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Mann AE, Aumend C, Crull S, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Rowe M, Blouin T, Soule A, Kelly C, Burne RA, Coker MO, Richards VP. HIV Infection and Exposure Increases Cariogenic Taxa, Reduces Taxonomic Turnover, and Homogenizes Spatial Differentiation for the Supragingival Microbiome. RESEARCH SQUARE 2024:rs.3.rs-4720457. [PMID: 39149457 PMCID: PMC11326420 DOI: 10.21203/rs.3.rs-4720457/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background The oral microbiome comprises distinct microbial communities that colonize diverse ecological niches across the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is regularly and directly exposed to the external environment and is therefore likely less stable over time. Cross sectional studies of the oral microbiome capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease. Results Here we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1,960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpoC gene. We found that both infection and exposure to HIV have significant effects on the stability of the supragingival plaque microbiome at both the spatial and temporal scale. Specifically, we detect (1) significantly lower taxonomic turnover of the oral community among exposed and infected children compared to unexposed children, (2) we find that HIV infection homogenizes the oral community across the anterior and posterior dentition, and (3) that impaired immunity (i.e., low CD4 count) and low taxonomic turnover over time in children living with HIV is associated with higher frequency of cariogenic taxa including Streptococcus mutans. Conclusions Our results document substantial community fluctuations over time in children unexposed to HIV independent of oral health status. This suggests that the oral community, under typical conditions, rapidly adapts to environmental perturbations to maintain homeostasis and that long-term taxonomic rigidity is a signal of community dysfunction, potentially leading to a higher incidence of oral disease including caries.
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Baek HJ, Kim KS, Kwoen M, Park ES, Lee HJ, Park KU. Saliva assay: a call for methodological standardization. J Periodontal Implant Sci 2024; 54:54.e13. [PMID: 39058348 DOI: 10.5051/jpis.2304180209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 07/28/2024] Open
Abstract
The oral cavity provides an ideal environment for microorganisms, including bacteria, viruses, and fungi, to flourish. Increasing attention has been focused on the connection between the oral microbiome and both oral and systemic diseases, spurring active research into the collection and analysis of specimens for healthcare purposes. Among the various methods for analyzing the oral microbiome, saliva analysis is especially prominent. Saliva samples, which can be collected non-invasively, provide information on the systemic health and oral microbiome composition of an individual. This review was performed to evaluate the current state of the relevant research through an examination of the literature and to suggest an appropriate assay method for investigating the oral microbiome. We analyzed articles published in English in SCI(E) journals after January 1, 2000, ultimately selecting 53 articles for review. Articles were identified through keyword searches in the PubMed, Embase, Cochrane, Web of Science, and CINAHL databases. Three experienced researchers conducted full-text assessments following title and abstract screening to select appropriate papers. Subsequently, they organized and analyzed the desired data. Our review revealed that most studies utilized unstimulated saliva samples for oral microbiome analysis. Of the 53 studies examined, 29 identified relationships between the oral microbiome and various diseases, such as oral disease, Behçet disease, cancer, and oral lichen planus. However, the studies employed diverse methods of collection and analysis, which compromised the reliability and accuracy of the findings. To address the limitations caused by methodological inconsistencies, a standardized saliva assay should be established.
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Affiliation(s)
- Hyeong-Jin Baek
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - MinJeong Kwoen
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eun-Sun Park
- Medical Library, College of Medicine, Seoul National University, Seoul, Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Kyoung-Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
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3
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Fan X, Monson KR, Peters BA, Whittington JM, Um CY, Oberstein PE, McCullough ML, Freedman ND, Huang WY, Ahn J, Hayes RB. Altered salivary microbiota associated with high-sugar beverage consumption. Sci Rep 2024; 14:13386. [PMID: 38862651 PMCID: PMC11167035 DOI: 10.1038/s41598-024-64324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 06/07/2024] [Indexed: 06/13/2024] Open
Abstract
The human oral microbiome may alter oral and systemic disease risk. Consuming high sugar content beverages (HSB) can lead to caries development by altering the microbial composition in dental plaque, but little is known regarding HSB-specific oral microbial alterations. Therefore, we conducted a large, population-based study to examine associations of HSB intake with oral microbiome diversity and composition. Using mouthwash samples of 989 individuals in two nationwide U.S. cohorts, bacterial 16S rRNA genes were amplified, sequenced, and assigned to bacterial taxa. HSB intake was quantified from food frequency questionnaires as low (< 1 serving/week), medium (1-3 servings/week), or high (> 3 servings/week). We assessed overall bacterial diversity and presence of specific taxa with respect to HSB intake in each cohort separately and combined in a meta-analysis. Consistently in the two cohorts, we found lower species richness in high HSB consumers (> 3 cans/week) (p = 0.027), and that overall bacterial community profiles differed from those of non-consumers (PERMANOVA p = 0.040). Specifically, presence of a network of commensal bacteria (Lachnospiraceae, Peptostreptococcaceae, and Alloprevotella rava) was less common in high compared to non-consumers, as were other species including Campylobacter showae, Prevotella oulorum, and Mycoplasma faucium. Presence of acidogenic bacteria Bifodobacteriaceae and Lactobacillus rhamnosus was more common in high consumers. Abundance of Fusobacteriales and its genus Leptotrichia, Lachnoanaerobaculum sp., and Campylobacter were lower with higher HSB consumption, and their abundances were correlated. No significant interaction was found for these associations with diabetic status or with microbial markers for caries (S. mutans) and periodontitis (P. gingivalis). Our results suggest that soft drink intake may alter the salivary microbiota, with consistent results across two independent cohorts. The observed perturbations of overrepresented acidogenic bacteria and underrepresented commensal bacteria in high HSB consumers may have implications for oral and systemic disease risk.
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Affiliation(s)
- Xiaozhou Fan
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, 180 Madison, New York, NY, 10016, USA
| | - Kelsey R Monson
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, 180 Madison, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brandilyn A Peters
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, 180 Madison, New York, NY, 10016, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Paul E Oberstein
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyoung Ahn
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, 180 Madison, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, 180 Madison, New York, NY, 10016, USA.
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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Chattopadhyay S, Malayil L, Chopyk J, Smyth E, Kulkarni P, Raspanti G, Thomas SB, Sapkota A, Mongodin EF, Sapkota AR. Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users. Sci Rep 2024; 14:10394. [PMID: 38710815 DOI: 10.1038/s41598-024-60730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
Tobacco use significantly influences the oral microbiome. However, less is known about how different tobacco products specifically impact the oral microbiome over time. To address this knowledge gap, we characterized the oral microbiome of cigarette users, smokeless tobacco users, and non-users over 4 months (four time points). Buccal swab and saliva samples (n = 611) were collected from 85 participants. DNA was extracted from all samples and sequencing was carried out on an Illumina MiSeq, targeting the V3-V4 region of the 16S rRNA gene. Cigarette and smokeless tobacco users had more diverse oral bacterial communities, including a higher relative abundance of Firmicutes and a lower relative abundance of Proteobacteria, when compared to non-users. Non-users had a higher relative abundance of Actinomyces, Granulicatella, Haemophilus, Neisseria, Oribacterium, Prevotella, Pseudomonas, Rothia, and Veillonella in buccal swab samples, compared to tobacco users. While the most abundant bacterial genera were relatively constant over time, some species demonstrated significant shifts in relative abundance between the first and last time points. In addition, some opportunistic pathogens were detected among tobacco users including Neisseria subflava, Bulleidia moorei and Porphyromonas endodontalis. Overall, our results provide a more holistic understanding of the structure of oral bacterial communities in tobacco users compared to non-users.
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Affiliation(s)
- Suhana Chattopadhyay
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Leena Malayil
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Jessica Chopyk
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Eoghan Smyth
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Prachi Kulkarni
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Greg Raspanti
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Stephen B Thomas
- Center for Health Equity, School of Public Health, University of Maryland, College Park, MD, USA
| | - Amir Sapkota
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD, USA
| | - Emmanuel F Mongodin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Lung Diseases, National Institutes of Health (NIH), National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Amy R Sapkota
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA.
