1
|
Long MB, Chotirmall SH, Shteinberg M, Chalmers JD. Rethinking bronchiectasis as an inflammatory disease. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00176-0. [PMID: 38971168 DOI: 10.1016/s2213-2600(24)00176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 07/08/2024]
Abstract
Bronchiectasis is understood to be the result of a complex interaction between infection, impaired mucociliary clearance, inflammation, and lung damage. Current therapeutic approaches to bronchiectasis are heavily focused on management of infection along with enhancing mucus clearance. Long-term antibiotics have had limited success in clinical trials, suggesting a need to re-evaluate the concept of bronchiectasis as an infective disorder. We invoke the example of asthma, for which treatment paradigms shifted away from targeting smooth muscle constriction, towards permanently suppressing airway inflammation, reducing risk and ultimately inducing remission with precision anti-inflammatory treatments. In this Review, we argue that bronchiectasis is primarily a chronic inflammatory disease, requiring early identification of at-risk individuals, and we introduce a novel concept of disease activity with important implications for clinical practice and future research. A new generation of novel anti-inflammatory treatments are under development and repurposing of anti-inflammatory agents from other diseases could revolutionise patient care.
Collapse
Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel; The Technion, Israel Institute of Technology, The B Rappaport Faculty of Medicine, Haifa, Israel
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK.
| |
Collapse
|
2
|
Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [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: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
Collapse
Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| |
Collapse
|
3
|
Zhang J, Zheng X, Luo W, Sun B. Cross-domain microbiomes: the interaction of gut, lung and environmental microbiota in asthma pathogenesis. Front Nutr 2024; 11:1346923. [PMID: 38978703 PMCID: PMC11229079 DOI: 10.3389/fnut.2024.1346923] [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: 12/01/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Recent experimental and epidemiological studies underscore the vital interaction between the intestinal microbiota and the lungs, an interplay known as the "gut-lung axis". The significance of this axis has been further illuminated following the identification of intestinal microbial metabolites, such as short-chain fatty acids (SCFA), as key mediators in setting the tone of the immune system. Through the gut-lung axis, the gut microbiota and its metabolites, or allergens, are directly or indirectly involved in the immunomodulation of pulmonary diseases, thereby increasing susceptibility to allergic airway diseases such as asthma. Asthma is a complex outcome of the interplay between environmental factors and genetic predispositions. The concept of the gut-lung axis may offer new targets for the prevention and treatment of asthma. This review outlines the relationships between asthma and the respiratory microbiome, gut microbiome, and environmental microbiome. It also discusses the current advancements and applications of microbiomics, offering novel perspectives and strategies for the clinical management of chronic respiratory diseases like asthma.
Collapse
Affiliation(s)
- Jiale Zhang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Xianhui Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Wenting Luo
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| |
Collapse
|
4
|
Natalini JG, Wong KK, Nelson NC, Wu BG, Rudym D, Lesko MB, Qayum S, Lewis TC, Wong A, Chang SH, Chan JCY, Geraci TC, Li Y, Wang C, Li H, Pamar P, Schnier J, Mahoney IJ, Malik T, Darawshy F, Sulaiman I, Kugler MC, Singh R, Collazo DE, Chang M, Patel S, Kyeremateng Y, McCormick C, Barnett CR, Tsay JCJ, Brosnahan SB, Singh S, Pass HI, Angel LF, Segal LN. Longitudinal Lower Airway Microbial Signatures of Acute Cellular Rejection in Lung Transplantation. Am J Respir Crit Care Med 2024; 209:1463-1476. [PMID: 38358857 PMCID: PMC11208954 DOI: 10.1164/rccm.202309-1551oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/14/2024] [Indexed: 02/17/2024] Open
Abstract
Rationale: Acute cellular rejection (ACR) after lung transplant is a leading risk factor for chronic lung allograft dysfunction. Prior studies have demonstrated dynamic microbial changes occurring within the allograft and gut that influence local adaptive and innate immune responses. However, the lung microbiome's overall impact on ACR risk remains poorly understood. Objectives: To evaluate whether temporal changes in microbial signatures were associated with the development of ACR. Methods: We performed cross-sectional and longitudinal analyses (joint modeling of longitudinal and time-to-event data and trajectory comparisons) of 16S rRNA gene sequencing results derived from lung transplant recipient lower airway samples collected at multiple time points. Measurements and Main Results: Among 103 lung transplant recipients, 25 (24.3%) developed ACR. In comparing samples acquired 1 month after transplant, subjects who never developed ACR demonstrated lower airway enrichment with several oral commensals (e.g., Prevotella and Veillonella spp.) than those with current or future (beyond 1 mo) ACR. However, a subgroup analysis of those who developed ACR beyond 1 month revealed delayed enrichment with oral commensals occurring at the time of ACR diagnosis compared with baseline, when enrichment with more traditionally pathogenic taxa was present. In longitudinal models, dynamic changes in α-diversity (characterized by an initial decrease and a subsequent increase) and in the taxonomic trajectories of numerous oral commensals were more commonly observed in subjects with ACR. Conclusions: Dynamic changes in the lower airway microbiota are associated with the development of ACR, supporting its potential role as a useful biomarker or in ACR pathogenesis.
Collapse
Affiliation(s)
- Jake G. Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Kendrew K. Wong
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Nathaniel C. Nelson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Benjamin G. Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Veterans Affairs New York Harbor Healthcare System, New York, New York
| | - Darya Rudym
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Melissa B. Lesko
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Seema Qayum
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Tyler C. Lewis
- New York University Langone Transplant Institute, New York, New York
| | - Adrian Wong
- New York University Langone Transplant Institute, New York, New York
| | - Stephanie H. Chang
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Justin C. Y. Chan
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Travis C. Geraci
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Chan Wang
- Department of Population Health, New York University Grossman School of Medicine, New York, New York
| | - Huilin Li
- Department of Population Health, New York University Grossman School of Medicine, New York, New York
| | - Prerna Pamar
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Joseph Schnier
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Ian J. Mahoney
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Tahir Malik
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Fares Darawshy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- The Institute of Pulmonology, Hadassah Medical Center, Jerusalem, Israel
- The Faculty of Medicine at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; and
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Matthias C. Kugler
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Rajbir Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Destiny E. Collazo
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Miao Chang
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Shrey Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Colin McCormick
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Clea R. Barnett
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Jun-Chieh J. Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Veterans Affairs New York Harbor Healthcare System, New York, New York
| | - Shari B. Brosnahan
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | | | - Luis F. Angel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| |
Collapse
|
5
|
Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin DA, Huang CY, Van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure. Nat Commun 2024; 15:4708. [PMID: 38830853 PMCID: PMC11148165 DOI: 10.1038/s41467-024-48819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/13/2024] [Indexed: 06/05/2024] Open
Abstract
Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.
Collapse
Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran's Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran's Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
6
|
Bongers KS, Massett A, O'Dwyer DN. The Oral-Lung Microbiome Axis in Connective Tissue Disease-Related Interstitial Lung Disease. Semin Respir Crit Care Med 2024; 45:449-458. [PMID: 38626906 DOI: 10.1055/s-0044-1785673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Connective tissue disease-related interstitial lung disease (CTD-ILD) is a frequent and serious complication of CTD, leading to high morbidity and mortality. Unfortunately, its pathogenesis remains poorly understood; however, one intriguing contributing factor may be the microbiome of the mouth and lungs. The oral microbiome, which is a major source of the lung microbiome through recurrent microaspiration, is altered in ILD patients. Moreover, in recent years, several lines of evidence suggest that changes in the oral and lung microbiota modulate the pulmonary immune response and thus may play a role in the pathogenesis of ILDs, including CTD-ILD. Here, we review the existing data demonstrating oral and lung microbiota dysbiosis and possible contributions to the development of CTD-ILD in rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, and systemic lupus erythematosus. We identify several areas of opportunity for future investigations into the role of the oral and lung microbiota in CTD-ILD.
