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Costa Silva A, Pina-Vaz T, Morgado A, Martins-Silva C, Antunes-Lopes T, Alturas Silva J. The Role of the Urobiome in Kidney Transplantation: A Systematic Review. Transplant Direct 2024; 10:e1643. [PMID: 38769976 PMCID: PMC11104728 DOI: 10.1097/txd.0000000000001643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 05/22/2024] Open
Abstract
Background The urinary microbiome, also known as the urobiome, was traditionally considered sterile. However, emerging evidence suggests its presence in the urinary tract. Urobiome dysbiosis has been associated with various urologic conditions, making it a topic of interest also in kidney transplantation. This systematic review examines the evidence of urobiome changes in kidney transplant recipients (KTRs). Methods Systematic literature searches in the PubMed and SCOPUS databases. Results Of the 770 articles identified, 8 met the inclusion criteria. The urobiome showed reduced diversity in KTRs compared with healthy controls and patients on dialysis. Proteobacteria enrichment was associated with graft stability or spontaneous tolerance in KTRs without immunological events. Kidney interstitial fibrosis and tubular atrophy were associated with changes in resident urinary microbes and increased pathogenic bacteria. Additionally, KTRs with chronic allograft dysfunction had a higher prevalence of Corynebacterium. Conclusions The review highlights the importance of studying the urobiome in KTRs and its potential impact on transplant outcomes. The field remains largely unexplored, and further research is needed to establish consistent study designs and objectives. Future studies could lead to biomarker discovery, personalized therapies, and improved outcomes and graft survival in KTRs.
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Affiliation(s)
- Alberto Costa Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Teresa Pina-Vaz
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Afonso Morgado
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Carlos Martins-Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Tiago Antunes-Lopes
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - João Alturas Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
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Sampaio S, Araujo R, Merino-Riba A, Lelouvier B, Servant F, Quelhas-Santos J, Pestana M, Sampaio-Maia B. Blood, Gut, and Oral Microbiome in Kidney Transplant Recipients. Indian J Nephrol 2023; 33:366-370. [PMID: 37881747 PMCID: PMC10593307 DOI: 10.4103/ijn.ijn_168_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/31/2023] [Indexed: 10/27/2023] Open
Abstract
Background and Objective Recent reports describe the existence of a blood microbiome profile not associated with an infection state. Given the high impact that the dysbiotic human microbiome appears to have in chronic kidney disease and, in particular, in the outcome of kidney transplant recipients (KTRs), we aimed to explore the variations and correlations of the gut, oral, and blood microbiome of recipients, 3 months after kidney transplantation. Materials and Methods We conducted a cross-sectional study where the microbiome of stool, saliva, and blood collected from recipients 3 months after kidney transplantation (N = 6) was analyzed by polymerase chain reaction (PCR) amplification and sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene using MiSeq Illumina® technology. Results Blood of KTRs harbors a distinct low-abundance microbiome dominated by Proteobacteria and Firmicutes. Gut and oral microbiome of KTRs also present distinct profiles. The existence of a proportion of shared operational taxonomic units among the different body sites is reported, mainly classified as Proteobacteria and Firmicutes. Conclusions This study provides evidence of existence a blood microbiome in KTRs, different from the gut and the oral microbiome profiles, with a small number of operational taxonomic units representing a shared microbiome. The clinical relevance of this observation should be further explored in these patients.
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Affiliation(s)
- Susana Sampaio
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
- Department of Nephrology, São João Hospital Center, EPE, Portugal
| | - Ricardo Araujo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
| | - Ana Merino-Riba
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Nephrology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | | | | | - Janete Quelhas-Santos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
| | - Manuel Pestana
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Medicine, University of Porto, EPE, Portugal
- Department of Nephrology, São João Hospital Center, EPE, Portugal
| | - Benedita Sampaio-Maia
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, EPE, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen, 208, 4200- 180 Porto, EPE, Portugal
- Faculty of Dental Medicine, University of Porto, Porto, Portugal
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Boopathi S, Priya PS, Haridevamuthu B, Nayak SPRR, Chandrasekar M, Arockiaraj J, Jia AQ. Expanding germ-organ theory: Understanding non-communicable diseases through enterobacterial translocation. Pharmacol Res 2023; 194:106856. [PMID: 37460001 DOI: 10.1016/j.phrs.2023.106856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/02/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Diverse microbial communities colonize different habitats of the human body, including gut, oral cavity, nasal cavity and tissues. These microbial communities are known as human microbiome, plays a vital role in maintaining the health. However, changes in the composition and functions of human microbiome can result in chronic low-grade inflammation, which can damage the epithelial cells and allows pathogens and their toxic metabolites to translocate into other organs such as the liver, heart, and kidneys, causing metabolic inflammation. This dysbiosis of human microbiome has been directly linked to the onset of several non-communicable diseases. Recent metabolomics studies have revealed that pathogens produce several uraemic toxins. These metabolites can serve as inter-kingdom signals, entering the circulatory system and altering host metabolism, thereby aggravating a variety of diseases. Interestingly, Enterobacteriaceae, a critical member of Proteobacteria, has been commonly associated with several non-communicable diseases, and the abundance of this family has been positively correlated with uraemic toxin production. Hence, this review provides a comprehensive overview of Enterobacterial translocation and their metabolites role in non-communicable diseases. This understanding may lead to the identification of novel biomarkers for each metabolic disease as well as the development of novel therapeutic drugs.
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Affiliation(s)
- Seenivasan Boopathi
- Hainan General Hospital, Hainan affiliated hospital of Hainan Medical University, Haikou 570311, China; Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - P Snega Priya
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - B Haridevamuthu
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - S P Ramya Ranjan Nayak
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India
| | - Munisamy Chandrasekar
- Department of Veterinary Clinical Medicine, Madras Veterinary College, Chennai, Tamil Nadu, India
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603 203, Chengalpattu District, Tamil Nadu, India.
| | - Ai-Qun Jia
- Hainan General Hospital, Hainan affiliated hospital of Hainan Medical University, Haikou 570311, China.
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吴 亚, 潘 亚. [Research Progress in Oral Diseases and Oral Microbiota of Organ Transplant Patients]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:61-65. [PMID: 36647644 PMCID: PMC10409052 DOI: 10.12182/20230160210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Indexed: 01/18/2023]
Abstract
Organ transplantation is an effective treatment for end-stage organ diseases. However, organ transplant recipients are susceptible to a wide variety of oral diseases, including gingival enlargement, periodontitis, oral mucosal diseases, oral malignant tumors, and dental caries. Oral microbiota may have played an important role in the organ transplant patients' increased susceptibility to oral diseases and is associated with adverse events after organ transplantation, which is gradually gaining more attention among scholars. We, herein, reviewed the common oral diseases, including periodontal tissue diseases, oral mucosal diseases, oral malignant tumors, and dental caries in organ transplantation patients. Furthermore, we discussed the characteristic changes in the oral microbiota of organ transplantation patients and the influencing factors of these changes. In-depth study of oral microbiota of organ transplant patients provides a reference for the prevention and treatment of relevant diseases after organ transplantation and serves an important role in oral and systemic health management of organ transplant patients.
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Affiliation(s)
- 亚红 吴
- 中国医科大学附属口腔医院 牙周病科 (沈阳 110002)Department of Periodontology, Hospital of Stomatology, China Medical University, Shenyang 110002, China
| | - 亚萍 潘
- 中国医科大学附属口腔医院 牙周病科 (沈阳 110002)Department of Periodontology, Hospital of Stomatology, China Medical University, Shenyang 110002, China
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5
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Sen T, Thummer RP. The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation. Front Immunol 2022; 13:932228. [PMID: 35874759 PMCID: PMC9300833 DOI: 10.3389/fimmu.2022.932228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interactions between the residents of the various human microbiotas and the human body. Since the gut microbiota is the densest, most popular, and most studied human microbiota, the impact of other human microbiotas such as the oral, lung, urinary, and genital microbiotas is often overshadowed. However, these microbiotas also provide critical and unique insights pertaining to transplantation success, rejection risk, and overall host health, across multiple different transplantation scenarios. Organ transplantation as well as the pre-, peri-, and post-transplant pharmacological regimens patients undergo is known to adversely impact the microbiotas, thereby increasing the risk of adverse patient outcomes. Over the past decade, holistic approaches to post-transplant patient care such as the administration of clinical and dietary interventions aiming at restoring deranged microbiota community structures have been gaining momentum. Examples of these include prebiotic and probiotic administration, fecal microbial transplantation, and bacteriophage-mediated multidrug-resistant bacterial decolonization. This review will discuss these perspectives and explore the role of different human microbiotas in the context of various transplantation scenarios.
