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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Kim J, Lee S, Moodley Y, Yagnik L, Birnie D, Dwivedi G. The role of the host-microbiome and metabolomics in sarcoidosis. Am J Physiol Cell Physiol 2023; 325:C1336-C1353. [PMID: 37746695 DOI: 10.1152/ajpcell.00316.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Sarcoidosis is a complex inflammatory fibrotic disease that affects multiple organ systems. It is characterized by the infiltration of lymphocytes and mononuclear phagocytes, which form non-caseating granulomas in affected organs. The lungs and intrathoracic lymph nodes are the most commonly affected organs. The underlying cause of sarcoidosis is unknown, but it is believed to occur in genetically predisposed individuals who are exposed to pathogenic organisms, environmental contaminants, or self and non-self-antigens. Recent research has suggested that the microbiome may play a role in the development of respiratory conditions, including sarcoidosis. Additionally, metabolomic studies have identified potential biomarkers for monitoring sarcoidosis progression. This review will focus on recent microbiome and metabolomic findings in sarcoidosis, with the goal of shedding light on the pathogenesis and possible diagnostic and therapeutic approaches.
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Affiliation(s)
- Junwoo Kim
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Yuben Moodley
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Lokesh Yagnik
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - David Birnie
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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Scurt FG, Bose K, Hammoud B, Brandt S, Bernhardt A, Gross C, Mertens PR, Chatzikyrkou C. Old known and possible new biomarkers of ANCA-associated vasculitis. J Autoimmun 2022; 133:102953. [PMID: 36410262 DOI: 10.1016/j.jaut.2022.102953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/06/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022]
Abstract
Antineutrophil cytoplasm antibody (ANCA)-associated vasculitis (AAV) comprises a group of multisystem disorders involving severe, systemic, small-vessel vasculitis with short- and long term serious and life-threating complications. Despite the simplification of treatment, fundamental aspects concerning assessment of its efficacy and its adaptation to encountered complications or to the relapsing/remitting/subclinical disease course remain still unknown. The pathogenesis of AAV is complex and unique, and despite the progress achieved in the last years, much has not to be learnt. Foremost, there is still no accurate marker enabling us to monitoring disease and guide therapy. Therefore, the disease management relays often on clinical judgment and follows a" trial and error approach". In the recent years, an increasing number of new molecules s have been explored and used for this purpose including genomics, B- and T-cell subpopulations, complement system factors, cytokines, metabolomics, biospectroscopy and components of our microbiome. The aim of this review is to discuss both the role of known historical and clinically established biomarkers of AAV, as well as to highlight potential new ones, which could be used for timely diagnosis and monitoring of this devastating disease, with the goal to improve the effectiveness and ameliorate the complications of its demanding therapy.
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Affiliation(s)
- Florian G Scurt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany.
| | - K Bose
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - Ben Hammoud
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - S Brandt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - A Bernhardt
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - C Gross
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
| | - Peter R Mertens
- University Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Germany
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Knudsen KS, Lehmann S, Nielsen R, Tangedal S, Paytuvi-Gallart A, Sanseverino W, Martinsen EMH, Hiemstra PS, Eagan TM. The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis. MICROBIOME 2022; 10:175. [PMID: 36258251 PMCID: PMC9580159 DOI: 10.1186/s40168-022-01362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND The role of the pulmonary microbiome in sarcoidosis is unknown. The objectives of this study were the following: (1) examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarcoidosis compared with controls; (2) examine whether there was an association between the microbiota and levels of the antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL). METHODS Thirty-five sarcoidosis patients and 35 healthy controls underwent bronchoscopy and were sampled with oral wash (OW), protected BAL (PBAL), and left protected sterile brushes (LPSB). The fungal ITS1 region and the V3V4 region of the bacterial 16S rRNA gene were sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 and hBD-2), were measured in PBAL by enzyme-linked immunosorbent assay (ELISA). RESULTS Aspergillus dominated the PBAL samples in sarcoidosis. Differences in bacterial taxonomy were minor. There was no significant difference in fungal alpha diversity between sarcoidosis and controls, but the bacterial alpha diversity in sarcoidosis was significantly lower in OW (p = 0.047) and PBAL (p = 0.03) compared with controls. The beta diversity for sarcoidosis compared with controls differed for both fungi and bacteria. AMP levels were significantly lower in sarcoidosis compared to controls (SLPI and hBD-1: p < 0.01). No significant correlations were found between alpha diversity and AMPs. CONCLUSIONS The pulmonary fungal and bacterial microbiota in sarcoidosis differed from in controls. Lower antimicrobial peptides levels were seen in sarcoidosis, indicating an interaction between the microbiota and the innate immune system. Whether this dysbiosis represents a pathogenic mechanism in sarcoidosis needs to be confirmed in experimental studies. Video Abstract.
