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Chen X, Zou T, Zeng Q, Chen Y, Zhang C, Jiang S, Ding G. Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries. J Dent 2024; 146:105059. [PMID: 38801939 DOI: 10.1016/j.jdent.2024.105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVES Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC. METHODS Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software. RESULTS 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome. CONCLUSIONS Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC. CLINICAL SIGNIFICANCE The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.
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Affiliation(s)
- Xin Chen
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China
| | - Ting Zou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China
| | - Qinglu Zeng
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Yubing Chen
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Chengfei Zhang
- Endodontology, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, PR China
| | - Shan Jiang
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China.
| | - Guicong Ding
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China.
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The virtual microbiome: A computational framework to evaluate microbiome analyses. PLoS One 2023; 18:e0280391. [PMID: 36753469 PMCID: PMC9907852 DOI: 10.1371/journal.pone.0280391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/28/2022] [Indexed: 02/09/2023] Open
Abstract
Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtual microbiomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information and optimizing the use of this information.
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Callahan N, Hattar M, Barbour T, Adami GR, Kawar N. Oral microbial taxa associated with risk for SARS-CoV-2 infection. FRONTIERS IN ORAL HEALTH 2022; 3:886341. [PMID: 36118052 PMCID: PMC9478458 DOI: 10.3389/froh.2022.886341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hypothesis and objective The oral and digestive tract microbial ecosystem has sparked interest because of its impact on various systemic diseases and conditions. The oral cavity serves not only as a reservoir for many potentially virulent microbiota but also as an important entry point and portal to the human body system. This is especially significant in the transmissibility of the virulent current pandemic virus SARS-CoV-2. The oral and digestive microbiome influences the inflammatory burden and effectiveness of the immune system and serves as a marker of activity of these host processes. The host immune response plays a role in infection susceptibility, including SARS-CoV-2. The purpose of this study is to investigate the role of specific salivary oral microbiome in susceptibility to SARS-CoV-2 infection. Methods and results One hundred six subjects of known medical and dental history who consented to provide saliva samples between January 2017 and December 2019 were included in this study. Sixteen had become COVID-19 positive based on the PCR test by 3/01/2021. A comparison of oral microbiome bacteria taxa profiles based on 16S rRNA sequencing revealed differences between the two groups in this pilot study. Conclusions These bacteria taxa may be markers of increased susceptibility to SARS-CoV-2 infection in the unvaccinated population.
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Affiliation(s)
- Nicholas Callahan
- Department of Oral and Maxillofacial Surgery, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Meryana Hattar
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Thawab Barbour
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Guy R. Adami
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
- *Correspondence: Guy R. Adami
| | - Nadia Kawar
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
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Zhu Y, Ma L, Wei W, Li X, Chang Y, Pan Z, Gao H, Yang R, Bi Y, Ding L. Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues. J Med Microbiol 2022; 71. [PMID: 35467501 DOI: 10.1099/jmm.0.001523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.
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Affiliation(s)
- Yubing Zhu
- Department of Colorectal Surgery and Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, PR China
| | - Ling Ma
- Department of Colorectal Surgery and Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, PR China
| | - Wenting Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Xiang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Yuxiao Chang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Hong Gao
- Department of Colorectal Surgery and Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, PR China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Lei Ding
- Department of Colorectal Surgery and Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, PR China
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5
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Schwartz JL, Peña N, Kawar N, Zhang A, Callahan N, Robles SJ, Griebel A, Adami GR. Old age and other factors associated with salivary microbiome variation. BMC Oral Health 2021; 21:490. [PMID: 34602059 PMCID: PMC8489047 DOI: 10.1186/s12903-021-01828-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/27/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Many factors can contribute to the exact makeup of the salivary microbiome. Differences in the oral microbiome occur with old age, which may be due to oral conditions and diseases associated with old age, such as edentulism, as well as other unknown causes. METHODS The salivary microbiome was sampled in patients from a large urban clinic. For all subjects age, gender, periodontal status, caries status, presence of edentulism, medications, and tobacco usage were recorded. Multifactor analysis was used to study variation in salivary microbiome profiles linked to these factors. RESULTS In the population sampled, there were significantly higher numbers of edentulous subjects, and increased levels of polypharmacy found with aging. Large differences in alpha diversity and beta diversity of the salivary microbiome in the old age group were largely linked to edentulism. However, multivariable analysis revealed, even after adjusting for differences in edentulism, polypharmacy, tobacco usage, periodontal disease, caries level, and gender, that old age itself was associated with lower levels of taxa Porphyromonas endodontalis, Alloprevotella tannerae, Filifactor alocis, Treponema, Lautropia Mirabilis and Pseudopropionibacterium sp._HMT_194. Surprisingly, of these taxa, most were ones known to reside on or near tooth surfaces. CONCLUSIONS Another factor or factors beyond edentulism, polypharmacy and periodontal disease play a role in the differences seen in oral microbiome with old age. The nature of this factor(s) is not known.
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Affiliation(s)
- Joel L Schwartz
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Natalia Peña
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Nadia Kawar
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrew Zhang
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Nicholas Callahan
- Department of Oral and Maxillofacial Surgery, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Steven J Robles
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA
| | - Andrew Griebel
- Department of Oral and Maxillofacial Surgery, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Guy R Adami
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, 60612, USA.
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Abstract
Measurement of saliva microbes is promoted as a way to detect oral and systemic disease, yet there is a multitude of factors that affect the oral microbiome. The salivary microbiome is influenced by biofilm of shedding (epithelial) and non-shedding (tooth) surfaces. Methods for study of the salivary microbiome are by no means standardized, and differences in sample collection, storage, and processing can all affect results to some degree. Here we describe one method of saliva collection that has been validated for reproducibility. Standard 16S rRNA gene analysis is done using the Human Oral Microbiome Database library which results in analysis that is straightforward. Everything about this procedure except the library synthesis and DNA sequencing itself can easily be done in-house. To gauge the ability of salivary microbial analytics to distinguish between edentulous and dentate oral conditions, differences in the saliva microbiome of subjects with and without teeth were examined. Fifty-two dentate and 49 edentulous subjects provided stimulated saliva samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analysis were done using several different analytical approaches to detect differences in the salivary microbiome between the two groups. Bacteria diversity was lower in the edentulous group. Remarkably, all 31 of the most significant differences in taxa were deficits that occurred in the edentulous group. As one might expect, many of these taxa are attributed to dental plaque and gingival sulcus-associated bacteria verifying that the measurement of 16S rRNA genes in the bacteria of the saliva can be used to reproducibly measure expected differences in the oral microbiome that occur with edentulism or other conditions and diseases.