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Affiliation(s)
| | - Rajkumar P. Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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6
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Long-Term Analysis of Resilience of the Oral Microbiome in Allogeneic Stem Cell Transplant Recipients. Microorganisms 2022; 10:microorganisms10040734. [PMID: 35456787 PMCID: PMC9030553 DOI: 10.3390/microorganisms10040734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
Stem cell transplantation (SCT) is associated with oral microbial dysbiosis. However, long-term longitudinal data are lacking. Therefore, this study aimed to longitudinally assess the oral microbiome in SCT patients and to determine if changes are associated with oral mucositis and oral chronic graft-versus-host disease. Fifty allogeneic SCT recipients treated in two Dutch university hospitals were prospectively followed, starting at pre-SCT, weekly during hospitalization, and at 3, 6, 12, and 18 months after SCT. Oral rinsing samples were taken, and oral mucositis (WHO score) and oral chronic graft-versus-host disease (NIH score) were assessed. The oral microbiome diversity (Shannon index) and composition significantly changed after SCT and returned to pre-treatment levels from 3 months after SCT. Oral mucositis was associated with a more pronounced decrease in microbial diversity and with several disease-associated genera, such as Mycobacterium, Staphylococcus, and Enterococcus. On the other hand, microbiome diversity and composition were not associated with oral chronic graft-versus-host disease. To conclude, dysbiosis of the oral microbiome occurred directly after SCT but recovered after 3 months. Diversity and composition were related to oral mucositis but not to oral chronic graft-versus-host disease.
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7
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Dong J, Li W, Wang Q, Chen J, Zu Y, Zhou X, Guo Q. Relationships Between Oral Microecosystem and Respiratory Diseases. Front Mol Biosci 2022; 8:718222. [PMID: 35071321 PMCID: PMC8767498 DOI: 10.3389/fmolb.2021.718222] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/09/2021] [Indexed: 02/05/2023] Open
Abstract
Oral microecosystem is a very complicated ecosystem that is located in the mouth and comprises oral microbiome, diverse anatomic structures of oral cavity, saliva and interactions between oral microbiota and between oral microbiota and the host. More and more evidence from studies of epidemiology, microbiology and molecular biology is establishing a significant link between oral microecosystem and respiratory diseases. Microbiota settling down in oral microecosystem is known as the main source of lung microbiome and has been associated with the occurrence and development of respiratory diseases like pneumonia, chronic obstructive pulmonary disease, lung cancer, cystic fibrosis lung disease and asthma. In fact, it is not only indigenous oral microbes promote or directly cause respiratory infection and inflammation when inhaled into the lower respiratory tract, but also internal environment of oral microecosystem serves as a reservoir for opportunistic respiratory pathogens. Moreover, poor oral health and oral diseases caused by oral microecological dysbiosis (especially periodontal disease) are related with risk of multiple respiratory diseases. Here, we review the research status on the respiratory diseases related with oral microecosystem. Potential mechanisms on how respiratory pathogens colonize oral microecosystem and the role of indigenous oral microbes in pathogenesis of respiratory diseases are also summarized and analyzed. Given the importance of oral plaque control and oral health interventions in controlling or preventing respiratory infection and diseases, we also summarize the oral health management measures and attentions, not only for populations susceptible to respiratory infection like the elderly and hospitalized patients, but also for dentist or oral hygienists who undertake oral health care. In conclusion, the relationship between respiratory diseases and oral microecosystem has been established and supported by growing body of literature. However, etiological evidence on the role of oral microecosystem in the development of respiratory diseases is still insufficient. Further detailed studies focusing on specific mechanisms on how oral microecosystem participate in the pathogenesis of respiratory diseases could be helpful to prevent and treat respiratory diseases.
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Affiliation(s)
- Jiajia Dong
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qi Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiahao Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yue Zu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiang Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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8
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Villar CC, Dongari-Bagtzoglou A. Fungal diseases: Oral dysbiosis in susceptible hosts. Periodontol 2000 2021; 87:166-180. [PMID: 34463992 DOI: 10.1111/prd.12378] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The oral cavity is colonized by a large number of microorganisms that are referred to collectively as the oral microbiota. These indigenous microorganisms have evolved in symbiotic relationships with the oral mucosal immune system and are involved in maintaining homeostasis in the oral cavity. Although Candida species are commonly found in the healthy oral cavity without causing infection, these fungi can become pathogenic. Recents advances indicate that the development of oral candidiasis is driven both by Candida albicans overgrowth in a dysbiotic microbiome and by disturbances in the host's immune system. Perturbation of the oral microbiota triggered by host-extrinsic (ie, medications), host-intrinsic (ie, host genetics), and microbiome-intrinsic (ie, microbial interactions) factors may increase the risk of oral candidiasis. In this review, we provide an overview of the oral mycobiome, with a particular focus on the interactions of Candida albicans with some of the most common oral bacteria and the oral mucosal immune system. Also, we present a summary of our current knowledge of the host-intrinsic and host-extrinsic factors that can predispose to oral candidiasis.
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Affiliation(s)
- Cristina Cunha Villar
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut School of Dental Medicine, Farmington, CT, USA
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9
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Joyce H, Taylor MR, Moffat A, Hong M, Isaac D, Fine N, Greenway SC. Changes in the Composition and Function of the Human Salivary Microbiome After Heart Transplantation: A Pilot Study. TRANSPLANT RESEARCH AND RISK MANAGEMENT 2021. [DOI: 10.2147/trrm.s328467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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10
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Bertolini M, Vazquez Munoz R, Archambault L, Shah S, Souza JGS, Costa RC, Thompson A, Zhou Y, Sobue T, Dongari-Bagtzoglou A. Mucosal Bacteria Modulate Candida albicans Virulence in Oropharyngeal Candidiasis. mBio 2021; 12:e0193721. [PMID: 34399623 PMCID: PMC8406182 DOI: 10.1128/mbio.01937-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 01/12/2023] Open
Abstract
Oropharyngeal candidiasis (OPC) is the most prevalent oral infection in immunocompromised patients, primarily associated with Candida albicans. Increasing evidence points to a significant role of mucosal bacteria on the transition of C. albicans from commensal to pathogenic. In this work, we hypothesized that changes in the abundance or composition of the mucosal bacterial microbiota induced by dietary sucrose during the development of OPC can modulate C. albicans virulence. C. albicans burdens and mucosal lesions were evaluated in a mouse cortisone immunosuppression model amended with sucrose. We also analyzed the mucosal bacterial composition using 16S rRNA gene sequencing and culture methods. In immunocompetent mice, sucrose significantly increased total bacterial burdens and reduced alpha diversity, by increasing the relative abundance of mitis group streptococci. In immunocompromised mice, C. albicans infection was associated with a significantly reduced bacterial alpha diversity due to an increase in the relative abundance of enterococci. When exposed to dietary sucrose, these mice had reduced C. albicans burdens and reduced bacterial alpha diversity, associated with an increase in the relative abundance of Lactobacillus. SparCC correlation networks showed a significant negative correlation between Lactobacillus and Enterococcus in all Candida-infected mice. Depletion of lactobacilli with antibiotic treatment partially restored C. albicans burdens in mice receiving sucrose. In coculture in vitro experiments, mouse oral Lactobacillus johnsonii isolates inhibited growth of Enterococcus faecalis isolates and C. albicans. These results support the hypothesis that the sucrose-induced attenuation of C. albicans virulence was a result of changes in the mucosal bacterial microbiome characterized by a reduction in enterococci and an increase in lactobacilli. IMPORTANCE By comparing Candida albicans virulence and the mucosal bacterial composition in a mouse oral infection model, we were able to dissect the effects of the host environment (immunosuppression), infection with C. albicans, and local modulating factors (availability of sucrose as a carbon source) on the mucosal bacterial microbiome and its role on fungal virulence. We showed that changes in endogenous microbial communities in response to sucrose can lead to attenuation of fungal disease. We also showed that Lactobacillus johnsonii may curtail Candida virulence both by inhibiting its growth and by inhibiting the growth of potentially synergistic bacteria such as enterococci. Our results support the concept that Candida pathogenesis should be viewed in the contexts of both a susceptible host and a mucosal bacterial microbiota conducive to virulence.