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Wang S, Song F, Song M, Wei X, Zhou Y, Jiang L, Wang Z, Sun C, Yao H, Liang W, Luo H. Explore variation of salivary bacteria across time and geolocations. Int J Legal Med 2024; 138:547-554. [PMID: 37353677 DOI: 10.1007/s00414-023-03045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Saliva is an informative body fluid that can be found at various crime scenes, and the salivary bacterial community has been revealed it is a potential auxiliary target for forensic identification. However, the variation of salivary bacterial community composition across time and geolocation needs to be explored. The study was designed to be carried out during the winter vacation that was across about 50 days and eight geographic locations. The high throughput sequencing was performed with the V3-V4 region of the16S rRNA gene to explore salivary bacterial community composition. An overall slight fluctuation of the salivary bacteria was observed, which primarily occurred in the relative abundance of the salivary bacterial taxa. The results of principal coordinate analysis and hierarchical clustering showed samples were clustered by the individuals. All individuals could be correctly identified with the random forest model. In summation, although the relative abundance of salivary bacteria varied across the changes of time and geolocation, the individualized characteristic of salivary bacteria remained steady, which is beneficial for the salivary bacterial application in personal identification.
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Affiliation(s)
- Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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Solfisburg QS, Baldini F, Baldwin-Hunter B, Austin GI, Lee HH, Park H, Freedberg DE, Lightdale CJ, Korem T, Abrams JA. The Salivary Microbiome and Predicted Metabolite Production Are Associated with Barrett's Esophagus and High-Grade Dysplasia or Adenocarcinoma. Cancer Epidemiol Biomarkers Prev 2024; 33:371-380. [PMID: 38117184 PMCID: PMC10955687 DOI: 10.1158/1055-9965.epi-23-0652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/05/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Esophageal adenocarcinoma (EAC) is rising in incidence, and established risk factors do not explain this trend. Esophageal microbiome alterations have been associated with Barrett's esophagus (BE) and dysplasia and EAC. The oral microbiome is tightly linked to the esophageal microbiome; this study aimed to identify salivary microbiome-related factors associated with BE, dysplasia, and EAC. METHODS Clinical data and oral health history were collected from patients with and without BE. The salivary microbiome was characterized, assessing differential relative abundance of taxa by 16S rRNA gene sequencing and associations between microbiome composition and clinical features. Microbiome metabolic modeling was used to predict metabolite production. RESULTS A total of 244 patients (125 non-BE and 119 BE) were analyzed. Patients with high-grade dysplasia (HGD)/EAC had a significantly higher prevalence of tooth loss (P = 0.001). There were significant shifts with increased dysbiosis associated with HGD/EAC, independent of tooth loss, with the largest shifts within the genus Streptococcus. Modeling predicted significant shifts in the microbiome metabolic capacities, including increases in L-lactic acid and decreases in butyric acid and L-tryptophan production in HGD/EAC. CONCLUSIONS Marked dysbiosis in the salivary microbiome is associated with HGD and EAC, with notable increases within the genus Streptococcus and accompanying changes in predicted metabolite production. Further work is warranted to identify the biological significance of these alterations and to validate metabolic shifts. IMPACT There is an association between oral dysbiosis and HGD/EAC. Further work is needed to establish the diagnostic, predictive, and causal potential of this relationship.
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Affiliation(s)
- Quinn S Solfisburg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Federico Baldini
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - George I Austin
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Harry H Lee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Microbiome and Pathogen Genomics Collaborative Center, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Daniel E Freedberg
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles J Lightdale
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
- CIFAR Azrieli Global Scholars Program, CIFAR, Toronto, Canada
| | - Julian A Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY USA
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7
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Schmiedová L, Černá K, Li T, Těšický M, Kreisinger J, Vinkler M. Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time. Int Microbiol 2024; 27:127-142. [PMID: 37222909 PMCID: PMC10830831 DOI: 10.1007/s10123-023-00372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.
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Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Kateřina Černá
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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8
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Solfisburg QS, Baldini F, Baldwin-Hunter BL, Lee HH, Park H, Freedberg DE, Lightdale CJ, Korem T, Abrams JA. The Salivary Microbiome and Predicted Metabolite Production are Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546733. [PMID: 37425673 PMCID: PMC10327009 DOI: 10.1101/2023.06.27.546733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Esophageal adenocarcinoma (EAC) is rising in incidence and associated with poor survival, and established risk factors do not explain this trend. Microbiome alterations have been associated with progression from the precursor Barrett's esophagus (BE) to EAC, yet the oral microbiome, tightly linked to the esophageal microbiome and easier to sample, has not been extensively studied in this context. We aimed to assess the relationship between the salivary microbiome and neoplastic progression in BE to identify microbiome-related factors that may drive EAC development. We collected clinical data and oral health and hygiene history and characterized the salivary microbiome from 250 patients with and without BE, including 78 with advanced neoplasia (high grade dysplasia or early adenocarcinoma). We assessed differential relative abundance of taxa by 16S rRNA gene sequencing and associations between microbiome composition and clinical features and used microbiome metabolic modeling to predict metabolite production. We found significant shifts and increased dysbiosis associated with progression to advanced neoplasia, with these associations occurring independent of tooth loss, and the largest shifts were with the genus Streptococcus. Microbiome metabolic models predicted significant shifts in the metabolic capacities of the salivary microbiome in patients with advanced neoplasia, including increases in L-lactic acid and decreases in butyric acid and L-tryptophan production. Our results suggest both a mechanistic and predictive role for the oral microbiome in esophageal adenocarcinoma. Further work is warranted to identify the biological significance of these alterations, to validate metabolic shifts, and to determine whether they represent viable therapeutic targets for prevention of progression in BE.
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Affiliation(s)
- Quinn S Solfisburg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Federico Baldini
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Harry H Lee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Microbiome and Pathogen Genomics Collaborative Center, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Daniel E Freedberg
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles J Lightdale
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
- CIFAR Azrieli Global Scholars Program, CIFAR, Toronto, Canada
| | - Julian A Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY USA
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Cameron SJS, Edwards A, Lambert RJ, Stroud M, Mur LAJ. Participants in the Trans-Antarctic Winter Traverse Expedition Showed Increased Bacterial Load and Diversity in Saliva but Maintained Individual Differences within Stool Microbiota and Across Metabolite Fingerprints. Int J Mol Sci 2023; 24:ijms24054850. [PMID: 36902282 PMCID: PMC10002533 DOI: 10.3390/ijms24054850] [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: 01/27/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Understanding the impact of long-term physiological and environmental stress on the human microbiota and metabolome may be important for the success of space flight. This work is logistically difficult and has a limited number of available participants. Terrestrial analogies present important opportunities to understand changes in the microbiota and metabolome and how this may impact participant health and fitness. Here, we present work from one such analogy: the Transarctic Winter Traverse expedition, which we believe is the first assessment of the microbiota and metabolome from different bodily locations during prolonged environmental and physiological stress. Bacterial load and diversity were significantly higher during the expedition when compared with baseline levels (p < 0.001) in saliva but not stool, and only a single operational taxonomic unit assigned to the Ruminococcaceae family shows significantly altered levels in stool (p < 0.001). Metabolite fingerprints show the maintenance of individual differences across saliva, stool, and plasma samples when analysed using flow infusion electrospray mass spectrometry and Fourier transform infrared spectroscopy. Significant activity-associated changes in terms of both bacterial diversity and load are seen in saliva but not in stool, and participant differences in metabolite fingerprints persist across all three sample types.
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Affiliation(s)
- Simon J. S. Cameron
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Chlorine Gardens, Belfast BT9 5DL, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
| | - Robert J. Lambert
- Department of Orthopaedics, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Mike Stroud
- NIHR BRC Nutrition, University of Southampton Medical School, Southampton SO16 6YD, UK
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK
- Correspondence: (S.J.S.C.); (L.A.J.M.)
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10
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Tong F, Tang G, Wang X. Characteristics of Human and Microbiome RNA Profiles in Saliva. RNA Biol 2023; 20:398-408. [PMID: 37401028 PMCID: PMC10321209 DOI: 10.1080/15476286.2023.2229596] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/08/2023] [Accepted: 06/17/2023] [Indexed: 07/05/2023] Open
Abstract
Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers. By comparing the expression profiles of total RNA from these fractions, we found that MV was most enriched in microbiome RNA (76.2% of total reads on average), whereas EV-D was notably enriched in human RNA (70.3% of total reads on average). As for human RNA composition, CFS and EV-D were both enriched in snoRNA and tRNA compared with the two EV fractions (EXO and MV, P < 0.05). Interestingly, EXO and MV had highly correlated expression profiles for various noncoding RNAs such as miRNA, tRNA, and yRNA. Our study revealed unique characteristics of circulating RNAs in various saliva fractions, which provides a guideline on preparing saliva samples to study specific RNA biomarkers of interest.