Collapse
Affiliation(s)
- Kale S Bongers
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Angeline Massett
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - David N O'Dwyer
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
7
|
Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation. Nat Med 2024:10.1038/s41591-024-02999-4. [PMID: 38783139 DOI: 10.1038/s41591-024-02999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 children's hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes.
Collapse
Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Courtney M Rowan
- Department of Pediatrics, Division of Critical Care Medicine, Indiana University, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, Benioff Children's Hospital Oakland, University of California, San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- Department of Pediatrics, Division of Critical Care Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Department of Pediatric Medicine, Division of Critical Care, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Division of Pediatric Oncology Harvard Medical School Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Department of Pediatrics, Division of Pediatric Critical Care, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Department of Pediatrics, Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Columbia University, New York, NY, USA
| | - Paul Castillo
- UF Health Shands Children's Hospital, University of Florida, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, Division of Critical Care Medicine, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Department of Pediatrics, Division of Infectious Diseases, Children's National Hospital, Washington DC, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Department of Pediatrics, Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
8
|
O’Dwyer DN, Kim JS, Ma SF, Ranjan P, Das P, Lipinski JH, Metcalf JD, Falkowski NR, Yow E, Anstrom K, Dickson RP, Huang Y, Gilbert JA, Martinez FJ, Noth I. Commensal Oral Microbiota, Disease Severity, and Mortality in Fibrotic Lung Disease. Am J Respir Crit Care Med 2024; 209:1101-1110. [PMID: 38051927 PMCID: PMC11092942 DOI: 10.1164/rccm.202308-1357oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis (IPF). Methods: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with IPF in the multicenter CleanUP-IPF (Study of Clinical Efficacy of Antimicrobial Therapy Strategy Using Pragmatic Design in IPF) trial. Buccal swabs were collected from usual care and antimicrobial cohorts. Microbiome data were correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan-Meier analysis, and Cox proportional hazards models. Measurements and Main Results: Greater buccal microbial diversity associated with lower FVC at baseline (mean difference, -3.60; 95% confidence interval [CI], -5.92 to -1.29% predicted FVC per 1-unit increment). The buccal proportion of Streptococcus correlated positively with FVC (mean difference, 0.80; 95% CI, 0.16 to 1.43% predicted per 10% increase) (n = 490). Greater microbial diversity was associated with an increased risk of death (hazard ratio, 1.73; 95% CI, 1.03-2.90), whereas a greater proportion of Streptococcus was associated with a reduced risk of death (HR, 0.85; 95% CI, 0.73 to 0.99). The Streptococcus genus was mainly composed of Streptococcus mitis species. Conclusions: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal S. mitis spp associates with preserved lung function and improved survival.
Collapse
Affiliation(s)
- David N. O’Dwyer
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - John S. Kim
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Piyush Ranjan
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Jay H. Lipinski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joseph D. Metcalf
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Nicole R. Falkowski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Eric Yow
- Department of Biostatistics, Duke University, Durham, North Carolina
| | - Kevin Anstrom
- Department of Biostatistics, University of North Carolina–Chapel Hill Gillings School of Global Public Health, Chapel Hill, North Carolina
| | - Robert P. Dickson
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, Michigan; and
| | - Yong Huang
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California
| | | | - Imre Noth
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| |
Collapse
|
9
|
Xiao W, Chen YL, Du LY, Wu J, Wang Z, Mao B, Wen FQ, Gibson PG, McDonald VM, Yu H, Fu JJ. Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations. Respir Res 2024; 25:173. [PMID: 38643126 PMCID: PMC11032604 DOI: 10.1186/s12931-024-02802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/03/2024] [Indexed: 04/22/2024] Open
Abstract
RATIONALE Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome. OBJECTIVES To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes. METHODS We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data. RESULTS Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota. CONCLUSIONS Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.
Collapse
Affiliation(s)
- Wei Xiao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Yi-Long Chen
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Jiqiu Wu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bing Mao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Fu-Qiang Wen
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Peter Gerard Gibson
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Vanessa M McDonald
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China.
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.
| |
Collapse
|
10
|
King A. Exploring the lung microbiome's role in disease. Nature 2024:10.1038/d41586-024-01123-3. [PMID: 38632423 DOI: 10.1038/d41586-024-01123-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
|
11
|
Lipinksi JH, Ranjan P, Dickson RP, O’Dwyer DN. The Lung Microbiome. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1269-1275. [PMID: 38560811 PMCID: PMC11073614 DOI: 10.4049/jimmunol.2300716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/01/2024] [Indexed: 04/04/2024]
Abstract
Although the lungs were once considered a sterile environment, advances in sequencing technology have revealed dynamic, low-biomass communities in the respiratory tract, even in health. Key features of these communities-composition, diversity, and burden-are consistently altered in lung disease, associate with host physiology and immunity, and can predict clinical outcomes. Although initial studies of the lung microbiome were descriptive, recent studies have leveraged advances in technology to identify metabolically active microbes and potential associations with their immunomodulatory by-products and lung disease. In this brief review, we discuss novel insights in airway disease and parenchymal lung disease, exploring host-microbiome interactions in disease pathogenesis. We also discuss complex interactions between gut and oropharyngeal microbiota and lung immunobiology. Our advancing knowledge of the lung microbiome will provide disease targets in acute and chronic lung disease and may facilitate the development of new therapeutic strategies.
Collapse
Affiliation(s)
- Jay H. Lipinksi
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Piyush Ranjan
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - David N. O’Dwyer
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| |
Collapse
|
12
|
Marrella V, Nicchiotti F, Cassani B. Microbiota and Immunity during Respiratory Infections: Lung and Gut Affair. Int J Mol Sci 2024; 25:4051. [PMID: 38612860 PMCID: PMC11012346 DOI: 10.3390/ijms25074051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Bacterial and viral respiratory tract infections are the most common infectious diseases, leading to worldwide morbidity and mortality. In the past 10 years, the importance of lung microbiota emerged in the context of pulmonary diseases, although the mechanisms by which it impacts the intestinal environment have not yet been fully identified. On the contrary, gut microbial dysbiosis is associated with disease etiology or/and development in the lung. In this review, we present an overview of the lung microbiome modifications occurring during respiratory infections, namely, reduced community diversity and increased microbial burden, and of the downstream consequences on host-pathogen interaction, inflammatory signals, and cytokines production, in turn affecting the disease progression and outcome. Particularly, we focus on the role of the gut-lung bidirectional communication in shaping inflammation and immunity in this context, resuming both animal and human studies. Moreover, we discuss the challenges and possibilities related to novel microbial-based (probiotics and dietary supplementation) and microbial-targeted therapies (antibacterial monoclonal antibodies and bacteriophages), aimed to remodel the composition of resident microbial communities and restore health. Finally, we propose an outlook of some relevant questions in the field to be answered with future research, which may have translational relevance for the prevention and control of respiratory infections.
Collapse
Affiliation(s)
- Veronica Marrella
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy;
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
| | - Federico Nicchiotti
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, 20089 Milan, Italy;
| | - Barbara Cassani
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, 20089 Milan, Italy;
| |
Collapse
|
13
|
Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
Collapse
Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
14
|
Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN, Chotirmall SH. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024; 18:111-125. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.
Collapse
Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| |
Collapse
|
15
|
Drigot ZG, Clark SE. Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia. Curr Opin Microbiol 2024; 77:102428. [PMID: 38277901 PMCID: PMC10922932 DOI: 10.1016/j.mib.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.
