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Lamont EI, Gadkari A, Kerns KA, To TT, Daubert D, Kotsakis G, Bor B, He X, McLean JS. Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. Mol Oral Microbiol 2020; 36:37-49. [PMID: 33174294 PMCID: PMC7984074 DOI: 10.1111/omi.12323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023]
Abstract
Developing a laboratory model of oral polymicrobial communities is essential for in vitro studies of the transition from healthy to diseased oral plaque. SHI medium is an enriched growth medium capable of supporting in vitro biofilms with similar diversity to healthy supragingival inocula; however, this medium does not maintain the diversity of gram‐negative bacteria more associated with subgingival plaque. Here, we systematically modified SHI medium components to investigate the impacts of varying nutrients and develop a medium capable of supporting a specific disease‐state subgingival community. A diseased subgingival plaque sample was inoculated in SHI medium with increasing concentrations of sucrose (0%, 0.1%, 0.5%), fetal bovine serum (FBS) (0%, 10%, 20%, 30%, 50%), and mucin (0.1, 2.5, 8.0 g/L) and grown for 48 hrs, then the 16S rRNA profiles of the resulting biofilms were examined. In total, these conditions were able to capture 89 of the 119 species and 43 of the 51 genera found in the subgingival inoculum. Interestingly, biofilms grown in high sucrose media, although dominated by acidogenic Firmicutes with a low final pH, contained several uncultured taxa from the genus Treponema, information that may aid culturing these periodontitis‐associated fastidious organisms. Biofilms grown in a modified medium (here named subSHI‐v1 medium) with 0.1% sucrose and 10% FBS had a high diversity closest to the inoculum and maintained greater proportions of many gram‐negative species of interest from the subgingival periodontal pocket (including members of the genera Prevotella and Treponema, and the Candidate Phyla Radiation phylum Saccharibacteria), and therefore best represented the disease community.
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Affiliation(s)
- Eleanor I Lamont
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Archita Gadkari
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | | | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Diane Daubert
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Georgios Kotsakis
- Department of Periodontics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, USA
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Lin W, Jiang W, Hu X, Gao L, Ai D, Pan H, Niu C, Yuan K, Zhou X, Xu C, Huang Z. Ecological Shifts of Supragingival Microbiota in Association with Pregnancy. Front Cell Infect Microbiol 2018; 8:24. [PMID: 29497601 PMCID: PMC5819318 DOI: 10.3389/fcimb.2018.00024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/18/2018] [Indexed: 02/05/2023] Open
Abstract
Pregnancy is a physiological process with pronounced hormonal fluctuations in females, and relatively little is known regarding how pregnancy influences the ecological shifts of supragingival microbiota. In this study, supragingival plaques and salivary hormones were collected from 11 pregnant women during pregnancy (P1, ≤14 weeks; P2, 20-25 weeks; P3, 33-37 weeks) and the postpartum period (P4, 6 weeks after childbirth). Seven non-pregnant volunteers were sampled at the same time intervals. The microbial genetic repertoire was obtained by 16S rDNA sequencing. Our results indicated that the Shannon diversity in P3 was significantly higher than in the non-pregnant group. The principal coordinates analysis showed distinct clustering according to gestational status, and the partial least squares discriminant analysis identified 33 genera that may contribute to this difference. There were differentially distributed genera, among which Neisseria, Porphyromonas, and Treponema were over-represented in the pregnant group, while Streptococcus and Veillonella were more abundant in the non-pregnant group. In addition, 53 operational taxonomic units were observed to have positive correlations with sex hormones in a redundancy analysis, with Prevotella spp. and Treponema spp. being most abundant. The ecological events suggest that pregnancy has a role in shaping an at-risk-for-harm microbiota and provide a basis for etiological studies of pregnancy-associated oral dysbiosis.