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Affiliation(s)
- Fangjia Tong
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
| | - Gongyu Tang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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12
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Li X, Zhao K, Chen J, Ni Z, Yu Z, Hu L, Qin Y, Zhao J, Peng W, Lu L, Gao X, Sun H. Diurnal changes of the oral microbiome in patients with alcohol dependence. Front Cell Infect Microbiol 2022; 12:1068908. [PMID: 36579346 PMCID: PMC9791055 DOI: 10.3389/fcimb.2022.1068908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background Saliva secretion and oral microbiota change in rhythm with our biological clock. Dysbiosis of the oral microbiome and alcohol consumption have a two-way interactive impact, but little is known about whether the oral microbiome undergoes diurnal changes in composition and function during the daytime in patients with alcohol dependence (AD). Methods The impact of alcohol consumption on the diurnal salivary microbiome was examined in a case-control study of 32 AD patients and 21 healthy control (HC) subjects. We tested the changes in microbial composition and individual taxon abundance by 16S rRNA gene sequencing. Results The present study is the first report showing that alcohol consumption enhanced the richness of the salivary microbiome and lowered the evenness. The composition of the oral microbiota changed significantly in alcohol-dependent patients. Additionally, certain genera were enriched in the AD group, including Actinomyces, Leptotrichia, Sphaerochaeta and Cyanobacteria, all of which have pathogenic effects on the host. There is a correlation between liver enzymes and oral microbiota. KEGG function analysis also showed obvious alterations during the daytime. Conclusion Alcohol drinking influences diurnal changes in the oral microbiota, leading to flora disturbance and related functional impairment. In particular, the diurnal changes of the oral microbiota may open avenues for potential interventions that can relieve the detrimental consequences of AD.
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Affiliation(s)
- Xiangxue Li
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Kangqing Zhao
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jie Chen
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Zhaojun Ni
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Zhoulong Yu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Lingming Hu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Ying Qin
- Addiction Medicine Department, The Second People’s Hospital of Guizhou Province, Guizhou, China
| | - Jingwen Zhao
- Addiction Medicine Department, The Second People’s Hospital of Guizhou Province, Guizhou, China
| | - Wenjuan Peng
- Addiction Medicine Department, The Second People’s Hospital of Guizhou Province, Guizhou, China
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xuejiao Gao
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China,*Correspondence: Xuejiao Gao, ; Hongqiang Sun,
| | - Hongqiang Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China,*Correspondence: Xuejiao Gao, ; Hongqiang Sun,
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13
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Shenker NS, Perdones-Montero A, Burke A, Stickland S, McDonald JAK, Cameron SJS. Human Milk from Tandem Feeding Dyads Does Not Differ in Metabolite and Metataxonomic Features When Compared to Single Nursling Dyads under Six Months of Age. Metabolites 2022; 12:metabo12111069. [PMID: 36355152 PMCID: PMC9696481 DOI: 10.3390/metabo12111069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Given the long-term advantages of exclusive breastfeeding to infants and their mothers, there is both an individual and public health benefit to its promotion and support. Data on the composition of human milk over the course of a full period of lactation for a single nursling is sparse, but data on human milk composition during tandem feeding (feeding children of different ages from different pregnancies) is almost entirely absent. This leaves an important knowledge gap that potentially endangers the ability of parents to make a fully informed choice on infant feeding. We compared the metataxonomic and metabolite fingerprints of human milk samples from 15 tandem feeding dyads to that collected from ten exclusively breastfeeding single nursling dyads where the nursling is under six months of age. Uniquely, our cohort also included three tandem feeding nursling dyads where each child showed a preferential side for feeding-allowing a direct comparison between human milk compositions for different aged nurslings. Across our analysis of volume, total fat, estimation of total microbial load, metabolite fingerprinting, and metataxonomics, we showed no statistically significant differences between tandem feeding and single nursling dyads. This included comparisons of preferential side nurslings of different ages. Together, our findings support the practice of tandem feeding of nurslings, even when feeding an infant under six months.
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Affiliation(s)
- Natalie S. Shenker
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Adam Burke
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Sarah Stickland
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Julie A. K. McDonald
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Simon J. S. Cameron
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
- Correspondence: ; Tel.: +44-(0)28-9097-6421
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14
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Jiang X, Zhang Y, Wang H, Wang Z, Hu S, Cao C, Xiao H. In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer. Research (Wash D C) 2022; 2022:9781578. [PMID: 36320634 PMCID: PMC9590273 DOI: 10.34133/2022/9781578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method, the number of interfering peptides decreased by 52.87%, whereas the bacterial peptides and species increased by 94.97% and 44.90%, respectively, compared to the conventional metaproteomics approach. We identified 3647 bacterial proteins, which is the most comprehensive oral metaproteomics study to date. Lung cancer-associated bacteria were validated among an independent cohort. The imbalanced Fusobacterium nucleatum and Prevotella histicola and their dysregulated functions in inhibiting immune response and maintaining cell redox homeostasis were revealed. The FFIEF-MS may serve as a valuable strategy to study the mechanisms between human diseases and microbiomes with broader applications.
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Affiliation(s)
- Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shen Hu
- School of Dentistry and Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles 90095, USA
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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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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16
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Liddle L, Monaghan C, Burleigh MC, Baczynska KA, Muggeridge DJ, Easton C. Reduced nitric oxide synthesis in winter: A potential contributing factor to increased cardiovascular risk. Nitric Oxide 2022; 127:1-9. [PMID: 35792235 DOI: 10.1016/j.niox.2022.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Nitric oxide is a key signalling molecule that elicits a range of biological functions to maintain vascular homeostasis. A reduced availability of nitric oxide is implicated in the progression of cardiovascular diseases and increases the risk of pathogenic events. AIMS To compare the concentration of nitric oxide metabolites in healthy adults between winter and summer months. DESIGN An observational study of healthy adults (age 32 ± 9 years) living in central Scotland. METHODS Thirty-four healthy adults (13 females) were monitored for 7 days in summer and winter to record sunlight exposure (ultraviolet-A (UV-A) radiation), diet, and physical activity. At the end of each phase, blood pressure was measured, and samples of blood and saliva collected. The samples were analysed to determine the concentrations of plasma and salivary nitrate and nitrite and serum 25-hydroxyvitamin D (25(OH)D). RESULTS The participants maintained similar diets in each measurement phase but were exposed to more UV-A radiation (550%) and undertook more moderate-vigorous physical activity (23%) in the summer than in winter. Plasma nitrite (46%) and serum 25(OH)D (59%) were higher and blood pressure was lower in the summer compared to winter months. Plasma nitrite concentration was negatively associated with systolic, diastolic, and mean arterial blood pressure. CONCLUSIONS Plasma nitrite, an established marker of nitric oxide synthesis, is higher in healthy adults during the summer than in winter. This may be mediated by a greater exposure to UV-A which stimulates the release of nitric oxide metabolites from skin stores. While it is possible that seasonal variation in nitric oxide availability may contribute to an increased blood pressure in the winter months, the overall impact on cardiovascular health remains to be determined.
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Affiliation(s)
- Luke Liddle
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK; School of Sport and Health Sciences, St. Luke's Campus, University of Exeter, Exeter, UK
| | - Christopher Monaghan
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK
| | - Mia C Burleigh
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK
| | - Katarzyna A Baczynska
- Laser and Optical Radiation Dosimetry Group, Centre for Radiation, Chemical and Environmental Hazards, UK Health Security Agency, Chilton, UK
| | | | - Chris Easton
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK.
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17
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Yabuuchi S, Oiki S, Minami S, Takase R, Watanabe D, Hashimoto W. Enhanced propagation of Granulicatella adiacens from human oral microbiota by hyaluronan. Sci Rep 2022; 12:10948. [PMID: 35768476 PMCID: PMC9243090 DOI: 10.1038/s41598-022-14857-9] [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: 10/29/2021] [Accepted: 06/14/2022] [Indexed: 11/29/2022] Open
Abstract
Host determinants for formation/composition of human oral microbiota remain to be clarified, although microorganisms entering the mouth cannot necessarily colonize the oral environment. Here we show that human oral-abundant bacteria degraded host glycosaminoglycans (GAGs) in saliva and gingiva, and certain bacteria significantly grew on hyaluronan (HA), a kind of GAGs. Microbial communities from teeth or gingiva of healthy donors assimilated HA. Metagenomic analysis of human oral microbiota under different carbon sources revealed HA-driven Granulicatella growth. HA-degrading bacterial strains independently isolated from teeth and gingiva were identified as Granulicatella adiacens producing extracellular 130 kDa polysaccharide lyase as a HA-degrading enzyme encoded in a peculiar GAG genetic cluster containing genes for isomerase KduI and dehydrogenase DhuD. These findings demonstrated that GAGs are one of the host determinants for formation/composition of oral microbiota not only for colonization but also for the adaptation to the host niche. Especially, HA enhanced the G. adiacens propagation.