Collapse
Affiliation(s)
- Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA.
| |
Collapse
|
16
|
Taylor SL, Crabbé A, Hoffman LR, Chalmers JD, Rogers GB. Understanding the clinical implications of the "non-classical" microbiome in chronic lung disease: a viewpoint. Eur Respir J 2024; 63:2302281. [PMID: 38387999 DOI: 10.1183/13993003.02281-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Steven L Taylor
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Luke R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Geraint B Rogers
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Leduc L, Costa M, Leclère M. The Microbiota and Equine Asthma: An Integrative View of the Gut-Lung Axis. Animals (Basel) 2024; 14:253. [PMID: 38254421 PMCID: PMC10812655 DOI: 10.3390/ani14020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Both microbe-microbe and host-microbe interactions can have effects beyond the local environment and influence immunological responses in remote organs such as the lungs. The crosstalk between the gut and the lungs, which is supported by complex connections and intricate pathways, is defined as the gut-lung axis. This review aimed to report on the potential role of the gut-lung gut-lung axis in the development and persistence of equine asthma. We summarized significant determinants in the development of asthma in horses and humans. The article discusses the gut-lung axis and proposes an integrative view of the relationship between gut microbiota and asthma. It also explores therapies for modulating the gut microbiota in horses with asthma. Improving our understanding of the horse gut-lung axis could lead to the development of techniques such as fecal microbiota transplants, probiotics, or prebiotics to manipulate the gut microbiota specifically for improving the management of asthma in horses.
Collapse
Affiliation(s)
- Laurence Leduc
- Clinical Sciences Department, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Marcio Costa
- Veterinary Department of Biomedical Sciences, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Mathilde Leclère
- Clinical Sciences Department, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| |
Collapse
|
19
|
Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
Collapse
Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| |
Collapse
|
20
|
Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299130. [PMID: 38077035 PMCID: PMC10705623 DOI: 10.1101/2023.11.29.23299130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes. In this multicenter study, we collected 278 bronchoalveolar lavage (BAL) samples from 229 patients treated at 32 children's hospitals between 2014-2022. Using paired metatranscriptomes and human gene expression data, we identified 4 patient clusters with varying BAL composition. Among those requiring respiratory support prior to sampling, in-hospital mortality varied from 22-60% depending on the cluster (p=0.007). The most common patient subtype, Cluster 1, showed a moderate quantity and high diversity of commensal microbes with robust metabolic activity, low rates of infection, gene expression indicating alveolar macrophage predominance, and low mortality. The second most common cluster showed a very high burden of airway microbes, gene expression enriched for neutrophil signaling, frequent bacterial infections, and moderate mortality. Cluster 3 showed significant depletion of commensal microbes, a loss of biodiversity, gene expression indicative of fibroproliferative pathways, increased viral and fungal pathogens, and high mortality. Finally, Cluster 4 showed profound microbiome depletion with enrichment of Staphylococci and viruses, gene expression driven by lymphocyte activation and cellular injury, and the highest mortality. BAL clusters were modeled with a random forest classifier and reproduced in a geographically distinct validation cohort of 57 patients from The Netherlands, recapitulating similar cluster-based mortality differences (p=0.022). Degree of antibiotic exposure was strongly associated with depletion of BAL microbes and enrichment of fungi. Potential pathogens were parsed from all detected microbes by analyzing each BAL microbe relative to the overall microbiome composition, which yielded increased sensitivity for numerous previously occult pathogens. These findings support personalized interpretation of the pulmonary microenvironment in pediatric HCT, which may facilitate biology-targeted interventions to improve outcomes.
Collapse
Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Y Mayday
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Departments of Laboratory Medicine and Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Gustavo Reyes
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Miriam R Simon
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Emma M Pearce
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Hanna Kim
- Division of Critical Care Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Shaw
- The Children`s Hospital at Westmead, Sydney, Australia
| | - Courtney M Rowan
- Indiana University, Department of Pediatrics, Division of Critical Care Medicine, Indianapolis, IN, USA
| | - Jeffrey J Auletta
- Hematology/Oncology/BMT and Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Paul L Martin
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Kamar Godder
- Cancer and Blood Disorders Center, Nicklaus Children's Hospital, Miami, FL, USA
| | - Christine N Duncan
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Nahal R Lalefar
- Division of Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, Oakland, CA, USA
| | - Erin M Kreml
- Department of Child Health, Division of Critical Care Medicine, University of Arizona, Phoenix, AZ, USA
| | - Janet R Hume
- University of Minnesota, Department of Pediatrics, Division of Critical Care Medicine, Minneapolis, MN, USA
| | - Hisham Abdel-Azim
- Department of Pediatrics, Division of Hematology/Oncology and Transplant and Cell Therapy, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Loma Linda University School of Medicine, Cancer Center, Children Hospital and Medical Center, Loma Linda, CA, USA
| | - Caitlin Hurley
- Division of Critical Care, Department of Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey D E Cuvelier
- CancerCare Manitoba, Manitoba Blood and Marrow Transplant Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Amy K Keating
- Center for Cancer and Blood Disorders, Children's Hospital Colorado and University of Colorado, Aurora, CO, USA
- Harvard Medical School, Boston, Massachusetts; Division of Pediatric Oncology, Department of Pediatrics, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Muna Qayed
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, GA, USA
| | - James S Killinger
- Division of Pediatric Critical Care, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Rabi Hanna
- Department of Pediatric Hematology, Oncology and Blood and Marrow Transplantation, Pediatric Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kris M Mahadeo
- Department of Pediatrics, Division of Hematology/Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Division of Pediatric and Cellular Therapy, Duke University Medical Center, Durham, NC, USA
| | - Troy C Quigg
- Pediatric Blood and Marrow Transplantation Program, Texas Transplant Institute, Methodist Children's Hospital, San Antonio, TX, USA
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Prakash Satwani
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Paul Castillo
- University of Florida, Gainesville, UF Health Shands Children's Hospital, Gainesville, FL, USA
| | - Shira J Gertz
- Department of Pediatrics, Division of Critical Care Medicine, Joseph M Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
- Department of Pediatrics, St. Barnabas Medical Center, Livingston, NJ, USA
| | - Theodore B Moore
- Department of Pediatric Hematology-Oncology, Mattel Children's Hospital, University of California, Los Angeles, CA, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Aly Abdel-Mageed
- Section of Pediatric BMT and Cellular Therapy, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Rachel Phelan
- Division of Pediatric Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Dereck B Davis
- Department of Pediatrics, Hematology/Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michelle P Hudspeth
- Adult and Pediatric Blood & Marrow Transplantation, Pediatric Hematology/Oncology, Medical University of South Carolina Children's Hospital/Hollings Cancer Center, Charleston, SC, USA
| | - Greg A Yanik
- Pediatric Blood and Bone Marrow Transplantation, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Pulsipher
- Division of Hematology, Oncology, Transplantation, and Immunology, Primary Children's Hospital, Huntsman Cancer Institute, Spense Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Imran Sulaiman
- Departments of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Leopoldo N Segal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
| | - Birgitta A Versluys
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Caroline A Lindemans
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, NY, USA
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap J Boelens
- Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
- Transplantation and Cellular Therapy, MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
21
|
Pragman AA. Investigating a Causal Role for Lung Microbiome Dysbiosis in Early Chronic Obstructive Pulmonary Disease Pathogenesis. Am J Respir Crit Care Med 2023; 208:1019-1021. [PMID: 37703423 PMCID: PMC10867932 DOI: 10.1164/rccm.202309-1599ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Affiliation(s)
- Alexa A Pragman
- Department of Medicine Minneapolis Veterans Affairs Medical Center Minneapolis, Minnesota and Department of Medicine University of Minnesota Minneapolis, Minnesota
| |
Collapse
|
22
|
Sulaiman I, Wu BG, Chung M, Isaacs B, Tsay JCJ, Holub M, Barnett CR, Kwok B, Kugler MC, Natalini JG, Singh S, Li Y, Schluger R, Carpenito J, Collazo D, Perez L, Kyeremateng Y, Chang M, Campbell CD, Hansbro PM, Oppenheimer BW, Berger KI, Goldring RM, Koralov SB, Weiden MD, Xiao R, D’Armiento J, Clemente JC, Ghedin E, Segal LN. Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2023; 208:1101-1114. [PMID: 37677136 PMCID: PMC10867925 DOI: 10.1164/rccm.202210-1865oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality, and healthcare costs. Cigarette smoke is a causative factor; however, not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advanced stages. Objectives: We investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis. Methods: We recruited 57 patients with a >10 pack-year smoking history: 26 had physiological evidence of COPD, and 31 had normal lung function (smoker control subjects). Bronchoscopy sampled the upper airways, lower airways, and environmental background. Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome, and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury. Measurements and Main Results: Compared with smoker control subjects, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis, such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1, and MUC4 in mild-to-moderate COPD. Finally, in a preclinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury, revealing transcriptomic signatures similar to those observed in human subjects with COPD. Conclusions: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.