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Soil Microbial Community Profiling and Bacterial Metabolic Activity of Technosols as an Effect of Soil Properties following Land Reclamation: A Case Study from the Abandoned Iron Sulphide and Uranium Mine in Rudki (South-Central Poland). AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10111795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.
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8
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Manoil D, Al‐Manei K, Belibasakis GN. A Systematic Review of the Root Canal Microbiota Associated with Apical Periodontitis: Lessons from Next‐Generation Sequencing. Proteomics Clin Appl 2020; 14:e1900060. [DOI: 10.1002/prca.201900060] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/14/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Manoil
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
| | - Khaled Al‐Manei
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
- Division of EndodonticsDepartment of Restorative Dental ScienceCollege of DentistryKing Saud University Riyadh 11545 Saudi Arabia
| | - Georgios N. Belibasakis
- Division of Oral DiseasesDepartment of Dental MedicineKarolinska Institute Huddinge 14152 Sweden
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9
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Yun JSW, Yap T, Martyres R, Kern JS, Varigos G, Scardamaglia L. The association of mycophenolate mofetil and human herpes virus infection. J DERMATOL TREAT 2019; 31:46-55. [DOI: 10.1080/09546634.2019.1572864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jenny Sung Won Yun
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Victoria, Australia
| | - Tami Yap
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Victoria, Australia
- Melbourne Dental School, University of Melbourne, Victoria, Australia
| | - Raymond Martyres
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Victoria, Australia
| | - Johannes S. Kern
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
| | - George Varigos
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Victoria, Australia
| | - Laura Scardamaglia
- Departments of Dermatology, Royal Melbourne Hospital, Victoria, Australia
- Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Victoria, Australia
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10
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Newman TM, Krishnan LP, Lee J, Adami GR. Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage. Sci Rep 2019; 9:12697. [PMID: 31481657 PMCID: PMC6722050 DOI: 10.1038/s41598-019-48768-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/01/2019] [Indexed: 01/08/2023] Open
Abstract
Marijuana smoke contains cannabinoids, immunosuppressants, and a mixture of potentially-mutagenic chemicals. In addition to systemic disease, it is thought to contribute to oral disease, such as tooth loss, tissue changes in the gums and throat, and possibly oral pharyngeal cancer. We used a cross-sectional study of 20 marijuana users and 19 control non-users, to determine if chronic inhalation-based exposure to marijuana was associated with a distinct oral microbiota at the two most common sites of head and neck squamous cell carcinoma (HNSCC), the lateral border of the tongue and the oral pharynx. At the tongue site, genera earlier shown to be enriched on HNSCC mucosa, Capnocytophaga, Fusobacterium, and Porphyromonas, were at low levels in marijuana users, while Rothia, which is found at depressed levels on HNSCC mucosa, was high. At the oral pharynx site, differences in bacteria were distinct, with higher levels of Selenomonas and lower levels of Streptococcus which is what is seen in HNSCC. No evidence was seen for a contribution of marijuana product contaminating bacteria to these differences. This study revealed differences in the surface oral mucosal microbiota with frequent smoking of marijuana.
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Affiliation(s)
- Taylor M Newman
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| | - Laya P Krishnan
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| | - Jessica Lee
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| | - Guy R Adami
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA.
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11
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Grine G, Royer A, Terrer E, Diallo OO, Drancourt M, Aboudharam G. Tobacco Smoking Affects the Salivary Gram-Positive Bacterial Population. Front Public Health 2019; 7:196. [PMID: 31380336 PMCID: PMC6659441 DOI: 10.3389/fpubh.2019.00196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/01/2019] [Indexed: 12/02/2022] Open
Abstract
The microbial communities of the oral fluid are in direct contact with tobacco smoke, which may thus affect these communities. Few culture-based studies have analyzed the effects of tobacco smoking on the oral fluid microbiota. Using bacterial culture we investigated whether tobacco smoking altered the microbial diversity of the oral fluid, focusing on aerobic and facultative anaerobic Gram-positive bacteria otherwise comprising of major pathogens. Among 90 oral fluid specimens collected in 19 tobacco-smokers and 71 controls, the diversity did not significantly differ with age and with sex. However, diversity was significantly lower in tobacco-smokers (nine different species) than in non-smokers (18 different species) with all the species cultured in tabocco-smokers being also cultured in non-smokers. We isolated the human pathogen Streptococcus australis for the first time from oral fluid. Tobacco smoking significantly alters the saliva Gram-positive bacterial microbiota, including pathogens with potential implication in the pathogenesis of tobacco-related diseases such as periodontitis and peri-implantitis.