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Affiliation(s)
- Shun Yabuuchi
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Sayoko Oiki
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Shuma Minami
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ryuichi Takase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Daisuke Watanabe
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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18
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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Hao Z, Zhu Y, Fu Y, Yang J, Meng C, Dong C, Liu H. Effects of Long-Term Enclosed Environment on Human Health Based on the Analysis of Salivary Microbiota and Cytokines. Microbiol Spectr 2022; 10:e0025422. [PMID: 35254118 PMCID: PMC9045383 DOI: 10.1128/spectrum.00254-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 11/20/2022] Open
Abstract
The long-term exposure to enclosed environments may lead to chronic stress in crewmembers and affect their physical and mental state. Salivary microbiome and biomarkers of immune function are increasingly used in human health research. The "Lunar Palace 365" project, which was a 370-day, multicrew, enclosed experiment carried out in a ground-based bioregenerative life support system platform named Lunar Palace 1 (LP1). We investigated the temporal dynamics of the salivary microbiota and cytokines in the third phase of the "Lunar Palace 365" experiment, including 1 month before entering LP1 and 1 month after leaving Lp1. Results reveal no regular temporal change pattern in these parameters (highly abundant phyla and genera) during the experiment. Although the crewmembers' oral microbiota temporally changed, it recovered quickly after the study subjects left the enclosed environment. The levels of IL-6, IL-10, and TNF-α in crewmembers' saliva decreased after leaving the normal environment for the enclosed environment, indicating that their oral inflammatory response level was reduced. There were significant individual differences in crewmembers' salivary microbiota, however, the shared living space reduced these differences. Moreover, air microbiota might have also played a significant role in reducing the individual differences. In summary, the enclosed environment did not result in persistent changes in human salivary microbiota and oral immunity. This study provides some insights for studying the effect of enclosed controlled environments on human immunity and microbiome. IMPORTANCE Long-term exposure to space environments may influence the human microbiome, the human immune system, and the intricate balance between the two, causing impaired immunity and increased disease susceptibility. It was previously believed that the main potential factors of long-term spaceflight on human health were microgravity and radiation. However, the effects of long-term enclosed environments on human health were unclear. Bioregenerative life support systems (BLSS) is a good experimental model for studying the effects of enclosed environments on human systemic microbiota and immune disorders. We monitored the microbiota and cytokines in the saliva of crewmembers before they entered BLSS, during their stay in BLSS, and after leaving BLSS. The results indicated long-term closed environment will not cause persistent changes in human salivary microbiota and immunity.
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Affiliation(s)
- Zikai Hao
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- State Key Laboratory of Software Development Environment, School of Computer Science and Engineering, Beihang University, Beijing, China
| | - Yinzhen Zhu
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Yuming Fu
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, China
| | - Jianlou Yang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Chen Meng
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Chen Dong
- Laboratory of Sport Nutrition and Intelligent Cooking, Shandong Sport University, Jinan, China
| | - Hong Liu
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, China
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20
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La X, Jiang H, Chen A, Zheng H, Shen L, Chen W, Yang F, Zhang L, Cai X, Mao H, Cheng L. Profile of the oral microbiota from preconception to the third trimester of pregnancy and its association with oral hygiene practices. J Oral Microbiol 2022; 14:2053389. [PMID: 35341210 PMCID: PMC8942530 DOI: 10.1080/20002297.2022.2053389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The oral microbiota plays vital roles in both oral and systemic health, but limited studies have explored the transition of the female oral microbiota from preconception to pregnancy along with pronounced hormonal fluctuations. Aim To characterize the oral microbiota among women in preconception and pregnancy through a prospective study and to explore the associations between the oral microbiota and oral hygiene practices. Methods A total of 202 unstimulated saliva samples were collected from 101 women in both preconception and late pregnancy. The oral microbiota was analyzed using 16S rRNA gene sequencing. Results The Ace and phylogenetic diversity (PD) index were significantly lower in the third trimester than preconception. The pathogenic taxa Prevotella and Atopobium parvulum were significantly higher during late pregnancy than preconception. Women with overall better oral hygiene practice showed lower richness and diversity in preconception compared to women with poorer oral hygiene practice. The abundance of pathogens such as Dialister during both preconception and pregnancy decreased among women with better oral hygiene practice. Conclusions The composition of the oral microbiota changed slightly from preconception to late pregnancy, with more pathogens in saliva samples during pregnancy. Improving oral hygiene practices has the potential to maintain oral micro-ecological balance.
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Affiliation(s)
- Xuena La
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China.,Department of Non-communicable Diseases Surveillance, Shanghai Municipal Center for Disease Control and Prevention (SCDC), Changning District, Shanghai,China
| | - Hong Jiang
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China
| | - An Chen
- Institute of Healthcare Engineering, Management and Architecture (HEMA), Department of Industrial Engineering and Management, Aalto University, Espoo, Finland
| | - Huajun Zheng
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Xuhui District, Shanghai,China
| | - Liandi Shen
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Weiyi Chen
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China
| | - Fengyun Yang
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Lifeng Zhang
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Xushan Cai
- Department of Woman Health care, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai, China
| | - Hongfang Mao
- Department of Woman Health care, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai, China
| | - Lu Cheng
- Department of Computer Science, Aalto University, Espoo, Finland
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21
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Chang S, Guo H, Li J, Ji Y, Jiang H, Ruan L, Du M. Comparative Analysis of Salivary Mycobiome Diversity in Human Immunodeficiency Virus-Infected Patients. Front Cell Infect Microbiol 2021; 11:781246. [PMID: 34926323 PMCID: PMC8671614 DOI: 10.3389/fcimb.2021.781246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Reports on alterations in the oral mycobiome of HIV-infected patients are still limited. This study was designed to compare the salivary mycobiome between 30 human immunodeficiency virus (HIV) infections and 30 healthy controls and explore the effect of antiretroviral therapy (ART) administration on the oral mycobiome of HIV infections. Results showed that the diversity and richness of salivary mycobiome in HIV-infected individuals were higher than those of controls (P < 0.05). After ART, the diversity and richness of salivary mycobiome in HIV-infected patients were reduced significantly (P < 0.05). Candida, Mortierella, Malassezia, Simplicillium, and Penicillium were significantly enriched in the HIV group and dramatically decreased after ART. While the relative abundance of Verticillium, Issatchenkia, and Alternaria significantly increased in patients with HIV after ART. Correlation analysis revealed that Mortierella, Malassezia, Simplicillium, and Chaetomium were positively correlated with viral load (VL), whereas Thyrostroma and Archaeorhizomyces were negatively related to VL and positively related to CD4+ T-cell counts. All results showed that HIV infection and ART administration affected the composition of salivary mycobiome communities. Furthermore, differences of salivary mycobiome in HIV infections after ART were complex and might mirror the immune state of the body.
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Affiliation(s)
- Shenghua Chang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Haiying Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jin Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaoting Ji
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Han Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lianguo Ruan
- Department of Infectious Diseases Treatment, Wuhan Medical Treatment Center, Wuhan, China
| | - Minquan Du
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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22
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Mishra K, Bukavina L, Ghannoum M. Symbiosis and Dysbiosis of the Human Mycobiome. Front Microbiol 2021; 12:636131. [PMID: 34630340 PMCID: PMC8493257 DOI: 10.3389/fmicb.2021.636131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.
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Affiliation(s)
- Kirtishri Mishra
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Laura Bukavina
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mahmoud Ghannoum
- Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Center for Medical Mycology, and Integrated Microbiome Core, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Dermatology, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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23
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Kim J, Lee M, Baldwin-Hunter B, Solfisburg QS, Lightdale CJ, Korem T, Hur C, Abrams JA. Minimal Associations between Short-Term Dietary Intake and Salivary Microbiome Composition. Microorganisms 2021; 9:microorganisms9081739. [PMID: 34442819 PMCID: PMC8401849 DOI: 10.3390/microorganisms9081739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 12/01/2022] Open
Abstract
Background: Increasing evidence points to the esophageal microbiome as an important co-factor in esophageal neoplasia. Esophageal microbiome composition is strongly influenced by the oral microbiome. Salivary microbiome assessment has emerged as a potential non-invasive tool to identify patients at risk for esophageal cancer, but key host and environmental factors that may affect the salivary microbiome have not been well-defined. This study aimed to evaluate the impact of short-term dietary intake on salivary microbiome composition. Methods: Saliva samples were collected from 69 subjects prior to upper endoscopy who completed the Automated Self-Administered 24-Hour (ASA24) Dietary Assessment. Salivary microbiome composition was determined using 16S rRNA amplicon sequencing. Results: There was no significant correlation between alpha diversity and primary measures of short-term dietary intake (total daily calories, fat, fiber, fruit/vegetables, red meat intake, and fasting time). There was no evidence of clustering on beta diversity analyses. Very few taxonomic alterations were found for short-term dietary intake; an increased relative abundance of Neisseria oralis and Lautropia sp. was associated with high fruit and vegetable intake, and an increased relative abundance of a taxon in the family Gemellaceae was associated with increased red meat intake. Conclusions: Short-term dietary intake was associated with only minimal salivary microbiome alterations and does not appear to have a major impact on the potential use of the salivary microbiome as a biomarker for esophageal neoplasia.
