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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.
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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
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2
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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.
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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
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3
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Chotirmall SH, Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [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: 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 in chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline searches between Jan 2010 and March 2024 were retrieved and summarized. The review examines clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, anti-inflammatories and antimicrobial strategies are 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 'pathogen-centric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving cross-disciplinary 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.
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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
| | - 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
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY
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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.
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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;
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5
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Kaur J, Sharma A, Passi G, Dey P, Khajuria A, Alajangi HK, Jaiswal PK, Barnwal RP, Singh G. Nanomedicine at the Pulmonary Frontier: Immune-Centric Approaches for Respiratory Disease Treatment. Immunol Invest 2024; 53:295-347. [PMID: 38206610 DOI: 10.1080/08820139.2023.2298398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Respiratory diseases (RD) are a group of common ailments with a rapidly increasing global prevalence, posing a significant threat to humanity, especially the elderly population, and imposing a substantial burden on society and the economy. RD represents an unmet medical need that requires the development of viable pharmacotherapies. While various promising strategies have been devised to advance potential treatments for RD, their implementation has been hindered by difficulties in drug delivery, particularly in critically ill patients. Nanotechnology offers innovative solutions for delivering medications to the inflamed organ sites, such as the lungs. Although this approach is enticing, delivering nanomedicine to the lungs presents complex challenges that require sophisticated techniques. In this context, we review the potential of novel nanomedicine-based immunomodulatory strategies that could offer therapeutic benefits in managing this pressing health condition.
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Affiliation(s)
- Jatinder Kaur
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Akanksha Sharma
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Gautam Passi
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Piyush Dey
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Akhil Khajuria
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Hema Kumari Alajangi
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Pradeep Kumar Jaiswal
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, USA
| | | | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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Kau AL, Rosen AL, Rosas-Salazar C. Can Therapeutic Targeting of the Human Microbiome Influence Asthma Management? A Pro/Con Debate. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:863-869. [PMID: 38224872 DOI: 10.1016/j.jaip.2023.12.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Asthma is a clinically heterogeneous disease, and despite substantial improvements in therapies, there remains an unmet need for well-tolerated, effective treatments. Observational studies have demonstrated that alterations in the respiratory and gut microbiome are associated with the development of asthma and its severity. These findings are supported by preclinical models demonstrating that respiratory and gut microbes can alter airway inflammation. Therapeutic approaches to target the human microbiome have been increasingly applied to a wide range of acute and chronic diseases, but there are currently no microbiome-based therapeutics approved for the treatment of asthma. This clinical commentary addresses the future role of microbiome-based therapeutics in asthma management from both a pro and con perspective. We examine (1) the prospects for clinical studies demonstrating a causal relationship between the human microbiome and the severity of asthma; (2) the challenges and potential solutions for designing, testing, and implementing a microbiome-based therapeutic; and (3) the possibility of microbiome-based therapeutics for conditions comorbid to asthma. We conclude by identifying research priorities that will help determine the future of microbiome-based therapeutics for the management of asthma.
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Affiliation(s)
- Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine, and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Mo.
| | - Anne L Rosen
- Division of Allergy and Immunology, Department of Medicine, and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Mo
| | - Christian Rosas-Salazar
- Division of Allergy, Immunology, and Pulmonary Medicine, Vanderbilt University Medical Center, Nashville, Tenn.
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Gavillet H, Hatfield L, Jones A, Maitra A, Horsley A, Rivett D, van der Gast C. Ecological patterns and processes of temporal turnover within lung infection microbiota. MICROBIOME 2024; 12:63. [PMID: 38523273 PMCID: PMC10962200 DOI: 10.1186/s40168-024-01780-6] [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: 07/10/2023] [Accepted: 02/22/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical 'one microbe, one disease' concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota. RESULTS The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend's rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function. CONCLUSIONS Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases. Video Abstract.
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Affiliation(s)
- Helen Gavillet
- Department of Applied Sciences, Northumbria University, Newcastle, UK
| | - Lauren Hatfield
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Andrew Jones
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anirban Maitra
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Alexander Horsley
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Damian Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.
| | - Christopher van der Gast
- Department of Applied Sciences, Northumbria University, Newcastle, UK.
- Department of Respiratory Medicine, Northern Care Alliance NHS Foundation Trust, Salford, UK.
