may provide insights into virulence mechanisms. Our study aimed to analyze and characterize the secretome of A. defectiva strain CCUG 27639. Methods Secretome of A. defectiva was prepared from broth cultures and subjected to mass spectrometry and proteomics for protein identification. Inflammatory potential of the secretome was assessed by ELISA. Results Eighty-four proteins were identified, with diverse subcellular localizations predicted by PSORTb. Notably, 20 were cytoplasmic, 12 cytoplasmic membrane, 5 extracellular, and 9 cell wall-anchored proteins. Bioinformatics tools revealed 54 proteins secreted via the 'Sec' pathway and 8 via a non-classical pathway. Moonlighting functions were found in 23 proteins, with over 20 exhibiting potential virulence properties, including peroxiredoxin and oligopeptide ABC transporter substrate-binding protein. Gene Ontology and KEGG analyses categorized protein sequences in various pathways. STRING analysis revealed functional protein association networks. Cytokine profiling demonstrated significant proinflammatory cytokine release (IL-8, IL-1β, and CCL5) from human PBMCs. Conclusions Our study provides a comprehensive understanding of A. defectiva's secretome, laying the foundation for insights into its pathogenicity.
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Affiliation(s)
- Radhika G Bhardwaj
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences College of Dentistry, Kuwait University, Safat, Kuwait
| | - Mai E Khalaf
- Department of General Dental Practice, College of Dentistry, Kuwait University, Safat, Kuwait
| | - Maribasappa Karched
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences College of Dentistry, Kuwait University, Safat, Kuwait
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2
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Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.
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Affiliation(s)
- Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
| | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, USA
| | - Keolu Fox
- Department of Anthropology, Global Health Program, and Indigenous Futures Institute, University of California, San Diego, CA, USA
| | - Emma Kowal
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Melbourne, Victoria, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, USA.
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3
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Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
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Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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4
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Cogulu D, Saglam C. Genetic aspects of dental caries. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.1060177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Dental caries is a common chronic disease affecting humans in all age groups. Various factors can affect the formation of caries including demineralization and remineralization processes with oral flora; dietary and oral hygiene habits; salivary composition, flow rate, pH and buffering capacity; morphological features of the teeth; fluoride exposures, environmental and socioeconomic factors. One of the most important factors causing inter-individual variations in caries susceptibility is the host genetics. Several genes affect individual caries susceptibility. Genes play a role in immune response, development of saliva and tooth enamel. The present review aims to overview the literature focusing on the genetic features of dental caries.
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5
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屠 叶, 徐 欣, 周 学. [Development and Influencing Factors of Oral Microbiota in Early Life]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2022; 53:220-225. [PMID: 35332721 PMCID: PMC10409358 DOI: 10.12182/20220360303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Oral cavity, an important component of and the gateway to the digestive system, is also the colonization site and the microecological environment of trillions of microorganisms. The establishment and succession of oral microbiota are of great importance for the development of human immune system, and function as a major determinant of oral and systemic health. Within a few hours after birth, early colonizers such as Streptococcus and Lactobacillus can be detected in an infant's mouth. The oral microbiota communities mature gradually along with the growth of the host, expanding in their species abundance and diversity. In addition to genetic factors, a number of cross-sectional studies have revealed that the development of oral microecosystems in early life is influenced and tuned by multiple external factors, including maternal health status, mode of delivery, feeding habits, antibiotics use, etc. The dysbiosis of oral microecology in early life is closely related to the pathogenesis and progression of oral and systemic diseases. Therefore, good oral hygiene habits are of vital importance to the early management of oral microbial diseases and their effective prevention and control. Herein, we summarized the colonization and succession of oral microbiota in early life and further discussed the key external factors that affect early life oral microecosystem, as well as the impact of early life oral microbiota on the host's health at a later stage, intending to help providing new insights into and new strategies for the management of the whole lifecycle oral and systemic health.
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Affiliation(s)
- 叶 屠
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 欣 徐
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 学东 周
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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6
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Blum J, Silva M, Byrne SJ, Butler CA, Adams GG, Reynolds EC, Dashper SG. Temporal development of the infant oral microbiome. Crit Rev Microbiol 2022; 48:730-742. [PMID: 35015598 DOI: 10.1080/1040841x.2021.2025042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human oral microbiome is becoming recognized as playing roles in health and disease well beyond the oral cavity over the lifetime of the individual. The oral microbiome is hypothesized to result from specific colonization events followed by a reproducible and ordered development of complex bacterial communities. Colonization events, proliferation, succession and subsequent community development are dependent on a range of host and environmental factors, most notably the neonate diet. It is now becoming apparent that early childhood and prenatal influences can have long term effects on the development of human oral microbiomes. In this review, the temporal development of the infant human oral microbiome is examined, with the effects of prenatal and postnatal influences and the roles of specific bacteria. Dietary and environmental factors, especially breastfeeding, have a significant influence on the development of the infant oral microbiome. The evidence available regarding the roles and functions of early colonizing bacteria is still limited, and gaps in knowledge where further research is needed to elucidate these specific roles in relation to health and disease still exist.
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Affiliation(s)
- Jordan Blum
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Mihiri Silva
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Samantha J Byrne
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Catherine A Butler
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Geoffrey G Adams
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Eric C Reynolds
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Stuart G Dashper
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
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7
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Yang SF, Lin CW, Chuang CY, Lee YC, Chung WH, Lai HC, Chang LC, Su SC. Host Genetic Associations with Salivary Microbiome in Oral Cancer. J Dent Res 2021; 101:590-598. [PMID: 34875929 DOI: 10.1177/00220345211051967] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite the growing recognition of a host genetic effect on shaping gut microbiota composition, the genetic determinants of oral microbiota remain largely unexplored, especially in the context of oral diseases. Here, we performed a microbiome genome-wide association study in 2 independent cohorts of patients with oral squamous cell carcinoma (OSCC, n = 144 and 67) and an additional group of noncancer individuals (n = 104). Besides oral bacterial dysbiosis and signatures observed in OSCC, associations of 3 loci with the abundance of genus-level taxa and 4 loci with β diversity measures were detected (q < 0.05) at the discovery stage. The most significant hit (rs10906082 with the genus Lachnoanaerobaculum, P = 3.55 × 10-9 at discovery stage) was replicated in a second OSCC cohort. Moreover, the other 2 taxonomical associations, rs10973953 with the genus Kingella (P = 1.38 × 10-9) and rs4721629 with the genus Parvimonas (P = 3.53 × 10-8), were suggestive in the meta-analysis combining 2 OSCC cohorts. Further pathway analysis revealed that these loci were enriched for genes in regulation of oncogenic and angiogenic responses, implicating a genetic anchor to the oral microbiome in estimation of casual relationships with OSCC. Our findings delineate the role of host genotypes in influencing the structure of oral microbial communities.