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Affiliation(s)
- Judith Kim
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; (J.K.); (B.B.-H.); (C.J.L.); (C.H.)
| | - Minyi Lee
- School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Brittany Baldwin-Hunter
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; (J.K.); (B.B.-H.); (C.J.L.); (C.H.)
| | - Quinn S. Solfisburg
- Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Charles J. Lightdale
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; (J.K.); (B.B.-H.); (C.J.L.); (C.H.)
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA;
| | - Chin Hur
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; (J.K.); (B.B.-H.); (C.J.L.); (C.H.)
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; (J.K.); (B.B.-H.); (C.J.L.); (C.H.)
- Correspondence:
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24
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Bacci G, Mengoni A, Emiliani G, Chiellini C, Cipriani EG, Bianconi G, Canganella F, Fani R. Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission. MICROBIOME 2021; 9:152. [PMID: 34193273 PMCID: PMC8247138 DOI: 10.1186/s40168-021-01070-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission, six crewmembers lived completely isolated from the outer world for 520 days following standardized diet regimes. The mission constitutes the first spaceflight simulation to Mars and was a unique experiment to determine, in a longitudinal study design, the composition and importance of the resident vs. a more variable microbiota-the fraction of the human microbiota that changes in time and according to environmental conditions-in humans. METHODS Here, we report the characterization of the salivary microbiota from 88 samples taken during and after Mars500 mission for a total of 720 days. Amplicon sequencing of the V3-V4 regions of 16S rRNA gene was performed, and results were analyzed monitoring the diversity of the microbiota while evaluating the effect of the three main variables present in the experimental system: time, diet, and individuality of each subject. RESULTS Results showed statistically significant effects for either time, diet, and individuality of each subject. The main contribution came from the individuality of each subject, emphasizing salivary microbiota-personalized features, and an individual-based resilience of the microbiota. CONCLUSIONS The uniqueness of Mars500 mission, allowed to dampen the effect of environmental variables on salivary microbiota, highlighting its pronounced personalization even after sharing the same physical space for more than a year. Video abstract.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
| | - Giovanni Emiliani
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Carolina Chiellini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Edoardo Giovanni Cipriani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
| | - Giovanna Bianconi
- Department of Biological, Agricultural and Forestry Sciences, Università della Tuscia, Via San Camillo de Lellis snc, I-01100 Viterbo, Italy
| | - Francesco Canganella
- Department of Biological, Agricultural and Forestry Sciences, Università della Tuscia, Via San Camillo de Lellis snc, I-01100 Viterbo, Italy
- Embassy of Italy, 98 Hannam-daero, Hannam-dong, Yongsan-gu, Seoul, South Korea
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
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25
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Abstract
The central theme of this volume of Periodontology 2000 is that the microbial dental plaque biofilm, specifically the subgingival dental plaque biofilm, mimics a human tissue in both structure and function. As a basis for this assertion we use the definition of a tissue as an aggregate of similar cells and cell products forming a defined structure with a specific function, in a multicellular organism. Accordingly, we propose that the dental plaque biofilm represents an acquired human tissue largely of bacterial origin that maintains the health of gingival tissue. Furthermore, we acknowledge that disease can be defined as a deviation from the normal structure or an interruption to the function of any body part, organ, or system, and that is manifested by a characteristic set of symptoms and signs whose etiology, pathology, and prognosis may be known or unknown. Therefore, in this volume we present the concept that periodontitis is a disruption of the normal function of the healthy subgingival plaque biofilm with concomitant disruption to its functional properties in relation to innate defense surveillance and tissue maintenance, leading to excessive, deregulated inflammation and tissue destruction.
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Affiliation(s)
- Richard P Darveau
- Department of Periodontics, University of Washington, Seattle, Washington, USA
| | - Michael A Curtis
- Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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26
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Hollingsworth BA, Cassatt DR, DiCarlo AL, Rios CI, Satyamitra MM, Winters TA, Taliaferro LP. Acute Radiation Syndrome and the Microbiome: Impact and Review. Front Pharmacol 2021; 12:643283. [PMID: 34084131 PMCID: PMC8167050 DOI: 10.3389/fphar.2021.643283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022] Open
Abstract
Study of the human microbiota has been a centuries-long endeavor, but since the inception of the National Institutes of Health (NIH) Human Microbiome Project in 2007, research has greatly expanded, including the space involving radiation injury. As acute radiation syndrome (ARS) is multisystemic, the microbiome niches across all areas of the body may be affected. This review highlights advances in radiation research examining the effect of irradiation on the microbiome and its potential use as a target for medical countermeasures or biodosimetry approaches, or as a medical countermeasure itself. The authors also address animal model considerations for designing studies, and the potential to use the microbiome as a biomarker to assess radiation exposure and predict outcome. Recent research has shown that the microbiome holds enormous potential for mitigation of radiation injury, in the context of both radiotherapy and radiological/nuclear public health emergencies. Gaps still exist, but the field is moving forward with much promise.
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Affiliation(s)
- Brynn A Hollingsworth
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - David R Cassatt
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Andrea L DiCarlo
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Carmen I Rios
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Merriline M Satyamitra
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Thomas A Winters
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
| | - Lanyn P Taliaferro
- Radiation and Nuclear Countermeasures Program (RNCP), Division of Allergy, Immunology and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States
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27
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Wang Y, Zhang Y, Wang Z, Tang J, Cao DX, Qian Y, Xie YH, Chen HY, Chen YX, Chen ZF, Fang JY. A clinical nomogram incorporating salivary Desulfovibrio desulfuricans level and oral hygiene index for predicting colorectal cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:754. [PMID: 34268367 PMCID: PMC8246182 DOI: 10.21037/atm-20-8168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023]
Abstract
Background Emerging evidence demonstrates that the salivary microbiome could serve as a biomarker for various diseases. To date, the oral microbiome’s role in the diagnosis of colorectal cancer (CRC) has not been fully elucidated. We aimed to illustrate the salivary microbiome’s role in diagnosing and predicting the risk of CRC. Methods We collected preoperational saliva from 237 patients [95 healthy controls (HCs) and 142 CRC patients] who underwent surgical resections or colorectal endoscopy in Renji Hospital from January 2018 to January 2020. Clinical demographics, comorbidities, and oral health conditions were obtained from medical records or questionnaires. Salivary microbial biomarkers were detected using quantitative polymerase chain reaction (qPCR) after DNA extraction. Multivariate logistic regression analysis was employed to analyze the risk factors for CRC. A predictive model for the risk of developing CRC was constructed based on logistic regression analysis. Predictive accuracy was internally validated by bootstrap resampling. A clinical nomogram was constructed to visualize the predictive model. Results Logistic regression analysis demonstrated that the risk factors associated with CRC included age at diagnosis, male sex, poor oral hygiene, and relative salivary Desulfovibrio desulfuricans abundance. The predictive model had good discriminative (0.866) and calibration abilities (0.834) after bias correction. Conclusions The model based on age, sex, oral hygiene index (OHI), and the salivary Desulfovibrio desulfuricans level, which is visualized by a clinical nomogram, can predict the risk of CRC. Developing good oral hygiene habits might reduce the risk of CRC.
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Affiliation(s)
- Yao Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yao Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zheng Wang
- Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Tang
- Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Xing Cao
- Department of General Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yuan-Hong Xie
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Hai-Ying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhao-Fei Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
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28
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales P, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand LA, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. eLife 2021; 10:e65113. [PMID: 33779548 PMCID: PMC8057811 DOI: 10.7554/elife.65113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification. The test has two steps: (1) heat saliva with a stabilization solution and (2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado BoulderBoulderUnited States
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado BoulderBoulderUnited States
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Patrick Gonzales
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Jack C Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado BoulderBoulderUnited States
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Leslie A Leinwand
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Roy Parker
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
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29
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Abstract
The human mouth harbors a complex microbiota, the composition of which is potentially influenced by a wide range of factors, including the intake of food and drink, the availability of endogenous nutrients, the host immune system, drug treatments, and systemic diseases. Despite these possible influences, the oral microbiota is remarkably resilient, particularly in comparison with the microbiota of the large intestine. Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community. The common oral diseases dental caries and the periodontal diseases is associated with modification of the oral microbiota primarily as a result of the ecological changes induced by excessive acid production and inflammation, respectively. Systemically-administered antimicrobials have only a small effect on the composition of the oral bacterial community, and while locally delivered antimicrobials can have some clinical benefits, the biofilm lifestyle of oral bacteria lends them substantial resistance to the agents used. Saliva plays an important role in oral microbial ecology, by supplying nutrients and providing protection against colonization by nonoral organisms. Dry mouth is one condition that has a major effect on the microbiota, resulting in increased colonization by opportunistic pathogens. Some systemic diseases do affect the oral microbiome, notably diabetes, in which raised levels of glucose in saliva and tissue impact on bacterial nutrition.