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Affiliation(s)
- M. Bertolini
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
| | - R. Vazquez Munoz
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
| | - L. Archambault
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
| | - S. Shah
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - J. G. S. Souza
- Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
- Dental Science School (Faculdade de Ciências Odontológicas [FCO]), Montes Claros, MG, Brazil
| | - R. C. Costa
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, SP, Brazil
| | - A. Thompson
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
| | - Y. Zhou
- Department of Medicine, UConn Health, Connecticut, Farmington, Connecticut, USA
| | - T. Sobue
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
| | - A. Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, Connecticut, USA
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Heidrich V, Bruno JS, Knebel FH, de Molla VC, Miranda-Silva W, Asprino PF, Tucunduva L, Rocha V, Novis Y, Arrais-Rodrigues C, Fregnani ER, Camargo AA. Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft- Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation. Front Immunol 2021; 12:692225. [PMID: 34220852 PMCID: PMC8250416 DOI: 10.3389/fimmu.2021.692225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/02/2021] [Indexed: 01/04/2023] Open
Abstract
Acute graft-versus-host disease (aGVHD) is one of the major causes of death after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Recently, aGVHD onset was linked to intestinal microbiota (IM) dysbiosis. However, other bacterial-rich gastrointestinal sites, such as the mouth, which hosts several distinctive microbiotas, may also impact the risk of GVHD. The dental biofilm microbiota (DBM) is highly diverse and, like the IM, interacts with host cells and modulates immune homeostasis. We characterized changes in the DBM of patients during allo-HSCT and evaluated whether the DBM could be associated with the risk of aGVHD. DBM dysbiosis during allo-HSCT was marked by a gradual loss of bacterial diversity and changes in DBM genera composition, with commensal genera reductions and potentially pathogenic bacteria overgrowths. High Streptococcus and high Corynebacterium relative abundance at preconditioning were associated with a higher risk of aGVHD (67% vs. 33%; HR = 2.89, P = 0.04 and 73% vs. 37%; HR = 2.74, P = 0.04, respectively), while high Veillonella relative abundance was associated with a lower risk of aGVHD (27% vs. 73%; HR = 0.24, P < 0.01). Enterococcus faecalis bloom during allo-HSCT was observed in 17% of allo-HSCT recipients and was associated with a higher risk of aGVHD (100% vs. 40%; HR = 4.07, P < 0.001) and severe aGVHD (60% vs. 12%; HR = 6.82, P = 0.01). To the best of our knowledge, this is the first study demonstrating that DBM dysbiosis is associated with the aGVHD risk after allo-HSCT.
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Affiliation(s)
- Vitor Heidrich
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Julia S Bruno
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Franciele H Knebel
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Vinícius C de Molla
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Oncologia Clínica e Experimental, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Paula F Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Vanderson Rocha
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo/Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, Brazil.,Churchill Hospital, National Health Service Blood and Transplant, Oxford, United Kingdom
| | - Yana Novis
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Celso Arrais-Rodrigues
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Oncologia Clínica e Experimental, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Anamaria A Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
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Kim MG, Yang J, Jo SK. Intestinal microbiota and kidney diseases. Kidney Res Clin Pract 2021; 40:335-343. [PMID: 34233442 PMCID: PMC8476297 DOI: 10.23876/j.krcp.21.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/12/2021] [Indexed: 11/15/2022] Open
Abstract
Large microbial communities reside in the gut as an endogenous organ and interact with the host physiology through symbiotic relationships, affecting health. Recent advances in high-throughput sequencing techniques have made it possible to better understand these complex microbial communities and their effects on hosts. Animal and clinical studies have provided considerable evidence to show that the microbiota plays an important role in chronic kidney disease, acute kidney injury, nephrolithiasis, and kidney transplantation by altering the functions of the intestinal barrier, regulating local and systemic inflammation, controlling production of metabolic components, and affecting immune responses. Although the exact mechanism underlying the microbial shift and its impact on disease progression remains uncertain, the kidney-gut interaction clearly plays a significant role in onset and progression of kidney disease and, therefore, holds promise as a therapeutic target. Here, we review recent literature pertaining to the bidirectional relationship between microbes and humans in various kidney diseases and discuss the future direction of microbial research in nephrology.
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Affiliation(s)
- Myung-Gyu Kim
- Division of Nephrology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Yang
- Division of Nephrology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sang-Kyung Jo
- Division of Nephrology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
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13
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Campbell PM, Humphreys GJ, Summers AM, Konkel JE, Knight CG, Augustine T, McBain AJ. Does the Microbiome Affect the Outcome of Renal Transplantation? Front Cell Infect Microbiol 2020; 10:558644. [PMID: 33425774 PMCID: PMC7785772 DOI: 10.3389/fcimb.2020.558644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/17/2020] [Indexed: 12/31/2022] Open
Abstract
The role of the human microbiome in health and disease is becoming increasingly apparent. Emerging evidence suggests that the microbiome is affected by solid organ transplantation. Kidney transplantation is the gold standard treatment for End-Stage Renal Disease (ESRD), the advanced stage of Chronic Kidney Disease (CKD). The question of how ESRD and transplantation affect the microbiome and vice versa includes how the microbiome is affected by increased concentrations of toxins such as urea and creatinine (which are elevated in ESRD), whether restoration of renal function following transplantation alters the composition of the microbiome, and the impact of lifelong administration of immunosuppressive drugs on the microbiome. Changes in microbiome composition and activity have been reported in ESRD and in therapeutic immunosuppression, but the effect on the outcome of transplantation is not well-understood. Here, we consider the current evidence that changes in kidney function and immunosuppression following transplantation influence the oral, gut, and urinary microbiomes in kidney transplant patients. The potential for changes in these microbiomes to lead to disease, systemic inflammation, or rejection of the organ itself is discussed, along with the possibility that restoration of kidney function might re-establish orthobiosis.
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Affiliation(s)
- Paul M Campbell
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Gavin J Humphreys
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Angela M Summers
- Department of Renal and Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Joanne E Konkel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Christopher G Knight
- School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Titus Augustine
- Department of Renal and Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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14
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Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant. Ann Am Thorac Soc 2020; 16:1383-1391. [PMID: 31415219 DOI: 10.1513/annalsats.201904-299oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rationale: The oropharyngeal microbiome is a primary source of lung microbiota, contributes to lower respiratory infection, and is also a driver of oral health.Objectives: We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics after lung transplantation, and ecological features of dysbiosis.Methods: Oropharyngeal wash samples were obtained from individuals with end-stage disease awaiting transplantation (n = 22) and longitudinally from individuals at 6 weeks, 3 months, and 6 months after transplantation (n = 33), along with healthy control subjects (n = 14). Bacterial 16S and fungal internal transcribed spacer rRNA regions were deep-sequenced, and bacterial community respiratory patterns were imputed from taxonomic composition.Results: Healthy subjects' oropharyngeal microbiomes showed a gradient of community types reflecting relative enrichment of strictly anaerobic, aerobic, or facultative anaerobic bacteria. Patients with end-stage lung disease showed severe dysbiosis by both taxonomic composition and respiration phenotypes, with reduced richness and diversity, increased facultative and decreased aerobic bacteria, and absence of communities characterized by obligate aerobes. In patients at 6 weeks and 3 months post-transplant, richness and diversity were intermediate between healthy and pretransplant subjects, with near-normal distribution of community types. However, by 6 months post-transplant, oropharyngeal wash resembled the low-diversity facultative-dominated profile of pretransplant subjects. Community ecotype correlated with Candida abundance.Conclusions: End-stage lung disease is associated with marked upper respiratory tract dysbiosis involving both community structure and respiratory metabolism profiles of constituent bacteria. Dynamic changes occur after lung transplantation, with partial normalization early but later appearance of severe dysbiosis similar to pretransplant patients. Aberrant oropharyngeal communities may predispose to abnormal lung microbiota and infection risk both in advanced lung disease and after transplantation.