Collapse
Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bradley Isaacs
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Jun-Chieh J. Tsay
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Meredith Holub
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Hartford Health Care, Hartford, Connecticut
| | - Clea R. Barnett
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Benjamin Kwok
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | - Jake G. Natalini
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Destiny Collazo
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Luisanny Perez
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Miao Chang
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Sydney, New South Wales, Australia
| | | | - Kenneth I. Berger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | | | - Michael D. Weiden
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rui Xiao
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jeanine D’Armiento
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, New York
| |
Collapse
|
23
|
Mao X, Li Y, Shi P, Zhu Z, Sun J, Xue Y, Wan Z, Yang D, Ma T, Wang J, Zhu R. Analysis of sputum microbial flora in chronic obstructive pulmonary disease patients with different phenotypes during acute exacerbations. Microb Pathog 2023; 184:106335. [PMID: 37673353 DOI: 10.1016/j.micpath.2023.106335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Increasing studies have shown that the imbalance of the respiratory microbial flora is related to the occurrence of COPD, the severity and frequency of exacerbations and mortality.However, it remains unclear how the sputum microbial flora differs during exacerbations in COPD patients manifesting emphysema phenotype, chronic bronchitis with emphysema phenotype and asthma-COPD overlap phenotype. METHODS Sputum samples were obtained from 29 COPD patients experiencing acute exacerbations who had not received antibiotics or systemic corticosteroids within the past four weeks.Patients were divided into three groups;emphysema phenotype(E);chronic bronchitis with emphysema phenotype(B+E) and asthma-COPD overlap phenotype(ACO).We utilized metagenomic Next Generation Sequencing (mNGS) technology to analyze the sputum microbial flora in COPD patients with different phenotypes during exacerbations. RESULTS There was no significant difference in alpha diversity and beta diversity among three groups.The microbial flora composition was similar in all three groups during exacerbations except for a significant increase in Streptococcus mitis in ACO.Through network analysis,we found Candidatus Saccharibacteria oral taxon TM7x and Fusobacterium necrophorum were the core nodes of the co-occurrence network in ACO and E respectively.They were positively correlated with some species and play a synergistic role.In B+E,Haemophilus pittmaniae and Klebsiella pneumoniae had a synergistic effect.Besides,some species among the three groups play a synergistic or antagonistic role.Through Spearman analysis,we found the relative abundance of Streptococcus mitis was negatively correlated with the number of hospitalizations in the past year(r = -0.410,P = 0.027).We also observed that the relative abundance of Prevotella and Prevotella melaninogenica was negatively correlated with age(r = -0.534,P = 0.003;r = -0.567,P = 0.001),while the relative abundance of Streptococcus oralis and Actinomyces odontolyticus was positively correlated with age(r = 0.570,P = 0.001;r = 0.480,P = 0.008).In addition,the relative abundance of Prevotella melaninogenica was negatively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio(r = -0.479,P = 0.009;r = -0.555,P = 0.002),while the relative abundance of Streptococcus sanguinis was positively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio (r = 0.450,P = 0.014;r = 0.501,P = 0.006).There was also a significant positive correlation between Oribacterium and blood eosinophil counts(r = 0.491,P = 0.007). CONCLUSION Overall,we analyzed the sputum microbiota of COPD patients with different phenotypes and its relationship with clinical indicators, and explored the relationships between microbiota and inflammation in COPD.We hope to alter the prognosis of patients by inhibiting specific bacterial taxa related to inflammation and using guide individualized treatment in the future research.
Collapse
Affiliation(s)
- Xiaoyan Mao
- Department of Intensive Care Unit, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, Jiangsu, 223002, China
| | - Yao Li
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Pengfei Shi
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Ziwei Zhu
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China
| | - Juan Sun
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Yu Xue
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Zongren Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Dan Yang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Ting Ma
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Jipeng Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu, 223300, China
| | - Rong Zhu
- Department of Respiratory and Critical Care Medicine, The Huaian Clinial College of Xuzhou Medical University, Huaian, Jiangsu, 223300, China.
| |
Collapse
|
24
|
Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23296086. [PMID: 37808745 PMCID: PMC10557814 DOI: 10.1101/2023.09.25.23296086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
Collapse
Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
25
|
Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Cruz CD, Okin DA, Huang CY, van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Prognostic Insights from Longitudinal Multicompartment Study of Host-Microbiota Interactions in Critically Ill Patients. RESEARCH SQUARE 2023:rs.3.rs-3338762. [PMID: 37841841 PMCID: PMC10571606 DOI: 10.21203/rs.3.rs-3338762/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Critical illness can disrupt the composition and function of the microbiome, yet comprehensive longitudinal studies are lacking. We conducted a longitudinal analysis of oral, lung, and gut microbiota in a large cohort of 479 mechanically ventilated patients with acute respiratory failure. Progressive dysbiosis emerged in all three body compartments, characterized by reduced alpha diversity, depletion of obligate anaerobe bacteria, and pathogen enrichment. Clinical variables, including chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, shaped dysbiosis. Notably, of the three body compartments, unsupervised clusters of lung microbiota diversity and composition independently predicted survival, transcending clinical predictors, organ dysfunction severity, and host-response sub-phenotypes. These independent associations of lung microbiota may serve as valuable biomarkers for prognostication and treatment decisions in critically ill patients. Insights into the dynamics of the microbiome during critical illness highlight the potential for microbiota-targeted interventions in precision medicine.
Collapse
Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W. Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
26
|
Mac Aogáin M, Narayana JK, Chotirmall SH. Reply to Ward et al.. Am J Respir Crit Care Med 2023; 208:631-632. [PMID: 37348125 PMCID: PMC10492252 DOI: 10.1164/rccm.202305-0872le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| |
Collapse
|
27
|
Vientós‐Plotts AI, Ericsson AC, Reinero CR. The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective. J Vet Intern Med 2023; 37:1641-1655. [PMID: 37551852 PMCID: PMC10473014 DOI: 10.1111/jvim.16824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.
Collapse
Affiliation(s)
- Aida I. Vientós‐Plotts
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
| | - Aaron C. Ericsson
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- University of Missouri Metagenomics CenterUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Pathobiology, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
| | - Carol R. Reinero
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
| |
Collapse
|
28
|
Kitsios GD, Nguyen VD, Sayed K, Al-Yousif N, Schaefer C, Shah FA, Bain W, Yang H, Fitch A, Li K, Wang X, Qin S, Gentry H, Zhang Y, Varon J, Arciniegas Rubio A, Englert JA, Baron RM, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ. The upper and lower respiratory tract microbiome in severe aspiration pneumonia. iScience 2023; 26:106832. [PMID: 37250794 PMCID: PMC10212968 DOI: 10.1016/j.isci.2023.106832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/24/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro-aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and performed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.