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Affiliation(s)
- William G Wade
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.,Department of Microbiology, Forsyth Institute, Cambridge, MA, USA
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30
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand L, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.16.20150250. [PMID: 33619503 PMCID: PMC7899473 DOI: 10.1101/2020.07.16.20150250] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification (RT-LAMP). The test has two steps: 1) heat saliva with a stabilization solution, and 2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Patrick K Gonzales
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Jack C Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Leslie Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
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Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load. mSystems 2021; 6:6/1/e01182-20. [PMID: 33594005 PMCID: PMC8561659 DOI: 10.1128/msystems.01182-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evaluating microbial community composition through next-generation sequencing has become increasingly accessible. However, metagenomic sequencing data sets provide researchers with only a snapshot of a dynamic ecosystem and do not provide information about the total microbial number, or load, of a sample. Additionally, DNA can be detected long after a microorganism is dead, making it unsafe to assume that all microbial sequences detected in a community came from living organisms. By combining relic DNA removal by propidium monoazide (PMA) with microbial quantification with flow cytometry, we present a novel workflow to quantify live microbial load in parallel with metagenomic sequencing. We applied this method to unstimulated saliva samples, which can easily be collected longitudinally and standardized by passive collection time. We found that the number of live microorganisms detected in saliva was inversely correlated with salivary flow rate and fluctuated by an order of magnitude throughout the day in healthy individuals. In an acute perturbation experiment, alcohol-free mouthwash resulted in a massive decrease in live bacteria, which would have been missed if we did not consider dead cell signal. While removing relic DNA from saliva samples did not greatly impact the microbial composition, it did increase our resolution among samples collected over time. These results provide novel insight into the dynamic nature of host-associated microbiomes and underline the importance of applying scale-invariant tools in the analysis of next-generation sequencing data sets. IMPORTANCE Human microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples. Microbial load was inversely correlated with salivary flow rate and fluctuated by an order of magnitude within a single participant throughout the day. Removing relic DNA improved our ability to distinguish samples over time and revealed that the percentage of sequenced bacteria in a given saliva sample that are alive can range from nearly 0% up to 100% throughout a typical day. These findings highlight the dynamic ecosystem of the human oral microbiome and the benefit of removing relic DNA signals in longitudinal microbiome study designs.
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Zaura E, Pappalardo VY, Buijs MJ, Volgenant CMC, Brandt BW. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. Periodontol 2000 2021; 85:210-236. [PMID: 33226702 PMCID: PMC7756869 DOI: 10.1111/prd.12359] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided.
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Affiliation(s)
- Egija Zaura
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Vincent Y. Pappalardo
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Mark J. Buijs
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Catherine M. C. Volgenant
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Bernd W. Brandt
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
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Bach LL, Ram A, Ijaz UZ, Evans TJ, Lindström J. A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease. Front Microbiol 2021; 11:573969. [PMID: 33552004 PMCID: PMC7861042 DOI: 10.3389/fmicb.2020.573969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.
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Affiliation(s)
- Lydia Luise Bach
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Asha Ram
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Thomas J. Evans
- Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Jan Lindström
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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Abstract
Evidence on the role of the oral microbiome in health and disease is changing the way we understand, diagnose, and treat ailments. Numerous studies on diseases affecting the oral cavity have revealed a large amount of data that is invaluable for the advancements in diagnosing and treating these diseases. However, the clinical translation of most of these exploratory data is stalled by variable methodology between studies and non-uniform reporting of the data.Understanding the key areas that are gateways to bias in microbiome studies is imperative to overcome this challenge faced by oral microbiome research. Bias can be multifactorial and may be introduced in a microbiome research study during the formulation of the study design, sample collection and storage, or the sample processing protocols before sequencing. This chapter summarizes the recommendations from literature to eliminate bias in the microbiome research studies and to ensure the reproducibility of the microbiome research data.
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Affiliation(s)
- Divya Gopinath
- Oral Diagnostic & Surgical Sciences Department, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia.
| | - Rohit Kunnath Menon
- Clinical Dentistry (Prosthodontics), School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
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35
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Metabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months. Nutrients 2020; 12:nu12113450. [PMID: 33187120 PMCID: PMC7697254 DOI: 10.3390/nu12113450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023] Open
Abstract
Sparse data exist regarding the normal range of composition of maternal milk beyond the first postnatal weeks. This single timepoint, observational study in collaboration with the ‘Parenting Science Gang’ citizen science group evaluated the metabolite and bacterial composition of human milk from 62 participants (infants aged 3–48 months), nearly 3 years longer than previous studies. We utilised rapid evaporative ionisation mass spectrometry (REIMS) for metabolic fingerprinting and 16S rRNA gene metataxonomics for microbiome composition analysis. Milk expression volumes were significantly lower beyond 24 months of lactation, but there were no corresponding changes in bacterial load, composition, or whole-scale metabolomic fingerprint. Some individual metabolite features (~14%) showed altered abundances in nursling age groups above 24 months. Neither milk expression method nor nursling sex affected metabolite and metataxonomic fingerprints. Self-reported lifestyle factors, including diet and physical traits, had minimal impact on metabolite and metataxonomic fingerprints. Our findings suggest remarkable consistency in human milk composition over natural-term lactation. The results add to previous studies suggesting that milk donation can continue up to 24 months postnatally. Future longitudinal studies will confirm the inter-individual and temporal nature of compositional variations and the use of donor milk as a personalised therapeutic.
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Verma D, Srivastava A, Garg PK, Akhter Y, Dubey AK, Mishra S, Deo SVS. Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population. Arch Microbiol 2020; 203:927-939. [PMID: 33084948 DOI: 10.1007/s00203-020-02084-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/26/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023]
Abstract
Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India.
| | - Ankita Srivastava
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Pankaj Kumar Garg
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, Uttrakhand, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Ashok Kumar Dubey
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - SukhDev Mishra
- Department of Bio-Statistics and Data Management, ICMR-National Institute of Occupational Health, Ahmedabad, India
| | - S V S Deo
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
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Eisenhofer R, Kanzawa-Kiriyama H, Shinoda KI, Weyrich LS. Investigating the demographic history of Japan using ancient oral microbiota. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190578. [PMID: 33012223 PMCID: PMC7702792 DOI: 10.1098/rstb.2019.0578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Raphael Eisenhofer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.,Department of Anthropology and the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
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38
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Omori M, Kato-Kogoe N, Sakaguchi S, Fukui N, Yamamoto K, Nakajima Y, Inoue K, Nakano H, Motooka D, Nakano T, Nakamura S, Ueno T. Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods. Clin Oral Investig 2020; 25:2779-2789. [PMID: 32975702 DOI: 10.1007/s00784-020-03592-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/15/2020] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis. MATERIALS AND METHODS Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data. RESULTS The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor. CONCLUSIONS Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected. CLINICAL RELEVANCE The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods.
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Affiliation(s)
- Michi Omori
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Nahoko Kato-Kogoe
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan.