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Affiliation(s)
- Ghiles Grine
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Arthur Royer
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Elodie Terrer
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, UFR Odontologie, Marseille, France
| | - Ousmane Oumou Diallo
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, UFR Odontologie, Marseille, France
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12
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Raju SC, Lagström S, Ellonen P, de Vos WM, Eriksson JG, Weiderpass E, Rounge TB. Gender-Specific Associations Between Saliva Microbiota and Body Size. Front Microbiol 2019; 10:767. [PMID: 31024514 PMCID: PMC6467948 DOI: 10.3389/fmicb.2019.00767] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE The human intestinal microbiota likely play an important role in the development of overweight and obesity. However, the associations between saliva microbiota and body mass index (BMI) have been sparsely studied. The aim of this study was to identify the associations between saliva microbiota and body size in Finnish children. METHODS The saliva microbiota of 900 Finnish children, aged 11-14 years with measured height and weight, was characterized using 16S rRNA (V3-V4) sequencing. RESULTS The core saliva microbiota consisted of 14 genera that were present in more than 95% of the Finnish children. The saliva microbiota profiles were gender-specific with higher alpha-diversity in boys than girls and significant differences between the genders in community composition and abundances. Alpha-diversity differed between normal weight and overweight girls and between normal weight and obese boys. The composition was dissimilar between normal weight and obese girls, but not in boys. The relative abundance profiles differed according to body size. Decrease in commensal saliva bacteria were observed in all the body sizes when compared to normal weight children. Notably, the relative abundance of bacteria related to, Veillonella, Prevotella, Selenomonas, and Streptococcus was reduced in obese children. CONCLUSION Saliva microbiota diversity and composition were significantly associated with body size and gender in Finnish children. Body size-specific saliva microbiota profiles open new avenues for studying the potential roles of microbiota in weight development and management.
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Affiliation(s)
- Sajan C. Raju
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sonja Lagström
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Johan G. Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Elisabete Weiderpass
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Research, Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Trine B. Rounge
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Research, Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
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13
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Gazdeck RK, Fruscione SR, Adami GR, Zhou Y, Cooper LF, Schwartz JL. Diversity of the oral microbiome between dentate and edentulous individuals. Oral Dis 2019; 25:911-918. [DOI: 10.1111/odi.13039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/20/2018] [Accepted: 12/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- R. Kyle Gazdeck
- Department of Prosthodontics and Implant Innovation University of Illinois at Chicago College of Dentistry Chicago Illinois
| | - Sarah R. Fruscione
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Guy R. Adami
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Yalu Zhou
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Lyndon F. Cooper
- Department of Oral Biology, College of Dentistry University of Illinois at Chicago Chicago Illinois
| | - Joel L. Schwartz
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry University of Illinois at Chicago Chicago Illinois
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14
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Marsh RL, Nelson MT, Pope CE, Leach AJ, Hoffman LR, Chang AB, Smith-Vaughan HC. How low can we go? The implications of low bacterial load in respiratory microbiota studies. Pneumonia (Nathan) 2018; 10:7. [PMID: 30003009 PMCID: PMC6033291 DOI: 10.1186/s41479-018-0051-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Background Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present. Main body Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed. Conclusion Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.
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Affiliation(s)
- Robyn L Marsh
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Maria T Nelson
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Chris E Pope
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Amanda J Leach
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Lucas R Hoffman
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Anne B Chang
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia.,3Department of Respiratory and Sleep Medicine, Children's Health Queensland and Queensland University of Technology, Brisbane, QLD Australia
| | - Heidi C Smith-Vaughan
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
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15
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Liu X, Xu Y, Li Z, Jiang S, Yao S, Wu R, An Y. A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species. Prep Biochem Biotechnol 2018; 48:378-382. [PMID: 29561226 DOI: 10.1080/10826068.2018.1451885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.
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Affiliation(s)
- Xia Liu
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Yongdong Xu
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Zhi Li
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Shengwei Jiang
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China.,b Qingshan Protection Bureau , Forestry Department of Liaoning Province , Shenyang , China
| | - Shuo Yao
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Rina Wu
- c College of Food Science , Shenyang Agricultural University , Shenyang , China
| | - Yingfeng An
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
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16
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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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17
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Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
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18
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Acharya A, Chan Y, Kheur S, Jin LJ, Watt RM, Mattheos N. Salivary microbiome in non-oral disease: A summary of evidence and commentary. Arch Oral Biol 2017; 83:169-173. [DOI: 10.1016/j.archoralbio.2017.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
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19
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Banerjee S, Tian T, Wei Z, Peck KN, Shih N, Chalian AA, O'Malley BW, Weinstein GS, Feldman MD, Alwine J, Robertson ES. Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas. Sci Rep 2017; 7:4036. [PMID: 28642609 PMCID: PMC5481414 DOI: 10.1038/s41598-017-03466-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022] Open
Abstract
The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.
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Affiliation(s)
- Sagarika Banerjee
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Tian Tian
- Department of Computer Science, New Jersey Institute of Technology, New Jersey, 07102, United States of America
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, New Jersey, 07102, United States of America
| | - Kristen N Peck
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Natalie Shih
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, Pennsylvania, United States of America
| | - Ara A Chalian
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Bert W O'Malley
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Gregory S Weinstein
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Michael D Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 19104, Philadelphia, Pennsylvania, United States of America
| | - James Alwine
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and neck surgery, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
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20
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Whiteson K, Agrawal S, Agrawal A. Differential responses of human dendritic cells to metabolites from the oral/airway microbiome. Clin Exp Immunol 2017; 188:371-379. [PMID: 28194750 DOI: 10.1111/cei.12943] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2017] [Indexed: 12/22/2022] Open
Abstract
Small molecule metabolites that are produced or altered by host-associated microbial communities are emerging as significant immune response modifiers. However, there is a key gap in our knowledge of how oral microbial metabolites affect the immune response. Here, we examined the effects of metabolites from five bacterial strains found commonly in the oral/airway microbial communities of humans. The five strains, each isolated from cystic fibrosis patient sputum, were Pseudomonas aeruginosa FLR01 non-mucoid (P1) and FLR02 mucoid (P2) forms, Streptococcus pneumoniae (Sp), S. salivarius (Ss) and Rothia mucilaginosa (Rm). The effect of bacterial metabolites on dendritic cell (DC) activation, T cell priming and cytokine secretion was determined by exposing DCs to bacterial supernatants and individual metabolites of interest. Supernatants from P1 and P2 induced high levels of tumour necrosis factor (TNF)-α, interleukin (IL)-12 and IL-6 from DCs and primed T cells to secrete interferon (IFN)-γ, IL-22 compared to supernatants from Sp, Ss and Rm. Investigations into the composition of supernatants using gas chromatography-mass spectroscopy (GC-MS) revealed signature metabolites for each of the strains. Supernatants from P1 and P2 contained high levels of putrescine and glucose, while Sp and Ss contained high levels of 2,3-butanediol. The individual metabolites replicated the results of whole supernatants, although the magnitudes of their effects were reduced significantly. Altogether, our data demonstrate for the first time that the signature metabolites produced by different bacteria have different effects on DC functions. The identification of signature metabolites and their effects on the host immune system can provide mechanistic insights into diseases and may also be developed as biomarkers.
