1
|
Muller E, Shiryan I, Borenstein E. Multi-omic integration of microbiome data for identifying disease-associated modules. Nat Commun 2024; 15:2621. [PMID: 38521774 PMCID: PMC10960825 DOI: 10.1038/s41467-024-46888-3] [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: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Multi-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and analyzing such complex datasets poses significant challenges. Most notably, current analysis methods often yield extensive lists of disease-associated features (e.g., species, pathways, or metabolites), without capturing the multi-layered structure of the data. Here, we address this challenge by introducing "MintTea", an intermediate integration-based approach combining canonical correlation analysis extensions, consensus analysis, and an evaluation protocol. MintTea identifies "disease-associated multi-omic modules", comprising features from multiple omics that shift in concord and that collectively associate with the disease. Applied to diverse cohorts, MintTea captures modules with high predictive power, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome study, MintTea identifies a module with serum glutamate- and TCA cycle-related metabolites, along with bacterial species linked to insulin resistance. In another dataset, MintTea identifies a module associated with late-stage colorectal cancer, including Peptostreptococcus and Gemella species and fecal amino acids, in line with these species' metabolic activity and their coordinated gradual increase with cancer development. This work demonstrates the potential of advanced integration methods in generating systems-level, multifaceted hypotheses underlying microbiome-disease interactions.
Collapse
Affiliation(s)
- Efrat Muller
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Itamar Shiryan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
| |
Collapse
|
2
|
Muller E, Shiryan I, Borenstein E. Multi-omic integration of microbiome data for identifying disease-associated modules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.03.547607. [PMID: 37461534 PMCID: PMC10349976 DOI: 10.1101/2023.07.03.547607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The human gut microbiome is a complex ecosystem with profound implications for health and disease. This recognition has led to a surge in multi-omic microbiome studies, employing various molecular assays to elucidate the microbiome's role in diseases across multiple functional layers. However, despite the clear value of these multi-omic datasets, rigorous integrative analysis of such data poses significant challenges, hindering a comprehensive understanding of microbiome-disease interactions. Perhaps most notably, multiple approaches, including univariate and multivariate analyses, as well as machine learning, have been applied to such data to identify disease-associated markers, namely, specific features (e.g., species, pathways, metabolites) that are significantly altered in disease state. These methods, however, often yield extensive lists of features associated with the disease without effectively capturing the multi-layered structure of multi-omic data or offering clear, interpretable hypotheses about underlying microbiome-disease mechanisms. Here, we address this challenge by introducing MintTea - an intermediate integration-based method for analyzing multi-omic microbiome data. MintTea combines a canonical correlation analysis (CCA) extension, consensus analysis, and an evaluation protocol to robustly identify disease-associated multi-omic modules. Each such module consists of a set of features from the various omics that both shift in concord, and collectively associate with the disease. Applying MintTea to diverse case-control cohorts with multi-omic data, we show that this framework is able to capture modules with high predictive power for disease, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome (MS) study, we found a MS-associated module comprising of a highly correlated cluster of serum glutamate- and TCA cycle-related metabolites, as well as bacterial species previously implicated in insulin resistance. In another cohort, we identified a module associated with late-stage colorectal cancer, featuring Peptostreptococcus and Gemella species and several fecal amino acids, in agreement with these species' reported role in the metabolism of these amino acids and their coordinated increase in abundance during disease development. Finally, comparing modules identified in different datasets, we detected multiple significant overlaps, suggesting common interactions between microbiome features. Combined, this work serves as a proof of concept for the potential benefits of advanced integration methods in generating integrated multi-omic hypotheses underlying microbiome-disease interactions and a promising avenue for researchers seeking systems-level insights into coherent mechanisms governing microbiome-related diseases.
Collapse
|
3
|
Rahnama-Hezavah M, Mertowska P, Mertowski S, Skiba J, Krawiec K, Łobacz M, Grywalska E. How Can Imbalance in Oral Microbiota and Immune Response Lead to Dental Implant Problems? Int J Mol Sci 2023; 24:17620. [PMID: 38139449 PMCID: PMC10743591 DOI: 10.3390/ijms242417620] [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: 11/16/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Dental implantology is one of the most dynamically developing fields of dentistry, which, despite developing clinical knowledge and new technologies, is still associated with many complications that may lead to the loss of the implant or the development of the disease, including peri-implantitis. One of the reasons for this condition may be the fact that dental implants cannot yield a proper osseointegration process due to the development of oral microbiota dysbiosis and the accompanying inflammation caused by immunological imbalance. This study aims to present current knowledge as to the impact of oral microflora dysbiosis and deregulation of the immune system on the course of failures observed in dental implantology. Evidence points to a strong correlation between these biological disturbances and implant complications, often stemming from improper osseointegration, pathogenic biofilms on implants, as well as an exacerbated inflammatory response. Technological enhancements in implant design may mitigate pathogen colonization and inflammation, underscoring implant success rates.
Collapse
Affiliation(s)
- Mansur Rahnama-Hezavah
- Chair and Department of Oral Surgery, Medical University of Lublin, 20-093 Lublin, Poland; (M.R.-H.); (M.Ł.)
| | - Paulina Mertowska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (S.M.); (E.G.)
| | - Sebastian Mertowski
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (S.M.); (E.G.)
| | - Julia Skiba
- Student Research Group of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Karol Krawiec
- Student Research Group of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Michał Łobacz
- Chair and Department of Oral Surgery, Medical University of Lublin, 20-093 Lublin, Poland; (M.R.-H.); (M.Ł.)
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland; (S.M.); (E.G.)
| |
Collapse
|
4
|
Button JE, Cosetta CM, Reens AL, Brooker SL, Rowan-Nash AD, Lavin RC, Saur R, Zheng S, Autran CA, Lee ML, Sun AK, Alousi AM, Peterson CB, Koh AY, Rechtman DJ, Jenq RR, McKenzie GJ. Precision modulation of dysbiotic adult microbiomes with a human-milk-derived synbiotic reshapes gut microbial composition and metabolites. Cell Host Microbe 2023; 31:1523-1538.e10. [PMID: 37657443 DOI: 10.1016/j.chom.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/13/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
Manipulation of the gut microbiome using live biotherapeutic products shows promise for clinical applications but remains challenging to achieve. Here, we induced dysbiosis in 56 healthy volunteers using antibiotics to test a synbiotic comprising the infant gut microbe, Bifidobacterium longum subspecies infantis (B. infantis), and human milk oligosaccharides (HMOs). B. infantis engrafted in 76% of subjects in an HMO-dependent manner, reaching a relative abundance of up to 81%. Changes in microbiome composition and gut metabolites reflect altered recovery of engrafted subjects compared with controls. Engraftment associates with increases in lactate-consuming Veillonella, faster acetate recovery, and changes in indolelactate and p-cresol sulfate, metabolites that impact host inflammatory status. Furthermore, Veillonella co-cultured in vitro and in vivo with B. infantis and HMO converts lactate produced by B. infantis to propionate, an important mediator of host physiology. These results suggest that the synbiotic reproducibly and predictably modulates recovery of a dysbiotic microbiome.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Martin L Lee
- Prolacta Bioscience, Duarte, CA 91010, USA; Department of Biostatistics, University of California Los Angeles, Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Adam K Sun
- Prolacta Bioscience, Duarte, CA 91010, USA
| | - Amin M Alousi
- Department of Stem Cell Transplantation, Division of Cancer Medicine, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B Peterson
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Y Koh
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | | |
Collapse
|
5
|
Zhou Q, Chen Y, Liu G, Qiao P, Tang C. A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure. PeerJ 2023; 11:e15537. [PMID: 37397022 PMCID: PMC10312199 DOI: 10.7717/peerj.15537] [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: 10/03/2022] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
Background The microbial community structure in saliva differs at different altitudes. However, the impact of acute high-altitude exposure on the oral microbiota is unclear. This study explored the impact of acute high-altitude exposure on the salivary microbiome to establish a foundation for the future prevention of oral diseases. Methods. Unstimulated whole saliva samples were collected from 12 male subjects at the following three time points: one day before entering high altitude (an altitude of 350 m, pre-altitude group), seven days after arrival at high altitude (an altitude of 4,500 m, altitude group) and seven days after returning to low altitude (an altitude of 350 m, post-altitude group). Thus, a total of 36 saliva samples were obtained. 16S rRNA V3-V4 region amplicon sequencing was used to analyze the diversity and structure of the salivary microbial communities, and a network analysis was employed to investigate the relationships among salivary microorganisms. The function of these microorganisms was predicted with a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Results In total, there were 756 operational taxonomic units (OTUs) identified, with 541, 613, and 615 OTUs identified in the pre-altitude, altitude, and post-altitude groups, respectively. Acute high-altitude exposure decreased the diversity of the salivary microbiome. Prior to acute high-altitude exposure, the microbiome mainly consisted of Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. After altitude exposure, the relative abundance of Streptococcus and Veillonella increased, and the relative abundance of Prevotella, Porphyromonas, and Alloprevotella decreased. The relationship among the salivary microorganisms was also affected by acute high-altitude exposure. The relative abundance of carbohydrate metabolism gene functions was upregulated, while the relative abundance of coenzyme and vitamin metabolism gene functions was downregulated. Conclusion Rapid high-altitude exposure decreased the biodiversity of the salivary microbiome, changing the community structure, symbiotic relationships among species, and abundance of functional genes. This suggests that the stress of acute high-altitude exposure influenced the stability of the salivary microbiome.