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Affiliation(s)
- S F Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - C W Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - C Y Chuang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Y C Lee
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - W H Chung
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - H C Lai
- Department of Medical Biotechnology and Laboratory Science, and Microbiota Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Central Research Laboratory, XiaMen Chang Gung Hospital, XiaMen, China
| | - L C Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - S C Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,Central Research Laboratory, XiaMen Chang Gung Hospital, XiaMen, China
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8
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Sivamaruthi BS, Kesika P, Chaiyasut C. A Review of the Role of Probiotic Supplementation in Dental Caries. Probiotics Antimicrob Proteins 2021; 12:1300-1309. [PMID: 32307660 DOI: 10.1007/s12602-020-09652-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dental diseases are among the common health issues experienced around the world. Dental caries is one of the most predominant oral diseases worldwide. Major factors associated with caries development include poor oral hygiene, the content of specific carbohydrates in the diet, dental biofilm formation, the cariogenic microbial load, reduction in salivary flow, insufficient fluoride exposure, gingival recession, genetic factors, and lack of personal attention to one's dental health. Several preventive measures have been implemented to reduce the risk of the development of caries. Probiotics are live microbes that when administered in suitable amounts confer health benefits on the host; they are recognized as potential adjunct therapeutic agents for several diseases. The present manuscript summarizes recent findings on the role of probiotics in dental caries prevention and the possible mechanisms of probiotic effects. Review of the literature indicates the regular consumption of probiotic products significantly reduced the risk of caries by inhibiting cariogenic bacteria and enriching commensal microbes in the oral cavity. Buffering the salivary pH, production of bacteriocin and enzymes (dextranase, mutanase, and urease), the capacity of competing for the adhesion and colonization on tooth surfaces are the possible mechanisms behind the beneficial effect of probiotics. Further studies are necessary to address the efficacy of long-term probiotic supplementation on the control of dental diseases and the influence of childhood probiotic supplementation on the risk of caries development.
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Affiliation(s)
- Bhagavathi Sundaram Sivamaruthi
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Periyanaina Kesika
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, 50200, Thailand.
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9
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Handsley-Davis M, Skelly E, Johnson NW, Kapellas K, Lalloo R, Kroon J, Weyrich LS. Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children. FRONTIERS IN ORAL HEALTH 2021; 2:641328. [PMID: 35047996 PMCID: PMC8757737 DOI: 10.3389/froh.2021.641328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4–17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences in microbial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management options for Australian Aboriginal and Torres Strait Islander children and communities.
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Affiliation(s)
- Matilda Handsley-Davis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
| | - Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Newell W. Johnson
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
- Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, United Kingdom
- Newell W. Johnson
| | - Kostas Kapellas
- Indigenous Oral Health Unit, Australian Research Centre for Population Oral Health, Adelaide Dental School, University of Adelaide, Adelaide, SA, Australia
| | - Ratilal Lalloo
- School of Dentistry, University of Queensland, Brisbane, QLD, Australia
| | - Jeroen Kroon
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
- microARCH Laboratory, Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Laura S. Weyrich
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10
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Abstract
Acquisition and establishment of the oral microbiota occur in a dynamic process over various stages and involve close and continuous interactions with the host and its environment. In the present review, we discuss the stages of this process in chronological order. We start with the prenatal period and address the following questions: ‘Is the fetus exposed to maternal microbiota during pregnancy?’ and ‘If so, what is the potential role of this exposure?’ We comment on recent reports of finding bacterial DNA in placenta during pregnancies, and provide current views on the potential functions of prenatal microbial encounters. Next, we discuss the physiological adaptations that take place in the newborn during the birth process and the effect of this phase of life on the acquisition of the oral microbiota. Is it really just exposure to maternal vaginal microbes that results in the difference between vaginally and Cesarian section‐born infants? Then, we review the postnatal phase, in which we focus on transmission of microbes, the intraoral niche specificity, the effects of the host behavior and environment, as well as the role of genetic background of the host on shaping the oral microbial ecosystem. We discuss the changes in oral microbiota during the transition from deciduous to permanent dentition and during puberty. We also address the finite knowledge on colonization of the oral cavity by microbes other than the bacterial component. Finally, we identify the main outstanding questions that limit our understanding of the acquisition and establishment of a healthy microbiome at an individual level.
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Affiliation(s)
- A M Marije Kaan
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Dono Kahharova
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
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11
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Widyarman AS, Udawatte NS, Theodorea CF, Apriani A, Richi M, Astoeti TE, Seneviratne CJ. Casein phosphopeptide-amorphous calcium phosphate fluoride treatment enriches the symbiotic dental plaque microbiome in children. J Dent 2021; 106:103582. [PMID: 33450310 DOI: 10.1016/j.jdent.2021.103582] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES The dysbiotic oral microbiome plays a key role in the pathogenesis of caries in children. Topical application of casein phosphopeptide-amorphous calcium phosphate containing fluoride (CPP-ACP/F) is an effective treatment modality for children with caries (CC). Hitherto the mechanism by which CPP-ACP/F modules the oral microbiome in CC has not been investigated. The study aimed to examine the CPP-ACP/F effect on the dental plaque microbiome of children group with caries. METHODS This preliminary prospective clinical cohort included 10 children with caries. The children received topical fluoride CPP-ACP/F once-a-week for one month. Plaque samples were collected before and after treatment and subjected to 16S rDNA-based next-generation-sequencing. Microbial composition, diversity and functional roles were analyzed in comparison to the clinical characteristics of cohort using standard bioinformatics tools. RESULTS CPP-ACP/F treatment modulated dysbiotic oral microbiome towards healthier community as the higher proportion of Proteobacteria and certain microbial protective species were enriched following CPP-ACP/F treatment. Despite overall uniformity of community structure in children with caries between the groups, some bacterial species were differentially represented in a statistically significant manner between pre- and post- treatments. Three bacterial species were found to be predictive of strongly sensitive to the CPP-ACP/F treatment, marked by decreased abundance of Lautropia mirabalis and increased abundance of Gemella haemolysans and Schwartzia succinivorans. CONCLUSION Within the limits of the current study, it could be concluded that the CPP-ACP/F varnish treatment modulated the microbial composition of the dental plaque microbiome towards symbiosis. These symbiotic changes may demonstrate the potential clinical significance of CPP-ACP/F varnish treatment.
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Affiliation(s)
- Armelia Sari Widyarman
- Department Head of Microbiology, Faculty of Dentistry, Trisakti University, Jln. Kyai Tapa 260, Grogol Jakarta Barat 11440, Indonesia.
| | - Nadeeka S Udawatte
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore (NDRIS), National Dental Centre Singapore, Oral Health ACP, Duke NUS Medical School, Singapore.
| | | | - Anie Apriani
- Department Pediatric Dentistry, Faculty of Dentistry, Maranatha University, Bandung, Indonesia.
| | - Mario Richi
- MiCORE Laboratory, Faculty of Dentistry, Trisakti University, Indonesia.
| | - Tri Erri Astoeti
- Department of Preventive and Public Health, Faculty of Dentistry, Trisakti University, Jln. Kyai Tapa 260, Grogol Jakarta Barat 11440, Indonesia.
| | - Chaminda Jayampath Seneviratne
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore (NDRIS), National Dental Centre Singapore, Oral Health ACP, Duke NUS Medical School, Singapore.