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Affiliation(s)
- K Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - S Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA, USA
| | - A Agrawal
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, CA, USA
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21
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Yang F, Ning K, Zeng X, Zhou Q, Su X, Yuan X. Characterization of saliva microbiota's functional feature based on metagenomic sequencing. SPRINGERPLUS 2016; 5:2098. [PMID: 28053828 PMCID: PMC5174016 DOI: 10.1186/s40064-016-3728-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 11/23/2016] [Indexed: 01/18/2023]
Abstract
Objective
Saliva, a mixture of exocrinally secretive fluids, amounts to ~1.5 L daily and harbors numerous microbial inhabitants. However, except the organismal structure of saliva microbiota, the functional profile of saliva microbiota remain elusive. Methods Here we used metagenomic sequencing to experimentally reconstruct the global genomic profile of saliva by sequencing total saliva DNA from two healthy and two caries-active (DMFT ≧ 6) adults. Results We found that saliva microbiota, representing 30–60% of total saliva DNA in our samples, might carry functional signatures that were site-specific and caries-state-specific. Among microbiota from different hosts, a prominent functional core, but not an organismal core, was identified. Each microbiota exhibited functional redundancy where dominant genomes tend to encode more functional diversity yet without necessarily contributing to dominant functions. Furthermore, genetic polymorphisms of hosts were also unraveled from salivary DNA without apparent physical or sequence bias in human chromosomes. Conclusions The microbial functional sensitivity to disease, links to specific functions, and permission of simultaneous genotyping of hosts and microbiota suggested sequencing salivary DNA might be an advantageous venue in uncovering both human and microbial basis of oral infections. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-3728-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fang Yang
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao, 266011 Shandong China
| | - Kang Ning
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Xiaowei Zeng
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Qian Zhou
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Xiaoquan Su
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 Shandong China
| | - Xiao Yuan
- Department of Stomatology, Qingdao Municipal Hospital, Qingdao, 266011 Shandong China
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22
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Belstrøm D, Jersie-Christensen RR, Lyon D, Damgaard C, Jensen LJ, Holmstrup P, Olsen JV. Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PeerJ 2016; 4:e2433. [PMID: 27672500 PMCID: PMC5028799 DOI: 10.7717/peerj.2433] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/12/2016] [Indexed: 01/10/2023] Open
Abstract
Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
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Affiliation(s)
- Daniel Belstrøm
- Section of Periodontology and Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rosa R Jersie-Christensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Damgaard
- Section of Periodontology and Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Palle Holmstrup
- Section of Periodontology and Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Enteric Viruses Ameliorate Gut Inflammation via Toll-like Receptor 3 and Toll-like Receptor 7-Mediated Interferon-β Production. Immunity 2016; 44:889-900. [DOI: 10.1016/j.immuni.2016.03.009] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/14/2015] [Accepted: 12/29/2015] [Indexed: 12/19/2022]
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24
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Belstrøm D, Holmstrup P, Bardow A, Kokaras A, Fiehn NE, Paster BJ. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples. J Oral Microbiol 2016; 8:30112. [PMID: 26987356 PMCID: PMC4796727 DOI: 10.3402/jom.v8.30112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/30/2022] Open
Abstract
Background and objective The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial composition may not reflect the more natural, unstimulated state. The purpose of this study was to validate whether stimulated saliva is an adequate surrogate for unstimulated saliva in determining salivary microbiomes. Design Unstimulated (n=20) and stimulated (n=20) saliva samples were collected from 20 orally and systemically healthy, non-smoking participants. Salivary bacterial profiles were analyzed by means of the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using Mann–Whitney test with Benjamini–Hochberg's correction for multiple comparison, cluster analysis, principal component analysis, and correspondence analysis. Results From a total of 40 saliva samples, 496 probe targets were identified with a mean number of targets per sample of 203 (range: 146–303), and a mean number of probe targets of 206 and 200 in unstimulated and stimulated saliva samples, respectively (p=0.62). Based on all statistical methods used for this study, the microbial profiles of unstimulated and stimulated saliva samples collected from the same person were not statistically significantly different. Conclusions Analysis of bacterial salivary profiles in unstimulated and stimulated saliva samples collected from the same individual showed comparable results. Thus, the results verify that stimulated saliva is an adequate surrogate of unstimulated saliva for microbiome-related studies.
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Affiliation(s)
- Daniel Belstrøm
- Section of Periodontology and Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;
| | - Palle Holmstrup
- Section of Periodontology and Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Bardow
- Section for Oral Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexis Kokaras
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Nils-Erik Fiehn
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bruce J Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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25
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Abstract
BACKGROUND Kingella kingae outbreaks occur sporadically in childcare centers but remain poorly understood and difficult to identify. METHODS To provide the basis of a better knowledge of K. kingae outbreaks patterns that may help to guide identification and management strategies, we collected epidemiological, clinical and laboratory data from all reported K. kingae outbreaks, and those from 2 new Israel outbreaks in 2014. RESULTS Nine outbreaks were identified in the USA, Israel and France from 2003 to 2014. Twenty-seven children with a median age of 14 ± 4.1 months were affected, male:female ratio of 1.4:1. Outbreaks demonstrated seasonal patterns from the 10th to the 45th weeks, a mean duration of 13.1 ± 8.4 days, a mean attack rate of 17.3 ± 5.1% and a case-fatality rate of 3.7% (1/27). Seventy-four percentage of children had fever (20/27), and the mean values of white blood cell count and C-reactive protein level were 14.6 ± 4.5 × 10/L and 23.8 ± 24.1 mg/L, respectively. Osteoarticular infections accounted for 88.9% of cases (24/27), bacteremia 7.4% (2/27), endocarditis 3.7% (1/27) and meningitis 3.7% (1/27). Specific real-time polymerase chain reaction demonstrated higher performance than culture methods in the diagnosis of case patients and investigations of oropharyngeal K. kingae carriage among close contacts, and multilocus sequence typing methods revealed that ST-6 and ST-25 invasive strains were responsible for multiple country-dependent outbreaks. Coviral infections were identified in the majority of K. kingae outbreaks, notably those causing oral ulcers. CONCLUSIONS K. kingae outbreaks displayed severe K. kingae diseases that were poorly confirmed with culture methods. We argue for the use of genomic technologies to investigate further K. kingae outbreaks.