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Nozomu Fukui
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Kayoko Yamamoto
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Yoichiro Nakajima
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Kazuya Inoue
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Hiroyuki Nakano
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Takaaki Ueno
- Department of Dentistry and Oral Surgery, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki City, Osaka, 569-8686, Japan
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Raju SC, Viljakainen H, Figueiredo RAO, Neuvonen PJ, Eriksson JG, Weiderpass E, Rounge TB. Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition. MICROBIOME 2020; 8:121. [PMID: 32825849 PMCID: PMC7441731 DOI: 10.1186/s40168-020-00893-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/13/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects by gender and AMs. We used data from 808 randomly selected children in the Finnish Health In Teens (Fin-HIT) cohort with register-based data on AM purchases from the Social Insurance Institution of Finland. Saliva microbiota was assessed with 16S rRNA (V3-V4) sequencing. The sequences were aligned to the SILVA ribosomal RNA database and classified and counted using the mothur pipeline. Associations between AM use and alpha-diversity (Shannon index) were identified with linear regression, while associations between beta-diversity (Bray-Curtis dissimilarity) and low, medium or high AM use were identified with PERMANOVA. RESULTS Of the children, 53.6% were girls and their mean age was 11.7 (0.4) years. On average, the children had 7.4 (ranging from 0 to 41) AM prescriptions during their lifespan. The four most commonly used AMs were amoxicillin (n = 2622, 43.7%), azithromycin (n = 1495, 24.9%), amoxicillin-clavulanate (n = 1123, 18.7%) and phenoxymethylpenicillin (n = 408, 6.8%). A linear inverse association was observed between the use of azithromycin and Shannon index (b - 0.015, p value = 0.002) in all children, the effect was driven by girls (b - 0.032, p value = 0.001), while not present in boys. Dissimilarities were marked between high, medium and low users of all AMs combined, in azithromycin users specifically, and in boys with amoxicillin use. Amoxicillin and amoxicillin-clavulanate use was associated with the largest decrease in abundance of Rikenellaceae. AM use in general and phenoxymethylpenicillin specifically were associated with a decrease of Paludibacter and pathways related to amino acid degradations differed in proportion between high and low AM users. CONCLUSIONS A systematic approach utilising reliable registry data on lifetime use of AMs demonstrated long-term effects on saliva microbiota diversity and composition. These effects are gender- and AM-dependent. We found that frequent lifelong use of AMs shifts bacterial profiles years later, which might have unforeseen health impacts in the future. Our findings emphasise a concern for high azithromycin use, which substantially decreases bacterial diversity and affects composition as well. Further studies are needed to determine the clinical implications of our findings. Video Abstract.
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Affiliation(s)
- Sajan C Raju
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Heli Viljakainen
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250, Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Rejane A O Figueiredo
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pertti J Neuvonen
- Department of Clinical Pharmacology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johan G Eriksson
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Trine B Rounge
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250, Helsinki, Finland.
- Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Research, Cancer Registry of Norway, Oslo, Norway.
- Department of Informatics, University of Oslo, Oslo, Norway.
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40
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Jiang X, Liu S, Zhang Y, Ji Y, Sohail A, Cao C, Wang P, Xiao H. Free-Flow Isoelectric Focusing for Comprehensive Separation and Analysis of Human Salivary Microbiome for Lung Cancer. Anal Chem 2020; 92:12017-12025. [DOI: 10.1021/acs.analchem.0c02627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Pharmaceutical Co., Ltd., Nanjing 210042, Jiangsu, China
| | - Amir Sohail
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Pharmaceutical Co., Ltd., Nanjing 210042, Jiangsu, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Yang J, Yao S, Cheng K, Xu L, Hou L, Wei Y, Feng H, Yu X, Zhang X, Tong X, Li Z, Zhao Y. Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS). Front Microbiol 2020; 11:1139. [PMID: 32582089 PMCID: PMC7283445 DOI: 10.3389/fmicb.2020.01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/05/2020] [Indexed: 01/27/2023] Open
Abstract
The early-life microbiota triggers life-long effects on physiological functions and health disorders. Previous studies in adult twins or animal models have revealed associations between host genetics and the harmonious microbiota. However, such associations may be obscured by the fact that each intra-pair of twins will continually encounter various environmental factors as they grow up. Here, we collected the meconium samples from nineteen dizygotic pairs (DZ, n = 38) and nine monozygotic pairs (MZ, n = 18) with cesarean delivery, and 16S rRNA gene sequencing was performed to profile the microbiome at birth. Diversity analysis showed that alpha diversity was not significantly different between two groups, whereas beta diversity of MZ twins was significantly lower than that of either DZ twins or unrelated individuals (i.e., randomly selected individual pairs of non-twinship) (p < 0.05). Two groups had very similar microbial classifications but different relative abundances of certain taxa including more Firmicutes (p = 0.05, Wilcoxon test) at the phylum level and lower abundances of five genera (p < 0.05) in DZ group compared to MZ group, including Rheinheimera, Proteus, SMB53, Sphingobium, and Megamonas. Co-occurrence analysis in each group showed slightly more complicated microbial interactions in DZ than MZ twins, although 22 shared bacterial genera co-existed in two groups, with both Rheinheimera and Megamonas having different centralities in their respective co-occurrence networks. Mean intra-class correlation coefficient (ICC) were also significantly higher for MZ (0.312) compared to DZ twins (0.138) (p < 0.05). The predicted microbial gene functions related to carbohydrate were higher in DZ group, whereas folding, sorting, degradation, cell motility pathways and energy metabolism were markedly over-represented in the microbiota of MZ group. In summary, our study uncovered that microbial diversity and components of the meconium microbiome between DZ and MZ twins were partially consistent with that in singleton neonates by cesarean delivery, but several distinctions related to the heritability supported genetic contributions to intestinal microbiome in early life.
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Affiliation(s)
- Jing Yang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Su Yao
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Kun Cheng
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Lili Xu
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Lingling Hou
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Huijun Feng
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xuejian Yu
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xin Zhang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xiaomei Tong
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Zailing Li
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
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42
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A Mediterranean Diet Intervention Reduces the Levels of Salivary Periodontopathogenic Bacteria in Overweight and Obese Subjects. Appl Environ Microbiol 2020; 86:AEM.00777-20. [PMID: 32276980 DOI: 10.1128/aem.00777-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
The human oral cavity is a complex ecosystem, and the alterations in salivary microbial communities are associated with both oral and nonoral diseases. The Mediterranean diet (MD) is a healthy dietary pattern useful for both prevention and treatment of several diseases. To further explore the effects of the MD on human health, in this study, we investigated the changes in the salivary microbial communities in overweight/obese subjects after an individually tailored MD-based nutritional intervention. Healthy overweight and obese subjects were randomized between two intervention groups. The MD group (Med-D group) increased their MD adherence during 8 weeks of intervention while the control diet (control-D) group did not change their dietary habits. The salivary microbiota was assessed at baseline and after 4 and 8 weeks of intervention. Despite no observed changes in the overall salivary microbiota composition, we found a significant decrease in the relative abundances of species-level operational taxonomic units annotated as Porphyromonas gingivalis, Prevotella intermedia, and Treponema denticola in the Med-D group compared to that in the control-D group after 8 weeks of intervention, which are known to be associated with periodontal disease. Such variations were significantly linked to dietary variables such as MD adherence rates and intakes of animal versus vegetable proteins. In addition, increased levels of Streptococcus cristatus were observed in the Med-D group, which has been reported as an antagonistic taxon inhibiting P. gingivalis gene expression. Our findings suggest that an MD-based nutritional intervention may be implicated in reducing periodontal bacteria, and an MD may be a dietary strategy supportive of oral homeostasis.IMPORTANCE Changes in dietary behavior with increased adherence to a Mediterranean diet can determine a reduction of periodontopathogenic bacterial abundances in the saliva of overweight subjects with cardiometabolic risk due to an unhealthy lifestyle, without any change in individual energy intake, nutrient intake, and physical activity.
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43
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Sundström K, Mishra PP, Pyysalo MJ, Lehtimäki T, Karhunen PJ, Pessi T. Similarity of salivary microbiome in parents and adult children. PeerJ 2020; 8:e8799. [PMID: 32296599 PMCID: PMC7151748 DOI: 10.7717/peerj.8799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Human saliva contains approximately 700 bacterial species. It has been reported that the salivary microbiome of a large family of closely related individuals consisting of multiple households is similar but the relatedness of salivary bacteria between generations of parents and their children has not yet been investigated. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between grandparents and their first daughter generations (F1) using 16S rRNA gene amplicon sequencing. Results The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13% of the variance between individuals’ bacterial communities (R2 = 0.13; P = 0.001). Mothers shared more OTUs with adult children compared to fathers, but this linkage seemed to be weaker in the nuclear family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between families, which accounted for 31% of the total identified genus level OTUs. Conclusions Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. The observed similarity in oral microbiome between parent–child pairs seemed to weaken over time. We suggest that our analysis approach is suitable for relatedness study of multigenerational salivary bacteria microbiome.