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12
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Handsley-Davis M, Jamieson L, Kapellas K, Hedges J, Weyrich LS. The role of the oral microbiota in chronic non-communicable disease and its relevance to the Indigenous health gap in Australia. BMC Oral Health 2020; 20:327. [PMID: 33198712 PMCID: PMC7670664 DOI: 10.1186/s12903-020-01308-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aboriginal Australians and Torres Strait Islanders (hereafter respectfully referred to as Indigenous Australians) experience disproportionately poor health and low life expectancy compared to non-Indigenous Australians. Poor oral health is a critical, but understudied, contributor to this health gap. A considerable body of evidence links poor oral health to increased risks of other chronic non-communicable conditions, such as diabetes, cardiovascular disease, chronic kidney disease, and poor emotional wellbeing. MAIN: The oral microbiota is indisputably associated with several oral diseases that disproportionately affect Indigenous Australians. Furthermore, a growing literature suggests direct and indirect links between the oral microbiota and systemic chronic non-communicable diseases that underpin much of the Indigenous health gap in Australia. Recent research indicates that oral microbial communities are shaped by a combination of cultural and lifestyle factors and are inherited from caregivers to children. Systematic differences in oral microbiota diversity and composition have been identified between Indigenous and non-Indigenous individuals in Australia and elsewhere, suggesting that microbiota-related diseases may be distinct in Indigenous Australians. CONCLUSION: Oral microbiota research involving Indigenous Australians is a promising new area that could benefit Indigenous communities in numerous ways. These potential benefits include: (1) ensuring equity and access for Indigenous Australians in microbiota-related therapies; (2) opportunities for knowledge-sharing and collaborative research between scientists and Indigenous communities; and (3) using knowledge about the oral microbiota and chronic disease to help close the gaps in Indigenous oral and systemic health.
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Affiliation(s)
- Matilda Handsley-Davis
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA, Australia.
| | - Lisa Jamieson
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Joanne Hedges
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Laura S Weyrich
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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13
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Abstract
Despite widely used preventive measures such as sealant programs to control caries prevalence, disparities are seen among ethnic groups. Supragingival plaque harbors hundreds of bacterial species, playing a significant role in oral health and disease. It is unknown whether the ethnic variation influences the supragingival microbiota in children. In our study, variations in microbiota of the supragingival plaque was investigated from 96 children between 6 and 11 years old in four ethnic groups (African American, Burmese, Caucasian, and Hispanic) from the same geographic location by 16S rRNA gene sequencing. We found that the microbial alpha and beta diversity of supragingival microbiota significantly differed between ethnic groups. The supragingival plaque microbiota had the most complex microbial community in Burmese children. Within-group microbiota similarity in Burmese or Caucasian children was significantly higher than between-groups similarity. We identified seven ethnic group-specific bacterial taxa after adjusting for dental plaque index, decayed missing filled teeth (DMFT) and the frequency of brushing. Children with high plaque index and high DMFT values were more similar to each other in the overall microbial community, compared to low plaque index or low DMFT groups in which inter-subject variation is high. Several bacterial taxa associated with high plaque index or high DMFT were ethnic group-specific. These results demonstrated that supragingival microbiota differed among ethnicity groups in children.
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14
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Esberg A, Haworth S, Kuja-Halkola R, Magnusson PK, Johansson I. Heritability of Oral Microbiota and Immune Responses to Oral Bacteria. Microorganisms 2020; 8:microorganisms8081126. [PMID: 32726935 PMCID: PMC7464143 DOI: 10.3390/microorganisms8081126] [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: 07/02/2020] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022] Open
Abstract
Maintaining a symbiotic oral microbiota is essential for oral and dental health, and host genetic factors may affect the composition or function of the oral microbiota through a range of possible mechanisms, including immune pathways. The study included 836 Swedish twins divided into separate groups of adolescents (n = 418) and unrelated adults (n = 418). Oral microbiota composition and functions of non-enzymatically lysed oral bacteria samples were evaluated using 16S rRNA gene sequencing and functional bioinformatics tools in the adolescents. Adaptive immune responses were assessed by testing for serum IgG antibodies against a panel of common oral bacteria in adults. In the adolescents, host genetic factors were associated with both the detection and abundance of microbial species, but with considerable variation between species. Host genetic factors were associated with predicted microbiota functions, including several functions related to bacterial sucrose, fructose, and carbohydrate metabolism. In adults, genetic factors were associated with serum antibodies against oral bacteria. In conclusion, host genetic factors affect the composition of the oral microbiota at a species level, and host-governed adaptive immune responses, and also affect the concerted functions of the oral microbiota as a whole. This may help explain why some people are genetically predisposed to the major dental diseases of caries and periodontitis.
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Affiliation(s)
- Anders Esberg
- Department of Odontology, Umeå University, 901 87 Umeå, Sweden;
- Correspondence:
| | - Simon Haworth
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK;
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, UK
| | - Ralf Kuja-Halkola
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden; (R.K.-H.); (P.K.M.)
| | - Patrik K.E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden; (R.K.-H.); (P.K.M.)
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15
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Freire M, Moustafa A, Harkins DM, Torralba MG, Zhang Y, Leong P, Saffery R, Bockmann M, Kuelbs C, Hughes T, Craig JM, Nelson KE. Longitudinal Study of Oral Microbiome Variation in Twins. Sci Rep 2020; 10:7954. [PMID: 32409670 PMCID: PMC7224172 DOI: 10.1038/s41598-020-64747-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 04/21/2020] [Indexed: 01/23/2023] Open
Abstract
Humans are host to a multitude of microorganisms that rapidly populate the body at birth, subject to a complex interplay that is dependent on host genetics, lifestyle, and environment. The host-associated microbiome, including the oral microbiome, presents itself in a complex ecosystem important to health and disease. As the most common chronic disease globally, dental caries is induced by host-microbial dysbiosis in children and adults. Multiple biological and environmental factors are likely to impact disease predisposition, onset, progression, and severity, yet longitudinal studies able to capture these influences are missing. To investigate how host genetics and environment influenced the oral microbial communities over time, we profiled supragingival plaque microbiomes of dizygotic and monozygotic twins during 3 visits over 12-months. Dental plaque DNA samples were amplified by targeting the 16S rRNA gene V4 region, and microbial findings were correlated with clinical, diet and genetic metadata. We observed that the oral microbiome variances were shaped primarily by the environment when compared to host genetics. Among the environmental factors shaping microbial changes of our subjects, significant metadata included age of the subject, and the age by which subjects initiated brushing habits, and the types of actions post-brushing. Relevant heritability of the microbiome included Actinomyces and Capnocytophaga in monozygotic twins and Kingella in dizygotic twins. Corynebacterium and Veillonella abundances were associated with age, whereas Aggregatibacter was associated with younger subjects. Streptococcus abundance showed an inverse association over time, and Selenomonas abundances increased with brushing frequency per day. Unraveling the exact biological mechanisms in caries has the potential to reveal novel host-microbial biomarkers, pathways, and targets important to effective preventive measures, and early disease control in children.