Collapse
Affiliation(s)
- Qian Zhou
- The fifth Clinical Medical College of Anhui Medical University, Clinical College of Anhui Medical University, Beijing, China
- Department of Stomatology, PLA Strategic Support Force Medical Center, Beijing, China
| | - Yuhui Chen
- Department of Stomatology, PLA Strategic Support Force Medical Center, Beijing, China
| | - Guozhu Liu
- The 32183 Military Hospital of PLA, Baicheng, Jilin, China
| | - Pengyan Qiao
- Department of Stomatology, PLA Strategic Support Force Medical Center, Beijing, China
| | - Chuhua Tang
- The fifth Clinical Medical College of Anhui Medical University, Clinical College of Anhui Medical University, Beijing, China
- Department of Stomatology, PLA Strategic Support Force Medical Center, Beijing, China
| |
Collapse
|
6
|
Yntema T, Koonen DPY, Kuipers F. Emerging Roles of Gut Microbial Modulation of Bile Acid Composition in the Etiology of Cardiovascular Diseases. Nutrients 2023; 15:nu15081850. [PMID: 37111068 PMCID: PMC10141989 DOI: 10.3390/nu15081850] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Despite advances in preventive measures and treatment options, cardiovascular disease (CVD) remains the number one cause of death globally. Recent research has challenged the traditional risk factor profile and highlights the potential contribution of non-traditional factors in CVD, such as the gut microbiota and its metabolites. Disturbances in the gut microbiota have been repeatedly associated with CVD, including atherosclerosis and hypertension. Mechanistic studies support a causal role of microbiota-derived metabolites in disease development, such as short-chain fatty acids, trimethylamine-N-oxide, and bile acids, with the latter being elaborately discussed in this review. Bile acids represent a class of cholesterol derivatives that is essential for intestinal absorption of lipids and fat-soluble vitamins, plays an important role in cholesterol turnover and, as more recently discovered, acts as a group of signaling molecules that exerts hormonal functions throughout the body. Studies have shown mediating roles of bile acids in the control of lipid metabolism, immunity, and heart function. Consequently, a picture has emerged of bile acids acting as integrators and modulators of cardiometabolic pathways, highlighting their potential as therapeutic targets in CVD. In this review, we provide an overview of alterations in the gut microbiota and bile acid metabolism found in CVD patients, describe the molecular mechanisms through which bile acids may modulate CVD risk, and discuss potential bile-acid-based treatment strategies in relation to CVD.
Collapse
Affiliation(s)
- Tess Yntema
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Debby P Y Koonen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| |
Collapse
|
7
|
Liu K, Yang L, Wang X, Huang Q, Tuerhong K, Yang M, Zhang R, Li Y, Yang S. Electroacupuncture regulates macrophage, neutrophil, and oral microbiota to alleviate alveolar bone loss and inflammation in experimental ligature-induced periodontitis. J Clin Periodontol 2023; 50:368-379. [PMID: 36356944 DOI: 10.1111/jcpe.13748] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022]
Abstract
AIM Electroacupuncture (EA) regulates distant body physiology through somatic sensory autonomic reflexes, balances the microbiome, and can promote the release of immune cells into bloodstream, thereby inhibiting severe systemic inflammation. This makes it possible to use EA as an integrated treatment for periodontitis. MATERIALS AND METHODS In this study, EA was applied to the ST36 acupoints in a ligature-induced periodontitis (LIP) mouse model. Then the effects of EA on periodontal myeloid cells, cytokines, and the microbiome were comprehensively analysed using flow cytometry, quantitative Polymerase Chain Reaction (PCR), and 16 S sequencing. RESULTS Results demonstrated that EA could significantly relieve periodontal bone resorption. EA also suppressed the infiltration of macrophages and neutrophils, reduced gene expression of the pro-inflammatory cytokines IL-1β, IL-6, IL-17 and TNF-α, and increased expression of the anti-inflammatory factors IL-4 and IL-10 in periodontal tissues. Moreover, composition of the periodontal microbiome was regulated by EA, finding that complex of microbiota, including supragingival Veillonella, subgingival Streptococcus, and subgingival Erysipelatoclostridium, were significantly reduced. Meanwhile, nitrate and nitrate-related activities of subgingival microbiota were reversed. Network analysis revealed close relationships among Veillonella, Streptococcus, and Bacteroides. CONCLUSIONS Our study indicates that EA can effectively alleviate inflammation and bone resorption in LIP mice, potentially via the regulation of myeloid cells, cytokines, and periodontal microbiome.
Collapse
Affiliation(s)
- Kehao Liu
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Liangjie Yang
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Xu Wang
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Qi Huang
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Kamoran Tuerhong
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Mingcong Yang
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Rong Zhang
- Neuroscience Research Institute, Peking University, Beijing, China.,Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Education, Beijing, China.,Key Laboratory for Neuroscience, Ministry of Health, Beijing, China.,Autism Research Center of Peking University Health Science Center, Beijing, China
| | - Yuzhou Li
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Sheng Yang
- Department of Prosthodontics, College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| |
Collapse
|
8
|
Hov JR, Karlsen TH. The microbiota and the gut-liver axis in primary sclerosing cholangitis. Nat Rev Gastroenterol Hepatol 2023; 20:135-154. [PMID: 36352157 DOI: 10.1038/s41575-022-00690-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/11/2022]
Abstract
Primary sclerosing cholangitis (PSC) offers unique opportunities to explore the gut-liver axis owing to the close association between liver disease and colonic inflammation. It is well established that the gut microbiota in people with PSC differs from that of healthy individuals, but details of the microbial factors that demarcate PSC from inflammatory bowel disease (IBD) without PSC are poorly understood. In this Review, we aim to provide an overview of the latest literature on the gut microbiome in PSC and PSC with IBD, critically examining hypotheses on how microorganisms could contribute to the pathogenesis of PSC. A particular emphasis will be put on pathogenic features of the gut microbiota that might explain the occurrence of bile duct inflammation and liver disease in the context of IBD, and we postulate the potential existence of a specific yet unknown factor related to the gut-liver axis as causative in PSC. Available data are scrutinized in the perspective of therapeutic approaches related to the gut-liver axis.
Collapse
Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center and Section of gastroenterology and Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| |
Collapse
|
9
|
Wang DH, Tsai FT, Tu HF, Yang CC, Hsu ML, Huang LJ, Lin CT, Hsu WE, Lin YC. Profiles of oral microbiome associated with nasogastric tube feeding. J Oral Microbiol 2023; 15:2200898. [PMID: 37063979 PMCID: PMC10101675 DOI: 10.1080/20002297.2023.2200898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Background Dysbiosis of oral microbiome causes chronic diseases including dental caries and periodontitis, which frequently affect older patient populations. Severely disabled individuals with impaired swallowing functions may require nutritional supply via nasogastric (NG) tubes, further impacting their oral condition and possibly microbial composition. However, little is known about the effect of NG tube on oral microbes and its potential ramification. Methods By using 16S rRNA amplicon sequencing, we characterized the tongue microbiome of 27 patients fed with NG tubes and 26 others fed orally. Results The microbial compositions of NG-tube and oral-feeding patients were substantially different, with more Gram-negative aerobes enriched in the presence of NG tube. Specifically, NG-tube patients presented more opportunistic pathogens like Pseudomonas and Corynebacterium associated with pneumonia and lower levels of commensal Streptococcus and Veillonella. Co-occurrence analysis further showed an inverse relationship between commensal and pathogenic species. Conclusion We present a systematic, high-throughput profiling of oral microbiome with regard to long-term NG tube feeding among the older patient population.
Collapse
Affiliation(s)
- Ding-Han Wang
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Fa-Tzu Tsai
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsi-Feng Tu
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
| | - Cheng-Chieh Yang
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ming-Lun Hsu
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lin-Jack Huang
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
| | - Chiu-Tzu Lin
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
| | - Wun-Eng Hsu
- Department of Dentistry, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- CONTACT Yu-Cheng Lin Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| |
Collapse
|
10
|
Blostein F, Bhaumik D, Davis E, Salzman E, Shedden K, Duhaime M, Bakulski KM, McNeil DW, Marazita ML, Foxman B. Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study. MICROBIOME 2022; 10:240. [PMID: 36567334 PMCID: PMC9791751 DOI: 10.1186/s40168-022-01442-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/01/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Early childhood caries (ECC)-dental caries (cavities) occurring in primary teeth up to age 6 years-is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a primary cause, but recent research promotes the ecologic hypothesis, in which a dysbiosis in the oral microbial community leads to caries. In this incident, density sampled case-control study of 189 children followed from 2 months to 5 years, we use the salivary bacteriome to (1) prospectively test the ecological hypothesis of ECC in salivary bacteriome communities and (2) identify co-occurring salivary bacterial communities predicting future ECC. RESULTS Supervised classification of future ECC case status using salivary samples from age 12 months using bacteriome-wide data (AUC-ROC 0.78 95% CI (0.71-0.85)) predicts future ECC status before S. mutans can be detected. Dirichlet multinomial community state typing and co-occurrence network analysis identified similar robust and replicable groups of co-occurring taxa. Mean relative abundance of a Haemophilus parainfluenzae/Neisseria/Fusobacterium periodonticum group was lower in future ECC cases (0.14) than controls (0.23, P value < 0.001) in pre-incident visits, positively correlated with saliva pH (Pearson rho = 0.33, P value < 0.001) and reduced in individuals who had acquired S. mutans by the next study visit (0.13) versus those who did not (0.20, P value < 0.01). In a subset of whole genome shotgun sequenced samples (n = 30), case plaque had higher abundances of antibiotic production and resistance gene orthologs, including a major facilitator superfamily multidrug resistance transporter (MFS DHA2 family PBH value = 1.9 × 10-28), lantibiotic transport system permease protein (PBH value = 6.0 × 10-6) and bacitracin synthase I (PBH value = 5.6 × 10-6). The oxidative phosphorylation KEGG pathway was enriched in case plaque (PBH value = 1.2 × 10-8), while the ABC transporter pathway was depleted (PBH value = 3.6 × 10-3). CONCLUSIONS Early-life bacterial interactions predisposed children to ECC, supporting a time-dependent interpretation of the ecological hypothesis. Bacterial communities which assemble before 12 months of age can promote or inhibit an ecological succession to S. mutans dominance and cariogenesis. Intragenera competitions and intergenera cooperation between oral taxa may shape the emergence of these communities, providing points for preventive interventions. Video Abstract.
