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Gregorczyk-Maga I, Fiema M, Kania M, Jachowicz-Matczak E, Romaniszyn D, Gerreth K, Klupa T, Wójkowska-Mach J. Oral Microbiota-One Habitat or Diverse Niches? A Pilot Study of Sampling and Identification of Oral Bacterial and Fungal Biota in Patients with Type I Diabetes Mellitus Treated with Insulin Pump. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2252. [PMID: 36767617 PMCID: PMC9914992 DOI: 10.3390/ijerph20032252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE The oral microbiota is a very complex and dynamic microbial ecosystem. Alterations of its balance can result in oral and systemic diseases. We aimed to characterize the microbiota in particular niches of the oral cavity in adult type 1 diabetes patients treated with continuous infusion of insulin with insulin pump (IP). In addition, we aimed to determine optimal sites of oral microbiota sampling in studies of large research groups of patients with DM I. DESIGN In this pilot study, we sampled the buccal and soft palate mucosa, tongue, palatal and buccal dental surfaces and gingival pockets of adult DM I patients treated with IP. RESULTS In total, 23 patients were recruited. The oral microbiota was dominated by Streptococus and Neisseria, with a low incidence of cariogenic S. mutans and Lactobacillus, as well as periodontal pathogens such as Prevotella. There were significant differences in overall CFU counts of all strains, Gram-positive, Staphylococci, Streptococci and S. oralis strains between mucosal and dental surface sites. The overall CFU counts of all strains and Gram-positive strains were higher in dental sites vs. mucosal sites (both p < 0.001). CFU counts of S. oralis were significantly higher in dental sites vs. gingival pocket sites (p = 0.013). Candida species were rare. The mucosal sites on the buccae presented lower diversity and bacterial counts. CONCLUSIONS In the study group of adult DM I patients treated with IP, the microbiota in particular niches of the oral cavity was significantly different. Three distinct and optimally appropriate sampling sites for oral microflora were identified: buccal and palatal mucosa, dental surface and gingival pockets. The results of this study may be the basis for further studies of large groups of patients with DM I.
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Affiliation(s)
- Iwona Gregorczyk-Maga
- Institute of Dentistry, Faculty of Medicine, Jagiellonian University Medical College, 31-155 Krakow, Poland
| | - Mateusz Fiema
- Department of Endocrinology, University Hospital, 30-688 Krakow, Poland
| | - Michal Kania
- Doctoral School of Medicine and Health Sciences, Jagiellonian University Medical College, 31-008 Krakow, Poland
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Estera Jachowicz-Matczak
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Dorota Romaniszyn
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Karolina Gerreth
- Department of Risk Group Dentistry, Chair of Pediatric Dentistry, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Tomasz Klupa
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Jadwiga Wójkowska-Mach
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
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2
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Butcher MC, Short B, Veena CLR, Bradshaw D, Pratten JR, McLean W, Shaban SMA, Ramage G, Delaney C. Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes. APMIS 2022; 130:763-777. [PMID: 36050830 PMCID: PMC9825849 DOI: 10.1111/apm.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/22/2022] [Indexed: 01/11/2023]
Abstract
As one of the most prevalent infective diseases worldwide, it is crucial that we not only know the constituents of the oral microbiome in dental caries but also understand its functionality. Herein, we present a reproducible meta-analysis to effectively report the key components and the associated functional signature of the oral microbiome in dental caries. Publicly available sequencing data were downloaded from online repositories and subjected to a standardized analysis pipeline before analysis. Meta-analyses identified significant differences in alpha and beta diversities of carious microbiomes when compared to healthy ones. Additionally, machine learning and receiver operator characteristic analysis showed an ability to discriminate between healthy and disease microbiomes. We identified from importance values, as derived from random forest analyses, a group of genera, notably containing Selenomonas, Aggregatibacter, Actinomyces and Treponema, which can be predictive of dental caries. Finally, we propose the most appropriate study design for investigating the microbiome of dental caries by synthesizing the studies, which had the most accurate differentiation based on random forest modelling. In conclusion, we have developed a non-biased, reproducible pipeline, which can be applied to microbiome meta-analyses of multiple diseases, but importantly we have derived from our meta-analysis a key group of organisms that can be used to identify individuals at risk of developing dental caries based on oral microbiome inhabitants.