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Affiliation(s)
- Marcelo Freire
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA.
| | - Ahmed Moustafa
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Department of Biology, The American University in Cairo, New Cairo, 11835, Egypt
| | - Derek M Harkins
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Manolito G Torralba
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Yun Zhang
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Pamela Leong
- IMPACT Strategic Research Centre, Deakin University School of Medicine, Geelong, VIC, 3220, Australia
| | - Richard Saffery
- IMPACT Strategic Research Centre, Deakin University School of Medicine, Geelong, VIC, 3220, Australia
| | - Michelle Bockmann
- Adelaide Dental School, The University of Adelaide Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Claire Kuelbs
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Toby Hughes
- Adelaide Dental School, The University of Adelaide Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Jeffrey M Craig
- IMPACT Strategic Research Centre, Deakin University School of Medicine, Geelong, VIC, 3220, Australia
| | - Karen E Nelson
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD, 20850, USA
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16
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Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L, Dowd JB. Sociodemographic variation in the oral microbiome. Ann Epidemiol 2019; 35:73-80.e2. [PMID: 31151886 PMCID: PMC6626698 DOI: 10.1016/j.annepidem.2019.03.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/18/2019] [Accepted: 03/15/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE Variations in the oral microbiome are potentially implicated in social inequalities in oral disease, cancers, and metabolic disease. We describe sociodemographic variation of oral microbiomes in a diverse sample. METHODS We performed 16S rRNA sequencing on mouthwash specimens in a subsample (n = 282) of the 2013-2014 population-based New York City Health and Nutrition Examination Study. We examined differential abundance of 216 operational taxonomic units, and alpha and beta diversity by age, sex, income, education, nativity, and race/ethnicity. For comparison, we examined differential abundance by diet, smoking status, and oral health behaviors. RESULTS Sixty-nine operational taxonomic units were differentially abundant by any sociodemographic variable (false discovery rate < 0.01), including 27 by race/ethnicity, 21 by family income, 19 by education, 3 by sex. We found 49 differentially abundant by smoking status, 23 by diet, 12 by oral health behaviors. Genera differing for multiple sociodemographic characteristics included Lactobacillus, Prevotella, Porphyromonas, Fusobacterium. CONCLUSIONS We identified oral microbiome variation consistent with health inequalities, more taxa differing by race/ethnicity than diet, and more by SES variables than oral health behaviors. Investigation is warranted into possible mediating effects of the oral microbiome in social disparities in oral and metabolic diseases and cancers.
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Affiliation(s)
- Audrey Renson
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC.
| | - Heidi E Jones
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY
| | - Francesco Beghini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Christine P Zolnik
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY; Department of Biology, Long Island University, Brooklyn, NY
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Thomas U Moody
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY; Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lorna Thorpe
- Department of Population Health, NYU School of Medicine, New York, NY
| | - Robert Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY; Departments of Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY; Institute for Implementation Science in Population Health, City University of New York, New York, NY
| | - Jennifer B Dowd
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY; Department of Global Health and Social Medicine, King's College London, London, UK
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17
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Mattos MG, Fernandez CA, Masterson D, Maia LC, Neves ADA. Is the caregivers’ oral health related to dental caries in children or adolescents? A systematic review. Clin Oral Investig 2019; 23:3843-3854. [DOI: 10.1007/s00784-019-02814-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/11/2019] [Indexed: 01/22/2023]
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18
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Cherkasov SV, Popova LY, Vivtanenko TV, Demina RR, Khlopko YA, Balkin AS, Plotnikov AO. Oral microbiomes in children with asthma and dental caries. Oral Dis 2019; 25:898-910. [PMID: 30561093 DOI: 10.1111/odi.13020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/07/2018] [Accepted: 12/04/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing. MATERIAL AND METHODS Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform. RESULTS There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The "caries-enriched" genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p < 0.05). CONCLUSIONS The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children.
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Affiliation(s)
- Sergey V Cherkasov
- Laboratory for the Research of the Mechanisms of Human Microbiocenoses Formation, Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia
| | - Larisa Yu Popova
- Department of Childhood Diseases, Orenburg State Medical University, Orenburg, Russia
| | - Tatyana V Vivtanenko
- Department of Childhood Diseases, Orenburg State Medical University, Orenburg, Russia
| | - Rimma R Demina
- Department of Therapeutic Dentistry, Orenburg State Medical University, Orenburg, Russia
| | - Yuri A Khlopko
- Center of Shared Scientific Equipment, Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia
| | - Alexander S Balkin
- Center of Shared Scientific Equipment, Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia
| | - Andrey O Plotnikov
- Center of Shared Scientific Equipment, Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia.,Department of Hygiene and Epidemiology, Orenburg State Medical University, Orenburg, Russia
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19
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Fakhruddin KS, Ngo HC, Samaranayake LP. Cariogenic microbiome and microbiota of the early primary dentition: A contemporary overview. Oral Dis 2018; 25:982-995. [PMID: 29969843 DOI: 10.1111/odi.12932] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 12/24/2022]
Abstract
Recent advances in the field of molecular microbiology provide an unprecedented opportunity to decipher the vast diversity of the oral microbiome in health and disease. Here, we provide a contemporary overview of the oral microbiome and the microbiota of early childhood caries (ECC) with particular reference to newer analytical techniques. A MEDLINE search revealed a total of 20 metagenomic studies describing cariogenic microbiomes of ECC, 10 of which also detailed the healthy microbiomes. In addition, seven studies on site-specific microbiomes, focusing on acidogenic and aciduric microbiota of deep-dentinal lesions, were also reviewed. These studies evaluated plaque and saliva of children aged 1.5-11 years, in cohorts of 12-485 individuals. These studies reveal a very rich and diverse microbial communities, with hundreds of different phylotypes and microbial species, including novel species and phyla such as Scardovia wiggsiae, Slackia exigua, Granulicatella elegans, Firmicutes in the plaque biofilms of children with ECC. On the contrary, bacteria such as Streptococcus cristatus, S. gordonii, S. sanguinis, Corynebacterium matruchotii, and Neisseria flavescens were common in plaque biofilm of noncarious, healthy, tooth surfaces in subjects with caries. The review illustrates the immense complexity and the diversity of the human oral microbiota of the cariogenic plaque microbiome in ECC, and the daunting prospect of its demystification.
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Affiliation(s)
| | - Hien Chi Ngo
- Department of Preventive and Restorative Dentistry, University of Sharjah, Sharjah, UAE
| | - Lakshman Perera Samaranayake
- Department of Preventive and Restorative Dentistry, University of Sharjah, Sharjah, UAE.,The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
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20
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Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE. Host Genetic Control of the Oral Microbiome in Health and Disease. Cell Host Microbe 2018; 22:269-278.e3. [PMID: 28910633 DOI: 10.1016/j.chom.2017.08.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/30/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
Abstract
Host-associated microbial communities are influenced by both host genetics and environmental factors. However, factors controlling the human oral microbiome and their impact on disease remain to be investigated. To determine the combined and relative effects of host genotype and environment on oral microbiome composition and caries phenotypes, we profiled the supragingival plaque microbiome of 485 dizygotic and monozygotic twins aged 5-11. Oral microbiome similarity always increased with shared host genotype, regardless of caries state. Additionally, although most of the variation in the oral microbiome was determined by environmental factors, highly heritable oral taxa were identified. The most heritable oral bacteria were not associated with caries state, did not tend to co-occur with other taxa, and decreased in abundance with age and sugar consumption frequency. Thus, while the human oral microbiome composition is influenced by host genetic background, potentially cariogenic taxa are likely not controlled by genetic factors.