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Affiliation(s)
- Wenzhen Lin
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Wenxin Jiang
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Xuchen Hu
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Li Gao
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Dongmei Ai
- Department of Information and Computational Sciences, University of Science and Technology Beijing, Beijing, China
| | - Hongfei Pan
- Department of Information and Computational Sciences, University of Science and Technology Beijing, Beijing, China
| | - Chenguang Niu
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Keyong Yuan
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Changen Xu
- Obstetrics Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
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Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, Lawson F, Folawiyo O, Michailidi C, Dziedzic A, Thangavel R, Hadar T, Noordhuis MG, Westra W, Koch W, Sidransky D. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment. Oncotarget 2018; 7:51320-51334. [PMID: 27259999 PMCID: PMC5239478 DOI: 10.18632/oncotarget.9710] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022] Open
Abstract
Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection.The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella, with lower numbers of Citrobacter and Neisseraceae genus Kingella. HNSCC patients had a significant loss in richness and diversity of microbiota species (p<0.05) compared to the controls. Overall, the Operational Taxonomic Units network shows that the relative abundance of OTU's within genus Streptococcus, Dialister, and Veillonella can be used to discriminate tumor from control samples (p<0.05). Tumor samples lost Neisseria, Aggregatibacter (Proteobacteria), Haemophillus (Firmicutes) and Leptotrichia (Fusobacteria). Paired taxa within family Enterobacteriaceae, together with genus Oribacterium, distinguish OCSCC samples from OPSCC and normal samples (p<0.05). Similarly, only HPV positive samples have an abundance of genus Gemellaceae and Leuconostoc (p<0.05). Longitudinal analyses of samples taken before and after surgery, revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred (p<0.05). These results suggest that microbiota may be used as HNSCC diagnostic and prognostic biomonitors.
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Affiliation(s)
- Rafael Guerrero-Preston
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Filipa Godoy-Vitorino
- Natural Sciences Department, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Anne Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| | - Arnold Rodríguez-Hilario
- Natural Sciences Department, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Herminio González
- Natural Sciences Department, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Jessica Bondy
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fahcina Lawson
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Oluwasina Folawiyo
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christina Michailidi
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| | - Rajagowthamee Thangavel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tal Hadar
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maartje G Noordhuis
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Otorhinolaryngology-Head and Neck Surgery, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - William Westra
- Department of Pathology-Surgical Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wayne Koch
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Visser M, Ellen R. New insights into the emerging role of oral spirochaetes in periodontal disease. Clin Microbiol Infect 2011; 17:502-12. [DOI: 10.1111/j.1469-0691.2011.03460.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
OBJECTIVES The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the human oral cavity. In this mini-review, we describe the impact of these culture-independent approaches on our knowledge of the ecology of the human oral cavity and provide directions for future studies that should emphasize the role of specific strains, species and groups of microbes in periodontal disease. MATERIALS AND METHODS Recent findings are summarized to elucidate the relationship between periodontal disease and human oral microbiota, including as-yet-to-be-cultured organisms. RESULTS The real-time polymerase chain reaction (PCR) method was developed to detect and quantify periodontopathic bacteria, such as Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis (formerly Bacteroides forsythus) and Treponema denticola. The checkerboard DNA-DNA hybridization technique allowed enumeration of large numbers of species in very large numbers of samples. 16S rRNA gene clone library analysis revealed the diversity of human oral microbiota and the existence of as-yet-to-be-cultured organisms that are presumed periodontal pathogens. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was applied for assessment of diversity of human oral microbiota. CONCLUSION Culture-independent approaches are useful for studying the microbial ecology in the human oral cavity and should be useful in the future to elucidate the etiology of periodontal disease.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan.
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Sakamoto M, Huang Y, Umeda M, Ishikawa I, Benno Y. Detection of novel oral phylotypes associated with periodontitis. FEMS Microbiol Lett 2002; 217:65-9. [PMID: 12445647 DOI: 10.1111/j.1574-6968.2002.tb11457.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A phylogenetic approach based on 16S rRNA (rDNA) has been recently applied to investigate the diversity of cultivable and uncultivable species in the human oral cavity without cultivation. In a previous study [Sakamoto et al. (2000) Microbiol. Immunol. 44, 643-652], we identified a number of novel oral phylotypes, representing as yet uncultured organisms. The purpose of this study was to design specific PCR primers for five phylotypes AP12, AP21, AP24, AP50, and RP58, which are deeply branched particularly in the phylogenetic tree, and determine the prevalence of these phylotypes in 45 patients with periodontitis and 18 healthy subjects. The specificity of each primer was validated by the sequence analysis of PCR products obtained from saliva and subgingival plaque samples. Among phylotypes tested, phylotype AP24, which is closely related to oral clone DA014 reported previously [Paster et al. (2001) J. Bacteriol. 183, 3770-3783], was significantly associated with saliva and subgingival plaque samples from patients with periodontitis (P<0.01), but the difference was not statistically significant in the presence of other phylotypes. These data suggest that phylotype AP24 may play an important role in periodontal disease.
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Affiliation(s)
- Mitsuo Sakamoto
- Japan Collection of Microorganisms, RIKEN, Wako, 351-0198, Saitama, Japan.
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