Collapse
Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Vi D. Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- University of California Los Angeles, Department of Medicine, Internal Medicine Residency Program, Los Angeles, CA90095, USA
| | - Khaled Sayed
- University of PittsburghDepartment of Computational & Systems Biology, Pittsburgh, PA15213, USA
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Nameer Al-Yousif
- University of Pittsburgh Medical Center Mercy, Department of Medicine, Pittsburgh, PA15219, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - Haopu Yang
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Heather Gentry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Antonio Arciniegas Rubio
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Joshua A. Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH43210, USA
| | - Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO63110, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| |
Collapse
|
29
|
Caparrós-Martín JA, Saladie M, Agudelo-Romero SP, Reen FJ, Ware RS, Sly PD, Stick SM, O'Gara F. Detection of bile acids in bronchoalveolar lavage fluid defines the inflammatory and microbial landscape of the lower airways in infants with cystic fibrosis. MICROBIOME 2023; 11:132. [PMID: 37312128 DOI: 10.1186/s40168-023-01543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/05/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cystic Fibrosis (CF) is a genetic condition characterized by neutrophilic inflammation and recurrent infection of the airways. How these processes are initiated and perpetuated in CF remains largely unknown. We have demonstrated a link between the intestinal microbiota-related metabolites bile acids (BA) and inflammation in the bronchoalveolar lavage fluid (BALF) from children with stable CF lung disease. To establish if BA indicate early pathological processes in CF lung disease, we combined targeted mass spectrometry and amplicon sequencing-based microbial characterization of 121 BALF specimens collected from 12-month old infants with CF enrolled in the COMBAT-CF study, a multicentre randomized placebo-controlled clinical trial comparing azithromycin versus placebo. We evaluated whether detection of BA in BALF is associated with the establishment of the inflammatory and microbial landscape of early CF lung disease, and whether azithromycin, a motilin agonist that has been demonstrated to reduce aspiration of gastric contents, alters the odds of detecting BA in BALF. We also explored how different prophylactic antibiotics regimens impact the early life BALF microbiota. RESULTS Detection of BA in BALF was strongly associated with biomarkers of airway inflammation, more exacerbation episodes during the first year of life, increased use of oral antibiotics with prolonged treatment periods, a higher degree of structural lung damage, and distinct microbial profiles. Treatment with azithromycin, a motilin agonist, which has been reported to reduce aspiration of gastric contents, did not reduce the odds of detecting BA in BALF. Culture and molecular methods showed that azithromycin does not alter bacterial load or diversity in BALF. Conversely, penicillin-type prophylaxis reduced the odds of detecting BAs in BALF, which was associated with elevated levels of circulating biomarkers of cholestasis. We also observed that environmental factors such as penicillin-type prophylaxis or BAs detection were linked to distinct early microbial communities of the CF airways, which were associated with different inflammatory landscapes but not with structural lung damage. CONCLUSIONS Detection of BA in BALF portend early pathological events in CF lung disease. Benefits early in life associated with azithromycin are not linked to its antimicrobial properties. Video Abstract.
Collapse
Affiliation(s)
- Jose A Caparrós-Martín
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
| | - Montserrat Saladie
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
- Present Address: Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Reus, Spain
| | - S Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Stephen M Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Fergal O'Gara
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia.
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland.
| |
Collapse
|
30
|
Xue Q, Xie Y, He Y, Yu Y, Fang G, Yu W, Wu J, Li J, Zhao L, Deng X, Li R, Wang F, Zheng Y, Gao Z. Lung microbiome and cytokine profiles in different disease states of COPD: a cohort study. Sci Rep 2023; 13:5715. [PMID: 37029178 PMCID: PMC10080507 DOI: 10.1038/s41598-023-32901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
Increasing evidence indicates that respiratory tract microecological disorders may play a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Understanding the composition of the respiratory microbiome in COPD and its relevance to respiratory immunity will help develop microbiome-based diagnostic and therapeutic approaches. One hundred longitudinal sputum samples from 35 subjects with acute exacerbation of COPD (AECOPD) were analysed for respiratory bacterial microbiome using 16S ribosomal RNA amplicon sequencing technology, and the sputum supernatant was analysed for 12 cytokines using a Luminex liquid suspension chip. Unsupervised hierarchical clustering was employed to evaluate the existence of distinct microbial clusters. In AECOPD, the respiratory microbial diversity decreased, and the community composition changed significantly. The abundances of Haemophilus, Moraxella, Klebsiella, and Pseudomonas increased significantly. Significant positive correlations between the abundance of Pseudomonas and TNF-α, abundance of Klebsiella and the percentage of eosinophils were observed. Furthermore, COPD can be divided into four clusters based on the respiratory microbiome. AECOPD-related cluster was characterized by the enrichment of Pseudomonas and Haemophilus and a high level of TNF-α. Lactobacillus and Veillonella are enriched in therapy-related phenotypes and may play potential probiotic roles. There are two inflammatory endotypes in the stable state: Gemella is associated with the Th2 inflammatory endotypes, whereas Prevotella is associated with the Th17 inflammatory endotypes. Nevertheless, no differences in clinical manifestations were found between these two endotypes. The sputum microbiome is associated with the disease status of COPD, allowing us to distinguish different inflammatory endotypes. Targeted anti-inflammatory and anti-infective therapies may improve the long-term prognosis of COPD.
Collapse
Affiliation(s)
- Qing Xue
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Yu Xie
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
- Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yan Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Guiju Fang
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Jianhui Wu
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Jiwei Li
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361101, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Xinyu Deng
- The Third Clinical Medical College, Fujian Medical University, Ningde Municipal Hospital, Ningde, Fujian, China
| | - Ran Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Fang Wang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361101, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, China.
| |
Collapse
|
31
|
Narayana JK, Aliberti S, Mac Aogáin M, Jaggi TK, Ali NABM, Ivan FX, Cheng HS, Yip YS, Vos MIG, Low ZS, Lee JXT, Amati F, Gramegna A, Wong SH, Sung JJY, Tan NS, Tsaneva-Atanasova K, Blasi F, Chotirmall SH. Microbial Dysregulation of the Gut-Lung Axis in Bronchiectasis. Am J Respir Crit Care Med 2023; 207:908-920. [PMID: 36288294 PMCID: PMC10111978 DOI: 10.1164/rccm.202205-0893oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Emerging data support the existence of a microbial "gut-lung" axis that remains unexplored in bronchiectasis. Methods: Prospective and concurrent sampling of gut (stool) and lung (sputum) was performed in a cohort of n = 57 individuals with bronchiectasis and subjected to bacteriome (16S rRNA) and mycobiome (18S Internal Transcribed Spacer) sequencing (total, 228 microbiomes). Shotgun metagenomics was performed in a subset (n = 15; 30 microbiomes). Data from gut and lung compartments were integrated by weighted similarity network fusion, clustered, and subjected to co-occurrence analysis to evaluate gut-lung networks. Murine experiments were undertaken to validate specific Pseudomonas-driven gut-lung interactions. Results: Microbial communities in stable bronchiectasis demonstrate a significant gut-lung interaction. Multibiome integration followed by unsupervised clustering reveals two patient clusters, differing by gut-lung interactions and with contrasting clinical phenotypes. A high gut-lung interaction cluster, characterized by lung Pseudomonas, gut Bacteroides, and gut Saccharomyces, is associated with increased exacerbations and greater radiological and overall bronchiectasis severity, whereas the low gut-lung interaction cluster demonstrates an overrepresentation of lung commensals, including Prevotella, Fusobacterium, and Porphyromonas with gut Candida. The lung Pseudomonas-gut Bacteroides relationship, observed in the high gut-lung interaction bronchiectasis cluster, was validated in a murine model of lung Pseudomonas aeruginosa infection. This interaction was abrogated after antibiotic (imipenem) pretreatment in mice confirming the relevance and therapeutic potential of targeting the gut microbiome to influence the gut-lung axis. Metagenomics in a subset of individuals with bronchiectasis corroborated our findings from targeted analyses. Conclusions: A dysregulated gut-lung axis, driven by lung Pseudomonas, associates with poorer clinical outcomes in bronchiectasis.
Collapse
Affiliation(s)
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | | | | | | | | | | | | | | | - Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Andrea Gramegna
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Sunny H. Wong
- Lee Kong Chian School of Medicine and
- Department of Gastroenterology and
| | - Joseph J. Y. Sung
- Lee Kong Chian School of Medicine and
- Department of Gastroenterology and
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine and
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Statistics and
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Francesco Blasi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore; and
| |
Collapse
|
32
|
Abstract
New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.
Collapse
|
33
|
Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W, Forslund SK. Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection. Microbiol Spectr 2023; 11:e0213921. [PMID: 36790203 PMCID: PMC10100697 DOI: 10.1128/spectrum.02139-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.