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15
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Roberts MB, Fishman JA. Immunosuppressive Agents and Infectious Risk in Transplantation: Managing the "Net State of Immunosuppression". Clin Infect Dis 2020; 73:e1302-e1317. [PMID: 32803228 DOI: 10.1093/cid/ciaa1189] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Successful solid organ transplantation reflects meticulous attention to the details of immunosuppression, balancing risks for graft rejection against risks for infection. The 'net state of immune suppression' is a conceptual framework of all factors contributing to infectious risk. Assays which measure immune function in the immunosuppressed transplant recipient relative to infectious risk and allograft function are lacking. The best measures of integrated immune function may be quantitative viral loads to assess the individual's ability to control latent viral infections. Few studies address adjustment of immunosuppression during active infections. Thus, confronted with infection in solid organ recipients, the management of immunosuppression is based largely on clinical experience. This review examines known measures of immune function and the immunologic effects of common immunosuppressive drugs and available studies reporting modification of drug regimens for specific infections. These data provide a conceptual framework for the management of immunosuppression during infection in organ recipients.
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Affiliation(s)
- Matthew B Roberts
- Transplant Infectious Disease and Compromised Host Program and Transplant Center, Massachusetts General Hospital, Boston MA
| | - Jay A Fishman
- Transplant Infectious Disease and Compromised Host Program and Transplant Center, Massachusetts General Hospital, Boston MA.,Harvard Medical School, Boston, MA
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16
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Colas L, Mongodin EF, Montassier E, Chesneau M, Guerif P, Hittle L, Giral M, Bromberg JS, Brouard S. Unique and specific Proteobacteria diversity in urinary microbiota of tolerant kidney transplanted recipients. Am J Transplant 2020; 20:145-158. [PMID: 31374143 DOI: 10.1111/ajt.15549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/25/2023]
Abstract
Host-microbiota interactions can modulate the immune system both at local and systemic levels, with potential consequences for organ transplantation outcomes. In this study, we hypothesized that differences in the urinary microbiome following kidney transplantation would be associated with posttransplantation status: stable, minimally immunosuppressed, or tolerant. One hundred thirteen urine samples from stable (n = 51), minimally immunosuppressed (n = 19), and spontaneously tolerant (n = 16) patients, paired with age-matched controls (n = 27) were profiled and compared to each other at a taxonomic level with special interest in the immunosuppressive regimen. All comparisons and correlations were adjusted on sex and time posttransplantation. Our results highlighted a unique and specific urinary microbiota associated with spontaneous tolerance characterized by a high diversity and a clear Proteobacteria profile. Finally, we report that this profile is (1) impacted by gender, (2) inversely correlated with immunosuppressive drugs (calcineurin inhibitors and mammalian target of rapamycin inhibitors), and (3) stable in time.
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Affiliation(s)
- Luc Colas
- Plateforme Transversale d'Allergologie et d'Immunologie Clinique, Institut du Thorax, CHU de Nantes, Nantes, France
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Mélanie Chesneau
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Pierrick Guerif
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Lauren Hittle
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Magali Giral
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Jonathan S Bromberg
- Departments of Surgery and Microbiology and Immunology, and the Center for Vascular and Inflammatory Diseases, University of Maryland, School of Medicine, Baltimore, Maryland
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
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17
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Sureda A, Daglia M, Argüelles Castilla S, Sanadgol N, Fazel Nabavi S, Khan H, Belwal T, Jeandet P, Marchese A, Pistollato F, Forbes-Hernandez T, Battino M, Berindan-Neagoe I, D'Onofrio G, Nabavi SM. Oral microbiota and Alzheimer's disease: Do all roads lead to Rome? Pharmacol Res 2019; 151:104582. [PMID: 31794871 DOI: 10.1016/j.phrs.2019.104582] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative pathology affecting milions of people worldwide associated with deposition of senile plaques. While the genetic and environmental risk factors associated with the onset and consolidation of late onset AD are heterogeneous and sporadic, growing evidence also suggests a potential link between some infectious diseases caused by oral microbiota and AD. Oral microbiota dysbiosis is purported to contribute either directly to amyloid protein production, or indirectly to neuroinflammation, occurring as a consequence of bacterial invasion. Over the last decade, the development of Human Oral Microbiome database (HOMD) has deepened our understanding of oral microbes and their different roles during the human lifetime. Oral pathogens mostly cause caries, periodontal disease, and edentulism in aged population, and, in particular, alterations of the oral microbiota causing chronic periodontal disease have been associated with the risk of AD. Here we describe how different alterations of the oral microbiota may be linked to AD, highlighting the importance of a good oral hygiene for the prevention of oral microbiota dysbiosis.
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Affiliation(s)
- Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress, University of Balearic Islands, CIBEROBN (Physiopathology of Obesity and Nutrition), and IdisBa, Palma de Mallorca, Balearic Islands, Spain.
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, Naples, Italy; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, China
| | | | - Nima Sanadgol
- Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran; Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Tarun Belwal
- Zhejiang University, College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agri-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Hangzhou, People's Republic of China
| | - Philippe Jeandet
- Induced Resistance and Plant Bioprotection, Faculty of Sciences, University of Reims Champagne-Ardenne, Reims Cedex 51687, France
| | | | - Francesca Pistollato
- Centre for Health & Nutrition, Universidad Europea del Atlantico, Santander, Spain
| | - Tamara Forbes-Hernandez
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo - Vigo Campus, Vigo, Spain
| | - Maurizio Battino
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo - Vigo Campus, Vigo, Spain; Dept of Clinical Sciences, Università Politecnica delle Marche, Ancona, Italy; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, "Iuliu-Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, Cluj-Napoca, Romania; Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, Cluj-Napoca, Romania
| | - Grazia D'Onofrio
- Unit of Geriatrics, Department of Medical Sciences, Fondazione Casa Sollievo della sofferenza, San Giovanni Rotondo, Italy
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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18
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The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis. J Fungi (Basel) 2019; 5:jof5040087. [PMID: 31546600 PMCID: PMC6958497 DOI: 10.3390/jof5040087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/28/2022] Open
Abstract
As more information emerges on oral microbiota using advanced sequencing methodologies, it is imperative to examine how organisms modulate the capacity of each other to colonize or trigger infection. Most mouse models of oral C. albicans infection have focused on interactions with single bacterial species. Thus, little is known about the microbiome-mediated interactions that control the switch of C. albicans from commensalism to infection. Evidence is accumulating that in immunosuppression where mucosal candidiasis is more prevalent, there is an altered oral bacterial microbiome with reduced diversity, but not an altered mycobiome. Oropharyngeal candidiasis in immunosuppressed humans and mice is associated with a further reduction in oral bacterial diversity and a dysbiotic shift with significant enrichment of streptococcal and enterococcal species. Our recent studies in a cancer chemotherapy mouse model supported the combined profound effect of immunosuppression and C. albicans in reducing oral bacterial diversity and provided the first direct evidence that these changes contribute to pathogenesis, representing dysbiosis. There is still a gap in understanding the relationship between Candida and the oral bacterial microbiome. We propose that certain oral commensal bacteria contribute to fungal pathogenesis and we identify gaps in our understanding of the mechanisms involved in this cooperative virulence.
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19
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Davanian H, Gaiser RA, Silfverberg M, Hugerth LW, Sobkowiak MJ, Lu L, Healy K, Sandberg JK, Näsman P, Karlsson J, Jansson L, Engstrand L, Sällberg Chen M. Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis. Int J Oral Sci 2019; 11:16. [PMID: 31068577 PMCID: PMC6506549 DOI: 10.1038/s41368-019-0049-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Opportunistic bacteria in apical periodontitis (AP) may pose a risk for systemic dissemination. Mucosal-associated invariant T (MAIT) cells are innate-like T cells with a broad and potent antimicrobial activity important for gut mucosal integrity. It was recently shown that MAIT cells are present in the oral mucosal tissue, but the involvement of MAIT cells in AP is unknown. Here, comparison of surgically resected AP and gingival tissues demonstrated that AP tissues express significantly higher levels of Vα7.2-Jα33, Vα7.2-Jα20, Vα7.2-Jα12, Cα and tumour necrosis factor (TNF), interferon (IFN)-γ and interleukin (IL)-17A transcripts, resembling a MAIT cell signature. Moreover, in AP tissues the MR1-restricted MAIT cells positive for MR1–5-OP-RU tetramer staining appeared to be of similar levels as in peripheral blood but consisted mainly of CD4+ subset. Unlike gingival tissues, the AP microbiome was quantitatively impacted by factors like fistula and high patient age and had a prominent riboflavin-expressing bacterial feature. When merged in an integrated view, the examined immune and microbiome data in the sparse partial least squares discriminant analysis could identify bacterial relative abundances that negatively correlated with Vα7.2-Jα33, Cα, and IL-17A transcript expressions in AP, implying that MAIT cells could play a role in the local defence at the oral tissue barrier. In conclusion, we describe the presence of MAIT cells at the oral site where translocation of oral microbiota could take place. These findings have implications for understanding the immune sensing of polymicrobial-related oral diseases.