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Affiliation(s)
- Mark C. Butcher
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Bryn Short
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Chandra Lekha Ramalingam Veena
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | | | | | - William McLean
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Suror Mohamad Ahmad Shaban
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Christopher Delaney
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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3
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Chatterjee S, Damle SG, Iyer N. A study on genetic and mutans streptococcal transmissibility of dental caries. J Oral Maxillofac Pathol 2022; 26:604. [PMID: 37082046 PMCID: PMC10112085 DOI: 10.4103/jomfp.jomfp_201_22] [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: 05/08/2022] [Revised: 06/10/2022] [Accepted: 07/06/2022] [Indexed: 04/22/2023] Open
Abstract
Background Dental caries is characterized by an interplay between environmental and genetic factors. Aim The aim of this study was to analyse the transmissibilities of high caries risk chromosomal loci at 5q 12.1-13.3 and low caries risk chromosomal loci at 13q31.1 and Streptococcus mutans (S. mutans) in family units. Materials This prospective cohort study was performed on 56 families grouped into four: (a) Group I: 18 families of children with caries affected primary teeth; (b) Group II: 21 families of children with caries in permanent teeth; (c) Group III: 6 families of children with no caries in primary teeth and (d) Group IV: 12 families of children with no caries in permanent teeth. Blood, saliva and plaque samples were collected from consenting study participants. Isolated DNAs were subjected to polymerase chain reactions using suitable primers. Data collected was analysed with ANOVA and Chi-squared test. Results Wide expression of chromosome loci 5q12.1-13.3 was obtained in both blood and saliva samples. For chromosome loci 13q31.1, no expression was found in saliva samples, hence indicating its local absence. For the GtfB expression, transmissibility was common for a single band expressing S. mutans. Conclusion This study reflects upon newer findings in the field of genetic research on dental caries.
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Affiliation(s)
- Shailja Chatterjee
- Department of Oral and Maxillofacial Pathology, Yamuna Institute of Dental Sciences and Research, Yamuna Nagar, Haryana, India
| | - Satyawan G. Damle
- Former Vice-chancellor, M. M. (Deemed to be) University, Mullana, Ambala, Haryana, India
| | - Nageshwar Iyer
- Former Principal, MM College of Dental Sciences and Research, M. M. (Deemed to be) University, Mullana, Ambala, Haryana, India
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4
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Dame-Teixeira N, de Lima AKA, Do T, Stefani CM. Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries. FRONTIERS IN ORAL HEALTH 2022; 2:770917. [PMID: 35048071 PMCID: PMC8757819 DOI: 10.3389/froh.2021.770917] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 02/01/2023] Open
Abstract
Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data. Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54–3.90); p = 0.01]. Conclusions:Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.
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Affiliation(s)
- Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brasilia, Brazil.,Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | | | - Thuy Do
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Cristine Miron Stefani
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brasilia, Brazil
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5
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Złoch M, Rodzik A, Pauter K, Szultka-Młyńska M, Rogowska A, Kupczyk W, Pomastowski P, Buszewski B. Problems with identifying and distinguishing salivary streptococci: a multi-instrumental approach. Future Microbiol 2021; 15:1157-1171. [PMID: 32954849 DOI: 10.2217/fmb-2020-0036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: The purpose of this study was to create an alternative protocol for the DNA-based identification of salivary microbiota focused on the distinguishing of Streptococcus species. Materials & methods: Salivary bacteria were identified using 16S rDNA sequencing and proteins and lipids profiling using MALDI-TOF/MS as well as FTIR analysis. Results: Most of the isolates belonged to streptococci - mostly the salivarious group indistinguishable by the molecular technique. In turn, MALDI analysis allowed for their fast and reliable classification. Although FTIR spectroscopy demonstrated the correct species classification, the spectra interpretation was time consuming and complicated. Conclusion: MALDI-TOF/MS demonstrated the biggest effectiveness in the identification and discrimination between the salivary streptococci, which could be easily incorporated in the workflow of routine microbiological laboratories.
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Affiliation(s)
- Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland
| | - Agnieszka Rodzik
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Katarzyna Pauter
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Agnieszka Rogowska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland.,Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological & Oncological Surgery, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland.,Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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6
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Zaura E, Pappalardo VY, Buijs MJ, Volgenant CMC, Brandt BW. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. Periodontol 2000 2021; 85:210-236. [PMID: 33226702 PMCID: PMC7756869 DOI: 10.1111/prd.12359] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided.