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26
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Belstrøm D, Paster BJ, Fiehn NE, Bardow A, Holmstrup P. Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique. J Oral Microbiol 2016; 8:30170. [PMID: 26782357 PMCID: PMC4717152 DOI: 10.3402/jom.v8.30170] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/01/2022] Open
Abstract
Background and objective The composition of the salivary microbiota, as determined using various molecular methods, has been reported to differentiate oral health from diseases. Thus, the purpose of this study was to utilize the newly developed molecular technique HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing) for comparison of the salivary microbiota in patients with periodontitis, patients with dental caries, and orally healthy individuals. The hypothesis was that this method could add on to the existing knowledge on salivary bacterial profiles in oral health and disease. Design Stimulated saliva samples (n=30) were collected from 10 patients with untreated periodontitis, 10 patients with untreated dental caries, and 10 orally healthy individuals. Salivary microbiota was analyzed using HOMINGS and statistical analysis was performed using Kruskal–Wallis test with Benjamini–Hochberg's correction. Results From a total of 30 saliva samples, a mean number of probe targets of 205 (range 120–353) were identified, and a statistically significant higher mean number of targets was registered in samples from patients with periodontitis (mean 220, range 143–306) and dental caries (mean 221, range 165–353) as compared to orally healthy individuals (mean 174, range 120–260) (p=0.04 and p=0.04). Nine probe targets were identified with a different relative abundance between groups (p<0.05). Conclusions Cross-sectional comparison of salivary bacterial profiles by means of HOMINGS analysis showed that different salivary bacterial profiles were associated with oral health and disease. Future large-scale prospective studies are needed to evaluate if saliva-based screening for disease-associated oral bacterial profiles may be used for identification of patients at risk of acquiring periodontitis and dental caries.
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Affiliation(s)
- Daniel Belstrøm
- Section of Periodontology and Microbiology, School of Dentistry, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark;
| | - Bruce J Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Nils-Erik Fiehn
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Allan Bardow
- Department of Oral Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Palle Holmstrup
- Section of Periodontology and Microbiology, School of Dentistry, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
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27
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Torres PJ, Fletcher EM, Gibbons SM, Bouvet M, Doran KS, Kelley ST. Characterization of the salivary microbiome in patients with pancreatic cancer. PeerJ 2015; 3:e1373. [PMID: 26587342 PMCID: PMC4647550 DOI: 10.7717/peerj.1373] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/13/2015] [Indexed: 12/15/2022] Open
Abstract
Clinical manifestations of pancreatic cancer often do not occur until the cancer has undergone metastasis, resulting in a very low survival rate. In this study, we investigated whether salivary bacterial profiles might provide useful biomarkers for early detection of pancreatic cancer. Using high-throughput sequencing of bacterial small subunit ribosomal RNA (16S rRNA) gene, we characterized the salivary microbiota of patients with pancreatic cancer and compared them to healthy patients and patients with other diseases, including pancreatic disease, non-pancreatic digestive disease/cancer and non-digestive disease/cancer. A total of 146 patients were enrolled at the UCSD Moores Cancer Center where saliva and demographic data were collected from each patient. Of these, we analyzed the salivary microbiome of 108 patients: 8 had been diagnosed with pancreatic cancer, 78 with other diseases and 22 were classified as non-diseased (healthy) controls. Bacterial 16S rRNA sequences were amplified directly from salivary DNA extractions and subjected to high-throughput sequencing (HTS). Several bacterial genera differed in abundance in patients with pancreatic cancer. We found a significantly higher ratio of Leptotrichia to Porphyromonas in the saliva of patients with pancreatic cancer than in the saliva of healthy patients or those with other disease (Kruskal–Wallis Test; P < 0.001). Leptotrichia abundances were confirmed using real-time qPCR with Leptotrichia specific primers. Similar to previous studies, we found lower relative abundances of Neisseria and Aggregatibacter in the saliva of pancreatic cancer patients, though these results were not significant at the P < 0.05 level (K–W Test; P = 0.07 and P = 0.09 respectively). However, the relative abundances of other previously identified bacterial biomarkers, e.g., Streptococcus mitis and Granulicatella adiacens, were not significantly different in the saliva of pancreatic cancer patients. Overall, this study supports the hypothesis that bacteria abundance profiles in saliva are useful biomarkers for pancreatic cancer though much larger patient studies are needed to verify their predictive utility.
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University , San Diego, CA , United States
| | - Erin M Fletcher
- Department of Medical Sciences, Harvard University , Boston, MA , United States
| | - Sean M Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago , Chicago, IL , United States ; Institute for Genomics and Systems Biology, Argonne National Laboratory , Lemont, IL , United States
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego , La Jolla, CA , United States
| | - Kelly S Doran
- Department of Biology, San Diego State University , San Diego, CA , United States ; Department of Pediatrics, University of California San Diego School of Medicine , La Jolla, CA , United States
| | - Scott T Kelley
- Department of Biology, San Diego State University , San Diego, CA , United States
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28
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Foulongne V. [The human virome]. ACTA ACUST UNITED AC 2015; 2015:59-65. [PMID: 32288819 PMCID: PMC7140283 DOI: 10.1016/s1773-035x(15)72822-4] [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: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 11/17/2022]
Abstract
The human virome is the collection of viruses found in human, including viruses that infect eucaryotic cells, bacteriophages and virus-derived genetic elements in host chromosomes that can influence host-genes expression. Most of the recent knowledges regarding the human virome were driven by advances in high-throughput, deep sequencing approaches. Thanks to these new technologies, many new human viruses were described with, furthermore, the evidence of the presence of a resident viral community in most human tissus. This new concept will have profound implications for understanding the biological role of viruses in the human body.