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Affiliation(s)
- Haleh Davanian
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | | | - Luisa W Hugerth
- Department of Microbiology, Tumor and Cell Biology and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Clinical Genomics Facility, Science for Life Laboratory, Solna, Sweden
| | | | - Liyan Lu
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Katie Healy
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | - Peggy Näsman
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Jörgen Karlsson
- Clinic of Endodontics and Periodontology, Eastman Institute Stockholm, Stockholm, Sweden
| | - Leif Jansson
- Clinic of Endodontics and Periodontology, Eastman Institute Stockholm, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Clinical Genomics Facility, Science for Life Laboratory, Solna, Sweden
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20
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Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, Townsley DM, Childs R, Paster BJ, Faller LL, Wallen GR. The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study. Ann Hematol 2019; 98:1351-1365. [PMID: 30919073 DOI: 10.1007/s00277-019-03599-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 01/07/2019] [Indexed: 12/11/2022]
Abstract
The microbiome, an intriguing component of the human body, composed of trillions of microorganisms, has prompted scientific exploration to identify and understand its function and role in health and disease. As associations between microbiome composition, disease, and symptoms accumulate, the future of medicine hinges upon a comprehensive knowledge of these microorganisms for patient care. The oral microbiome may provide valuable and efficient insight for predicting future changes in disease status, infection, or treatment course. The main aim of this pilot study was to characterize the oral microbiome in patients with severe aplastic anemia (SAA) during their therapeutic course. SAA is a hematologic disease characterized by bone marrow failure which if untreated is fatal. Treatment includes either hematopoietic stem cell transplantation (HSCT) or immunosuppressive therapy (IST). In this study, we examined the oral microbiome composition of 24 patients admitted to the National Institutes of Health (NIH) Clinical Center for experimental SAA treatment. Tongue brushings were collected to assess the effects of treatment on the oral microbiome. Twenty patients received standard IST (equine antithymocyte globulin and cyclosporine) plus eltrombopag. Four patients underwent HSCT. Oral specimens were obtained at three time points during treatment and clinical follow-up. Using a novel approach to 16S rRNA gene sequence analysis encompassing seven hypervariable regions, results demonstrated a predictable decrease in microbial diversity over time among the transplant patients. Linear discriminant analysis or LefSe reported a total of 14 statistically significant taxa (p < 0.05) across time points in the HSCT patients. One-way plots of relative abundance for two bacterial species (Haemophilus parainfluenzae and Rothia mucilaginosa) in the HSCT group, show the differences in abundance between time points. Only one bacterial species (Prevotella histicola) was noted in the IST group with a p value of 0.065. The patients receiving immunosuppressive therapy did not exhibit a clear change in diversity over time; however, patient-specific changes were noted. In addition, we compared our findings to tongue dorsum samples from healthy participants in the Human Microbiome Project (HMP) database and found among HSCT patients, approximately 35% of bacterial identifiers (N = 229) were unique to this study population and were not present in tongue dorsum specimens obtained from the HMP. Among IST-treated patients, 45% (N = 351) were unique to these patients and not identified by the HMP. Although antibiotic use may have likely influenced bacterial composition and diversity, some literature suggests a decreased impact of antimicrobials on the oral microbiome as compared to their effect on the gut microbiome. Future studies with larger sample sizes that focus on the oral microbiome and the effects of antibiotics in an immunosuppressed patient population may help establish these potential associations.
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Affiliation(s)
- N J Ames
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, MD, USA.
| | - J J Barb
- Mathematical and Statistical Computing Lab, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA
| | - A Ranucci
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, MD, USA.,Tulane University School of Medicine, New Orleans, LA, USA
| | - H Kim
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, USA
| | - S E Mudra
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, MD, USA.,University of Louisville School of Medicine, Louisville, KY, USA
| | - A K Cashion
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, USA
| | - D M Townsley
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - R Childs
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - B J Paster
- Forsyth Institute, Cambridge, MA, USA.,Harvard School of Dental Medicine, Boston, MA, USA
| | - L L Faller
- Forsyth Institute, Cambridge, MA, USA.,Ginkgo Bioworks, Boston, MA, USA
| | - G R Wallen
- Clinical Center Nursing Department, National Institutes of Health, Bethesda, MD, USA
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21
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Proal A, Marshall T. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity. Front Pediatr 2018; 6:373. [PMID: 30564562 PMCID: PMC6288442 DOI: 10.3389/fped.2018.00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.
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Affiliation(s)
- Amy Proal
- Autoimmunity Research Foundation, Thousand Oaks, CA, United States
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22
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Sarier M, Sepin Ozen N, Guler H, Duman I, Yüksel Y, Tekin S, Yavuz AH, Yucetin L, Erdogan Yilmaz M. Prevalence of Sexually Transmitted Diseases in Asymptomatic Renal Transplant Recipients. EXP CLIN TRANSPLANT 2018. [PMID: 29619908 DOI: 10.6002/ect.2017.0232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Sexually transmitted diseases, which may be asymptomatic, have the potential to cause serious health problems in renal transplant recipients. The aim of this study was to determine the prevalence of sexually transmitted diseases in sexually active asymptomatic renal transplant patients by using real-time multiplex polymerase chain reaction assays. MATERIALS AND METHODS This prospective controlled study was conducted between November 2016 and January 2017 in our hospital. Our study group included 80 consecutive, sexually active asymptomatic patients (40 men and 40 women) who had undergone renal transplant in our hospital and who presented to our outpatient clinic for routine follow-up. We also included a control group of 80 consecutive, sexually active nontransplant patients (40 men and 40 women). All patient samples were tested for Gardnerella vaginalis and obligate anaerobes (Prevotella bivia, Porphyromonas species), Candida species, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma species, Trichomonas vaginalis, Neisseria gonorrhoeae, Chlamydia trachomatis, herpes simplex virus 1 and 2, and Cytomegalovirus by real-time multiplex polymerase chain reaction. RESULTS The prevalences of infection with Gardnerella vaginalis and obligate anaerobes (P = .043), Ureaplasma species (P = .02), and Cytomegalovirus (P = .016) were found to be significantly higher in the study group versus the control group. However, there was no difference between the 2 groups regarding the prevalence of Mycoplasma infection (P = .70). CONCLUSIONS Sexually transmitted diseases may occur more frequently in sexually active asymptomatic renal transplant recipients than in nontransplanted individuals. Real-time multiplex polymerase chain reaction analysis may be a suitable method for determining these pathogens.
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Affiliation(s)
- Mehmet Sarier
- From the Department of Urology, Altinbas University, Istanbul, Turkey
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23
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Abstract
For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.
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Reemergence of Lower-Airway Microbiota in Lung Transplant Patients with Cystic Fibrosis. Ann Am Thorac Soc 2018; 13:2132-2142. [PMID: 27925791 DOI: 10.1513/annalsats.201606-431oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RATIONALE Chronic lung infections are a hallmark of cystic fibrosis; they are responsible for progressive airway destruction and ultimately lead to respiratory death or the requirement for life-saving bilateral lung transplant. Furthermore, recurrent isolation of airway pathogens such as Pseudomonas aeruginosa in the allograft after transplant is associated with adverse outcomes, including bronchiolitis obliterans syndrome and acute infections. Little information exists on the impact of bilateral lung transplant on the lower-airway microbiota. OBJECTIVES To compare, at a microbiome and single-pathogen level (P. aeruginosa), the bacterial communities in pre- and post-transplant samples. METHODS We retrospectively accessed our biobank of sputum samples and sputum-derived bacterial pathogens for patients who had matched samples, including those who were clinically stable before transplant, those who had a pulmonary exacerbation before transplant, and those who had pulmonary exacerbation after transplant. We used 16S ribosomal RNA gene sequencing to characterize the lower-airway microbiome of 14 adult transplant patients with cystic fibrosis. Genotyping and phenotyping of P. aeruginosa isolates from 12 of these patients with matched isolates was performed. MEASUREMENTS AND MAIN RESULTS Although α-diversity (richness and evenness) of patient microbiomes was similar before and after transplant, β- diversity (core microbiome composition) measures stratified patients evenly into two groups with more similar and more dissimilar communities. P. aeruginosa strains isolated before transplant were found to reemerge in 11 of 12 patients; however, phenotypic variation was observed. CONCLUSIONS These findings indicate that recolonization by P. aeruginosa after transplant is almost always strain specific, suggesting a within-host source. The polymicrobial colonization of the airways after transplant does not always reflect the pretransplant sputum microbiota.