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Affiliation(s)
- Egija Zaura
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Vincent Y. Pappalardo
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Mark J. Buijs
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Catherine M. C. Volgenant
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Bernd W. Brandt
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
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7
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Low levels of salivary metals, oral microbiome composition and dental decay. Sci Rep 2020; 10:14640. [PMID: 32887894 PMCID: PMC7474081 DOI: 10.1038/s41598-020-71495-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Salivary microbiome composition can change following exposure to environmental toxicants, e.g., heavy metals. We hypothesized that levels of salivary nutrients and metals would correlate with salivary microbiome composition and be associated with dental decay. Here we assess the salivary concentrations of 5 essential minerals (cobalt, copper, manganese, molybdenum, and zinc), 4 metals with some evidence of normal physiological function (chromium, nickel, tungsten, and vanadium), and 12 with known toxicity (antimony, arsenic, barium, beryllium, cadmium, cesium, lead, mercury, platinum, thallium, tin, and uranium), and their associations with salivary microbiome composition and dental decay in 61 children and adults. 16 metals were detected in 54% of participants; 8 were found in all. Marked differences in salivary bacterial taxa were associated with levels of antimony, arsenic, and mercury, after adjusting for multiple testing. Further, antimony levels were associated with the presence of decayed teeth. Thus, salivary metal levels, even at low concentrations, may impact oral health.
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8
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Ramadugu K, Bhaumik D, Luo T, Gicquelais RE, Lee KH, Stafford EB, Marrs CF, Neiswanger K, McNeil DW, Marazita ML, Foxman B. Maternal Oral Health Influences Infant Salivary Microbiome. J Dent Res 2020; 100:58-65. [PMID: 32859139 DOI: 10.1177/0022034520947665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Oral microbiomes vary in cariogenic potential; these differences may be established early in life. A major concern is whether mothers transmit cariogenic bacteria to their children. Here we characterize early salivary microbiome development and the potential associations of that development with route of delivery, breastfeeding, and mother's oral health, and we evaluate transmission of microbes between mother and child. We analyzed saliva and metadata from the Center for Oral Health Research in Appalachia. For this cohort study, we sequenced the V6 region of the 16S rRNA gene and used quantitative polymerase chain reaction to detect Streptococcus mitis, Streptococcus sobrinus, Streptococcus mutans, Streptococcus oralis, and Candida albicans in the saliva from mothers and their infants, collected at 2, 9, and 12 mo (Pennsylvania site) and 2, 12, and 24 mo (West Virginia site). Breastfed children had lower relative abundances of Prevotella and Veillonella. If mothers had decayed, missing, or filled teeth, children had greater abundances of Veillonella and Actinomyces. There was little evidence of maternal transmission of selected microbes. At 12 mo, children's microbiomes were more similar to other children's than to their mothers'. Infants' salivary microbiomes became more adult-like with age but still differed with mothers' microbiomes at 12 mo. There was little evidence supporting transmission of selected microbes from mothers to children, but risk of colonization was associated with tooth emergence. Children are likely to acquire cariogenic bacteria from a variety of sources, including foods and contact with other children and adults.
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Affiliation(s)
- K Ramadugu
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - D Bhaumik
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - T Luo
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - R E Gicquelais
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - K H Lee
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - E B Stafford
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - C F Marrs
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - K Neiswanger
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - D W McNeil
- Center for Oral Health Research in Appalachia, Department of Psychology, Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - B Foxman
- Center of Molecular and Clinical Epidemiology of Infectious Diseases, Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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9
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Uchida-Fukuhara Y, Ekuni D, Islam MM, Kataoka K, Taniguchi-Tabata A, Fukuhara D, Toyama N, Kobayashi T, Fujimori K, Sawada N, Iwasaki Y, Morita M. Caries Increment and Salivary Microbiome during University Life: A Prospective Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103713. [PMID: 32466124 PMCID: PMC7277743 DOI: 10.3390/ijerph17103713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022]
Abstract
The purpose of this 3-year prospective cohort study was to explore the relationship between an increase in dental caries and oral microbiome among Japanese university students. We analyzed 487 students who volunteered to receive oral examinations and answer baseline (2013) and follow-up (2016) questionnaires. Of these students, salivary samples were randomly collected from 55 students at follow-up and analyzed using next-generation sequencing. Students were divided into two groups: increased group (Δdecayed, missing, and filled teeth (ΔDMFT) score increased during the 3-year period) and non-increased group (ΔDMFT did not increase). Thirteen phyla, 21 classes, 32 orders, 48 families, 72 genera, and 156 species were identified. Microbial diversity in the increased group (n = 14) was similar to that in the non-increased group (n = 41). Relative abundances of the family Prevotellaceae (p = 0.007) and genera Alloprevotella (p = 0.007) and Dialister (p = 0.039) were enriched in the increased group compared with the non-increased group. Some bacterial taxonomic clades were differentially present between the two groups. These results may contribute to the development of new dental caries prevention strategies, including the development of detection kits and enlightenment activities for these bacteria.