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Affiliation(s)
- Vincent Foulongne
- Pôle Biologie et pathologie, Unité de virologie, Centre hospitalier universitaire de Montpellier, Hôpital Saint-Eloi, Université de Montpellier I - INSERM U1058, 34295 Montpellier cedex 5
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Emerging horizons of salivary diagnostics for periodontal disease. Br Dent J 2014; 217:567-73. [DOI: 10.1038/sj.bdj.2014.1005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2014] [Indexed: 12/20/2022]
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Lazarevic V, Gaïa N, Emonet S, Girard M, Renzi G, Despres L, Wozniak H, Yugueros Marcos J, Veyrieras JB, Chatellier S, van Belkum A, Pugin J, Schrenzel J. Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients. Front Cell Infect Microbiol 2014; 4:65. [PMID: 24904840 PMCID: PMC4033159 DOI: 10.3389/fcimb.2014.00065] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/06/2014] [Indexed: 12/02/2022] Open
Abstract
The spread of microorganisms in hospitals is an important public health threat, and yet few studies have assessed how human microbial communities (microbiota) evolve in the hospital setting. Studies conducted so far have mainly focused on a limited number of bacterial species, mostly pathogenic ones and primarily during outbreaks. We explored the bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit and we discuss the technical challenges that may arise while using culture-independent approaches to study these types of samples.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | - Stéphane Emonet
- Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland ; Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | - Gesuele Renzi
- Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | - Lena Despres
- Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | - Hannah Wozniak
- Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
| | | | | | - Sonia Chatellier
- Research and Development Microbiology, BioMérieux La Balme-les-Grottes, France
| | - Alex van Belkum
- Research and Development Microbiology, BioMérieux La Balme-les-Grottes, France
| | - Jérôme Pugin
- Laboratory of Intensive Care, Department of Anaesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland ; Clinical Microbiology Laboratory, Department of Genetics and Laboratory Medicine and Department of Medical Specialties, Geneva University Hospitals Geneva, Switzerland
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Hasan NA, Young BA, Minard-Smith AT, Saeed K, Li H, Heizer EM, McMillan NJ, Isom R, Abdullah AS, Bornman DM, Faith SA, Choi SY, Dickens ML, Cebula TA, Colwell RR. Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS One 2014; 9:e97699. [PMID: 24846174 PMCID: PMC4028220 DOI: 10.1371/journal.pone.0097699] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/22/2014] [Indexed: 11/23/2022] Open
Abstract
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUSand BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.
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Affiliation(s)
- Nur A. Hasan
- CosmosID, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
| | | | | | - Kelly Saeed
- CosmosID, College Park, Maryland, United States of America
| | - Huai Li
- CosmosID, College Park, Maryland, United States of America
| | | | | | - Richard Isom
- CosmosID, College Park, Maryland, United States of America
| | | | | | | | - Seon Young Choi
- CosmosID, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
| | | | - Thomas A. Cebula
- CosmosID, College Park, Maryland, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rita R. Colwell
- CosmosID, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Salivary biomarkers: toward future clinical and diagnostic utilities. Clin Microbiol Rev 2014; 26:781-91. [PMID: 24092855 DOI: 10.1128/cmr.00021-13] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The pursuit of timely, cost-effective, accurate, and noninvasive diagnostic methodologies is an endeavor of urgency among clinicians and scientists alike. Detecting pathologies at their earliest stages can significantly affect patient discomfort, prognosis, therapeutic intervention, survival rates, and recurrence. Diagnosis and monitoring often require painful invasive procedures such as biopsies and repeated blood draws, adding undue stress to an already unpleasant experience. The discovery of saliva-based microbial, immunologic, and molecular biomarkers offers unique opportunities to bypass these measures by utilizing oral fluids to evaluate the condition of both healthy and diseased individuals. Here we discuss saliva and its significance as a source of indicators for local, systemic, and infectious disorders. We highlight contemporary innovations and explore recent discoveries that deem saliva a mediator of the body's physiological condition. Additionally, we examine the current state of salivary diagnostics and its associated technologies, future aspirations, and potential as the preferred route of disease detection, monitoring, and prognosis.
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Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U. Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma. PLoS One 2014; 9:e92297. [PMID: 24642836 PMCID: PMC3958540 DOI: 10.1371/journal.pone.0092297] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/20/2014] [Indexed: 01/01/2023] Open
Abstract
Mycoplasma salivarium belongs to the class of the smallest self-replicating Tenericutes and is predominantly found in the oral cavity of humans. In general it is considered as a non-pathogenic commensal. However, some reports point to an association with human diseases. M. salivarium was found e.g. as causative agent of a submasseteric abscess, in necrotic dental pulp, in brain abscess and clogged biliary stent. Here we describe the detection of M. salivarium on the surface of a squamous cell carcinoma of the tongue of a patient with Fanconi anaemia (FA). FA is an inherited bone marrow failure syndrome based on defective DNA-repair that increases the risk of carcinomas especially oral squamous cell carcinoma. Employing high coverage, massive parallel Roche/454-next-generation-sequencing of 16S rRNA gene amplicons we analysed the oral microbiome of this FA patient in comparison to that of an FA patient with a benign leukoplakia and five healthy individuals. The microbiota of the FA patient with leukoplakia correlated well with that of the healthy controls. A dominance of Streptococcus, Veillonella and Neisseria species was typically observed. In contrast, the microbiome of the cancer bearing FA patient was dominated by Pseudomonas aeruginosa at the healthy sites, which changed to a predominance of 98% M. salivarium on the tumour surface. Quantification of the mycoplasma load in five healthy, two tumour- and two leukoplakia-FA patients by TaqMan-PCR confirmed the prevalence of M. salivarium at the tumour sites. These new findings suggest that this mycoplasma species with its reduced coding capacity found ideal breeding grounds at the tumour sites. Interestingly, the oral cavity of all FA patients and especially samples at the tumour sites were in addition positive for Candida albicans. It remains to be elucidated in further studies whether M. salivarium can be used as a predictive biomarker for tumour development in these patients.