Collapse
Affiliation(s)
- Freida Blostein
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Deesha Bhaumik
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Elyse Davis
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Elizabeth Salzman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Kerby Shedden
- Department of Statistics, University of Michigan, Ann Arbor, MI USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Melissa Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI USA
| | - Kelly M. Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| | - Daniel W. McNeil
- Department of Psychology, West Virginia University, WVA, Morgantown, USA
- Department of Dental Practice & Rural Health, West Virginia University, Morgantown, WV USA
| | - Mary L. Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA USA
- Clinical and Translational Sciences Institute, and Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI USA
| |
Collapse
|
11
|
Deng Z, Guo K, Cao F, Fan T, Liu B, Shi M, Liu Y, Ma Z. Altered dental plaque microbiota correlated with salivary inflammation in female methamphetamine users. Front Immunol 2022; 13:999879. [PMID: 36524108 PMCID: PMC9745308 DOI: 10.3389/fimmu.2022.999879] [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: 07/21/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Poor oral health is the most immediate and overlooked hazard of methamphetamine abuse in humans. Previous studies have reported methamphetamine-associated alterations in saliva microbiota, but the cause of methamphetamine-induced alterations in the oral microenvironment remains unclear. The present study aimed to investigate the alterations in dental plaque microbiota in methamphetamine users, and to explore their relationship with local immune inflammation in the oral cavity. This may provide new ideas on the development of methamphetamine-related oral microenvironment changes. Questionnaires and samples were obtained from 30 female methamphetamine users and 15 sex- and age-matched healthy controls. Microbial profiles of supragingival dental plaque were analyzed using 16S rRNA gene sequencing. Inflammatory factors in saliva were measured using enzyme-linked immunosorbent assay. Methamphetamine users had worse oral self-evaluation. Compared with healthy controls, methamphetamine users showed no differences in oral dental plaque microbial diversity but exhibited differences in the relative abundance of several microbial taxa. At the phylum level, a higher abundance of Proteobacteria and a lower abundance of Firmicutes were detected in methamphetamine users. Moreover, function prediction using the MetaCyc database showed that 33 pathways were significantly upregulated in methamphetamine users; Only the glycolytic (Pyrococcus) pathway was enriched in the C group. Importantly, salivary inflammatory factors showed complex significant associations with bacterial genera in methamphetamine users. Specifically, the genus Neisseria was positively correlated with IL-17 levels in saliva, and both were high in methamphetamine users. In contrast, the genus Streptococcus, with a lower abundance, was positively correlated with lower IL-10 levels. Overall, This study is the first to provide evidence for a link between altered dental plaque microbiota and salivary inflammation in methamphetamine users. Further elucidation of the interactions between methamphetamine use and oral microenvironment would be beneficial for appropriate interventions to improve oral health.
Collapse
|
12
|
Abstract
Oral commensal streptococci are primary colonizers of the oral cavity. These streptococci produce many adhesins, metabolites, and antimicrobials that modulate microbial succession and diversity within the oral cavity. Often, oral commensal streptococci antagonize cariogenic and periodontal pathogens such as Streptococcus mutans and Porphyromonas gingivalis, respectively. Mechanisms of antagonism are varied and range from the generation of hydrogen peroxide, competitive metabolite scavenging, the generation of reactive nitrogen intermediates, and bacteriocin production. Furthermore, several oral commensal streptococci have been shown to alter the host immune response at steady state and in response to oral pathogens. Collectively, these features highlight the remarkable ability of oral commensal streptococci to regulate the structure and function of the oral microbiome. In this review, we discuss mechanisms used by oral commensal streptococci to interact with diverse oral pathogens, both physically and through the production of antimicrobials. Finally, we conclude by exploring the critical roles of oral commensal streptococci in modulating the host immune response and maintaining health and homeostasis.
Collapse
|
13
|
Zhu J, Chu W, Luo J, Yang J, He L, Li J. Dental Materials for Oral Microbiota Dysbiosis: An Update. Front Cell Infect Microbiol 2022; 12:900918. [PMID: 35846759 PMCID: PMC9280126 DOI: 10.3389/fcimb.2022.900918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
The balance or dysbiosis of the microbial community is a major factor in maintaining human health or causing disease. The unique microenvironment of the oral cavity provides optimal conditions for colonization and proliferation of microbiota, regulated through complex biological signaling systems and interactions with the host. Once the oral microbiota is out of balance, microorganisms produce virulence factors and metabolites, which will cause dental caries, periodontal disease, etc. Microbial metabolism and host immune response change the local microenvironment in turn and further promote the excessive proliferation of dominant microbes in dysbiosis. As the product of interdisciplinary development of materials science, stomatology, and biomedical engineering, oral biomaterials are playing an increasingly important role in regulating the balance of the oral microbiome and treating oral diseases. In this perspective, we discuss the mechanisms underlying the pathogenesis of oral microbiota dysbiosis and introduce emerging materials focusing on oral microbiota dysbiosis in recent years, including inorganic materials, organic materials, and some biomolecules. In addition, the limitations of the current study and possible research trends are also summarized. It is hoped that this review can provide reference and enlightenment for subsequent research on effective treatment strategies for diseases related to oral microbiota dysbiosis.
Collapse
Affiliation(s)
- Jieyu Zhu
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenlin Chu
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Jun Luo
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Jiaojiao Yang
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Jiaojiao Yang, ; Libang He,
| | - Libang He
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Jiaojiao Yang, ; Libang He,
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
14
|
Mechanisms underlying interactions between two abundant oral commensal bacteria. THE ISME JOURNAL 2022; 16:948-957. [PMID: 34732850 PMCID: PMC8940909 DOI: 10.1038/s41396-021-01141-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/21/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
Complex polymicrobial biofilm communities are abundant in nature particularly in the human oral cavity where their composition and fitness can affect health. While the study of these communities during disease is essential and prevalent, little is known about interactions within the healthy plaque community. Here we describe interactions between two of the most abundant species in this healthy microbiome, Haemophilus parainfluenzae and Streptococcus mitis. We discovered that H. parainfluenzae typically exists adjacent to mitis group streptococci in vivo with which it is also positively correlated based on microbiome data. By comparing in vitro coculture data to ex vivo microscopy we revealed that this co-occurrence is density dependent and further influenced by H2O2 production. We discovered that H. parainfluenzae utilizes a more redundant, multifactorial response to H2O2 than related microorganisms and that this system's integrity enhances streptococcal fitness. Our results indicate that mitis group streptococci are likely the in vivo source of NAD for H. parainfluenzae and also evoke patterns of carbon utilization in vitro for H. parainfluenzae similar to those observed in vivo. Our findings describe mechanistic interactions between two of the most abundant and prevalent members of healthy supragingival plaque that contribute to their in vivo survival.
Collapse
|
15
|
Roles of oral microbiota and oral-gut microbial transmission in hypertension. J Adv Res 2022; 43:147-161. [PMID: 36585105 PMCID: PMC9811375 DOI: 10.1016/j.jare.2022.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Considerable evidence has linked periodontitis (PD) to hypertension (HTN), but the nature behind this connection is unclear. Dysbiosis of oral microbiota leading to PD is known to aggravate different systematic diseases, but the alteration of oral microbiota in HTN and their impacts on blood pressure (BP) remains to be discovered. OBJECTIVES To characterize the alterations of oral and gut microbiota and their roles in HTN. METHODS We performed a cross-sectional (95 HTN participants and 39 controls) and a 6-month follow-up study (52 HTN participants and 26 controls) to analyze the roles of oral and gut microbiota in HTN. Saliva, subgingival plaques, and feces were collected for 16S rRNA gene sequencing or metagenomic analysis. C57BL/6J mice were pretreated with antibiotics to deplete gut microbiota, and then transplanted with human saliva by gavage to test the impacts of abnormal oral-gut microbial transmission on HTN. RESULTS BP in participants with PD was higher than no PD in both cross-sectional and follow-up cohort. Relative abundances of 14 salivary genera, 15 subgingival genera and 10 gut genera significantly altered in HTN and those of 7 salivary genera, 12 subgingival genera and 6 gut genera significantly correlated with BP. Sixteen species under 5 genera were identified as oral-gut transmitters, illustrating the presence of oral-gut microbial transmission in HTN. Veillonella was a frequent oral-gut transmitter stably enriched in HTN participants of both cross-sectional and follow-up cohorts. Saliva from HTN participants increased BP in hypertensive mice. Human saliva-derived Veillonella successfully colonized in mouse gut, more abundantly under HTN condition. CONCLUSIONS PD and oral microbiota are strongly associated with HTN, likely through oral-gut transmission of microbes. Ectopic colonization of saliva-derived Veillonella in the gut may aggravate HTN. Therefore, precise manipulations of oral microbiota and/or oral-gut microbial transmission may be useful strategies for better prevention and treatment of HTN.
Collapse
|
16
|
Incidence of Postoperative Pneumonia and Oral Microbiome for Patients with Cancer Operation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Postoperative pneumonia is a serious problem for patients and medical staff. In Japan, many hospitals introduced perioperative oral care management for the efficient use of medical resources. However, a high percentage of postoperative pneumonia still developed. Therefore, there is a need to identify the specific respiratory pathogens to predict the incidence of pneumonia The purpose of this study was to find out the candidate of bacterial species for the postoperative pneumonia. This study applied case-control study design for the patients who had a cancer operation with or without postoperative pneumonia. A total of 10 patients undergoing a cancer operation under general anesthesia participated in this study. The day before a cancer operation, preoperative oral care management was applied. Using the next generation sequence, oral microbiome of these patients was analyzed at the time of their first visit, the day before and after a cancer operation. Porphyromonas gingivalis and Fusobacterium nucleatum group can be a high risk at first visit. Atopobium parvulum and Enterococcus faecalis before a cancer operation can be a high risk. Poor oral hygiene increased the risk of incidence of postoperative pneumonia. Increased periodontal pathogens can be a high risk of the incidence of postoperative pneumonia. In addition, increased intestinal bacteria after oral care management can also be a high risk for the incidence of postoperative pneumonia.