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Affiliation(s)
- Yoko Uchida-Fukuhara
- Department of Preventive Dentistry, Okayama University Hospital, Okayama 700-8558, Japan; (A.T.-T.); (D.F.)
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
- Correspondence: ; Tel.: +81-86-235-6712
| | - Daisuke Ekuni
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Md Monirul Islam
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Kota Kataoka
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan;
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Ayano Taniguchi-Tabata
- Department of Preventive Dentistry, Okayama University Hospital, Okayama 700-8558, Japan; (A.T.-T.); (D.F.)
| | - Daiki Fukuhara
- Department of Preventive Dentistry, Okayama University Hospital, Okayama 700-8558, Japan; (A.T.-T.); (D.F.)
| | - Naoki Toyama
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Terumasa Kobayashi
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Kohei Fujimori
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Nanami Sawada
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
| | - Yoshiaki Iwasaki
- Health Service Center, Okayama University, Okayama 700-8530, Japan;
| | - Manabu Morita
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (D.E.); (M.M.I.); (N.T.); (T.K.); (K.F.); (N.S.); (M.M.)
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10
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Hurley E, Mullins D, Barrett MP, O'Shea CA, Kinirons M, Ryan CA, Stanton C, Whelton H, Harris HMB, O'Toole PW. The microbiota of the mother at birth and its influence on the emerging infant oral microbiota from birth to 1 year of age: a cohort study. J Oral Microbiol 2019; 11:1599652. [PMID: 32128038 PMCID: PMC7034431 DOI: 10.1080/20002297.2019.1599652] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/12/2019] [Accepted: 03/22/2019] [Indexed: 01/11/2023] Open
Abstract
Background: The acquisition of microbial communities and the influence of delivery mode on the oral microbiota of the newborn infant remains poorly characterised. Methods: A cohort of pregnant women were enrolled in the study (n = 84). All infants were born full term, by Spontaneous vaginal delivery (SVD) or by Caesarean section (CS). At delivery a saliva sample along with a vaginal/skin sample from the mother. Saliva samples were the taken from the infant within one week of birth, and at week 4, week 8, 6 months and 1 year of age. We used high-throughput sequencing of V4-V5 region 16S rRNA amplicons to compare the microbiota of all samples. Results: The vaginal microbiota had a lower alpha diversity than the skin microbiota of the mother, while the infant oral microbiota diversity remained relatively stable from birth to 8 weeks of age. The oral microbiota of the neonate differed by birth modality up to 1 week of age (p < 0.05), but birth modality did not have any influence on the infant oral microbiota beyond this age. Conclusions: We conclude thatbirth mode does not have an effect on the infant oral microbiota beyond 4 weeks of age, and the oral microbiota of infants continues to develop until 1 year of age.
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Affiliation(s)
- Eimear Hurley
- School of Microbiology, University College Cork, Cork, Ireland.,Cork University Dental School & Hospital, Cork University Hospital, Wilton, Cork, Ireland
| | - David Mullins
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Maurice P Barrett
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Carol Anne O'Shea
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | - Martin Kinirons
- Cork University Dental School & Hospital, Cork University Hospital, Wilton, Cork, Ireland
| | - C Anthony Ryan
- Department of Neonatology, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | | | - Helen Whelton
- Cork University Dental School & Hospital, Cork University Hospital, Wilton, Cork, Ireland.,College of Medicine and Health, UCC, Cork, Ireland
| | - Hugh M B Harris
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
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11
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Štšepetova J, Truu J, Runnel R, Nõmmela R, Saag M, Olak J, Nõlvak H, Preem JK, Oopkaup K, Krjutškov K, Honkala E, Honkala S, Mäkinen K, Mäkinen PL, Vahlberg T, Vermeiren J, Bosscher D, de Cock P, Mändar R. Impact of polyols on Oral microbiome of Estonian schoolchildren. BMC Oral Health 2019; 19:60. [PMID: 30999906 PMCID: PMC6471963 DOI: 10.1186/s12903-019-0747-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/26/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Oral microbiome has significant impact on both oral and general health. Polyols have been promoted as sugar substitutes in prevention of oral diseases. We aimed to reveal the effect of candies containing erythritol, xylitol or control (sorbitol) on salivary microbiome. METHODS Ninety children (11.3 ± 0.6 years) consumed candies during 3 years. Microbial communities were profiled using Illumina HiSeq 2000 sequencing and real-time PCR. RESULTS The dominant phyla in saliva were Firmicutes (39.1%), Proteobacteria (26.1%), Bacteroidetes (14.7%), Actinobacteria (12%) and Fusobacteria (6%). The microbiome of erythritol group significantly differed from that of the other groups. Both erythritol and xylitol reduced the number of observed bacterial phylotypes in comparison to the control group. The relative abundance of the genera Veillonella, Streptococcus and Fusobacterium were higher while that of Bergeyella lower after erythritol intervention when comparing with control. The lowest prevalence of caries-related mutans streptococci corresponded with the lowest clinical caries markers in the erythritol group. CONCLUSIONS Daily consumption of erythritol, xylitol or control candies has a specific influence on the salivary microbiome composition in schoolchildren. Erythritol is associated with the lowest prevalence of caries-related mutans streptococci and the lowest levels of clinical caries experience. TRIAL REGISTRATION ClinicalTrials.gov Identifier NCT01062633.