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Affiliation(s)
- Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail:
| | - Madis Rumming
- Department of Paediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Computational Metagenomics, Faculty of Technology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alexander Sczyrba
- Computational Metagenomics, Faculty of Technology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Eunike Velleuer
- Department of Paediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | | | - Wolfgang Gerlach
- Genome Informatics, Faculty of Technology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Michael Gombert
- Department of Paediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Sebastian Rahn
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jens Stoye
- Genome Informatics, Faculty of Technology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Ute Fischer
- Department of Paediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Cuevas-Córdoba B, Santiago-García J. Saliva: a fluid of study for OMICS. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:87-97. [PMID: 24404837 DOI: 10.1089/omi.2013.0064] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Saliva is a fluid that can be collected easily and noninvasively. Its functions in the oral cavity are well known. Advances in molecular biology and technology, as well as research conducted by the various disciplines of omics (genomics, transcriptomics, proteomics, metabolomics, and metagenomics) have contributed to the identification and characterization of salivary components, including DNA, RNA, proteins, metabolites, and microorganisms. These biomolecules enter the saliva through extracellular and intracellular routes, providing information from several organs and systems and raising the possibility of their use as disease biomarkers. In recent years, these factors have expanded the potential use of saliva as a diagnostic fluid for oral and systemic diseases. This review integrates information regarding salivary biomolecules studied through omics and explores their utility as biomarkers for the diagnosis of several infectious and noninfectious diseases, and the opportunity they represent for the development of point of care devices for clinical application. We also discuss the advantages, disadvantages, and challenges to be overcome in order to establish saliva as a useful fluid for the accurate diagnosis and monitoring of a wide range of diseases.
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Pereira JV, Leomil L, Rodrigues-Albuquerque F, Pereira JO, Astolfi-Filho S. Bacterial diversity in the saliva of patients with different oral hygiene indexes. Braz Dent J 2013. [PMID: 23207858 DOI: 10.1590/s0103-64402012000400017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.
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Resident viruses and their interactions with the immune system. Nat Immunol 2013; 14:654-9. [PMID: 23778792 PMCID: PMC3760236 DOI: 10.1038/ni.2614] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/16/2013] [Indexed: 02/08/2023]
Abstract
The human body is colonized with a diverse resident microflora that includes viruses. Recent studies of metagenomes have begun to characterize the composition of the human 'virobiota' and its associated genes (the 'virome'), and have fostered the emerging field of host-virobiota interactions. In this Perspective, we explore how resident viruses interact with the immune system. We review recent findings that highlight the role of the immune system in shaping the composition of the virobiota and consider how resident viruses may impact host immunity. Finally, we discuss the implications of virobiota-immune system interactions for human health.
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Xu Y, Teng F, Huang S, Lin Z, Yuan X, Zeng X, Yang F. Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy. Arch Oral Biol 2013; 59:176-86. [PMID: 24370189 DOI: 10.1016/j.archoralbio.2013.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 10/22/2013] [Accepted: 10/27/2013] [Indexed: 01/05/2023]
Abstract
OBJECTIVE A growing body of evidence has implicated human oral microbiota in the aetiology of oral and systemic diseases. Nasopharyngeal carcinoma (NPC), an epithelial-originated malignancy, has a complex aetiology not yet fully understood. Chemoradiation therapy of NPC can affect oral microbiota and is usually accompanied by plaque accumulation. Thus, the study aimed to understand the diversity, divergence and development of the oral microbiota in NPC patients and their associated treatment, which might provide useful insights into disease aetiology and treatment side effects. DESIGN A longitudinal study was designed that included three Chinese adults with NPC. Saliva samples were collected at three time points: prior to the chemoradiation treatment (carcinoma baseline, or CB), 7 months post-treatment (carcinoma-after-therapy phase 1 or CA1) and 12 months post-treatment (carcinoma-after-therapy phase 2 or CA2). Pyrosequencing of the bacterial 16S ribosomal DNA (rDNA) V1-V3 hypervariable region was employed to characterise the microbiota. Saliva samples of three healthy subjects from our former study were employed as healthy controls. Principal coordinates analysis (PCoA), Metastats and random forest prediction models were used to reveal the key microbial members associated with NPC and its treatment programme. RESULTS (1) In total, 412 bacterial species from at least 107 genera and 13 phyla were found in the saliva samples of the NPC patients. (2) PCoA revealed that not only were the microbiota from NPC patients distinct from those of healthy controls (p<0.001) but also that separation was found on the saliva microbiota between pre- and post-therapy (p<0.001) in the NPC samples. (3) At the genus level and the operational taxonomic unit (OTU) level, Streptococcus was found with lower abundance in NPC samples. (4) Chemoradiation therapy did not incur similar changes in microbiota structure among the three NPC patients; the microbiota in one of them stayed largely steady, while those in the other two showed significant alteration. CONCLUSIONS This is the first study employing culture-independent techniques to interrogate the phylogenetic diversity, divergence and temporal development of oral microbiota in NPC patients. Our results indicated that certain bacterial taxa might be associated with NPC and that oral microbiota of NPC patients might respond to the chemoradiation therapy in a host-specific manner. Further investigation with larger sample size should help to validate the links between oral microbiota and NPC.
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Affiliation(s)
- Yuan Xu
- Department of Stomatology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Fei Teng
- Department of Operative Dentistry and Endodontics, Guanghua School and Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shi Huang
- Bioenergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Zhengmei Lin
- Department of Operative Dentistry and Endodontics, Guanghua School and Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao Yuan
- Oral Research Center, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Xiaowei Zeng
- Bioenergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Fang Yang
- Oral Research Center, Qingdao Municipal Hospital, Qingdao, Shandong, China.