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Affiliation(s)
- Andres Gomez
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Josh L Espinoza
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Derek M Harkins
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Pamela Leong
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michelle Bockmann
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Manolito Torralba
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Claire Kuelbs
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Rohith Kodukula
- JCVI Summer Intern Program, Torrey Pines High School, San Diego, CA 9213, USA
| | - Jason Inman
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Toby Hughes
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Sarah K Highlander
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Chris L Dupont
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Karen E Nelson
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA; Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA.
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21
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Sharma N, Bhatia S, Sodhi AS, Batra N. Oral microbiome and health. AIMS Microbiol 2018; 4:42-66. [PMID: 31294203 PMCID: PMC6605021 DOI: 10.3934/microbiol.2018.1.42] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/03/2018] [Indexed: 12/12/2022] Open
Abstract
The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, “Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual”.
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Affiliation(s)
- Neetu Sharma
- Department of Microbiology, GGDSD College, Sector 32 C Chandigarh, India
| | - Sonu Bhatia
- Department of Biotechnology, GGDSD College, Sector 32 C Chandigarh, India
| | | | - Navneet Batra
- Department of Biotechnology, GGDSD College, Sector 32 C Chandigarh, India
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22
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Demmitt BA, Corley RP, Huibregtse BM, Keller MC, Hewitt JK, McQueen MB, Knight R, McDermott I, Krauter KS. Genetic influences on the human oral microbiome. BMC Genomics 2017; 18:659. [PMID: 28836939 PMCID: PMC5571580 DOI: 10.1186/s12864-017-4008-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/02/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The human oral microbiome is formed early in development. Its composition is influenced by environmental factors including diet, substance use, oral health, and overall health and disease. The influence of human genes on the composition and stability of the oral microbiome is still poorly understood. We studied both environmental and genetic characteristics on the oral microbiome in a large twin sample as well as in a large cohort of unrelated individuals. We identify several significantly heritable features of the oral microbiome. The heritability persists in twins even when their cohabitation changes. The heritability of these traits correlates with the cumulative genetic contributions of over half a million single nucleotide sequence variants measured in a different population of unrelated individuals. Comparison of same-sex and opposite sex cotwins showed no significant differences. We show that two new loci on chromosomes 7 and 12 are associated with the most heritable traits. RESULTS An analysis of 752 twin pairs from the Colorado Twin Registry, shows that the beta-diversity of monozygotic twins is significantly lower than for dizygotic or unrelated individuals. This is independent of cohabitation status. Intraclass correlation coefficients of nearly all taxa examined were higher for MZ than DZ twin pairs. A comparison of individuals sampled over 2-7 years confirmed previous reports that the oral microbiome remains relatively more stable in individuals over that time than to unrelated people. Twin modeling shows that a number of microbiome phenotypes were more than 50% heritable consistent with the hypothesis that human genes influence microbial populations. To identify loci that could influence microbiome phenotypes, we carried out an unbiased GWAS analysis which identified one locus on chromosome 7 near the gene IMMPL2 that reached genome-wide significance after correcting for multiple testing. Another locus on chromosome 12 near the non-coding RNA gene INHBA-AS1 achieved genome-wide significance when analyzed using KGG4 that sums SNP significance across coding genes. DISCUSSION Using multiple methods, we have demonstrated that some aspects of the human oral microbiome are heritable and that with a relatively small sample we were able to identify two previously unidentified loci that may be involved.
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Affiliation(s)
- Brittany A. Demmitt
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80304 USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
| | - Robin P. Corley
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO USA
| | - Brooke M. Huibregtse
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO USA
| | - Matthew C. Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO USA
| | - John K. Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO USA
| | - Matthew B. McQueen
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
- Department of Integrative Physiology and Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
| | - Rob Knight
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093 USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093 USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093 USA
| | - Ivy McDermott
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80304 USA
| | - Kenneth S. Krauter
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80304 USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO USA
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23
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Gomez A, Nelson KE. The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health. MICROBIAL ECOLOGY 2017; 73:492-503. [PMID: 27628595 PMCID: PMC5274568 DOI: 10.1007/s00248-016-0854-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/01/2016] [Indexed: 05/05/2023]
Abstract
In the era of applied meta-omics and personalized medicine, the oral microbiome is a valuable asset. From biomarker discovery to being a powerful source of therapeutic targets and to presenting an opportunity for developing non-invasive approaches to health care, it has become clear that oral microbes may hold the answer for understanding disease, even beyond the oral cavity. Although our understanding of oral microbiome diversity has come a long way in the past 50 years, there are still many areas that need to be fine-tuned for better risk assessment and diagnosis, especially in early developmental stages of human life. Here, we discuss the factors that impact development of the oral microbiome and explore oral markers of disease, with a focus on the early oral cavity. Our ultimate goal is to put different experimental and methodological views into perspective for better assessment of early oral and systemic disease at an early age and discuss how oral microbiomes-at the community level-could provide improved assessment in individuals and populations at risk.
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Affiliation(s)
- Andres Gomez
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, 92037, CA, USA.
| | - Karen E Nelson
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, 92037, CA, USA
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24
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Sampaio-Maia B, Caldas IM, Pereira ML, Pérez-Mongiovi D, Araujo R. The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:171-210. [PMID: 27926431 DOI: 10.1016/bs.aambs.2016.08.002] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The oral microbiome can alter the balance between health and disease, locally and systemically. Within the oral cavity, bacteria, archaea, fungi, protozoa, and viruses may all be found, each having a particular role, but strongly interacting with each other and with the host, in sickness or in health. A description on how colonization occurs and how the oral microbiome dynamically evolves throughout the host's life is given. In this chapter the authors also address oral and nonoral conditions in which oral microorganisms may play a role in the etiology and progression, presenting the up-to-date knowledge on oral dysbiosis as well as the known underlying pathophysiologic mechanisms involving oral microorganisms in each condition. In oral pathology, oral microorganisms are associated with several diseases, namely dental caries, periodontal diseases, endodontic infections, and also oral cancer. In systemic diseases, nonoral infections, adverse pregnancy outcomes, cardiovascular diseases, and diabetes are among the most prevalent pathologies linked with oral cavity microorganisms. The knowledge on how colonization occurs, how oral microbiome coevolves with the host, and how oral microorganisms interact with each other may be a key factor to understand diseases etiology and progression.