Collapse
Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Theda Ulrike Patricia Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Till Birkner
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Lajos Markó
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Edgar Kigozi
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Carolyne Atugonza
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Richard Munana
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Denis Mawanda
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Sekibira
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Uwimaana
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Patricia Alupo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Kalyesubula
- African Community Center for Social Sustainability (ACCESS), Department of Research, Nakaseke, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Trishul Siddharthan
- University of Miami, School of Medicine, Division of pulmonary and critical care medicine, Miami, Florida, USA
| | - Bernard S. Bagaya
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - David P. Kateete
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Nelson K. Sewankambo
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Daudi Jjingo
- Makerere University, College of Computing and Information Sciences, Department of Computer Science, Kampala, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Global Non-Communicable Disease Research and Training, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sofia K. Forslund
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| |
Collapse
|
34
|
Kayongo A, Robertson NM, Siddharthan T, Ntayi ML, Ndawula JC, Sande OJ, Bagaya BS, Kirenga B, Mayanja-Kizza H, Joloba ML, Forslund SK. Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease. Front Immunol 2023; 13:1085551. [PMID: 36741369 PMCID: PMC9890194 DOI: 10.3389/fimmu.2022.1085551] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.
Collapse
Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, United States
| | | | - Trishul Siddharthan
- Division of Pulmonary Medicine, School of Medicine, University of Miami, Miami, FL, United States
| | - Moses Levi Ntayi
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Josephine Caren Ndawula
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Obondo J. Sande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bernard S. Bagaya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Experimental and Clinical Research Center, a cooperation of Charité - Universitatsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany,Charité-Universitatsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,*Correspondence: Sofia K. Forslund,
| |
Collapse
|
35
|
Melo-Dias S, Cabral M, Furtado A, Souto-Miranda S, Mendes MA, Cravo J, Almeida CR, Marques A, Sousa A. Responsiveness to pulmonary rehabilitation in COPD is associated with changes in microbiota. Respir Res 2023; 24:29. [PMID: 36698137 PMCID: PMC9875510 DOI: 10.1186/s12931-023-02339-z] [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: 12/21/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Pulmonary Rehabilitation (PR) is one of the most cost-effective therapies for chronic obstructive pulmonary disease (COPD) management. There are, however, people who do not respond to PR and reasons for non-response are mostly unknown. PR is likely to change the airway microbiota and this could play a role in its responsiveness. In this study we have explored the association between PR effectiveness and specific alterations in oral microbiota and inflammation. METHODS A prospective longitudinal study was conducted. Data on exercise capacity, dyspnoea, impact of disease and 418 saliva samples were collected from 76 patients, half of whom participated in a 12-weeks PR programme. Responders and non-responders to PR (dyspnoea, exercise-capacity and impact of disease) were defined based on minimal clinically important differences. RESULTS Changes in microbiota, including Prevotella melaninogenica and Streptococcus were observed upon PR. Prevotella, previously found to be depleted in severe COPD, increased during the first month of PR in responders. This increase was negatively correlated with Streptococcus and Lautropia, known to be enriched in severe cases of COPD. Simultaneously, an anti-inflammatory commensal of the respiratory tract, Rothia, correlated strongly and negatively with several pro-inflammatory markers, whose levels were generally boosted by PR. Conversely, in non-responders, the observed decline in Prevotella correlated negatively with Streptococcus and Lautropia whose fluctuations co-occurred with several pro-inflammatory markers. CONCLUSIONS PR is associated with changes in oral microbiota. Specifically, PR increases salivary Prevotella melaninogenica and avoids the decline in Rothia and the increase in Streptococcus and Lautropia in responders, which may contribute to the benefits of PR.
Collapse
Affiliation(s)
- Sara Melo-Dias
- grid.7311.40000000123236065Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal ,grid.7311.40000000123236065Lab3R – Respiratory Research and Rehabilitation Laboratory, School of Health Sciences (ESSUA), University of Aveiro, Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Miguel Cabral
- grid.7311.40000000123236065Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Andreia Furtado
- grid.7311.40000000123236065Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Sara Souto-Miranda
- grid.7311.40000000123236065Lab3R – Respiratory Research and Rehabilitation Laboratory, School of Health Sciences (ESSUA), University of Aveiro, Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal ,grid.5012.60000 0001 0481 6099Department of Respiratory Medicine, Maastricht University Medical Centre, NUTRIM School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Maria Aurora Mendes
- grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal ,Department of Pulmonology, Hospital Center of Baixo Vouga, Aveiro, Portugal
| | - João Cravo
- Department of Pulmonology, Hospital Center of Baixo Vouga, Aveiro, Portugal
| | - Catarina Rodrigues Almeida
- grid.7311.40000000123236065Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Alda Marques
- grid.7311.40000000123236065Lab3R – Respiratory Research and Rehabilitation Laboratory, School of Health Sciences (ESSUA), University of Aveiro, Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Ana Sousa
- grid.7311.40000000123236065Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| |
Collapse
|
36
|
Affiliation(s)
- Alexa A. Pragman
- Infectious Disease SectionMinneapolis Veterans Affairs Health Care SystemMinneapolis, Minnesota,Division of Infectious Diseases and International MedicineUniversity of MinnesotaMinneapolis, Minnesota
| |
Collapse
|
37
|
Yu X, Chen Y, He L, Liu H, Yang Z, Lin Y. Transcriptome and metabolome analyses reveal the interweaving of immune response and metabolic regulation in pelvic organ prolapse. Int Urogynecol J 2022:10.1007/s00192-022-05357-5. [PMID: 36136109 DOI: 10.1007/s00192-022-05357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION AND HYPOTHESIS The pathogenesis of pelvic organ prolapse (POP) remains unknown. Herein, we aim to reveal the molecular profile of POP by transcriptomic and metabolomic analysis. METHODS We selected 12 samples of uterosacral ligaments (USLs) from 6 POP patients and 6 controls for transcriptomic and metabolomic analyses. Differentially expressed genes (DEGs) were identified using the R package edgeR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using clusterProfiler, and a protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape. Metabolomic profiling was performed by a liquid chromatography-tandem mass spectrometry system. RESULTS Transcriptomic analysis identified 487 DEGs between the POP and control groups. Functional enrichment analysis revealed that they were mostly related to immune response terms, including "adaptive immune response," "T cell differentiation," and "T cell activation." In addition, PTPRC, LCK, CD247, IL2RB, CD2, CXR5, JUN, CD3E, IL2RG, and PRF1 were the 10 nodes with the highest node degrees in the PPI network. Metabolomic profiling revealed 290 differentially expressed metabolites, which significantly enriched in "glycerophospholipid metabolism," "nicotinate and nicotinamide metabolism," "glycine, serine, and threonine metabolism," "arginine and proline metabolism," "pyrimidine metabolism," and "purine metabolism." Finally, integrated analysis revealed that the DEGs involved in these significantly enriched metabolic pathways included NT5C1A, GMPR, SDS, ALAS2, CARNS1, PYCR1, P4HA3, PGS1, and NMRK2. CONCLUSIONS Our findings demonstrate that the immune response and metabolic regulatory pathways are intertwined in POP and might provide new therapeutic targets.
Collapse
Affiliation(s)
- Xia Yu
- Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ying Chen
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, No.1617 Ri Yue Street, Chengdu, 610091, Sichuan, China
| | - Li He
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, No.1617 Ri Yue Street, Chengdu, 610091, Sichuan, China
| | - Hong Liu
- Department of Surgical, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No.32 The First Ring Road West 2, Chengdu, 610071, Sichuan, China.
| | - Yonghong Lin
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, No.1617 Ri Yue Street, Chengdu, 610091, Sichuan, China.
| |
Collapse
|
38
|
Li L, Mac Aogáin M, Xu T, Jaggi TK, Chan LLY, Qu J, Wei L, Liao S, Cheng HS, Keir HR, Dicker AJ, Tan KS, De Yun W, Koh MS, Ong TH, Lim AYH, Abisheganaden JA, Low TB, Hassan TM, Long X, Wark PAB, Oliver B, Drautz-Moses DI, Schuster SC, Tan NS, Fang M, Chalmers JD, Chotirmall SH. Neisseria species as pathobionts in bronchiectasis. Cell Host Microbe 2022; 30:1311-1327.e8. [PMID: 36108613 DOI: 10.1016/j.chom.2022.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/30/2022] [Accepted: 07/18/2022] [Indexed: 02/07/2023]
Abstract
Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.