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8
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024:S0966-842X(24)00057-X. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [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: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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9
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Zheng L, Liu C, Wang H, Zhang J, Mao L, Dong X, Hu S, Li N, Pi D, Qiu J, Xu F, Chen C, Zou Z. Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury. MICROBIOME 2024; 12:56. [PMID: 38494479 PMCID: PMC10946114 DOI: 10.1186/s40168-024-01772-6] [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: 06/07/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Accumulating clinical evidence suggests that lung microbiome is closely linked to the progression of pulmonary diseases; however, it is still controversial which specimen type is preferred for the evaluation of lung microbiome. METHODS AND RESULTS To address this issue, we established a classical acute lung injury (ALI) mice model by intratracheal instillation of lipopolysaccharides (LPS). We found that the bacterial DNA obtained from the bronchoalveolar lavage fluid (BALF), intact lung tissue [Lung(i)], lung tissue after perfused [Lung(p)], and feces of one mouse were enough for 16S rRNA sequencing, except the BALF of mice treated with phosphate buffer saline (PBS), which might be due to the biomass of lung microbiome in the BALF were upregulated in the mice treated with LPS. Although the alpha diversity among the three specimens from lungs had minimal differences, Lung(p) had higher sample-to-sample variation compared with BALF and Lung(i). Consistently, PCoA analysis at phylum level indicated that BALF was similar to Lung(i), but not Lung(p), in the lungs of mice treated with LPS, suggesting that BALF and Lung(i) were suitable for the evaluation of lung microbiome in ALI. Importantly, Actinobacteria and Firmicutes were identified as the mostly changed phyla in the lungs and might be important factors involved in the gut-lung axis in ALI mice. Moreover, Actinobacteria and Proteobacteria might play indicative roles in the severity of lung injury. CONCLUSION This study shows both Lung(i) and BALF are suitable for the evaluation of murine lung microbiome in ALI, and several bacterial phyla, such as Actinobacteria, may serve as potential biomarkers for the severity of ALI. Video Abstract.
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Affiliation(s)
- Lijun Zheng
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Chengjun Liu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Hongjing Wang
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jun Zhang
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Lejiao Mao
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xiaomei Dong
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Siyao Hu
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Na Li
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Dandan Pi
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Jingfu Qiu
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Feng Xu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Chengzhi Chen
- Department of Occupational and Environmental Health, School of Public Health, Chongqing Medical University, Chongqing, 400016, People's Republic of China
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
- Research Center for Environment and Human Health, School of Public Health, Chongqing, 400016, People's Republic of China.
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10
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Lee SH, Lee JH, Lee SW. Application of Microbiome-Based Therapies in Chronic Respiratory Diseases. J Microbiol 2024; 62:201-216. [PMID: 38635003 DOI: 10.1007/s12275-024-00124-1] [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: 12/14/2023] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.
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Affiliation(s)
- Se Hee Lee
- Department of Pulmonology, Allergy and Critical Care Medicine, CHA Bundang Medical Center, CHA University, Seongnam, 13496, Republic of Korea
| | - Jang Ho Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Sei Won Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.
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11
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O’Farrell HE, Kok HC, Goel S, Chang AB, Yerkovich ST. Endotypes of Paediatric Cough-Do They Exist and Finding New Techniques to Improve Clinical Outcomes. J Clin Med 2024; 13:756. [PMID: 38337450 PMCID: PMC10856076 DOI: 10.3390/jcm13030756] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Chronic cough is a common symptom of many childhood lung conditions. Given the phenotypic heterogeneity of chronic cough, better characterization through endotyping is required to provide diagnostic certainty, precision therapies and to identify pathobiological mechanisms. This review summarizes recent endotype discoveries in airway diseases, particularly in relation to children, and describes the multi-omic approaches that are required to define endotypes. Potential biospecimens that may contribute to endotype and biomarker discoveries are also discussed. Identifying endotypes of chronic cough can likely provide personalized medicine and contribute to improved clinical outcomes for children.
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Affiliation(s)
- Hannah E. O’Farrell
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Hing Cheong Kok
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Department of Paediatrics, Sabah Women and Children’s Hospital, Kota Kinabalu 88996, Sabah, Malaysia
| | - Suhani Goel
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Anne B. Chang
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Department of Respiratory and Sleep Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
| | - Stephanie T. Yerkovich
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
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12
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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13
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van Beveren GJ, Said H, van Houten MA, Bogaert D. The respiratory microbiome in childhood asthma. J Allergy Clin Immunol 2023; 152:1352-1367. [PMID: 37838221 DOI: 10.1016/j.jaci.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
Asthma is the most prevalent noncommunicable disease in childhood, characterized by reversible airway constriction and inflammation of the lower airways. The respiratory tract consists of the upper and lower airways, which are lined with a diverse community of microbes. The composition and density of the respiratory microbiome differs across the respiratory tract, with microbes adapting to the gradually changing physiology of the environment. Over the past decade, both the upper and lower respiratory microbiomes have been implicated in the etiology and disease course of asthma, as well as in its severity and phenotype. We have reviewed the literature on the role of the respiratory microbiome in asthma, making a careful distinction between the relationship of the microbiome with development of childhood asthma and its relationship with the disease course, while accounting for age and the microbial niches studied. Furthermore, we have assessed the literature regarding the underlying asthma endotypes and the impact of the microbiome on the host immune response. We have identified distinct microbial signatures across the respiratory tract associated with asthma development, stability, and severity. These data suggest that the respiratory microbiome may be important for asthma development and severity and may therefore be a potential target for future microbiome-based preventive and treatment strategies.