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Acharya A, Chan Y, Kheur S, Jin LJ, Watt RM, Mattheos N. Salivary microbiome in non-oral disease: A summary of evidence and commentary. Arch Oral Biol 2017; 83:169-173. [DOI: 10.1016/j.archoralbio.2017.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
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Riella LV, Bagley J, Iacomini J, Alegre ML. Impact of environmental factors on alloimmunity and transplant fate. J Clin Invest 2017; 127:2482-2491. [PMID: 28481225 DOI: 10.1172/jci90596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although gene-environment interactions have been investigated for many years to understand people's susceptibility to autoimmune diseases or cancer, a role for environmental factors in modulating alloimmune responses and transplant outcomes is only now beginning to emerge. New data suggest that diet, hyperlipidemia, pollutants, commensal microbes, and pathogenic infections can all affect T cell activation, differentiation, and the kinetics of graft rejection. These observations reveal opportunities for novel therapeutic interventions to improve graft outcomes as well as for noninvasive biomarker discovery to predict or diagnose graft deterioration before it becomes irreversible. In this Review, we will focus on the impact of these environmental factors on immune function and, when known, on alloimmune function, as well as on transplant fate.
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Affiliation(s)
- Leonardo V Riella
- Schuster Family Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jessamyn Bagley
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Sackler School of Biomedical Sciences Programs in Immunology and Genetics, Boston, Massachusetts, USA
| | - John Iacomini
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Sackler School of Biomedical Sciences Programs in Immunology and Genetics, Boston, Massachusetts, USA
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Lin L, Zhang J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol 2017; 18:2. [PMID: 28061847 PMCID: PMC5219689 DOI: 10.1186/s12865-016-0187-3] [Citation(s) in RCA: 414] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/20/2016] [Indexed: 12/12/2022] Open
Abstract
Background A vast diversity of microbes colonizes in the human gastrointestinal tract, referred to intestinal microbiota. Microbiota and products thereof are indispensable for shaping the development and function of host innate immune system, thereby exerting multifaceted impacts in gut health. Methods This paper reviews the effects on immunity of gut microbe-derived nucleic acids, and gut microbial metabolites, as well as the involvement of commensals in the gut homeostasis. We focus on the recent findings with an intention to illuminate the mechanisms by which the microbiota and products thereof are interacting with host immunity, as well as to scrutinize imbalanced gut microbiota (dysbiosis) which lead to autoimmune disorders including inflammatory bowel disease (IBD), Type 1 diabetes (T1D) and systemic immune syndromes such as rheumatoid arthritis (RA). Results In addition to their well-recognized benefits in the gut such as occupation of ecological niches and competition with pathogens, commensal bacteria have been shown to strengthen the gut barrier and to exert immunomodulatory actions within the gut and beyond. It has been realized that impaired intestinal microbiota not only contribute to gut diseases but also are inextricably linked to metabolic disorders and even brain dysfunction. Conclusions A better understanding of the mutual interactions of the microbiota and host immune system, would shed light on our endeavors of disease prevention and broaden the path to our discovery of immune intervention targets for disease treatment.
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Affiliation(s)
- Lan Lin
- Department of Bioengineering, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
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Cree BAC, Spencer CM, Varrin-Doyer M, Baranzini SE, Zamvil SS. Gut microbiome analysis in neuromyelitis optica reveals overabundance of Clostridium perfringens. Ann Neurol 2016; 80:443-7. [PMID: 27398819 PMCID: PMC5053302 DOI: 10.1002/ana.24718] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 12/17/2022]
Abstract
T cells from neuromyelitis optica (NMO) patients, which recognize the immunodominant epitope of aquaporin‐4, exhibit Th17 polarization and cross‐react with a homologous sequence of a Clostridium perfringens adenosine triphosphate‐binding cassette transporter. Therefore, this commensal microbe might participate in NMO pathogenesis. We examined the gut microbiome by PhyloChip G3 from 16 NMO patients, 16 healthy controls (HC), and 16 multiple sclerosis patients. A significant difference in the abundance of several microbial communities was observed between NMO and HC (Adonis test, p = 0.001). Strikingly, C. perfringens was overrepresented in NMO (p = 5.24 × 10−8). These observations support a potential role for C. perfringens in NMO pathogenesis. Ann Neurol 2016;80:443–447
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Affiliation(s)
- Bruce A C Cree
- Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Collin M Spencer
- Department of Neurology, University of California, San Francisco, San Francisco, CA.,Program in Immunology, University of California, San Francisco, San Francisco, CA
| | - Michel Varrin-Doyer
- Department of Neurology, University of California, San Francisco, San Francisco, CA.,Program in Immunology, University of California, San Francisco, San Francisco, CA
| | - Sergio E Baranzini
- Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Scott S Zamvil
- Department of Neurology, University of California, San Francisco, San Francisco, CA. .,Program in Immunology, University of California, San Francisco, San Francisco, CA.
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Abstract
Diverse effects of the microbiome on solid organ transplantation are beginning to be recognized. In allograft recipients, microbial networks are disrupted by immunosuppression, nosocomial and community-based infectious exposures, antimicrobial therapies, surgery, and immune processes. Shifting microbial patterns, including acute infectious exposures, have dynamic and reciprocal interactions with local and systemic immune systems. Both individual microbial species and microbial networks have central roles in the induction and control of innate and adaptive immune responses, in graft rejection, and in ischemia-reperfusion injury. Understanding the diverse interactions between the microbiome and the immune system of allograft recipients may facilitate clinical management in the future.
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Li M, Zou Y, Jiang Q, Jiang L, Yu Q, Ding X, Yu Y. A preliminary study of the oral microbiota in Chinese patients with Sjögren's syndrome. Arch Oral Biol 2016; 70:143-148. [PMID: 27351333 DOI: 10.1016/j.archoralbio.2016.06.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 05/30/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To investigate the oral microbiota in Sjögren's syndrome (SS) as opposed to that of healthy subjects. STUDY DESIGN Ten patients with primary SS, [6 patients daily taking stable dosage of hydroxychloroquine (HC) and 4 patients taking hydroxychloroquine combined with Prednisone acetas (HC+PA)], along with 10 age-matched healthy controls were examined in regard of number of teeth, stimulated/unstimulated saliva secretion rate. Microflora on bilateral buccal mucosa was analyzed by high throughput sequencing. Statistical analyses were performed using the chi-square test, t test and Mann-Whitney U test. The Venn diagrams and Redundancy Analysis (RDA) were also used to evaluate effects of the disease and treatment on the bacterial community composition. RESULTS The relative abundance of Proteobacteria in SS group was lower compared to controls (P=0.002). The total richness of genera for all groups was 339. The numbers of genera in SS group and in control group were 248 and 270, respectively. Some taxa with different prevalence and/or relative abundance were found between two groups. CONCLUSIONS SS affects the oral microbiota and SS patients carry a different and less diverse microorganism community compared with healthy subjects. Prednisone acetas is an influence on the oral microbiome. This study provides a basic data on the oral flora in SS patients.
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Affiliation(s)
- Miaoran Li
- Department of Stomatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
| | - Yan Zou
- Department of Stomatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
| | - Qian Jiang
- Department of Stomatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
| | - Lindi Jiang
- Department of Rheumatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
| | - Qiang Yu
- Department of Rheumatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
| | - Xiaojun Ding
- Department of Stomatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital, Shanghai Medical School, Fudan University, 111 Yixueyuan Road, Shanghai 200032, China
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Coit P, Mumcu G, Ture-Ozdemir F, Unal AU, Alpar U, Bostanci N, Ergun T, Direskeneli H, Sawalha AH. Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease. Clin Immunol 2016; 169:28-35. [PMID: 27283393 DOI: 10.1016/j.clim.2016.06.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 12/14/2022]
Abstract
Behçet's disease (BD) is characterized by recurrent oro-genital ulcers, mucocutaneous lesions, and serious organ involvement. We investigated the salivary microbiome in BD using high-throughput sequencing of the 16S rRNA V4 region. Stimulated saliva samples were collected from 31 BD patients and 15 healthy controls, and in 9 BD patients, a second saliva sample was collected following dental and periodontal treatment. Sequence analysis identified a total of 908 operational taxonomic units (OTUs) present across all samples. Patients had a microbial community structure that is significantly less diverse than healthy controls. The most overabundant species in BD was Haemophilus parainfluenzae, while the most depleted included Alloprevotella rava and species in the genus Leptotrichia. Periodontal treatment improved oral health indices in BD but had no short-term effect on bacterial community structure. Neither the BD-associated genetic risk locus within the HLA-B/MICA region nor being on immunosuppressive medications explained the differences between patients and controls.