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Affiliation(s)
| | - I M Caldas
- Universidade do Porto, Portugal; Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal; Universidade de Coimbra, Portugal
| | | | - D Pérez-Mongiovi
- Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
| | - R Araujo
- Universidade do Porto, Portugal; Flinders University, Adelaide, SA, Australia
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Lee HS, Lee JH, Kim SO, Song JS, Kim BI, Kim YJ, Lee JH. Comparison of the oral microbiome of siblings using next-generation sequencing: a pilot study. Oral Dis 2016; 22:549-56. [DOI: 10.1111/odi.12491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 04/05/2016] [Accepted: 04/10/2016] [Indexed: 01/06/2023]
Affiliation(s)
- H-S Lee
- Department of Pediatric Dentistry; School of Dentistry; Kyung Hee University; Seoul Korea
| | - JH Lee
- Department of Clinical Pharmacology and Therapeutics; College of Medicine; Kyung Hee University; Seoul Korea
| | - S-O Kim
- Department of Pediatric Dentistry; College of Dentistry; Yonsei University; Seoul Korea
- Oral Science Research Center; College of Dentistry; Yonsei University; Seoul Korea
| | - JS Song
- Department of Pediatric Dentistry; College of Dentistry; Yonsei University; Seoul Korea
- Oral Science Research Center; College of Dentistry; Yonsei University; Seoul Korea
| | - BI Kim
- Oral Science Research Center; College of Dentistry; Yonsei University; Seoul Korea
- Department of Preventive Dentistry and Public Oral Health; College of Dentistry; Yonsei University; Seoul Korea
| | - YJ Kim
- Department of Pediatric Dentistry; School of Dentistry; Seoul National University; Seoul Korea
| | - J-H Lee
- Department of Pediatric Dentistry; College of Dentistry; Yonsei University; Seoul Korea
- Oral Science Research Center; College of Dentistry; Yonsei University; Seoul Korea
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Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes. PLoS One 2015; 10:e0141310. [PMID: 26524687 PMCID: PMC4629883 DOI: 10.1371/journal.pone.0141310] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022] Open
Abstract
Despite recent successes in the control of dental caries, the mechanism of caries development remains unclear. To investigate the causes of dental decay, especially in early childhood caries, the supragingival microflora composition of 20 twins with discordant caries phenotypes were analyzed using high-throughput pyrosequencing. In addition, the parents completed a lifestyle questionnaire. A total of 228,789 sequencing reads revealed 10 phyla, 84 genera, and 155 species of microflora, the relative abundances of these strains varied dramatically among the children, Comparative analysis between groups revealed that Veillonella, Corynebacterium and Actinomyces were presumed to be caries-related genera, Fusobacterium, Kingella and Leptotrichia were presumed to be healthy-related genus, yet this six genera were not statistically significant (P>0.05). Moreover, a cluster analysis revealed that the microbial composition of samples in the same group was often dissimilar but that the microbial composition observed in twins was usually similar. Although the genetic and environmental factors that strongly influence the microbial composition of dental caries remains unknown, we speculate that genetic factors primarily influence the individual's susceptibility to dental caries and that environmental factors primarily regulate the microbial composition of the dental plaque and the progression to caries. By using improved twins models and increased sample sizes, our study can be extended to analyze the specific genetic and environmental factors that affect the development of caries.
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Opal S, Garg S, Jain J, Walia I. Genetic factors affecting dental caries risk. Aust Dent J 2015; 60:2-11. [DOI: 10.1111/adj.12262] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/29/2022]
Affiliation(s)
- S Opal
- Department of Pediatric and Preventive Dentistry; BRS Dental College; Panchkula Haryana India
| | - S Garg
- Department of Pediatric and Preventive Dentistry; Maharishi Markandeshwar College of Dental Sciences and Research, Mullana; Ambala Haryana India
| | - J Jain
- Department of Conservative Dentistry and Endodontics; Maharishi Markandeshwar College of Dental Sciences and Research, Mullana; Ambala Haryana India
| | - I Walia
- Department of Oral Medicine and Radiology; BRS Dental College; Panchkula Haryana India
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Sampaio-Maia B, Monteiro-Silva F. Acquisition and maturation of oral microbiome throughout childhood: An update. Dent Res J (Isfahan) 2014; 11:291-301. [PMID: 25097637 PMCID: PMC4119360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Traditional microbiology concepts are being renewed since the development of new microbiological technologies, such as, sequencing and large-scale genome analysis. Since the entry into the new millennium, a lot of new information has emerged regarding the oral microbiome. This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. Throughout childhood, the oral microbial load increases, but the microbial diversity decreases. The initial colonizers are related to the type of delivery, personal relationships, and living environment. These first colonizers seem to condition the subsequent colonization, which will lead to more complex and stable ecosystems in adulthood. These early oral microbial communities, therefore, play a major role in the development of the adult oral microbiota and may represent a source of both pathogenic and protective microorganisms in a very early stage of human life. The implications of this knowledge on the daily clinical practice of odontopediatrics are highlighted.
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Affiliation(s)
- Benedita Sampaio-Maia
- Department of Microbiology, Faculty of Dental Medicine, University of Porto, Porto, Portugal
| | - Filipa Monteiro-Silva
- Department of Microbiology, Faculty of Dental Medicine, University of Porto, Porto, Portugal
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Jiang W, Ling Z, Lin X, Chen Y, Zhang J, Yu J, Xiang C, Chen H. Pyrosequencing analysis of oral microbiota shifting in various caries states in childhood. MICROBIAL ECOLOGY 2014; 67:962-969. [PMID: 24504329 DOI: 10.1007/s00248-014-0372-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
Dental caries is one of the most prevalent childhood diseases worldwide, but little is known about the dynamic characteristics of oral microbiota in the development of dental caries. To investigate the shifting bacterial profiles in different caries states, 60 children (3-7-year-old) were enrolled in this study, including 30 caries-free subjects and 30 caries-active subjects. Supragingival plaques were collected from caries-active subjects on intact enamel, white spot lesions and carious dentin lesions. Plaques from caries-free subjects were used as a control. All samples were analyzed by 454 pyrosequencing based on 16S rRNA gene V1-V3 hypervariable regions. A total of 572,773 pyrosequencing reads passed the quality control and 25,444 unique phylotypes were identified, which represented 18 phyla and 145 genera. Reduced bacterial diversity in the cavitated dentin was observed as compared with the other groups. Thirteen genera (including Capnocytophaga, Fusobacterium, Porphyromonas, Abiotrophia, Comamonas, Tannerella, Eikenella, Paludibacter, Treponema, Actinobaculum, Stenotrophomonas, Aestuariimicrobium, and Peptococcus) were found to be associated with dental health, and the bacterial profiles differed considerably depending on caries status. Eight genera (including Cryptobacterium, Lactobacillus, Megasphaera, Olsenella, Scardovia, Shuttleworthia, Cryptobacterium, and Streptococcus) were increased significantly in cavitated dentin lesions, and Actinomyces and Corynebacterium were present at significant high levels in white spot lesions (P < 0.05), while Flavobacterium, Neisseria, Bergeyella, and Derxia were enriched in the intact surfaces of caries individuals (P < 0.05). Our results showed that oral bacteria were specific at different stages of caries progression, which contributes to informing the prevention and treatment of childhood dental caries.