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Affiliation(s)
- Jelena Štšepetova
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Jaak Truu
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Riina Runnel
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Rita Nõmmela
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Mare Saag
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Jana Olak
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Hiie Nõlvak
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Jens-Konrad Preem
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Kristjan Oopkaup
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | | | - Eino Honkala
- Institute of Clinical Dentistry, University of Tromso, Tromso, Norway
| | - Sisko Honkala
- Institute of Clinical Dentistry, University of Tromso, Tromso, Norway
| | - Kauko Mäkinen
- Institute of Dentistry, University of Turku, Turku, Finland
| | | | - Tero Vahlberg
- Faculty of Medicine, University of Turku, Turku, Finland
| | | | | | | | - Reet Mändar
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
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12
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Mervish NA, Hu J, Hagan LA, Arora M, Frau C, Choi J, Attaie A, Ahmed M, Teitelbaum SL, Wolff MS. Associations of the Oral Microbiota with Obesity and Menarche in Inner City Girls. JOURNAL OF CHILDHOOD OBESITY 2019; 4. [PMID: 31535093 DOI: 10.21767/2572-5394.100068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Objective Alterations of the oral microbiome have been associated with obesity, possibly based on inflammatory processes mediated by bacteria. Specific bacterial strains have been associated with obesity and periodontal disease. Little is known about the oral microbiome in children. Understanding the relationship between oral health and childhood growth could help identify preventable factors contributing to obesity and related conditions, including onset of menarche which is associated with obesity. Methods In this pilot study, we investigated the saliva microbiome among 25 girls 7-15 years old (mean 11.1) and their mothers in an inner city dental clinic in New York City. The main outcome measures were body size, presence or absence of menarche and dental practices. We examined associations of microbiome richness, diversity, and relative abundance with pubertal and demographic factors and oral health. Results Girls had good dental health and a typical rich oral microbiome, based on the Shannon Index of all species detected. Older girls flossed more often and younger girls had more frequent dental check-ups. Microbiome richness among girls was similar to their mothers', but diversity was greater among mothers than girls. Richness was reduced among mothers with gum bleeding, flossing and increased teeth brushing. Overweight girls had greater diversity and less richness than normal weight girls. Certain bacterial species differed in abundance with respect to whether girls had reached menarche (Flavobacteria, Actinobacteria), overweight (Megasphaera, Lactorbacillales, Lactobacillus) and gingivitis in the girls (Scardovia, Bifidobacteriales, Gemellaceae). Conclusions Differences found in specific bacteria in the oral microbiome were related to body size and menarche. With increasing interest on studying microbiome variability related to the multifactorial etiology of obesity in children, saliva is capable of providing clinically informative markers of this and related conditions.