Collapse
|
17
|
Patel VC, Lee S, McPhail MJW, Da Silva K, Guilly S, Zamalloa A, Witherden E, Støy S, Manakkat Vijay GK, Pons N, Galleron N, Huang X, Gencer S, Coen M, Tranah TH, Wendon JA, Bruce KD, Le Chatelier E, Ehrlich SD, Edwards LA, Shoaie S, Shawcross DL. Rifaximin-α reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial. J Hepatol 2022; 76:332-342. [PMID: 34571050 DOI: 10.1016/j.jhep.2021.09.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/20/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Rifaximin-α is efficacious for the prevention of recurrent hepatic encephalopathy (HE), but its mechanism of action remains unclear. We postulated that rifaximin-α reduces gut microbiota-derived endotoxemia and systemic inflammation, a known driver of HE. METHODS In a placebo-controlled, double-blind, mechanistic study, 38 patients with cirrhosis and HE were randomised 1:1 to receive either rifaximin-α (550 mg BID) or placebo for 90 days. PRIMARY OUTCOME 50% reduction in neutrophil oxidative burst (OB) at 30 days. SECONDARY OUTCOMES changes in psychometric hepatic encephalopathy score (PHES) and neurocognitive functioning, shotgun metagenomic sequencing of saliva and faeces, plasma and faecal metabolic profiling, whole blood bacterial DNA quantification, neutrophil toll-like receptor (TLR)-2/4/9 expression and plasma/faecal cytokine analysis. RESULTS Patients were well-matched: median MELD (11 rifaximin-α vs. 10 placebo). Rifaximin-α did not lead to a 50% reduction in spontaneous neutrophil OB at 30 days compared to baseline (p = 0.48). However, HE grade normalised (p = 0.014) and PHES improved (p = 0.009) after 30 days on rifaximin-α. Rifaximin-α reduced circulating neutrophil TLR-4 expression on day 30 (p = 0.021) and plasma tumour necrosis factor-α (TNF-α) (p <0.001). Rifaximin-α suppressed oralisation of the gut, reducing levels of mucin-degrading sialidase-rich species, Streptococcus spp, Veillonella atypica and parvula, Akkermansia and Hungatella. Rifaximin-α promoted a TNF-α- and interleukin-17E-enriched intestinal microenvironment, augmenting antibacterial responses to invading pathobionts and promoting gut barrier repair. Those on rifaximin-α were less likely to develop infection (odds ratio 0.21; 95% CI 0.05-0.96). CONCLUSION Rifaximin-α led to resolution of overt and covert HE, reduced the likelihood of infection, reduced oralisation of the gut and attenuated systemic inflammation. Rifaximin-α plays a role in gut barrier repair, which could be the mechanism by which it ameliorates bacterial translocation and systemic endotoxemia in cirrhosis. CLINICAL TRIAL NUMBER ClinicalTrials.gov NCT02019784. LAY SUMMARY In this clinical trial, we examined the underlying mechanism of action of an antibiotic called rifaximin-α which has been shown to be an effective treatment for a complication of chronic liver disease which effects the brain (termed encephalopathy). We show that rifaximin-α suppresses gut bacteria that translocate from the mouth to the intestine and cause the intestinal wall to become leaky by breaking down the protective mucus barrier. This suppression resolves encephalopathy and reduces inflammation in the blood, preventing the development of infection.
Collapse
Affiliation(s)
- Vishal C Patel
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK; Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK; The Roger Williams Institute of Hepatology (Foundation for Liver Research), 111 Coldharbour Lane, London, SE5 9NT, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, UK; Science for Life Laboratory, KTH - Royal Institute of Technology, 171 21, Stockholm, Sweden; School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Mark J W McPhail
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK; Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK; Imperial College London, Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, London, UK
| | - Kevin Da Silva
- University Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, 78350, France
| | - Susie Guilly
- University Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, 78350, France
| | - Ane Zamalloa
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Elizabeth Witherden
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, UK
| | - Sidsel Støy
- Aarhus University Hospital, Department of Hepatology and Gastroenterology, Aarhus, Denmark
| | - Godhev Kumar Manakkat Vijay
- Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Nicolas Pons
- University Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, 78350, France
| | - Nathalie Galleron
- University Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, 78350, France
| | - Xaiohong Huang
- Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Selin Gencer
- Imperial College London, Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, London, UK
| | - Muireann Coen
- Imperial College London, Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, London, UK
| | - Thomas Henry Tranah
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK; Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Julia Alexis Wendon
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK; Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, 5th Floor Franklin-Wilkins Building, London, UK
| | | | | | - Lindsey Ann Edwards
- Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, UK; Science for Life Laboratory, KTH - Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Debbie Lindsay Shawcross
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK; Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK.
| |
Collapse
|
18
|
Schulz-Weidner N, Weigel M, Turujlija F, Komma K, Mengel JP, Schlenz MA, Bulski JC, Krämer N, Hain T. Microbiome Analysis of Carious Lesions in Pre-School Children with Early Childhood Caries and Congenital Heart Disease. Microorganisms 2021; 9:microorganisms9091904. [PMID: 34576799 PMCID: PMC8469307 DOI: 10.3390/microorganisms9091904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/23/2021] [Accepted: 09/02/2021] [Indexed: 12/04/2022] Open
Abstract
Oral bacteria have been associated with several systemic diseases. Moreover, the abundance of bacteria associated with caries has been found to be higher in patients with congenital heart disease (CHD) than in healthy control groups (HCGs). Therefore, this study aimed to evaluate the dental microbiota in children with CHD compared to a HCG. The aim was to describe and compare the carious microbiome regarding the composition, diversity, and taxonomic patterns in these two groups. Twenty children with CHD and a HCG aged between two and six years participated. All of them were affected by early childhood caries. Microbiome profiling indicated that Fusobacterium, Prevotella, Capnocytophaga, and Oribacterium were more abundant in the CHD group, whereas Lactobacillus and Rothia were predominant in the HCG. Furthermore, microbiome analysis revealed three distinct clusters for the CHD and HCG samples. In the first cluster, we found mainly the genera Lactobacillus and Coriobacteriaceae. The second cluster showed a higher relative abundance of the genus Actinomyces and a more diverse composition consisting of more genera with a smaller relative lot. The third cluster was characterized by two genera, Streptococcus and Veillonella. These data can help us to understand the oral microbial community structures involved in caries and endodontic infections of pre-school children in relation to the general health of these high-risk patients.
Collapse
Affiliation(s)
- Nelly Schulz-Weidner
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Markus Weigel
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Filip Turujlija
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Kassandra Komma
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Jan Philipp Mengel
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
| | - Maximiliane Amelie Schlenz
- Dental Clinic—Department of Prosthodontics, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany;
| | - Julia Camilla Bulski
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Norbert Krämer
- Dental Clinic—Department of Pediatric Dentistry, Justus Liebig University, Schlangenzahl 14, 35392 Giessen, Germany; (N.S.-W.); (J.C.B.); (N.K.)
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany; (M.W.); (F.T.); (K.K.); (J.P.M.)
- Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany
- Correspondence: ; Tel.: +49-641-9939860
| |
Collapse
|
19
|
Sisk-Hackworth L, Ortiz-Velez A, Reed MB, Kelley ST. Compositional Data Analysis of Periodontal Disease Microbial Communities. Front Microbiol 2021; 12:617949. [PMID: 34079525 PMCID: PMC8165185 DOI: 10.3389/fmicb.2021.617949] [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: 10/15/2020] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies’ original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more “random” microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.
Collapse
Affiliation(s)
| | - Adrian Ortiz-Velez
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Micheal B Reed
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States
| |
Collapse
|
20
|
Abstract
Recent advances in our understanding of the microbial populations that colonize the human mouth, their acquisition, interdependency, and coevolution with the host, bring a different perspective to the mechanisms underpinning the maintenance of periodontal health and the development of disease. In this work we suggest that our knowledge map of the etiology of periodontal health and disease can be viewed as a broad, highly connected, and integrated system that spans the entire spectrum of microbe/host/clinical interactions. The overall concept of present Periodontology 2000, that the microbial biofilm can be considered a human tissue of bacteriological origin, is entirely consistent with this integrated system view. The health-associated community structure of microbial biofilms can be considered a system that is normally resilient to perturbation. Equally, there is evidence to suggest that the dysbiotic community structure in disease may share similar resilience properties. In both instances, the resilience may be governed by the precise makeup of the acquired microbiome and by the genetics of the host. Understanding the mechanisms that enable the resistance to change of healthy and dysbiotic microbial populations may be important in the development of approaches to prevent the progression of disease and to restore health in diseased individuals.
Collapse
Affiliation(s)
- Susan Joseph
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| |
Collapse
|
21
|
Wilbert SA, Mark Welch JL, Borisy GG. Spatial Ecology of the Human Tongue Dorsum Microbiome. Cell Rep 2021; 30:4003-4015.e3. [PMID: 32209464 PMCID: PMC7179516 DOI: 10.1016/j.celrep.2020.02.097] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/29/2020] [Accepted: 02/26/2020] [Indexed: 11/17/2022] Open
Abstract
A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. A test bed for examining this question is the tongue dorsum, which harbors a complex and important microbial community. Here, we use multiplexed fluorescence spectral imaging to investigate the organization of the tongue microbiome at micron to hundred-micron scales. We design oligonucleotide probes for taxa both abundant and prevalent, as determined by sequence analysis. Imaging reveals a highly structured spatial organization of microbial consortia, ranging in linear dimension from tens to hundreds of microns. The consortia appear to develop from a core of epithelial cells, with taxa clustering in domains suggestive of clonal expansion. Quantitative proximity analysis provides the basis for a model of tongue dorsum microbiome organization and dynamics. Our work illustrates how high-resolution analysis of micron-scale organization provides insights into physiological functions and microbiome-host interactions. How microbes are spatially organized is a fundamental question in microbial ecology about which little is known. Using fluorescence spectral imaging, Wilbert et al. discover dense, highly structured microbial consortia on the human tongue. Analysis of the organization of these consortia permits inferences about community dynamics and oral microbial ecology.
Collapse
Affiliation(s)
| | - Jessica L Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Gary G Borisy
- The Forsyth Institute, Cambridge, MA 02139, USA; Harvard School of Dental Medicine, Boston, MA 02115, USA.
| |
Collapse
|
22
|
Lamoureux C, Guilloux CA, Beauruelle C, Gouriou S, Ramel S, Dirou A, Le Bihan J, Revert K, Ropars T, Lagrafeuille R, Vallet S, Le Berre R, Nowak E, Héry-Arnaud G. An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches. Sci Rep 2021; 11:6845. [PMID: 33767218 PMCID: PMC7994387 DOI: 10.1038/s41598-021-85592-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella. These results raise the question of the potential impact of anaerobes on lung function.