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Affiliation(s)
- Wen Jiang
- Department of Conservative Dentistry and Periodontics, Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, No. 395 Yanan Road, Hangzhou, Zhejiang, 310006, China
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Du Q, Wang Y, Xu X, Li Y, Li M, Zou J, Zhou X. [Analysis of the oral microbiota in twin children]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2014; 32:182-185. [PMID: 24881216 PMCID: PMC7030792 DOI: 10.7518/hxkq.2014.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 12/20/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To analyze the differences between the oral microbiota of monozygotic and dizygotic twins by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). METHODS A total of 20 pairs of twin children were included in this study, in which 10 pairs were monozygotic (MZ) twins, and 10 pairs were dizygotic (DZ) twins. Of the 20 pairs, 10 pairs of twins had primary dentition, and 10 pairs had mixed dentition; 17 children had caries, and 23 children had no caries. Genomic DNA was extracted from saliva samples. The 16s rRNA was amplified and analyzed by PCR-DGGE. The PCR-DGGE band number and Shannon index were calculated. RESULTS Cluster analysis showed high similarity in the oral bacterial community seen in co-twins. However, no significant difference was seen between MZ and DZ twins. In the primary dentition, the PCR-DGGE band number and Shannon index of children with caries (11.00 +/- 1.56, 1.05 +/- 0.36) were lower than those of children without caries (14.00 +/- 2.74, 1.44 +/- 0.37) (P < 0.05). In mixed dentition, the PCR-DGGE band number and Shannon index of children with caries (11.88 +/- 4.05, 1.18 +/- 0.36) were lower than those of children without caries (14.31 +/- 5.71, 1.28 +/- 0.47), but the differences were not statistically significant (P > 0.05). CONCLUSION Environmental factors may have a stronger effect on the constitution of oral microbiota in children compared with genetic factors. Children without caries may have a richer microbial diversity compared with children with caries.
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Edlund A, Yang Y, Hall AP, Guo L, Lux R, He X, Nelson KE, Nealson KH, Yooseph S, Shi W, McLean JS. An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. MICROBIOME 2013; 1:25. [PMID: 24451062 PMCID: PMC3971625 DOI: 10.1186/2049-2618-1-25] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/17/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level. RESULTS Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories. CONCLUSIONS Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms.
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Affiliation(s)
- Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Youngik Yang
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Adam P Hall
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Lihong Guo
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Renate Lux
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Xuesong He
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Karen E Nelson
- Department of Human Genomic Medicine, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kenneth H Nealson
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
- Department of Earth Sciences, USC, ZHS 117, Los Angeles, CA 90089, USA
| | - Shibu Yooseph
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Wenyuan Shi
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Jeffrey S McLean
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
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Li J, Nasidze I, Quinque D, Li M, Horz HP, André C, Garriga RM, Halbwax M, Fischer A, Stoneking M. The saliva microbiome of Pan and Homo. BMC Microbiol 2013; 13:204. [PMID: 24025115 PMCID: PMC3848470 DOI: 10.1186/1471-2180-13-204] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 09/09/2013] [Indexed: 12/19/2022] Open
Abstract
Background It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors. Results To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals. Conclusions The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild.
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Affiliation(s)
- Jing Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D-04103, Germany.
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Peterson SN, Snesrud E, Liu J, Ong AC, Kilian M, Schork NJ, Bretz W. The dental plaque microbiome in health and disease. PLoS One 2013; 8:e58487. [PMID: 23520516 PMCID: PMC3592792 DOI: 10.1371/journal.pone.0058487] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/05/2013] [Indexed: 12/21/2022] Open
Abstract
Dental decay is one of the most prevalent chronic diseases worldwide. A variety of factors, including microbial, genetic, immunological, behavioral and environmental, interact to contribute to dental caries onset and development. Previous studies focused on the microbial basis for dental caries have identified species associated with both dental health and disease. The purpose of the current study was to improve our knowledge of the microbial species involved in dental caries and health by performing a comprehensive 16S rDNA profiling of the dental plaque microbiome of both caries-free and caries-active subjects. Analysis of over 50,000 nearly full-length 16S rDNA clones allowed the identification of 1,372 operational taxonomic units (OTUs) in the dental plaque microbiome. Approximately half of the OTUs were common to both caries-free and caries-active microbiomes and present at similar abundance. The majority of differences in OTU's reflected very low abundance phylotypes. This survey allowed us to define the population structure of the dental plaque microbiome and to identify the microbial signatures associated with dental health and disease. The deep profiling of dental plaque allowed the identification of 87 phylotypes that are over-represented in either caries-free or caries-active subjects. Among these signatures, those associated with dental health outnumbered those associated with dental caries by nearly two-fold. A comparison of this data to other published studies indicate significant heterogeneity in study outcomes and suggest that novel approaches may be required to further define the signatures of dental caries onset and progression.
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Affiliation(s)
- Scott N Peterson
- J. Craig Venter Institute, Rockville, Maryland, United States of America.
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Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res 2012; 22:2146-52. [PMID: 23064750 PMCID: PMC3483544 DOI: 10.1101/gr.140608.112] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/24/2012] [Indexed: 01/05/2023]
Abstract
Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We examined the salivary microbiome in up to three time-points during 10 yr spanning adolescence, and determined the influence of human genotype, gender, age, and weight class. Participants, including 27 monozygotic and 18 dizygotic twin pairs, were sampled mainly at ages 12-13, 17-18, and 22-24, with a few sampled as early as 8 yr of age. In contrast to gut or skin microbiomes, there is a core genus-level salivary microbiome. Individuals are more similar to themselves and their co-twins in the 12-17 and in the 17-22 cohorts than to the whole sample population, but not over the 10 yr from 12 to 22; and monozygotic twin pairs are statistically not more similar than dizygotic twin pairs. The data are most consistent with shared environment serving as the main determinant of microbial populations. Twins resemble each other more closely than the whole population at all time-points, but become less similar to each other when they age and no longer cohabit. Several organisms have age-specific abundance profiles, including members of the genera Veillonella, Actinomyces, and Streptococcus. There is no clear effect of weight class and gender. The results of this work will provide a basis to further study oral microbes and human health.
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Affiliation(s)
- Simone S. Stahringer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Jose C. Clemente
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Robin P. Corley
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309, USA
| | - John Hewitt
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309, USA
| | - Dan Knights
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
| | - William A. Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Kenneth S. Krauter
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309, USA
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Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis. PLoS One 2012; 7:e47722. [PMID: 23091642 PMCID: PMC3472979 DOI: 10.1371/journal.pone.0047722] [Citation(s) in RCA: 326] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/14/2012] [Indexed: 11/19/2022] Open
Abstract
Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have implications for bacterial community resilience and the restoration of oral health.
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Bretz WA, Biesbrock A, Corby PM, Corby AL, Bretz WG, Wessel J, Schork NJ. Environmental and genetic contributions to indicators of oral malodor in twins. Twin Res Hum Genet 2012; 14:568-72. [PMID: 22506313 DOI: 10.1375/twin.14.6.568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study aimed to: (1) determine concordance rates of self-reported and subjectively determined indicators of oral malodor in twins; (2) determine the relative contributions of genetic and environmental factors to levels of volatile sulfur compounds (VSCs) in intraoral and exhaled breath. Fifty-one twin pairs participated in the study. Measurements of VSCs were obtained by a halimeter. The presence of tongue coatings was determined and twins filled out a 32-item questionnaire on oral malodor indicators independently of one another. Estimates of heritability (h2) for halimeter measurements were computed by SOLAR. The concordance rates for the presence of tongue coating among identical and fraternal twins were 67% and 11%, respectively. In the 10 most informative items, 70% exhibited higher concordance rates for identical than for fraternal twins. Of particular interest were the differences in concordance rates for dry mouth, sinus infection and unusual sweating. The h2 for intraoral breath was 0.28 +/- 0.17 (NS), whereas the h2 for exhaled breath was 0.50 +/- 0.20 (p = .0207). The concordance rates of tongue coatings and malodor indicators were higher in identical twins than in fraternal twins. Intraoral breath VSC values were primarily attributable to environmental factors, whereas exhaled breath VSC values were partially explained by genetic factors.