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Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, Dimalanta ET, Amaral-Zettler LA, Davis T, Quail MA, Pradhan S. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS One 2013; 8:e76096. [PMID: 24204593 PMCID: PMC3810253 DOI: 10.1371/journal.pone.0076096] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/20/2013] [Indexed: 12/05/2022] Open
Abstract
DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we used a methyl-CpG binding domain (MBD) to separate methylated host DNA from microbial DNA based on differences in CpG methylation density. MBD fused to the Fc region of a human antibody (MBD-Fc) binds strongly to protein A paramagnetic beads, forming an effective one-step enrichment complex that was used to remove human or fish host DNA from bacterial and protistan DNA for subsequent sequencing and analysis. We report enrichment of DNA samples from human saliva, human blood, a mock malaria-infected blood sample and a black molly fish. When reads were mapped to reference genomes, sequence reads aligning to host genomes decreased 50-fold, while bacterial and Plasmodium DNA sequences reads increased 8-11.5-fold. The Shannon-Wiener diversity index was calculated for 149 bacterial species in saliva before and after enrichment. Unenriched saliva had an index of 4.72, while the enriched sample had an index of 4.80. The similarity of these indices demonstrates that bacterial species diversity and relative phylotype abundance remain conserved in enriched samples. Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types.
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Affiliation(s)
- George R. Feehery
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Erbay Yigit
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | | | - Victor T. Schmidt
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Fiona J. Stewart
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | - Linda A. Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
- Department of Geological Sciences, Brown University, Providence, Rhode Island, United States of America
| | - Theodore Davis
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | | | - Sriharsa Pradhan
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
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Lazarevic V, Gaïa N, Girard M, François P, Schrenzel J. Comparison of DNA extraction methods in analysis of salivary bacterial communities. PLoS One 2013; 8:e67699. [PMID: 23844068 PMCID: PMC3701005 DOI: 10.1371/journal.pone.0067699] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
Culture-independent high-throughput sequencing-based methods are widely used to study bacterial communities. Although these approaches are superior to traditional culture-based methods, they introduce bias at the experimental and bioinformatics levels. We assessed the diversity of the human salivary microbiome by pyrosequencing of the 16S rDNA V1–3 amplicons using metagenomic DNA extracted by two different protocols: a simple proteinase K digestion without a subsequent DNA clean-up step, and a bead-beating mechanical lysis protocol followed by column DNA purification. A high degree of congruence was found between the two extraction methods, most notably in regard to the microbial community composition. The results showed that for a given bioinformatics pipeline, all the taxa with an average proportion >0.12% in samples processed using one extraction method were also detected in samples extracted using the other method. The same taxa tended to be abundant and frequent for both extraction methods. The relative abundance of sequence reads assigned to the phyla Actinobacteria, Spirochaetes, TM7, Synergistetes, and Tenericutes was significantly higher in the mechanically-treated samples than in the enzymatically-treated samples, whereas the phylum Firmicutes showed the opposite pattern. No significant differences in diversity indices were found between the extraction methods, although the mechanical lysis method revealed higher operational taxonomic unit richness. Differences between the extraction procedures outweighed the variations due to the bioinformatics analysis pipelines used.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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41
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Neelakanta G, Sultana H. The use of metagenomic approaches to analyze changes in microbial communities. Microbiol Insights 2013; 6:37-48. [PMID: 24826073 PMCID: PMC3987754 DOI: 10.4137/mbi.s10819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, and sequence-alignment tools. In summary, we provide a snapshot for the recent advances in metagenomics approach for analyzing changes in the microbial communities in different ecosystems.
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Affiliation(s)
- Girish Neelakanta
- Center for Molecular Medicine, Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Hameeda Sultana
- Center for Molecular Medicine, Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
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42
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Cockburn AF, Dehlin JM, Ngan T, Crout R, Boskovic G, Denvir J, Primerano D, Plassman BL, Wu B, Cuff CF. High throughput DNA sequencing to detect differences in the subgingival plaque microbiome in elderly subjects with and without dementia. INVESTIGATIVE GENETICS 2012; 3:19. [PMID: 22998923 PMCID: PMC3488532 DOI: 10.1186/2041-2223-3-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 08/30/2012] [Indexed: 12/20/2022]
Abstract
Background To investigate the potential association between oral health and cognitive function, a pilot study was conducted to evaluate high throughput DNA sequencing of the V3 region of the 16S ribosomal RNA gene for determining the relative abundance of bacterial taxa in subgingival plaque from older adults with or without dementia. Methods Subgingival plaque samples were obtained from ten individuals at least 70 years old who participated in a study to assess oral health and cognitive function. DNA was isolated from the samples and a gene segment from the V3 portion of the 16S bacterial ribosomal RNA gene was amplified and sequenced using an Illumina HiSeq1000 DNA sequencer. Bacterial populations found in the subgingival plaque were identified and assessed with respect to the cognitive status and oral health of the participants who provided the samples. Results More than two million high quality DNA sequences were obtained from each sample. Individuals differed greatly in the mix of phylotypes, but different sites from different subgingival depths in the same subject were usually similar. No consistent differences were observed in this small sample between subjects separated by levels of oral health, sex, or age; however a consistently higher level of Fusobacteriaceae and a generally lower level of Prevotellaceae was seen in subjects without dementia, although the difference did not reach statistical significance, possibly because of the small sample size. Conclusions The results from this pilot study provide suggestive evidence that alterations in the subgingival microbiome are associated with changes in cognitive function, and provide support for an expanded analysis of the role of the oral microbiome in dementia.
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Affiliation(s)
- Andrew F Cockburn
- Microbiology, Immunology & Cell Biology, School of Medicine, Robert C, Byrd Health Sciences Center, West Virginia University, P,O, Box 4622, Morgantown, WV, 26506-4622, USA.
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Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 2012; 13:682-95. [PMID: 22786784 DOI: 10.1093/bib/bbs036] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
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Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
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