Collapse
Affiliation(s)
- Claudie Lamoureux
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Clémence Beauruelle
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Sophie Ramel
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Anne Dirou
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Jean Le Bihan
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Krista Revert
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Thomas Ropars
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | | | - Sophie Vallet
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | - Rozenn Le Berre
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Pulmonary and Internal Medicine, Brest University Hospital, Brest, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest, France
| | - Geneviève Héry-Arnaud
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France. .,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France.
| |
Collapse
|
23
|
Feng D, Neuweiler I, Nogueira R, Nackenhorst U. Modeling of Symbiotic Bacterial Biofilm Growth with an Example of the Streptococcus-Veillonella sp. System. Bull Math Biol 2021; 83:48. [PMID: 33760986 PMCID: PMC7990864 DOI: 10.1007/s11538-021-00888-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
We present a multi-dimensional continuum mathematical model for modeling the growth of a symbiotic biofilm system. We take a dual-species namely, the Streptococcus-Veillonella sp. biofilm system as an example for numerical investigations. The presented model describes both the cooperation and competition between these species of bacteria. The coupled partial differential equations are solved by using an integrative finite element numerical strategy. Numerical examples are carried out for studying the evolution and distribution of the bio-components. The results demonstrate that the presented model is capable of describing the symbiotic behavior of the biofilm system. However, homogenized numerical solutions are observed locally. To study the homogenization behavior of the model, numerical investigations regarding on how random initial biomass distribution influences the homogenization process are carried out. We found that a smaller correlation length of the initial biomass distribution leads to faster homogenization of the solution globally, however, shows more fluctuated biomass profiles along the biofilm thickness direction. More realistic scenarios with bacteria in patches are also investigated numerically in this study.
Collapse
Affiliation(s)
- Dianlei Feng
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany.
| | - Insa Neuweiler
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten 1, 30163, Hannover, Germany
| | - Udo Nackenhorst
- Institute of Mechanics and Computational Mechanics, Leibniz Universität Hannover, Appelstraße 9a, 30167, Hannover, Germany
| |
Collapse
|
24
|
Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 2020; 113:659-671. [PMID: 31975449 DOI: 10.1111/mmi.14469] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.
Collapse
Affiliation(s)
- Daniela Megrian
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Ecole Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | - Najwa Taib
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jerzy Witwinowski
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Christophe Beloin
- Department of Microbiology, Genetics of Biofilm Unit, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| |
Collapse
|
25
|
Suzuki I, Shimizu T, Senpuku H. Short chain fatty acids induced the type 1 and type 2 fimbrillin-dependent and fimbrillin-independent initial attachment and colonization of Actinomyces oris monoculture but not coculture with streptococci. BMC Microbiol 2020; 20:329. [PMID: 33129273 PMCID: PMC7603776 DOI: 10.1186/s12866-020-01976-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Actinomyces oris is an early colonizer and has two types of fimbriae on its cell surface, type 1 fimbriae (FimP and FimQ) and type 2 fimbriae (FimA and FimB), which contribute to the attachment and coaggregation with other bacteria and the formation of biofilm on the tooth surface, respectively. Short-chain fatty acids (SCFAs) are metabolic products of oral bacteria including A. oris and regulate pH in dental plaques. To clarify the relationship between SCFAs and fimbrillins, effects of SCFAs on the initial attachment and colonization (INAC) assay using A. oris wild type and fimbriae mutants was investigated. INAC assays using A. oris MG1 strain cells were performed with SCFAs (acetic, butyric, propionic, valeric and lactic acids) or a mixture of them on human saliva-coated 6-well plates incubated in TSB with 0.25% sucrose for 1 h. The INAC was assessed by staining live and dead cells that were visualized with a confocal microscope. RESULTS Among the SCFAs, acetic, butyric and propionic acids and a mixture of acetic, butyric and propionic acids induced the type 1 and type 2 fimbriae-dependent and independent INAC by live A. oris, but these cells did not interact with streptococci. The main effects might be dependent on the levels of the non-ionized acid forms of the SCFAs in acidic stress conditions. GroEL was also found to be a contributor to the FimA-independent INAC by live A. oris cells stimulated with non-ionized acid. CONCLUSION SCFAs affect the INAC-associated activities of the A. oris fimbrillins and non-fimbrillins during ionized and non-ionized acid formations in the form of co-culturing with other bacteria in the dental plaque but not impact the interaction of A. oris with streptococci.
Collapse
Affiliation(s)
- Itaru Suzuki
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,Department of Pediatric Dentistry, Nihon University Graduate School of Dentistry at Matsudo, Chiba, Japan
| | - Takehiko Shimizu
- Department of Pediatric Dentistry, Nihon University Graduate School of Dentistry at Matsudo, Chiba, Japan
| | - Hidenobu Senpuku
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
| |
Collapse
|
26
|
Luo YX, Sun ML, Shi PL, Liu P, Chen YY, Peng X. [Research progress in the relationship between Veillonella and oral diseases]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2020; 38:576-582. [PMID: 33085245 DOI: 10.7518/hxkq.2020.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Veillonella species, known as the early colonizer of oral biofilm, are prevalent in oral microbiota. Seven Veillonella species have been isolated from oral cavity. Their distribution varies not only with different people but also with different sites in the oral cavity. Oral Veillonella are associated with oral diseases. They contribute to the adhesion of Streptococcus mutans and consume the lactate generated by streptococci. Veillonella species play an important role in the occurrence and development of periodontal diseases by providing adhesion sites for Porphyromonas gingivalis and boosting immune responses. The production of lipopolysaccharide and H2S is related to other oral diseases, such as pulpitis, periapical periodontitis, and halitosis. Several studies have been conducted on the relationship between Veillonella and oral diseases and the interaction between Veillonella and other pathological microorganisms, but limited knowledge is available at the molecular level. This article reviews the research progress in the relationship between Veillonella and oral infectious diseases, such as dental caries and periodontal diseases.
Collapse
Affiliation(s)
- Yu-Xue Luo
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| | - Man-Lin Sun
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| | - Pei-Lei Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| | - Pan Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| | - Yi-Yin Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Dental Basic Medicine, West China School of Stomatology, Chengdu 610041, China
| |
Collapse
|
27
|
Khosravi Y, Kandukuri RDP, Palmer SR, Gloag ES, Borisov SM, Starke EM, Ward MT, Kumar P, de Beer D, Chennu A, Stoodley P. Use of an oxygen planar optode to assess the effect of high velocity microsprays on oxygen penetration in a human dental biofilms in-vitro. BMC Oral Health 2020; 20:230. [PMID: 32825831 PMCID: PMC7441732 DOI: 10.1186/s12903-020-01217-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dental plaque biofilms are the causative agents of caries, gingivitis and periodontitis. Both mechanical and chemical strategies are used in routine oral hygiene strategies to reduce plaque build-up. If allowed to mature biofilms can create anoxic microenvironments leading to communities which harbor pathogenic Gram-negative anaerobes. When subjected to high velocity fluid jets and sprays biofilms can be fluidized which disrupts the biofilm structure and allows the more efficient delivery of antimicrobial agents. METHODS To investigate how such jets may disrupt anoxic niches in the biofilm, we used planar optodes to measure the dissolved oxygen (DO) concentration at the base of in-vitro biofilms grown from human saliva and dental plaque. These biofilms were subject to "shooting" treatments with a commercial high velocity microspray (HVM) device. RESULTS HVM treatment resulted in removal of much of the biofilm and a concurrent rapid shift from anoxic to oxic conditions at the base of the surrounding biofilm. We also assessed the impact of HVM treatment on the microbial community by tracking 7 target species by qPCR. There was a general reduction in copy numbers of the universal 16S RNA by approximately 95%, and changes of individual species in the target region ranged from approximately 1 to 4 log reductions. CONCLUSION We concluded that high velocity microsprays removed a sufficient amount of biofilm to disrupt the anoxic region at the biofilm-surface interface.
Collapse
Affiliation(s)
- Yalda Khosravi
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA
| | | | - Sara R Palmer
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Erin S Gloag
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA
| | - Sergey M Borisov
- Institute of Analytical Chemistry and Food Chemistry Graz University of Technology Stremayrgasse, Graz, Austria
| | | | - Marilyn T Ward
- Philips Oral Healthcare, Bothell, Washington, 98021, USA
| | - Purnima Kumar
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA. .,Department Orthopaedics, Ohio State University, Columbus, USA. .,National Centre for Advanced Tribology (nCATS), Mechanical Engineering, University of Southampton, Southampton, UK.
| |
Collapse
|
28
|
Debelius JW, Huang T, Cai Y, Ploner A, Barrett D, Zhou X, Xiao X, Li Y, Liao J, Zheng Y, Huang G, Adami HO, Zeng Y, Zhang Z, Ye W. Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk. mSystems 2020; 5:e00065-20. [PMID: 32636333 PMCID: PMC7343305 DOI: 10.1128/msystems.00065-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/18/2020] [Indexed: 12/24/2022] Open
Abstract
Oral health and changes in the oral microbiome have been associated with both local and systemic cancer. Poor oral hygiene is a known risk factor for nasopharyngeal carcinoma (NPC), a virally associated head and neck cancer endemic to southern China. We explored the relationship between NPC and the oral microbiome using 16S rRNA sequencing in a study of 499 NPC patients and 495 population-based age and sex frequency-matched controls from an area of endemicity of Southern China. We found a significant reduction in community richness in cases compared to that in controls. Differences in the overall microbial community structure between cases and controls could not be explained by other potential confounders; disease status explained 5 times more variation in the unweighted UniFrac distance than the next most explanatory variable. In feature-based analyses, we identified a pair of coexcluding Granulicatella adiacens amplicon sequence variants (ASVs) which were strongly associated with NPC status and differed by a single nucleotide. The G. adiacens variant an individual carried was also associated with the overall microbial community based on beta diversity. Co-occurrence analysis suggested the two G. adiacens ASVs sit at the center of two coexcluding clusters of closely related organisms. Our results suggest there are differences in the oral microbiomes between NPC patients and healthy controls, and these may be associated with both a loss of microbial diversity and niche specialization among closely related commensals.IMPORTANCE The relationship between oral health and the risk of nasopharyngeal carcinoma (NPC) was previously established. However, the role of oral microbiome has not been evaluated in the disease in a large epidemiological study. This paper clearly establishes a difference in the oral microbiomes between NPC patients and healthy controls which cannot be explained by other confounding factors. It furthermore identifies a pair of closely related coexcluding organisms associated with the disease, highlighting the importance of modern methods for single-nucleotide resolution in 16S rRNA sequence characterization. To the best of our knowledge, this is one of the first examples of cancer-associated niche specialization of the oral microbiome.