Collapse
Affiliation(s)
- Liang Li
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China; Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland; Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Tengfei Xu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PRC
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jing Qu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lan Wei
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shumin Liao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hong Sheng Cheng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Holly R Keir
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Alison J Dicker
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Kai Sen Tan
- Department of Otolaryngology, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wang De Yun
- Department of Otolaryngology, Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Thun How Ong
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Albert Yick Hou Lim
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - John A Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Teck Boon Low
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | | | - Xiang Long
- Department of Respiratory Medicine and Critical Care, Peking University Shenzhen Hospital, Shenzhen, China
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia; Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Brian Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia; School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - James D Chalmers
- University of Dundee, Ninewells Hospital, Medical School, Dundee, Scotland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore.
| |
Collapse
|
39
|
Chotirmall SH, Bogaert D, Chalmers JD, Cox MJ, Hansbro PM, Huang YJ, Molyneaux PL, O’Dwyer DN, Pragman AA, Rogers GB, Segal LN, Dickson RP. Therapeutic Targeting of the Respiratory Microbiome. Am J Respir Crit Care Med 2022; 206:535-544. [PMID: 35549655 PMCID: PMC9716896 DOI: 10.1164/rccm.202112-2704pp] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Debby Bogaert
- Center for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Paediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, United Kingdom
| | - Michael J. Cox
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, New South Wales, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, New South Wales, Australia
| | - Yvonne J. Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - David N. O’Dwyer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Alexa A. Pragman
- Department of Medicine, Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Geraint B. Rogers
- Microbiome and Host Health, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, New York; and
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, Michigan
| |
Collapse
|
40
|
Yi X, Gao J, Wang Z. The human lung microbiome-A hidden link between microbes and human health and diseases. IMETA 2022; 1:e33. [PMID: 38868714 PMCID: PMC10989958 DOI: 10.1002/imt2.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome. The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.
Collapse
Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| |
Collapse
|
41
|
Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions. Nat Microbiol 2022; 7:1361-1375. [PMID: 35995842 DOI: 10.1038/s41564-022-01196-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 patients with COPD and 36 healthy individuals in China. Multi-omics data were integrated using sequential mediation analysis, to assess in silico associations of the microbiome with two primary COPD inflammatory endotypes, neutrophilic or eosinophilic inflammation, mediated through microbial metabolic interaction with host gene expression. Hypotheses of microbiome-metabolite-host interaction were identified by leveraging microbial genetic information and established metabolite-human gene pairs. A prominent hypothesis for neutrophil-predominant COPD was altered tryptophan metabolism in airway lactobacilli associated with reduced indole-3-acetic acid (IAA), which was in turn linked to perturbed host interleukin-22 signalling and epithelial cell apoptosis pathways. In vivo and in vitro studies showed that airway microbiome-derived IAA mitigates neutrophilic inflammation, apoptosis, emphysema and lung function decline, via macrophage-epithelial cell cross-talk mediated by interleukin-22. Intranasal inoculation of two airway lactobacilli restored IAA and recapitulated its protective effects in mice. These findings provide the rationale for therapeutically targeting microbe-host interaction in COPD.
Collapse
|
42
|
Liu C, Wu K, Sun T, Chen B, Yi Y, Ren R, Xie L, Xiao K. Effect of invasive mechanical ventilation on the diversity of the pulmonary microbiota. Crit Care 2022; 26:252. [PMID: 35996150 PMCID: PMC9394019 DOI: 10.1186/s13054-022-04126-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
Pulmonary microbial diversity may be influenced by biotic or abiotic conditions (e.g., disease, smoking, invasive mechanical ventilation (MV), etc.). Specially, invasive MV may trigger structural and physiological changes in both tissue and microbiota of lung, due to gastric and oral microaspiration, altered body posture, high O2 inhalation-induced O2 toxicity in hypoxemic patients, impaired airway clearance and ventilator-induced lung injury (VILI), which in turn reduce the diversity of the pulmonary microbiota and may ultimately lead to poor prognosis. Furthermore, changes in (local) O2 concentration can reduce the diversity of the pulmonary microbiota by affecting the local immune microenvironment of lung. In conclusion, systematic literature studies have found that invasive MV reduces pulmonary microbiota diversity, and future rational regulation of pulmonary microbiota diversity by existing or novel clinical tools (e.g., lung probiotics, drugs) may improve the prognosis of invasive MV treatment and lead to more effective treatment of lung diseases with precision.
Collapse
Affiliation(s)
- Chang Liu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Kang Wu
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Tianyu Sun
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bin Chen
- MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Yaxing Yi
- MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Ruotong Ren
- MatriDx Biotechnology Co., Ltd, Hangzhou, China.
- Foshan Branch, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Lixin Xie
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China.
- School of Medicine, Nankai University, Tianjin, China.
| | - Kun Xiao
- College of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, China.
| |
Collapse
|
43
|
Madapoosi SS, Cruickshank-Quinn C, Opron K, Erb-Downward JR, Begley LA, Li G, Barjaktarevic I, Barr RG, Comellas AP, Couper DJ, Cooper CB, Freeman CM, Han MK, Kaner RJ, Labaki W, Martinez FJ, Ortega VE, Peters SP, Paine R, Woodruff P, Curtis JL, Huffnagle GB, Stringer KA, Bowler RP, Esther CR, Reisdorph N, Huang YJ. Lung Microbiota and Metabolites Collectively Associate with Clinical Outcomes in Milder Stage Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2022; 206:427-439. [PMID: 35536732 DOI: 10.1164/rccm.202110-2241oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is variable in its development. Lung microbiota and metabolites collectively may impact COPD pathophysiology, but relationships to clinical outcomes in milder disease are unclear. Objectives: Identify components of the lung microbiome and metabolome collectively associated with clinical markers in milder stage COPD. Methods: We analyzed paired microbiome and metabolomic data previously characterized from bronchoalveolar lavage fluid in 137 participants in the SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study), or (GOLD [Global Initiative for Chronic Obstructive Lung Disease Stage 0-2). Datasets used included 1) bacterial 16S rRNA gene sequencing; 2) untargeted metabolomics of the hydrophobic fraction, largely comprising lipids; and 3) targeted metabolomics for a panel of hydrophilic compounds previously implicated in mucoinflammation. We applied an integrative approach to select features and model 14 individual clinical variables representative of known associations with COPD trajectory (lung function, symptoms, and exacerbations). Measurements and Main Results: The majority of clinical measures associated with the lung microbiome and metabolome collectively in overall models (classification accuracies, >50%, P < 0.05 vs. chance). Lower lung function, COPD diagnosis, and greater symptoms associated positively with Streptococcus, Neisseria, and Veillonella, together with compounds from several classes (glycosphingolipids, glycerophospholipids, polyamines and xanthine, an adenosine metabolite). In contrast, several Prevotella members, together with adenosine, 5'-methylthioadenosine, sialic acid, tyrosine, and glutathione, associated with better lung function, absence of COPD, or less symptoms. Significant correlations were observed between specific metabolites and bacteria (Padj < 0.05). Conclusions: Components of the lung microbiome and metabolome in combination relate to outcome measures in milder COPD, highlighting their potential collaborative roles in disease pathogenesis.