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Affiliation(s)
- Nancy A Mervish
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Loy A Hagan
- Department of Dentistry/Oral Maxillofacial Surgery, Otolaryngogoly and Surgery (Division of Plastic and Reconstructive Surgery), Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA.,Department of Dentistry/Oral Maxillofacial Surgery, Otolaryngogoly and Surgery (Division of Plastic and Reconstructive Surgery), Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Catalina Frau
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Julee Choi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Ali Attaie
- Department of Dentistry/Oral Maxillofacial Surgery, Otolaryngogoly and Surgery (Division of Plastic and Reconstructive Surgery), Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, USA.,Department Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Mairaj Ahmed
- Department of Dentistry/Oral Maxillofacial Surgery, Otolaryngogoly and Surgery (Division of Plastic and Reconstructive Surgery), Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
| | - Mary S Wolff
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, 1 Gustave L. Levy Place, New York, USA
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13
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Abstract
The microbiome is defined as the total of cellular microorganisms of baczerial, viral or e. g., parasite origin living on the surface of a body. Within the anatomical areas of otorhinolaryngology, a significant divergence and variance can be demonstrated. For ear, nose, throat, larynx and cutis different interactions of microbiome and common factors like age, diet and live style factors (e. g., smoking) have been detected in recent years. Besides, new insights hint at a passible pathognomic role of the microbiome towards diseases in the ENT area. This review article resumes the present findings of this rapidly devloping scientific area.
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Affiliation(s)
- Achim G Beule
- HNO-Uniklinik Münster.,Klinik und Poliklinik für Hals-Nasen-Ohrenkrankheiten der Universitätsmedizin Greifswald
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14
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Sarkar A, Stoneking M, Nandineni MR. Unraveling the human salivary microbiome diversity in Indian populations. PLoS One 2017; 12:e0184515. [PMID: 28886168 PMCID: PMC5590957 DOI: 10.1371/journal.pone.0184515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/27/2017] [Indexed: 12/21/2022] Open
Abstract
The importance of studying the salivary microbiome has been highlighted for its connection to health and disease and as a potential tool for supplementing human genetic diversity studies. While the salivary microbiome has been studied in various world populations, Indian populations have not been examined. We therefore analyzed microbiome diversity in saliva samples from 92 volunteers from eight different sampling locations in India by amplifying and sequencing variable regions (V1 and V2) of the bacterial 16S rRNA gene. The results showed immense bacterial richness in Indian populations; we identified 165 bacterial genera and 785 unique Operational Taxonomic Units (OTUs), with substantial sharing among the populations. There were small, but significant correlations in the abundance of bacterial genera in sampling locations from the same geographic region. Most of the core OTUs detected were also observed previously in other populations, but Solobacterium spp., Lachnoanaerobaculum spp. and Alloprevotella spp. were observed to be a component of the saliva microbiome unique to Indian populations. Importantly, nine bacterial genera were observed that were not listed in the Human Oral Microbiome Database (HOMD). These results highlight the importance of analyzing underrepresented populations like those of India.
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Affiliation(s)
- Anujit Sarkar
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana. India
- Graduate studies, Manipal University, Manipal. Karnataka, India
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana. India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana. India
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15
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Eriksson L, Lif Holgerson P, Johansson I. Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community. Sci Rep 2017; 7:5861. [PMID: 28724921 PMCID: PMC5517611 DOI: 10.1038/s41598-017-06221-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/08/2017] [Indexed: 12/16/2022] Open
Abstract
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates. Caries was scored at 17 and 19 years of age. Both sequencing platforms revealed that Firmicutes dominated in the saliva, whereas Firmicutes and Actinobacteria abundances were similar in tooth biofilm. Saliva microbiota discriminated caries-affected from caries-free adolescents, with enumeration of Scardovia wiggsiae, Streptococcus mutans, Bifidobacterium longum, Leptotrichia sp. HOT498, and Selenomonas spp. in caries-affected participants. Adolescents with B. longum in saliva had significantly higher 2-year caries increment. PacBio SMRT revealed Corynebacterium matruchotii as the most prevalent species in tooth biofilm. In conclusion, both sequencing methods were reliable and valid for oral samples, and saliva microbiota was associated with cross-sectional caries prevalence, especially S. wiggsiae, S. mutans, and B. longum; the latter also with the 2-year caries incidence.
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Affiliation(s)
- Linda Eriksson
- Department of Odontology, section of Cariology, Umeå University, Umeå, Sweden
- Department of Odontology,section of Pedodontics, Umeå University, Umeå, Sweden
| | | | - Ingegerd Johansson
- Department of Odontology, section of Cariology, Umeå University, Umeå, Sweden.
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16
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Foxman B, Seitz SM, Rothenberg R. Epidemiology and the microbiome. Ann Epidemiol 2016; 26:386-7. [PMID: 27180115 PMCID: PMC10519180 DOI: 10.1016/j.annepidem.2016.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/09/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Betsy Foxman
- Department of Epidemiology, University of Michigan, Ann Arbor.
| | | | - Richard Rothenberg
- Division of Epidemiology and Biostatistics, Georgia State University, Atlanta
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