Collapse
Affiliation(s)
- Justine W Debelius
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tingting Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yonglin Cai
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Donal Barrett
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoying Zhou
- Life Science Institute, Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, People's Republic of China
| | - Xue Xiao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yancheng Li
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Jian Liao
- Cangwu Institute for Nasopharyngeal Carcinoma Control and Prevention, Wuzhou, People's Republic of China
| | - Yuming Zheng
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Guangwu Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Clinical Effectiveness Research Group, Institute of Health, University of Oslo, Oslo, Norway
| | - Yi Zeng
- State Key Laboratory for Infectious Diseases Prevention and Control, Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhe Zhang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
29
|
Vandeplassche E, Sass A, Ostyn L, Burmølle M, Kragh KN, Bjarnsholt T, Coenye T, Crabbé A. Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm. Biofilm 2020; 2:100031. [PMID: 33447816 PMCID: PMC7798459 DOI: 10.1016/j.bioflm.2020.100031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.
Collapse
Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Mette Burmølle
- Department of Microbiology, University of Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| |
Collapse
|
30
|
Liu S, Chen M, Wang Y, Zhou X, Peng X, Ren B, Li M, Cheng L. Effect of Veillonella parvula on the physiological activity of Streptococcus mutans. Arch Oral Biol 2020; 109:104578. [DOI: 10.1016/j.archoralbio.2019.104578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022]
|
31
|
Katagiri S, Shiba T, Tohara H, Yamaguchi K, Hara K, Nakagawa K, Komatsu K, Watanabe K, Ohsugi Y, Maekawa S, Iwata T. Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities. Front Cell Infect Microbiol 2019; 9:434. [PMID: 31956606 PMCID: PMC6951430 DOI: 10.3389/fcimb.2019.00434] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/05/2019] [Indexed: 11/22/2022] Open
Abstract
Stroke is associated with multiple forms of disability, including dysphagia. Post-stroke dysphagia increases the risks of pneumonia and mortality and often results in cessation of oral feeding. However, appropriate rehabilitation methods can eventually lead to resumption of oral food intake. This study tried to clarify that re-initiating oral food intake could modify the composition of oral/gut microbial communities in patients with dysphagia. From 78 patients with sub-acute stage of stroke, 11 complete tube feeding subjects without taking antibiotics were enrolled and received rehabilitation for re-initiation of oral food intake, and 8 subjects were brought back to complete oral feeding. Oral and gut microbiota community profiles were evaluated using 16S rRNA sequencing of the saliva and feces samples before and after re-initiation of oral food intake in patients recovering from enteral nutrition under the same nutrient condition. Standard nutrition in the hospital was 1,840 kcal, including protein = 75 g, fat = 45 g, and carbohydrates = 280 g both for tube and oral feeding subjects. Oral food intake increased oral and gut microbiome diversity and altered the composition of the microbiome. Oral and gut microbiome compositions were drastically different; however, the abundance of family Carnobacteriaceae and genus Granulicatella was increased in both the oral and gut microbiome after re-initiation of oral food intake. Although oral microbiota showed more significant changes than the gut microbiota, metagenome prediction revealed the presence of more differentially enriched pathways in the gut. In addition, simpler co-occurrence networks of oral and gut microbiomes, indicating improved dysbiosis of the microbiome, were observed during oral feeding as compared to that during tube feeding. Oral food intake affects oral and gut microbiomes in patients recovering from enteral nutrition. Rehabilitation for dysphagia can modify systemic health by increasing the diversity and altering the composition and co-occurrence network structure of oral and gut microbial communities.
Collapse
Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruka Tohara
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Yamaguchi
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koji Hara
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuharu Nakagawa
- Gerodontology and Oral Rehabilitation, Department of Gerontology and Gerodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuki Watanabe
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shogo Maekawa
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
32
|
Abstract
Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.
Collapse
Affiliation(s)
- J L Baker
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - X He
- The Forsyth Institute, Cambridge, MA, USA
| | - W Shi
- The Forsyth Institute, Cambridge, MA, USA
| |
Collapse
|
33
|
Brown JL, Johnston W, Delaney C, Rajendran R, Butcher J, Khan S, Bradshaw D, Ramage G, Culshaw S. Biofilm-stimulated epithelium modulates the inflammatory responses in co-cultured immune cells. Sci Rep 2019; 9:15779. [PMID: 31673005 PMCID: PMC6823452 DOI: 10.1038/s41598-019-52115-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
The gingival epithelium is a physical and immunological barrier to the microbiota of the oral cavity, which interact through soluble mediators with the immune cells that patrol the tissue at the gingival epithelium. We sought to develop a three-dimensional gingivae-biofilm interface model using a commercially available gingival epithelium to study the tissue inflammatory response to oral biofilms associated with “health”, “gingivitis” and “periodontitis”. These biofilms were developed by sequential addition of microorganisms to mimic the formation of supra- and sub-gingival plaque in vivo. Secondly, to mimic the interactions between gingival epithelium and immune cells in vivo, we integrated peripheral blood mononuclear cells and CD14+ monocytes into our three-dimensional model and were able to assess the inflammatory response in the immune cells cultured with and without gingival epithelium. We describe a differential inflammatory response in immune cells cultured with epithelial tissue, and more so following incubation with epithelium stimulated by “gingivitis-associated” biofilm. These results suggest that gingival epithelium-derived soluble mediators may control the inflammatory status of immune cells in vitro, and therefore targeting of the epithelial response may offer novel therapies. This multi-cellular interface model, both of microbial and host origin, offers a robust in vitro platform to investigate host-pathogens at the epithelial surface.
Collapse
Affiliation(s)
- Jason L Brown
- Institute of Biomedical and Environmental Health Research, School of Science and Sport, University of the West of Scotland, Paisley, PA1 2BE, UK.,Oral Sciences Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - William Johnston
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Chris Delaney
- Institute of Biomedical and Environmental Health Research, School of Science and Sport, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - Ranjith Rajendran
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Butcher
- Institute of Biomedical and Environmental Health Research, School of Science and Sport, University of the West of Scotland, Paisley, PA1 2BE, UK.,Department of Life Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, G4 0BA, UK
| | - Shaz Khan
- Oral Healthcare R&D, GlaxoSmithKline Consumer Healthcare, Weybridge, KT13 0DE, UK
| | - David Bradshaw
- Oral Healthcare R&D, GlaxoSmithKline Consumer Healthcare, Weybridge, KT13 0DE, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| | - Shauna Culshaw
- Oral Sciences Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| |
Collapse
|
34
|
Valm AM. The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease. J Mol Biol 2019; 431:2957-2969. [PMID: 31103772 PMCID: PMC6646062 DOI: 10.1016/j.jmb.2019.05.016] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/27/2019] [Accepted: 05/09/2019] [Indexed: 01/01/2023]
Abstract
The human oral cavity harbors diverse communities of microbes that live as biofilms: highly ordered, surface-associated assemblages of microbes embedded in an extracellular matrix. Oral microbial communities contribute to human health by fine-tuning immune responses and reducing dietary nitrate. Dental caries and periodontal disease are together the most prevalent microbially mediated human diseases worldwide. Both of these oral diseases are known to be caused not by the introduction of exogenous pathogens to the oral environment, but rather by a homeostasis breakdown that leads to changes in the structure of the microbial communities present in states of health. Both dental caries and periodontal disease are mediated by synergistic interactions within communities, and both diseases are further driven by specific host inputs: diet and behavior in the case of dental caries and immune system interactions in the case of periodontal disease. Changes in community structure (taxonomic identity and abundance) are well documented during the transition from health to disease. In this review, changes in biofilm physical structure during the transition from oral health to disease and the concomitant relationship between structure and community function will be emphasized.
Collapse
Affiliation(s)
- Alex M Valm
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA.
| |
Collapse
|
35
|
Selective pressures during chronic infection drive microbial competition and cooperation. NPJ Biofilms Microbiomes 2019; 5:16. [PMID: 31263568 PMCID: PMC6555799 DOI: 10.1038/s41522-019-0089-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic infections often contain complex mixtures of pathogenic and commensal microorganisms ranging from aerobic and anaerobic bacteria to fungi and viruses. The microbial communities present in infected tissues are not passively co-existing but rather actively interacting with each other via a spectrum of competitive and/or cooperative mechanisms. Competition versus cooperation in these microbial interactions can be driven by both the composition of the microbial community as well as the presence of host defense strategies. These interactions are typically mediated via the production of secreted molecules. In this review, we will explore the possibility that microorganisms competing for nutrients at the host–pathogen interface can evolve seemingly cooperative mechanisms by controlling the production of subsets of secreted virulence factors. We will also address interspecies versus intraspecies utilization of community resources and discuss the impact that this phenomenon might have on co-evolution at the host–pathogen interface.