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Affiliation(s)
- Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Gonca Mumcu
- Faculty of Health Sciences, Marmara University, Istanbul, Turkey
| | - Filiz Ture-Ozdemir
- Department of Immunology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Ali Ugur Unal
- Department of Rheumatology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Ugur Alpar
- Faculty of Dentistry, Marmara University, Istanbul, Turkey
| | - Nagihan Bostanci
- Division of Periodontology, Department of Dental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Tulin Ergun
- Department of Dermatology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Haner Direskeneli
- Department of Rheumatology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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Gulcan A, Gulcan E, Keles M, Aktas E. Oral yeast colonization in peritoneal dialysis and hemodialysis patients and renal transplant recipients. Comp Immunol Microbiol Infect Dis 2016; 46:47-52. [PMID: 27260810 DOI: 10.1016/j.cimid.2016.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/29/2016] [Accepted: 04/11/2016] [Indexed: 10/22/2022]
Abstract
OBJECTIVE We aimed to investigate the frequency of oral yeast colonization (OYC) and the risk factors for patients who received continuous ambulatory peritoneal dialysis (CAPD) or hemodialysis (HD) or were renal transplant recipients (RTRs). The patients admitted to the Nephrology Clinic at Ataturk University Medical School from January through April 2013 were included in the study. A questionnaire about risk factors was filled out, and swab cultures were taken from the tongue surface of each participant. OYC was detected in 32.1% of the RTRs, 40% of the HD patients, 20.9% of the CAPD patients, and 18% of the healthy control (HC) group. Of the 42 yeast strains isolated from the renal replacement therapy groups, 26 strains (61.9%) were Candida albicans, nine (21.4%) were Candida glabrata, two (4.7%) were Candida krusei, two (4.7%) were Candida kefyr, one (2.38%) was Candida parapsilosis, and two (4.7%) were Geotrichum candidum. Risk factors for OYC in the RTRs group included antibiotic use and the presence of dental prostheses; however, in patients with chronic renal failure undergoing CAPD, only the presence of dental prostheses was found to be a statistically significant risk factor. Although OYC was mostly detected in patients with chronic kidney disease (undergoing HD, a variety of isolated yeast strains in the RTRs was noted. The rates of OYC and isolated Candida species in CAPD were similar to those of the HC group.
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Affiliation(s)
- Aynur Gulcan
- Dumlupinar University Medical Faculty, Microbiology and Clinical Microbiology, Kutahya, Turkey.
| | - Erim Gulcan
- Dumlupinar University Medical Faculty, Department of Nephrology, Kutahya, Turkey
| | - Mustafa Keles
- Mevlana University Medical Faculty, Department of Nephrology, Konya, Turkey
| | - Esin Aktas
- Yıldırım Beyazıt University Medical Faculty,Microbiology and Clinical Microbiology, Ankara, Turkey
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Shaping the oral mycobiota: interactions of opportunistic fungi with oral bacteria and the host. Curr Opin Microbiol 2015; 26:65-70. [PMID: 26100661 DOI: 10.1016/j.mib.2015.06.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/02/2015] [Accepted: 06/04/2015] [Indexed: 12/13/2022]
Abstract
The oral mycobiota is an important component of the oral microbiota that has only recently received increased attention. The diversity and complexity of the oral mycobiota in healthy humans is greater than any other body site. Dysbiotic imbalance of indigenous fungal communities in immunosuppressed hosts has been proposed to lead to oropharyngeal fungal infections. As in other body sites, to survive and thrive in the oral cavity fungi have to maintain mutually beneficial relationships with the resident bacterial microbiota and the host. Here we review our current understanding of the composition of the oral mycobiota and how it may be influenced by oral commensal bacteria and the host environment.
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Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. Clin Microbiol Rev 2015; 27:927-48. [PMID: 25278578 DOI: 10.1128/cmr.00044-14] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.
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Araújo MVF, Hong BY, Fava PL, Khan S, Burleson JA, Fares G, Samson W, Strausbaugh LD, Diaz PI, Ioannidou E. End stage renal disease as a modifier of the periodontal microbiome. BMC Nephrol 2015; 16:80. [PMID: 26055269 PMCID: PMC4460699 DOI: 10.1186/s12882-015-0081-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Evidence supports high prevalence of periodontitis in patients with chronic kidney disease. Several renal factors have been proposed as possible modifiers of periodontitis pathogenesis in this population. In this cross sectional study, we investigated whether distinct microbial profiles in renal patients could explain high periodontitis prevalence. METHODS We characterized the subgingival microbiome in 14 End Stage Renal Disease (ESRD) and 13 control individuals with chronic periodontitis with similar demographic and clinical parameters. Medical, demographic and periodontal parameters were recorded. Subgingival biofilm samples were collected from the deepest pocket in two different quadrants and characterized via 454-pyrosequencing of the 16S rRNA gene. RESULTS We found 874 species-level operational taxonomic units (OTU) across samples. Renal and control groups did not differ in the individual proportions of periodontitis-associated taxa. However, in principal coordinate plots of distance among samples based on OTU prevalence, some renal patients clustered apart from controls, with the microbial communities of these outlier subjects showing less diversity. Univariate correlation analysis showed a significant negative correlation between dialysis vintage and community diversity. CONCLUSIONS Within the study limitations, dialysis vintage was associated with a less diverse periodontal microbial community in ESRD suggesting the need for further research.
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Affiliation(s)
- Michel V Furtado Araújo
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
| | - Bo-Young Hong
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
| | - Philip L Fava
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
| | - Shiza Khan
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
| | - Joseph A Burleson
- Department of Community Medicine and Health Care, University of Connecticut Health Center, Farmington, CT, USA.
| | | | - Wilner Samson
- Division of Nephrology, Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Linda D Strausbaugh
- Center for Applied Genetics and Technologies, University of Connecticut, Storrs, CT, USA.
| | - Patricia I Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
| | - Effie Ioannidou
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030-1710, USA.
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Abstract
Each individual harbours a unique set of commensal microorganisms, collectively referred to as the microbiota. Notably, these microorganisms exceed the number of cells in the human body by 10-fold. This finding has accelerated a shift in our understanding of human physiology, with the realization that traits necessary for health are both encoded and influenced by the human genome and the microbiota. Our understanding of the aetiology of complex diseases has, therefore, evolved with increasing awareness that the human microbiota has an active and critical role in maintaining health and inducing disease. Indeed, findings from bioinformatic studies indicate that the microbiota and microbiome have multiple effects on the innate and adaptive immune systems, with effects on infection, autoimmune disease and cancer. In this Review, we first address the important statistical and informatics aspects that should be considered when characterizing the composition of microbiota. We next highlight the effects of the microbiota on the immune system and the implications of these effects on organ failure and transplantation. Finally, we reflect on the future perspectives for studies of the microbiota, including novel diagnostic tests and therapeutics.
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Jacobs JP, Braun J. Immune and genetic gardening of the intestinal microbiome. FEBS Lett 2014; 588:4102-11. [PMID: 24613921 PMCID: PMC4156569 DOI: 10.1016/j.febslet.2014.02.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 12/19/2022]
Abstract
The mucosal immune system - consisting of adaptive and innate immune cells as well as the epithelium - is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to non-pathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility.