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Affiliation(s)
| | - Sverre Lehmann
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Nielsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Solveig Tangedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | | | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Tomas M. Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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Oral Microbiota Profile in Patients with Anti-Neutrophil Cytoplasmic Antibody–Associated Vasculitis. Microorganisms 2022; 10:microorganisms10081572. [PMID: 36013990 PMCID: PMC9412476 DOI: 10.3390/microorganisms10081572] [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: 07/02/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
Microbiota has been associated with autoimmune diseases, with nasal Staphylococcus aureus being implicated in the pathogenesis of anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). Little is known about the role of oral microbiota in AAV. In this study, levels of IgG antibodies to 53 oral bacterial species/subspecies were screened using immunoblotting in plasma/serum in pre-symptomatic AAV-individuals (n = 85), matched controls, and established AAV-patients (n = 78). Saliva microbiota from acute-AAV and controls was sequenced from 16s rDNA amplicons. Information on dental status was extracted from a national register. IgG levels against oral bacteria were lower in established AAV versus pre-AAV and controls. Specifically, pre-AAV samples had, compared to controls, a higher abundance of periodontitis-associated species paralleling more signs of periodontitis in established AAV-patients than controls. Saliva microbiota in acute-AAV showed higher within-sample diversity but fewer detectable amplicon-sequence variants and taxa in their core microbiota than controls. Acute-AAV was not associated with increased abundance of periodontal bacteria but species in, e.g., Arthrospira, Staphylococcus, Lactobacillus, and Scardovia. In conclusion, the IgG profiles against oral bacteria differed between pre-AAV, established AAV, and controls, and microbiota profiles between acute AAV and controls. The IgG shift from a pre-symptomatic stage to established disease cooccurred with treatment of immunosuppression and/or antibiotics.
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Abstract
PURPOSE OF REVIEW To summarize recent evidence regarding the presence and potential role of the microbiome in systemic vasculitides. RECENT FINDINGS Microbiomic descriptions are now available in patients with small, medium and large vessel vasculitis. The majority of studies have evaluated gastrointestinal inhabitants, with a smaller number of studies describing the nasal, pulmonary or vascular microbiomes. Most published studies are observational and cross-sectional. Dysbiosis is seen frequently in vasculitis patients with reduced microbial diversity observed in nasal, fecal and vascular samples compared with disease and/or healthy controls. Predominant bacteria vary, but overall, patients with vasculitis tend to have more pathogenic and less commensal bacteria in active disease. In the few longitudinal studies available, improvement or resolution of dysbiosis has been observed following vasculitis treatment and improved disease activity. SUMMARY Dysbiosis and reduced microbial diversity has been identified in patients with small, medium and large vessel vasculitis. Although limited data suggests microbiomes may 'normalize' following immunosuppression, cause or effect cannot be determined. It is hypothesized that microbial disruption in a genetically susceptible individual may trigger excessive host immune activation and vasculitis; however, larger studies with longitudinal and translational design are needed to further our current understanding.
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Dekkema GJ, Rutgers A, Sanders JS, Stegeman CA, Heeringa P. The Nasal Microbiome in ANCA-Associated Vasculitis: Picking the Nose for Clues on Disease Pathogenesis. Curr Rheumatol Rep 2021; 23:54. [PMID: 34196846 PMCID: PMC8249244 DOI: 10.1007/s11926-021-01015-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 01/21/2023]
Abstract
PURPOSE OF REVIEW The onset and progression of small vessel vasculitis associated with anti-neutrophil cytoplasmic antibodies has been linked to microbial infections. Here, we provide a brief overview of the association of nasal colonization of Staphylococcus aureus with ANCA-associated vasculitis (AAV) and discuss several recent studies mapping the nasal microbiome in AAV patients in particular. RECENT FINDINGS Nasal microbiome studies revealed dysbiosis as a common trait in active AAV which tends to normalize upon immunosuppressive treatment and quiescent disease. However, due to differences in study design, patient selection, and methodology, the reported microbiome profiles differ considerably precluding conclusions on causal relationships. The microbiome is an emerging area of research in AAV warranting further investigation. Ideally, such studies should be combined with mechanistic studies to unravel key elements related to host-microbe interactions and their relevance for AAV pathogenesis.
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Affiliation(s)
- G J Dekkema
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A Rutgers
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J S Sanders
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - C A Stegeman
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P Heeringa
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 EA11, 9713, GZ, Groningen, The Netherlands.
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