Collapse
|
36
|
Yu XL, Chan Y, Zhuang L, Lai HC, Lang NP, Keung Leung W, Watt RM. Intra-oral single-site comparisons of periodontal and peri-implant microbiota in health and disease. Clin Oral Implants Res 2019; 30:760-776. [PMID: 31102416 DOI: 10.1111/clr.13459] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Periodontitis and peri-implantitis are oral infectious-inflammatory diseases that share similarities in their pathology and etiology. Our objective was to characterize the single-site subgingival and submucosal microbiomes of implant-rehabilitated, partially dentate Chinese subjects (n = 18) presenting with both periodontitis and peri-implantitis. MATERIALS AND METHODS Subgingival/submucosal plaque samples were collected from four clinically distinct sites in each subject: peri-implantitis submucosa (DI), periodontal pocket (DT), clinically healthy (unaffected) peri-implant submucosa (HI), and clinically healthy (unaffected) subgingival sulcus (HT). The bacterial microbiota present was analyzed using Illumina MiSeq sequencing. RESULTS Twenty-six phyla and 5,726 operational taxonomic units (OTUs, 97% sequence similarity cutoff) were identified. Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Synergistetes, TM7, and Spirochaetes comprised 99.6% of the total reads detected. Bacterial communities within the DI, DT, HI, and HT sites shared high levels of taxonomic similarity. Thirty-one "core species" were present in >90% sites, with Streptococcus infantis/mitis/oralis (HMT-070/HMT-071/HMT-638/HMT-677) and Fusobacterium sp. HMT-203/HMT-698 being particularly prevalent and abundant. Beta-diversity analyses (PERMANOVA test, weighted UniFrac) revealed the largest variance in the microbiota was at the subject level (46%), followed by periodontal health status (4%). Differing sets of OTUs were associated with periodontitis and peri-implantitis sites, respectively. This included putative "periodontopathogens," such as Prevotella, Porphyromonas, Tannerella, Bacteroidetes [G-5], and Treponema spp. Interaction network analysis identified several putative patterns underlying dysbiosis in periodontitis/peri-implantitis sites. CONCLUSIONS Species (OTU) composition of the periodontal and peri-implant microbiota varied widely between subjects. The inter-subject variations in subgingival/submucosal microbiome composition outweighed differences observed between implant vs. tooth sites, or between diseased vs. healthy (unaffected) peri-implant/periodontal sites.
Collapse
Affiliation(s)
- Xiao-Lin Yu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.,Department of Oral Implantology, Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Yuki Chan
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | | | - Hong-Chang Lai
- Department of Oral and Maxillo-facial Implantology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | | | - Wai Keung Leung
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Rory M Watt
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
37
|
Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq. Sci Rep 2019; 9:7664. [PMID: 31113978 PMCID: PMC6529473 DOI: 10.1038/s41598-019-43979-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
Many oral bacteria form macroscopic clumps known as coaggregates when mixed with a different species. It is thought that these cell-cell interactions are critical for the formation of mixed-species biofilms such as dental plaque. Here, we assessed the impact of coaggregation between two key initial colonizers of dental plaque, Streptococcus gordonii and Veillonella parvula, on gene expression in each partner. These species were shown to coaggregate in buffer or human saliva. To monitor gene regulation, coaggregates were formed in human saliva and, after 30 minutes, whole-transcriptomes were extracted for sequencing and Dual RNA-Seq analysis. In total, 272 genes were regulated in V. parvula, including 39 genes in oxidoreductase processes. In S. gordonii, there was a high degree of inter-sample variation. Nevertheless, 69 genes were identified as potentially regulated by coaggregation, including two phosphotransferase system transporters and several other genes involved in carbohydrate metabolism. Overall, these data indicate that responses of V. parvula to coaggregation with S. gordonii are dominated by oxidative stress-related processes, whereas S. gordonii responses are more focussed on carbohydrate metabolism. We hypothesize that these responses may reflect changes in the local microenvironment in biofilms when S. gordonii or V. parvula immigrate into the system.
Collapse
|
38
|
A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis. mSystems 2019; 4:mSystems00177-19. [PMID: 31098396 PMCID: PMC6517690 DOI: 10.1128/msystems.00177-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/26/2019] [Indexed: 11/20/2022] Open
Abstract
The European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae. The esophagus was dominated by a single ASV of the genus Vibrio. Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites. IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.
Collapse
|
39
|
Abstract
Periodontal disease (PD) is a common dental disease associated with the interaction between dysbiotic oral microbiota and host immunity. It is a prevalent disease, resulting in loss of gingival tissue, periodontal ligament, cementum and alveolar bone. PD is a major form of tooth loss in the adult population. Experimental animal models have enabled the study of PD pathogenesis and are used to test new therapeutic approaches for treating the disease. The ligature-induced periodontitis model has several advantages as compared with other models, including rapid disease induction, predictable bone loss and the capacity to study periodontal tissue and alveolar bone regeneration because the model is established within the periodontal apparatus. Although mice are the most convenient and versatile animal models used in research, ligature-induced periodontitis has been more frequently used in large animals. This is mostly due to the technical challenges involved in consistently placing ligatures around murine teeth. To reduce the technical challenge associated with the traditional ligature model, we previously developed a simplified method to easily install a bacterially retentive ligature between two molars for inducing periodontitis. In this protocol, we provide detailed instructions for placement of the ligature and demonstrate how the model can be used to evaluate gingival tissue inflammation and alveolar bone loss over a period of 18 d after ligature placement. This model can also be used on germ-free mice to investigate the role of human oral bacteria in periodontitis in vivo. In conclusion, this protocol enables the mechanistic study of the pathogenesis of periodontitis in vivo.
Collapse
|
40
|
Nakazawa F, Mashima I, Theodorea C, Thaweboon B, Thaweboon S, Vichayanrat T, Scannapieco F. Characterization of the salivary microbiome in healthy Thai children. ASIAN PAC J TROP MED 2019. [DOI: 10.4103/1995-7645.257116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
41
|
Edlund A, Yang Y, Yooseph S, He X, Shi W, McLean JS. Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation. MICROBIOME 2018; 6:217. [PMID: 30522530 PMCID: PMC6284299 DOI: 10.1186/s40168-018-0591-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 11/06/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation. RESULTS Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum. CONCLUSION It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.
Collapse
Affiliation(s)
- Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92137, USA.
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, 75, Jansang-ro 101beon-gil, Janghang-eup, Seocheon-gun, Chungcheongnam-do, 33662, Korea
| | - Shibu Yooseph
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL, 32816, USA
| | - Xuesong He
- The Forsyth Institute, Cambridge, MA, 02142, USA
| | - Wenyuan Shi
- The Forsyth Institute, Cambridge, MA, 02142, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
42
|
Xu L, Chen X, Wang Y, Jiang W, Wang S, Ling Z, Chen H. Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study. Front Physiol 2018; 9:342. [PMID: 29670544 PMCID: PMC5893825 DOI: 10.3389/fphys.2018.00342] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 03/20/2018] [Indexed: 12/16/2022] Open
Abstract
Dynamic alterations in oral microbiota are closely related to the development of dental caries;however, changes in salivary microbiota during this process have not been extensively studied. In addition, increasing evidence suggests that oral microbiome profiles differ according to dentition stages, but it is unclear whether they change with age during the same dentition, such as deciduous dentition. These two aspects were investigated in a 2-year follow-up study, and caries-free preschool children with complete deciduous dentition were enrolled. Saliva was collected and oral examination was conducted at the beginning of this trial, and then every subsequent 6 months for a total of five time points (T0, T1, T2, T3, and T4). Based on the clinical examination of teeth at the end of the trial, subjects were divided into health-to-health (H-H, N = 11) and health-to-caries (H-C, N = 12) groups at every time point. A total of 115 saliva samples from 23 subjects was detected by sequencing 16S rDNA V3-V4 hypervariable regions with the Illumina MiSeq platform to obtain microbiome profiles, and 100 samples finally passed quality control for further analyses. A total of 4,328,852 high-quality sequencing reads passed quality-control testing, representing 14 phyla, 27 classes, 43 orders, 67 families, and 127 genera. An α diversity analysis showed that salivary microbial diversity was similar in all groups, and a β diversity analysis showed that salivary microbial community structure changed with dental caries. Linear discriminant analysis effect size (LEfSe) analysis revealed that the abundance of the genera Atopobium, Megasphaera, and Veillonella increased significantly, while that of the genera Shuttleworthia and Rothia decreased significantly with the development of dental caries. Megasphaera and Veillonella were enriched at the early stage of deciduous dentition whereas Peptococcus, Rothia, and Treponema were enriched at the later stage. The core microbiome in the H-H and H-C groups comprised 26 and 29 genera, respectively, with statistical differences observed in 11 shared core genera. These results provide new insights into variations in the salivary microbiome related to dental caries and age in the deciduous dentition period.
Collapse
Affiliation(s)
- Lei Xu
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xi Chen
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yuan Wang
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Wen Jiang
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sa Wang
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hui Chen
- Department of Conservative Dentistry and Periodontics, The Affiliated Hospital of Stomatology, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
43
|
Sharma N, Bhatia S, Sodhi AS, Batra N. Oral microbiome and health. AIMS Microbiol 2018; 4:42-66. [PMID: 31294203 PMCID: PMC6605021 DOI: 10.3934/microbiol.2018.1.42] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/03/2018] [Indexed: 12/12/2022] Open
Abstract
The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, “Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual”.
Collapse
Affiliation(s)
- Neetu Sharma
- Department of Microbiology, GGDSD College, Sector 32 C Chandigarh, India
| | - Sonu Bhatia
- Department of Biotechnology, GGDSD College, Sector 32 C Chandigarh, India
| | | | - Navneet Batra
- Department of Biotechnology, GGDSD College, Sector 32 C Chandigarh, India
| |
Collapse
|
44
|
Guo L, Edlund A. Targeted Antimicrobial Peptides: A Novel Technology to Eradicate Harmful Streptococcus Mutans. JOURNAL OF THE CALIFORNIA DENTAL ASSOCIATION 2017; 45:557-564. [PMID: 29899655 PMCID: PMC5994769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Lihong Guo
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Anna Edlund
- J Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA
| |
Collapse
|
45
|
Veillonella Catalase Protects the Growth of Fusobacterium nucleatum in Microaerophilic and Streptococcus gordonii-Resident Environments. Appl Environ Microbiol 2017; 83:AEM.01079-17. [PMID: 28778894 DOI: 10.1128/aem.01079-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/26/2017] [Indexed: 12/16/2022] Open
Abstract
The oral biofilm is a multispecies community in which antagonism and mutualism coexist among friends and foes to keep an ecological balance of community members. The pioneer colonizers, such as Streptococcus gordonii, produce H2O2 to inhibit the growth of competitors, like the mutans streptococci, as well as strict anaerobic middle and later colonizers of the dental biofilm. Interestingly, Veillonella species, as early colonizers, physically interact (coaggregate) with S. gordonii A putative catalase gene (catA) is found in most sequenced Veillonella species; however, the function of this gene is unknown. In this study, we characterized the ecological function of catA from Veillonella parvula PK1910 by integrating it into the only transformable strain, Veillonella atypica OK5, which is catA negative. The strain (OK5-catA) became more resistant to H2O2 Further studies demonstrated that the catA gene expression is induced by the addition of H2O2 or coculture with S. gordonii Mixed-culture experiments further revealed that the transgenic OK5-catA strain not only enhanced the growth of Fusobacterium nucleatum, a strict anaerobic periodontopathogen, under microaerophilic conditions, but it also rescued F. nucleatum from killing by S. gordonii A potential role of catalase in veillonellae in biofilm ecology and pathogenesis is discussed here.IMPORTANCEVeillonella species, as early colonizers, can coaggregate with many bacteria, including the initial colonizer Streptococcus gordonii and periodontal pathogen Fusobacterium nucleatum, during various stages of oral biofilm formation. In addition to providing binding sites for many microbes, our previous study also showed that Veillonella produces nutrients for the survival and growth of periodontal pathogens. These findings indicate that Veillonella plays an important "bridging" role in the development of oral biofilms and the ecology of the human oral cavity. In this study, we demonstrated that the reducing activity of Veillonella can rescue the growth of Fusobacterium nucleatum not only under microaerophilic conditions, but also in an environment in which Streptococcus gordonii is present. Thus, this study will provide a new insight for future studies on the mechanisms of human oral biofilm formation and the control of periodontal diseases.