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Affiliation(s)
- Walter A Bretz
- New York University College of Dentistry, 345 East 24th Street, Room 1005, New York, NY 10010, USA.
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Bockmann MR, Harris AV, Bennett CN, Odeh R, Hughes TE, Townsend GC. Timing of colonization of caries-producing bacteria: an approach based on studying monozygotic twin pairs. Int J Dent 2011; 2011:571573. [PMID: 22028714 PMCID: PMC3199088 DOI: 10.1155/2011/571573] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/10/2011] [Indexed: 11/23/2022] Open
Abstract
Findings are presented from a prospective cohort study of timing of primary tooth emergence and timing of oral colonization of Streptococcus mutans (S. mutans) in Australian twins. The paper focuses on differences in colonization timing in genetically identical monozygotic (MZ) twins. Timing of tooth emergence was based on parental report. Colonization timing of S. mutans were established by plating samples of plaque and saliva on selective media at 3 monthly intervals and assessing colony morphology. In 25% of individuals colonization occurred prior to emergence of the first tooth. A significant proportion of MZ pairs (21%) was discordant for colonization occurring before or after first tooth emergence, suggesting a role of environmental or epigenetic factors in timing of tooth emergence, colonization by S. mutans, or both. These findings and further application of the MZ co-twin model should assist in development of strategies to prevent or delay infection with S. mutans in children.
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Affiliation(s)
- Michelle R. Bockmann
- Craniofacial Biology Research Group, School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
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Papapostolou A, Kroffke B, Tatakis DN, Nagaraja HN, Kumar PS. Contribution of host genotype to the composition of health-associated supragingival and subgingival microbiomes. J Clin Periodontol 2011; 38:517-24. [PMID: 21488931 DOI: 10.1111/j.1600-051x.2011.01718.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AIM Periodontitis and caries are two of the most prevalent diseases to affect humans, however; the individual susceptibility to these diseases varies significantly in the population. The aim of this investigation, therefore, was to examine the influence of host genotype on the composition of health-associated supragingival and subgingival microbiomes. MATERIALS AND METHODS Subgingival and supragingival plaque was collected from orally and systemically healthy adult monozygotic and dizygotic twin pairs. Zygosity was determined by multiplexed PCR amplification of 13 short tandem repeats. Terminal restriction fragment length polymorphism was used for bacterial community profiling. The number of species shared by the twin pairs as well as the similarity of the microbial communities between the twins was computed and compared using two-sample t-test RESULTS There was no difference in the number of species shared by the twin pairs as well as the similarity of the microbial communities between the twin dyads. Age was not a modifier of genetic influence on these microbial parameters. There was no difference between monozygotic and dizygotic twin pairs in the correlation between supragingival and subgingival community similarity. CONCLUSION The contributory role of host genotype, if any, is not apparent on an established, health-associated oral microbial community.
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Affiliation(s)
- Anastasia Papapostolou
- Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
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Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJF. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics 2011; 4:22. [PMID: 21371338 PMCID: PMC3058002 DOI: 10.1186/1755-8794-4-22] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 03/04/2011] [Indexed: 11/16/2022] Open
Abstract
Background An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays. Results Pyrosequencing reads (126174 reads, 1045 unique sequences) represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae) than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus Prevotella), Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age. Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93) probes per individual sample. A caries-free oral status significantly associated with the higher signal of the probes targeting Porphyromonas catoniae and Neisseria flavescens. Conclusions The potential role of P. catoniae and N. flavescens as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.
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Affiliation(s)
- Wim Crielaard
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Utrechtseweg 48, Zeist, the Netherlands
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Abstract
Previous studies have confirmed the association of the acid producers Streptococcus mutans and Lactobacillus spp. with childhood caries, but they also suggested these microorganisms are not sufficient to explain all cases of caries. In addition, health-associated bacterial community profiles are not well understood, including the importance of base production and acid catabolism in pH homeostasis. The bacterial community composition in health and in severe caries of the young permanent dentition was compared using Sanger sequencing of the ribosomal 16S rRNA genes. Lactobacillus species were dominant in severe caries, and levels rose significantly as caries progressed from initial to deep lesions. S. mutans was often observed at high levels in the early stages of caries but also in some healthy subjects and was not statistically significantly associated with caries progression in the overall model. Lactobacillus or S. mutans was found either at low levels or not present in several samples. Other potential acid producers observed at high levels in these subjects included strains of Selenomonas, Neisseria, and Streptococcus mitis. Propionibacterium FMA5 was significantly associated with caries progression but was not found at high levels. An overall loss of community diversity occurred as caries progressed, and species that significantly decreased included the Streptococcus mitis-S. pneumoniae-S. infantis group, Corynebacterium matruchotii, Streptococcus gordonii, Streptococcus cristatus, Capnocytophaga gingivalis, Eubacterium IR009, Campylobacter rectus, and Lachnospiraceae sp. C1. The relationship of acid-base metabolism to 16S rRNA gene-based species assignments appears to be complex, and metagenomic approaches that would allow functional profiling of entire genomes will be helpful in elucidating the microbial pathogenesis of caries.
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Abstract
The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
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Nasidze I, Li J, Quinque D, Tang K, Stoneking M. Global diversity in the human salivary microbiome. Genome Res 2009; 19:636-43. [PMID: 19251737 DOI: 10.1101/gr.084616.108] [Citation(s) in RCA: 309] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The human salivary microbiome may play a role in diseases of the oral cavity and interact with microbiomes from other parts of the human body (in particular, the intestinal tract), but little is known about normal variation in the salivary microbiome. We analyzed 14,115 partial ( approximately 500 bp) 16S ribosomal RNA (rRNA) sequences from saliva samples from 120 healthy individuals (10 individuals from each of 12 worldwide locations). These sequences could be assigned to 101 known bacterial genera, of which 39 were not previously reported from the human oral cavity; phylogenetic analysis suggests that an additional 64 unknown genera are present. There is high diversity in the salivary microbiome within and between individuals, but little geographic structure. Overall, approximately 13.5% of the total variance in the composition of genera is due to differences among individuals, which is remarkably similar to the fraction of the total variance in neutral genetic markers that can be attributed to differences among human populations. Investigation of some environmental variables revealed a significant association between the genetic distances among locations and the distance of each location from the equator. Further characterization of the enormous diversity revealed here in the human salivary microbiome will aid in elucidating the role it plays in human health and disease, and in the identification of potentially informative species for studies of human population history.
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Affiliation(s)
- Ivan Nasidze
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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