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Affiliation(s)
- Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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Abstract
Lung transplantation survival remains significantly impacted by infections and the development of chronic rejection manifesting as bronchiolitis obliterans syndrome (BOS). Traditional microbiologic data has provided insight into the role of infections in BOS. Now, new non-culture-based techniques have been developed to characterize the entire population of microbes resident on the surfaces of the body, also known as the human microbiome. Early studies have identified that lung transplant patients have a different lung microbiome and have demonstrated the important finding that the transplant lung microbiome changes over time. Furthermore, both unique bacterial populations and longitudinal changes in the lung microbiome have now been suggested to play a role in the development of BOS. In the future, this technology will need to be combined with functional assays and assessment of the immune responses in the lung to help further explain the microbiome's role in the failing lung allograft.
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Affiliation(s)
- Julia Becker
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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Zaura E, Nicu EA, Krom BP, Keijser BJF. Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Microbiol 2014; 4:85. [PMID: 25019064 PMCID: PMC4071637 DOI: 10.3389/fcimb.2014.00085] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/08/2014] [Indexed: 12/15/2022] Open
Abstract
The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift toward a disease, e.g., periodontitis or caries. Although processes that underlie oral diseases have been studied extensively, processes involved in maintaining of a normal, healthy microbiome are poorly understood. In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained. We introduce our view on the prenatal development of tolerance for the normal oral microbiome: we propose that development of fetal tolerance toward the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome. We describe the processes that influence the establishment of such microbiome, followed by our perspective on the process of sustaining a healthy oral microbiome. We divide microbiome-maintenance factors into host-derived and microbe-derived, while focusing on the host. Finally, we highlight the need and directions for future research.
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Affiliation(s)
- Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Elena A Nicu
- Department of Periodontology, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam Amsterdam, Netherlands
| | - Bart J F Keijser
- Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences Zeist, Netherlands ; Top Institute Food and Nutrition Wageningen, Netherlands
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Dickson RP, Erb-Downward JR, Freeman CM, Walker N, Scales BS, Beck JM, Martinez FJ, Curtis JL, Lama VN, Huffnagle GB. Changes in the lung microbiome following lung transplantation include the emergence of two distinct Pseudomonas species with distinct clinical associations. PLoS One 2014; 9:e97214. [PMID: 24831685 PMCID: PMC4022512 DOI: 10.1371/journal.pone.0097214] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 04/16/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multiple independent culture-based studies have identified the presence of Pseudomonas aeruginosa in respiratory samples as a positive risk factor for bronchiolitis obliterans syndrome (BOS). Yet, culture-independent microbiological techniques have identified a negative association between Pseudomonas species and BOS. Our objective was to investigate whether there may be a unifying explanation for these apparently dichotomous results. METHODS We performed bronchoscopies with bronchoalveolar lavage (BAL) on lung transplant recipients (46 procedures in 33 patients) and 26 non-transplant control subjects. We analyzed bacterial communities in the BAL fluid using qPCR and pyrosequencing of 16S rRNA gene amplicons and compared the culture-independent data with the clinical metadata and culture results from these subjects. FINDINGS Route of bronchoscopy (via nose or via mouth) was not associated with changes in BAL microbiota (p = 0.90). Among the subjects with positive Pseudomonas bacterial culture, P. aeruginosa was also identified by culture-independent methods. In contrast, a distinct Pseudomonas species, P. fluorescens, was often identified in asymptomatic transplant subjects by pyrosequencing but not detected via standard bacterial culture. The subject populations harboring these two distinct pseudomonads differed significantly with respect to associated symptoms, BAL neutrophilia, bacterial DNA burden and microbial diversity. Despite notable differences in culturability, a global database search of UM Hospital Clinical Microbiology Laboratory records indicated that P. fluorescens is commonly isolated from respiratory specimens. INTERPRETATION We have reported for the first time that two prominent and distinct Pseudomonas species (P. fluorescens and P. aeruginosa) exist within the post-transplant lung microbiome, each with unique genomic and microbiologic features and widely divergent clinical associations, including presence during acute infection.
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Affiliation(s)
- Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - John R. Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christine M. Freeman
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Research Service, Department of Veterans Affairs Health Care System, Ann Arbor, Michigan, United States of America
| | - Natalie Walker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brittan S. Scales
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - James M. Beck
- Department of Medicine, University of Colorado Denver, Aurora, Colorado and Medicine Service, Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, United States of America
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jeffrey L. Curtis
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Pulmonary & Critical Care Medicine Section, Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - Vibha N. Lama
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Gary B. Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal. PLoS One 2014; 9:e90899. [PMID: 24614173 PMCID: PMC3948697 DOI: 10.1371/journal.pone.0090899] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/05/2014] [Indexed: 01/20/2023] Open
Abstract
Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments. We have revised current practices in sequence-based taxonomy assignments and employed the improvements to address the question of the fungal genera present in the healthy human mouth. The human oral mycobiome was surveyed using massively parallel, high throughput sequencing of internal transcribed spacer 1 (ITS1) amplicons from saliva following robust extraction methods. Taxonomy was assigned by comparison to a curated reference dataset, followed by filtering with an empirically determined BLAST E-value match statistic (10−42). Nomenclature corrections further refined results by conjoining redundant names for a single fungal genus. Following these curation steps, about two-thirds of the initially identified genera were eliminated. In comparison with the one similar metagenomic study and several earlier culture-based ones, our findings change the current conception of the oral mycobiome, especially with the discovery of the high prevalence and abundance of the genus Malassezia. Previously identified as an important pathogen of the skin, and recently reported as the predominant fungal genus at the nostril and backs of the head and ear, this is the first account of Malassezia in the human mouth. Findings from this study were in good agreement with others on the existence of many consensus members of the core mycobiome, and on unique patterns for individual subjects. This research offered a cautionary note about unconditional acceptance of lengthy lists of community members produced by automated assignments, provided a roadmap for enhancing the likely biological relevance of sequence-based fungal surveys, and built the foundation for understanding the role of fungi in health and disease of the oral cavity.
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Fricke WF, Maddox C, Song Y, Bromberg JS. Human microbiota characterization in the course of renal transplantation. Am J Transplant 2014; 14:416-27. [PMID: 24373208 DOI: 10.1111/ajt.12588] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/13/2013] [Accepted: 11/14/2013] [Indexed: 02/07/2023]
Abstract
Recent studies demonstrate that the human microbiota, the collection of microorganisms growing on and in individuals, have numerous bidirectional interactions with the host, influencing immunity, resistance to infection, inflammation and metabolism. Little has been done to study the potential associations between microbiota composition and transplant outcome. Here, we investigated the longitudinal changes in the blood, urinary, oral and rectal microbiota of renal allograft recipients before and at 1 and 6 months after transplantation. The results showed major changes in microbiota composition as a result of the transplant episode and associated medications, and these changes persisted over time. The high interindividual variation as well as differences in response to transplantation suggested that it is unlikely that the same specific microbiota members can serve as universal diagnostic markers. Rather, longitudinal changes in each individual's microbiota have the potential to be indicative of health or disease. Use of sensitive nucleic acid-based testing showed that urine, irrespective of disease states, more often harbors a diverse microbiota than appreciated by conventional culture techniques. These results lay the groundwork to construct more comprehensive future investigations to identify microbiota characteristics that can serve as diagnostic markers for transplant health and to guide intervention strategies to improve transplant outcome.
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Affiliation(s)
- W F Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Scherer A. Clinical and ethical considerations of massively parallel sequencing in transplantation science. World J Transplant 2013; 3:62-67. [PMID: 24392310 PMCID: PMC3879525 DOI: 10.5500/wjt.v3.i4.62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/16/2013] [Accepted: 10/12/2013] [Indexed: 02/05/2023] Open
Abstract
Massively parallel sequencing (MPS), alias next-generation sequencing, is making its way from research laboratories into applied sciences and clinics. MPS is a framework of experimental procedures which offer possibilities for genome research and genetics which could only be dreamed of until around 2005 when these technologies became available. Sequencing of a transcriptome, exome, even entire genomes is now possible within a time frame and precision that we could only hope for 10 years ago. Linking other experimental procedures with MPS enables researchers to study secondary DNA modifications across the entire genome, and protein binding sites, to name a few applications. How the advancements of sequencing technologies can contribute to transplantation science is subject of this discussion: immediate applications are in graft matching via human leukocyte antigen sequencing, as part of systems biology approaches which shed light on gene expression processes during immune response, as biomarkers of graft rejection, and to explore changes of microbiomes as a result of transplantation. Of considerable importance is the socio-ethical aspect of data ownership, privacy, informed consent, and result report to the study participant. While the technology is advancing rapidly, legislation is lagging behind due to the globalisation of data requisition, banking and sharing.
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