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Affiliation(s)
- Kati Sundström
- Department of Forensic Medicine, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories Ltd, Tampere, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories Ltd, Tampere, Finland
| | - Mikko J Pyysalo
- Department of Otorhinolaryngology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Oral and Maxillofacial Diseases, Tampere University Hospital, Tampere, Finland.,Oral Health Services, City of Tampere, Tampere, Finland.,Department of Molecule Microbiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories Ltd, Tampere, Finland
| | - Pekka J Karhunen
- Department of Forensic Medicine, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories Ltd, Tampere, Finland
| | - Tanja Pessi
- Department of Forensic Medicine, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Department of Molecule Microbiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Science Centre, Tampere, Finland
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Carlson-Jones JAP, Kontos A, Kennedy D, Martin J, Lushington K, McKerral J, Paterson JS, Smith RJ, Dann LM, Speck P, Mitchell JG. The microbial abundance dynamics of the paediatric oral cavity before and after sleep. J Oral Microbiol 2020; 12:1741254. [PMID: 32341758 PMCID: PMC7170375 DOI: 10.1080/20002297.2020.1741254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/12/2020] [Accepted: 02/16/2020] [Indexed: 01/12/2023] Open
Abstract
Objective: Microhabitats in the oral cavity differ in microbial taxonomy. However, abundance variations of bacterial and viral communities within these microhabitats are not fully understood. Aims and Hypothesis: To assess the spatial distribution and dynamics of the microbial abundances within 6 microhabitats of the oral cavity before and after sleep. We hypothesise that the abundance distributions of these microbial communities will differ among oral sites. Methods: Using flow cytometry, bacterial and virus-like particle (VLP) abundances were enumerated for 6 oral microhabitats before and after sleep in 10 healthy paediatric sleepers. Results: Bacterial counts ranged from 7.2 ± 2.8 × 105 at the palate before sleep to 1.3 ± 0.2 × 108 at the back of the tongue after sleep, a difference of 187 times. VLPs ranged from 1.9 ± 1.0 × 106 at the palate before sleep to 9.2 ± 5.0 × 107 at the back of the tongue after sleep, a difference of 48 times. Conclusion: The oral cavity is a dynamic numerically heterogeneous environment where microbial communities can increase by a count of 100 million during sleep. Quantification of the paediatric oral microbiome complements taxonomic diversity information to show how biomass varies and shifts in space and time.
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Affiliation(s)
- Jessica A P Carlson-Jones
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia.,Robinson Research Institute, School of Paediatrics and Reproductive Health, the University of Adelaide, Adelaide, Australia.,College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Anna Kontos
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia.,Robinson Research Institute, School of Paediatrics and Reproductive Health, the University of Adelaide, Adelaide, Australia
| | - Declan Kennedy
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia.,Robinson Research Institute, School of Paediatrics and Reproductive Health, the University of Adelaide, Adelaide, Australia
| | - James Martin
- Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, Australia.,Robinson Research Institute, School of Paediatrics and Reproductive Health, the University of Adelaide, Adelaide, Australia
| | - Kurt Lushington
- School of Psychology, Social Work and Social Policy, University of South Australia, Adelaide, Australia
| | - Jody McKerral
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - James S Paterson
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Renee J Smith
- College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Lisa M Dann
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Peter Speck
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - James G Mitchell
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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45
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Murugesan S, Al Ahmad SF, Singh P, Saadaoui M, Kumar M, Al Khodor S. Profiling the Salivary microbiome of the Qatari population. J Transl Med 2020; 18:127. [PMID: 32169076 PMCID: PMC7071716 DOI: 10.1186/s12967-020-02291-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions. MATERIALS AND METHODS We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene. RESULTS In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers. CONCLUSION This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.
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Affiliation(s)
| | | | - Parul Singh
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
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46
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Belstrøm D. The salivary microbiota in health and disease. J Oral Microbiol 2020; 12:1723975. [PMID: 32128039 PMCID: PMC7034443 DOI: 10.1080/20002297.2020.1723975] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022] Open
Abstract
The salivary microbiota (SM), comprising bacteria shed from oral surfaces, has been shown to be individualized, temporally stable and influenced by diet and lifestyle. SM reflects local bacterial alterations of the supragingival and subgingival microbiota, and periodontitis and dental-caries associated characteristics of SM have been reported. Also, data suggest an impact of systemic diseases on SM as demonstrated in patients with a wide variety of systemic diseases including diabetes, cancer, HIV and rheumatoid arthritis. The presence of systemic diseases seems to influence salivary levels of specific bacterial species, as well as α- and β-diversity of SM. The composition of SM might thereby potentially mirror oral and general health status. The contentious development of advanced molecular techniques such as metagenomics, metatranscriptomics and metabolomics has enabled the possibility to address bacterial functions rather than presence in microbial samples. However, at present only a few studies have employed such techniques on SM to reveal functional and metabolic characteristics in oral health and disease. Future studies are therefore warranted to illuminate the possible impact of metabolic functions of SM on oral and general health status. Ultimately, such an approach has the possibility to reveal novel and personalized therapeutic avenues in oral and general medicine.
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Affiliation(s)
- Daniel Belstrøm
- Section for Periodontology and Microbiology, Department of Odontology, University of Copenhagen, Copenhagen, Denmark
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47
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Rosa N, Campos B, Esteves AC, Duarte AS, Correia MJ, Silva RM, Barros M. Tracking the functional meaning of the human oral-microbiome protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:199-235. [PMID: 32312422 DOI: 10.1016/bs.apcsb.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.
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Affiliation(s)
- Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Bruno Campos
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Cristina Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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48
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Rabe A, Gesell Salazar M, Michalik S, Fuchs S, Welk A, Kocher T, Völker U. Metaproteomics analysis of microbial diversity of human saliva and tongue dorsum in young healthy individuals. J Oral Microbiol 2019; 11:1654786. [PMID: 31497257 PMCID: PMC6720020 DOI: 10.1080/20002297.2019.1654786] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background: The human oral microbiome influences initiation or progression of diseases like caries or periodontitis. Metaproteomics approaches enable the simultaneous investigation of microbial and host proteins and their interactions to improve understanding of oral diseases. Objective: In this study, we provide a detailed metaproteomics perspective of the composition of salivary and tongue microbial communities of young healthy subjects. Design: Stimulated saliva and tongue samples were collected from 24 healthy volunteers, subjected to shotgun nLC-MS/MS and analyzed by the Trans-Proteomic Pipeline and the Prophane tool. Results: 3,969 bacterial and 1,857 human proteins could be identified from saliva and tongue, respectively. In total, 1,971 bacterial metaproteins and 1,154 human proteins were shared in both sample types. Twice the amount of bacterial metaproteins were uniquely identified for the tongue dorsum compared to saliva. Overall, 107 bacterial genera of seven phyla formed the microbiome. Comparative analysis identified significant functional differences between the microbial biofilm on the tongue and the microbiome of saliva. Conclusion: Even if the microbial communities of saliva and tongue dorsum showed a strong similarity based on identified protein functions and deduced bacterial composition, certain specific characteristics were observed. Both microbiomes exhibit a great diversity with seven genera being most abundant.
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Affiliation(s)
- Alexander Rabe
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch-Institute, Wernigerode, Germany
| | - Alexander Welk
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Kocher
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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49
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Mumcu G, Direskeneli H. Triggering agents and microbiome as environmental factors on Behçet's syndrome. Intern Emerg Med 2019; 14:653-660. [PMID: 30523495 DOI: 10.1007/s11739-018-2000-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022]
Abstract
Environmental and other triggering factors are suggested to cause the onset and the clinical relapses of Behçet's syndrome (BS), a multi-systemic inflammatory disorder. In this review, environmental factors are discussed according to their interactions with etiopathogenesis, immune response and disease activity. Stress is a common self-triggering factor for most BS patients. Stimuli such as some foods can activate oral ulcers, and may be linked to the histamine content of the food. Oral/skin trauma and menstruation associated with hormonal factors aggravate, whereas allergy/atopy seem to alleviate the symptoms of BS. Infections are associated with BS, and microbial stimuli can activate inflammation in mucosal surfaces with increased Th1/Th17 responses. Fecal and oral microbiome patterns change in diversity and composition in BS. Better oral hygiene applications and anti-microbial interventions might be helpful to suppress oral ulcers in BS.
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Affiliation(s)
- Gonca Mumcu
- Department of Health Management, Faculty of Health Sciences, Marmara University, Istanbul, Turkey
| | - Haner Direskeneli
- Department of Internal Medicine, Division of Rheumatology, School of Medicine, Marmara University, Istanbul, Turkey.
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50
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Krüger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Fungal-Bacterial Interactions in Health and Disease. Pathogens 2019; 8:E70. [PMID: 31117285 PMCID: PMC6630686 DOI: 10.3390/pathogens8020070] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 12/28/2022] Open
Abstract
Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.
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Affiliation(s)
- Wibke Krüger
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Sarah Vielreicher
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
| | - Ilse D Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
- Institute of Microbiology, Friedrich Schiller University, Jena 07743, Germany.
| | - Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
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