Collapse
Affiliation(s)
| | | | - Kristopher Opron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Lesa A Begley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Gen Li
- Department of Biostatistics, School of Public Health
| | | | - R Graham Barr
- Department of Medicine and
- Department of Epidemiology, Columbia University Medical Center, New York, New York
| | | | | | | | | | - MeiLan K Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Wassim Labaki
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Victor E Ortega
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | - Stephen P Peters
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | | | - Prescott Woodruff
- University of California at San Francisco, San Francisco, California
| | - Jeffrey L Curtis
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Molecular, Cellular and Developmental Biology
| | | | - Russell P Bowler
- School of Medicine, University of Colorado, Aurora, Colorado; and
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Charles R Esther
- Division of Pediatric Pulmonology, and
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nichole Reisdorph
- Department of Pharmaceutical Sciences, University of Colorado, Anschutz Campus, Aurora, Colorado
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
44
|
Singh S, Allwood BW, Chiyaka TL, Kleyhans L, Naidoo CC, Moodley S, Theron G, Segal LN. Immunologic and imaging signatures in post tuberculosis lung disease. Tuberculosis (Edinb) 2022; 136:102244. [PMID: 36007338 PMCID: PMC10061373 DOI: 10.1016/j.tube.2022.102244] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/24/2022] [Accepted: 07/31/2022] [Indexed: 11/25/2022]
Abstract
Post Tuberculosis Lung Disease (PTLD) affects millions of tuberculosis survivors and is a global health burden. The immune mechanisms that drive PTLD are complex and have historically been under investigated. Here, we discuss two immune-mediated paradigms that could drive human PTLD. We review the characteristics of a fibrotic granuloma that favors the development of PTLD via an abundance of T-helper-2 and T-regulatory cells and an upregulation of TGF-β mediated collagen deposition. Next, we discuss the post-primary tuberculosis paradigm and the complex mixture of caseous pneumonia, cavity formation and fibrosis that can also lead to PTLD. We review the delicate balance between cellular subsets and cytokines of the innate and adaptive immune system in conjunction with host-derived proteases that can perpetuate the parenchymal lung damage seen in PTLD. Next, we discuss the role of novel host directed therapies (HDT) to limit the development of PTLD and in particular, the recent repurposing of established medications such as statins, metformin and doxycycline. Finally, we review the emerging role of novel imaging techniques as a non-invasive modality for the early recognition of PTLD. While access to computed tomography imaging is unlikely to be available widely in countries with a high TB burden, its use in research settings can help phenotype PTLD. Due to a lack of disease-specific biomarkers and controlled clinical trials, there are currently no evidence-based recommendations for the management of PTLD. It is likely that an integrated antifibrotic strategy that could simultaneously target inflammatory and pro-fibrotic pathways will probably emerge as a successful way to treat this complex condition. In a disease spectrum as wide as PTLD, a single immunologic or radiographic marker may not be sufficient and a combination is more likely to be a successful surrogate that could aid in the development of successful HDTs.
Collapse
Affiliation(s)
- S Singh
- NYU Langone Translational Lung Biology Laboratory, Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University School of Medicine, NYU Langone Health, 550 First Avenue, MSB 594, New York, NY, USA.
| | - B W Allwood
- Division of Pulmonology, Department of Medicine, Stellenbosch University & Tygerberg Hospital, South Africa.
| | - T L Chiyaka
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
| | - L Kleyhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
| | - C C Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
| | - S Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
| | - G Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
| | - L N Segal
- NYU Langone Translational Lung Biology Laboratory, Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University School of Medicine, NYU Langone Health, 550 First Avenue, MSB 594, New York, NY, USA.
| |
Collapse
|
45
|
Horn KJ, Schopper MA, Drigot ZG, Clark SE. Airway Prevotella promote TLR2-dependent neutrophil activation and rapid clearance of Streptococcus pneumoniae from the lung. Nat Commun 2022; 13:3321. [PMID: 35680890 PMCID: PMC9184549 DOI: 10.1038/s41467-022-31074-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
This study investigates how specific members of the lung microbiome influence the early immune response to infection. Prevotella species are a major component of the endogenous airway microbiota. Increased abundance of Prevotella melaninogenica correlates with reduced infection with the bacterial pathogen Streptococcus pneumoniae, indicating a potentially beneficial role. Here, we show that P. melaninogenica enhances protection against S. pneumoniae, resulting in rapid pathogen clearance from the lung and improved survival in a mouse lung co-infection model. This response requires recognition of P. melaninogenica lipoproteins by toll-like receptor (TLR)2, the induction of TNFα, and neutrophils, as the loss of any of these factors abrogates Prevotella-induced protection. Improved clearance of S. pneumoniae is associated with increased serine protease-mediated killing by lung neutrophils and restraint of P. melaninogenica-induced inflammation by IL-10 in co-infected mice. Together, these findings highlight innate immune priming by airway Prevotella as an important protective feature in the respiratory tract. How the airway microbiome protects against bacterial pneumonia remains unclear. Here, the authors identify airway bacterial species that activate the immune system to facilitate rapid clearance of the pathogen Streptococcus pneumoniae from the lung.
Collapse
Affiliation(s)
- Kadi J Horn
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA
| | - Melissa A Schopper
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA
| | - Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA.,University of Colorado Boulder, College of Arts and Sciences, Boulder, CO, 80309, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA.
| |
Collapse
|
46
|
de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [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: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
Collapse
Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
| |
Collapse
|
47
|
Targeting the Pulmonary Microbiota to Fight against Respiratory Diseases. Cells 2022; 11:cells11050916. [PMID: 35269538 PMCID: PMC8909000 DOI: 10.3390/cells11050916] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/26/2022] [Accepted: 03/01/2022] [Indexed: 02/08/2023] Open
Abstract
The mucosal immune system of the respiratory tract possesses an effective “defense barrier” against the invading pathogenic microorganisms; therefore, the lungs of healthy organisms are considered to be sterile for a long time according to the strong pathogens-eliminating ability. The emergence of next-generation sequencing technology has accelerated the studies about the microbial communities and immune regulating functions of lung microbiota during the past two decades. The acquisition and maturation of respiratory microbiota during childhood are mainly determined by the birth mode, diet structure, environmental exposure and antibiotic usage. However, the formation and development of lung microbiota in early life might affect the occurrence of respiratory diseases throughout the whole life cycle. The interplay and crosstalk between the gut and lung can be realized by the direct exchange of microbial species through the lymph circulation, moreover, the bioactive metabolites produced by the gut microbiota and lung microbiota can be changed via blood circulation. Complicated interactions among the lung microbiota, the respiratory viruses, and the host immune system can regulate the immune homeostasis and affect the inflammatory response in the lung. Probiotics, prebiotics, functional foods and fecal microbiota transplantation can all be used to maintain the microbial homeostasis of intestinal microbiota and lung microbiota. Therefore, various kinds of interventions on manipulating the symbiotic microbiota might be explored as novel effective strategies to prevent and control respiratory diseases.
Collapse
|
48
|
|
49
|
Könönen E, Gursoy UK. Oral Prevotella Species and Their Connection to Events of Clinical Relevance in Gastrointestinal and Respiratory Tracts. Front Microbiol 2022; 12:798763. [PMID: 35069501 PMCID: PMC8770924 DOI: 10.3389/fmicb.2021.798763] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 12/19/2022] Open
Abstract
Prevotella is recognized as one of the core anaerobic genera in the oral microbiome. In addition, members of this genus belong to microbial communities of the gastrointestinal and respiratory tracts. Several novel Prevotella species, most of them of oral origin, have been described, but limited knowledge is still available of their clinical relevance. Prevotella melaninogenica is among the anaerobic commensals on oral mucosae from early months of life onward, and other early colonizing Prevotella species in the oral cavity include Prevotella nigrescens and Prevotella pallens. Oral Prevotella species get constant access to the gastrointestinal tract via saliva swallowing and to lower airways via microaspiration. At these extra-oral sites, they play a role as commensals but also as potentially harmful agents on mucosal surfaces. The aim of this narrative review is to give an updated overview on the involvement of oral Prevotella species in gastrointestinal and respiratory health and disease.
Collapse
Affiliation(s)
- Eija Könönen
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi K Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
| |
Collapse
|
50
|
The Airway Microbiome: Present and Future Applications. Arch Bronconeumol 2022; 58:8-10. [DOI: 10.1016/j.arbres.2021.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 01/07/2023]
|