Collapse
|
46
|
Mashima I, Nakazawa F. Role of an autoinducer-2-like molecule from Veillonella tobetsuensis in Streptococcus gordonii biofilm formation. J Oral Biosci 2017. [DOI: 10.1016/j.job.2017.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
47
|
Anbalagan R, Srikanth P, Mani M, Barani R, Seshadri KG, Janarthanan R. Next generation sequencing of oral microbiota in Type 2 diabetes mellitus prior to and after neem stick usage and correlation with serum monocyte chemoattractant-1. Diabetes Res Clin Pract 2017. [PMID: 28648853 DOI: 10.1016/j.diabres.2017.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Oral microbiome impacts health and disease. T2DM and periodontitis are associated. Neem (Azadiracta indica) has antibacterial activity against oral microbiota. OBJECTIVES To characterize oral microbiota (OMB) in saliva samples of T2DM patients by Next generation sequencing. To analyze MCP-1 levels among the T2DM patients before and after a month of neem stick usage as a toothbrush. MATERIALS AND METHODS Blood and saliva samples were collected from adult T2DM patients before and after the neem stick usage. Metagenomic sequencing was performed on saliva samples targeting V6 region of 16s rRNA. Serum MCP-1 levels were determined using a quantitative sandwich Human MCP-1 standard ABTS development kit (Peprotech, USA). RESULTS The profile of oral microbiota of T2DM patients (n=24) consists of Streptococcus (95.8%) counts ranging from 2644 to 27,214, Veillonella (72.2%, counts 25-19,709, Neisseria (87.5%) 453-33,445), Rothia (63.6%, 233-6734), Actinomycetes (25%, 161-3730), Fusobacterium (21%, 2252-21,334), and Pigmentiphaga (12.5% 3-16,644). Oral microbiota in healthy controls (n=10), consists of Streptococcus (26.1%), Veillonella (21.9%), Neisseria (16.9%), Haemophilus (10.7%), Actinomycetes (2.6%), Rothia (3.1%), Oribacterium (1.7%). Post neem samples showed drastic reduction in the load of bacteria which was statistically significant. The mean serum MCP-1 before the use of neem stick was 265.18±79.44 (range 141.6-980.5pg/ml) and dropped to 33.6±7.35 after a month of neem stick usage (P value>0.001). CONCLUSION OMB of T2DM patients and healthy controls were similar, however bacterial loads were significantly higher in T2DM patients. Use of neem stick has a statistically significant reduction on bacterial loads and MCP-1 levels in T2DM patients.
Collapse
Affiliation(s)
- Rubini Anbalagan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India.
| | - Monika Mani
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Ramya Barani
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Krishna G Seshadri
- Department of Endocrinology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - R Janarthanan
- Shrimpex Biotech Services Private Limited, Sholinganallur, Chennai, Tamil Nadu, India
| |
Collapse
|
48
|
Interbacterial Adhesion Networks within Early Oral Biofilms of Single Human Hosts. Appl Environ Microbiol 2017; 83:AEM.00407-17. [PMID: 28341674 DOI: 10.1128/aem.00407-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/16/2017] [Indexed: 02/04/2023] Open
Abstract
Specific interbacterial adhesion, termed coaggregation, is well established for three early colonizers of the plaque biofilm: streptococci, actinomyces, and veillonellae. However, little is known about interactions of other early colonizers and about the extent of interactions within the bacterial community from a single host. To address these gaps, subject-specific culture collections from two individuals were established using an intraoral biofilm retrieval device. Molecular taxonomy (Human Oral Microbe Identification Microarray [HOMIM]) analysis of biofilm samples confirmed the integrity and completeness of the collections. HOMIM analysis verified the isolation of Streptococcus gordonii and S. anginosus from only one subject, as well as isolation of a previously uncultivated streptococcal phylotype from the other subject. Strains representative of clonal diversity within each collection were further characterized. Greater than 70% of these streptococcal strains from each subject coaggregated with at least one other coisolate. One-third of the strains carry a known coaggregation mediator: receptor polysaccharide (RPS). Almost all nonstreptococcal isolates coaggregated with other coisolates. Importantly, certain Rothia strains demonstrated more coaggregations with their coisolated bacteria than did any Streptococcus or Actinomyces strain, and certain Haemophilus isolates participated in twice as many. Confocal microscopy of undisturbed biofilms showed that Rothia and Haemophilus each occur in small multispecies microcolonies. However, in confluent high-biomass regions, Rothia occurred in islands whereas Haemophilus was distributed throughout. Together, the data demonstrate that coaggregation networks within an individual's oral microflora are extensive and that Rothia and Haemophilus can be important initiators of cell-cell interactions in the early biofilm.IMPORTANCE Extensive involvement of specific interbacterial adhesion in dental plaque biofilm formation has been postulated based on in vitro coaggregation between oral bacteria from culture collections that are not subject specific. In the present study, subject-specific culture collections were obtained from early plaque biofilm of two volunteers, and coaggregations within each culture collection were assayed. Coaggregations, several of which involved a coaggregation-mediating cell surface molecule known from well-studied streptococci, were widespread. Unexpectedly, the little-studied organisms Haemophilus and Rothia participated in the greatest numbers of interactions with community members; these two organisms showed different distributions within the undisturbed biofilm. The data show that coaggregation networks encompass most organisms within the biofilm community of each individual, and they indicate prominent participation of organisms such as Haemophilus and Rothia in early plaque biofilm formation.
Collapse
|
49
|
Conrads G, Barth S, Möckel M, Lenz L, van der Linden M, Henne K. Streptococcus tigurinus is frequent among gtfR-negative Streptococcus oralis isolates and in the human oral cavity, but highly virulent strains are uncommon. J Oral Microbiol 2017; 9:1307079. [PMID: 28473881 PMCID: PMC5405715 DOI: 10.1080/20002297.2017.1307079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 11/25/2022] Open
Abstract
Streptococcus tigurinus is a new member of the Mitis group and is associated with infective endocarditis. Low and high virulent variants have been described. A search was made in the national reference collection of endocarditis isolates for S. tigurinus–like strains by sequencing housekeeping genes (16S rRNA-gene, gdh, groEL, sodA). The strains were further profiled by polymerase chain reaction (PCR) targeting a choice of virulence genes (rib-like, cshA-like, gtfR, int, pitA, hylA). To study the prevalence and abundance of S. tigurinus in the saliva and on the mucosal membranes of 35 healthy adults, PCRs detecting two variants of the 16S operon and virulence genes were applied. Among the endocarditis isolates, eight strains (all gtfR-negative and former S. oralis) holding the specific S. tigurinus 16S motif were found, but the pattern of genes related to high virulence found in the S. tigurinus type strain could not be detected in any of these strains. A close phylogenetic proximity between S. tigurinus and S. oralis was observed, with intersectional hybrid strains formed. This was supported by concatenated housekeeping sequences, in silico DNA–DNA hybridization, pathogenomic profiling, and multidimensional scaling. In the oral samples, S. tigurinus could be detected frequently, especially in the most common operon variant, but none of the type strain–related virulence factors were found. Low virulent S. tigurinus–like strains can be found frequently and in high prevalence (66%) and abundance (12.5%) in the oral cavity of healthy adults. In strain collections, they are among the formerly known gtfR-negative S. oralis. Highly virulent strains seem to be uncommon. Though closely related, S. oralis and S. tigurinus can be separated by the presence or absence of gtfR and dextran production. Hybrids of both species can be found. The variable arsenal of virulence genes found in this study emphasizes the genetic plasticity of Mitis group streptococci.
Collapse
Affiliation(s)
- Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Svenja Barth
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Maureen Möckel
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Lucas Lenz
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Mark van der Linden
- Institute of Medical Microbiology and National Reference Center for Streptococci, RWTH Aachen University Hospital, Aachen, Germany
| | - Karsten Henne
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| |
Collapse
|
50
|
Reynolds-Campbell G, Nicholson A, Thoms-Rodriguez CA. Oral Bacterial Infections: Diagnosis and Management. Dent Clin North Am 2017; 61:305-318. [PMID: 28317568 DOI: 10.1016/j.cden.2016.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The human oral cavity contains more than 500 different bacterial species. These organisms belong to several phyla including Bacteroidetes, Firmicutes, Tenericutes, Actinobacteria, Proteobacteria, Euryarchaeota, Chlamydiae, and Spirochaetes. Many of these have the ability to colonize the gingival crevices and the outer surface of the tooth forming biofilms often leading to dental plaque formation. These bacteria produce acid that erode teeth causing cavities or infections. The diagnosis of these infections is often clinical and antibiotics are used empirically to treat some infections or as prophylaxis. The characterization, definitive diagnosis, and susceptibility testing of oral bacterial infections are valuable in guiding appropriate therapy and in prevention of disease.
Collapse
Affiliation(s)
| | - Alison Nicholson
- Department of Microbiology, The University of the West Indies, Mona, KGN 7, Jamaica, West Indies
| | | |
Collapse
|