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Affiliation(s)
- Gina J van Beveren
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, Hoofddorp, The Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hager Said
- Department of Pediatrics, Spaarne Gasthuis Haarlem
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, Hoofddorp, The Netherlands; Department of Pediatrics, Spaarne Gasthuis Haarlem
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands; Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
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14
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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.
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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
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15
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Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med 2023; 29:2793-2804. [PMID: 37957375 DOI: 10.1038/s41591-023-02617-9] [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: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 11/15/2023]
Abstract
Respiratory microbial dysbiosis is associated with acute respiratory distress syndrome (ARDS) and hospital-acquired pneumonia (HAP) in critically ill patients. However, we lack reproducible respiratory microbiome signatures that can increase our understanding of these conditions and potential treatments. Here, we analyze 16S rRNA sequencing data from 2,177 respiratory samples collected from 1,029 critically ill patients (21.7% with ARDS and 26.3% with HAP) and 327 healthy controls, sourced from 17 published studies. After data harmonization and pooling of individual patient data, we identified microbiota signatures associated with ARDS, HAP and prolonged mechanical ventilation. Microbiota signatures for HAP and prolonged mechanical ventilation were characterized by depletion of a core group of microbes typical of healthy respiratory samples, and the ARDS microbiota signature was distinguished by enrichment of potentially pathogenic respiratory microbes, including Pseudomonas and Staphylococcus. Using machine learning models, we identified clinically informative, three- and four-factor signatures that predicted ARDS, HAP and prolonged mechanical ventilation with relatively high accuracy (area under the curve of 0.751, 0.72 and 0.727, respectively). We validated the signatures in an independent prospective cohort of 136 patients on mechanical ventillation and found that patients with microbiome signatures associated with ARDS, HAP or prolonged mechanical ventilation had longer times to successful extubation than patients lacking these signatures (hazard ratios of 1.56 (95% confidence interval (CI) 1.07-2.27), 1.51 (95% CI 1.02-2.23) and 1.50 (95% CI 1.03-2.18), respectively). Thus, we defined and validated robust respiratory microbiome signatures associated with ARDS and HAP that may help to identify promising targets for microbiome therapeutic modulation in critically ill patients.
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Affiliation(s)
- Emmanuel Montassier
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service des Urgences, Nantes Université, CHU Nantes, Nantes, France.
| | - 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
| | - Josiah E 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
| | | | - Brendan J Kelly
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariane Panzer
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Robert P Dickson
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - Antoine Roquilly
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service d'Anesthesie Réanimation, Nantes Université, CHU Nantes, Nantes, France.
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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16
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Cazzola M, Rogliani P, Blasi F. Can Treatable Traits Be the Approach to Addressing the Complexity and Heterogeneity of COPD? Int J Chron Obstruct Pulmon Dis 2023; 18:1959-1964. [PMID: 37705673 PMCID: PMC10497043 DOI: 10.2147/copd.s428391] [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: 06/30/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
The complexity of COPD implies the need to identify groups of patients with similar clinical characteristics and prognosis or treatment requirements. This is why much attention has been paid to identifying the different clinical phenotypes by investigating the clinical expression of the disease, and endotypes by studying the biological networks that enable and limit reactions. However, this approach is complicated because one endotype gives rise to one or more clinical characteristics, and clinical phenotypes can be derived from several endotypes. To simplify the approach, a new taxonomic classification of COPD based on the different causes (or etiotypes) has been proposed, but these etiotypes have not yet been validated. A simpler method is the so-called tractable traits approach, which is free from any designation of the disorder to be treated and does not present the criticality of using etiotypes. A large randomised controlled trial on using the treatable traits approach in COPD is still lacking. Nevertheless, this approach is already applied by following the GOLD strategy. However, its application is complicated because several potentially treatable traits have been identified within the pulmonary domain, the extrapulmonary domain, and the behavioural/risk factor domain. In addition, the hierarchy of the dominant treatable traits has not yet been established, and they change over time both spontaneously and because of treatment. This means that the patients being treated according to the tractable traits approach must be constantly followed over time so that the therapy is focused on their temporal needs.
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Affiliation(s)
- Mario Cazzola
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesco Blasi
- Pulmonology and Cystic Fibrosis Unit, Internal Medicine Department, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico of Milan, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
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17
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Lloyd CM, Saglani S. Early-life respiratory infections and developmental immunity determine lifelong lung health. Nat Immunol 2023; 24:1234-1243. [PMID: 37414905 DOI: 10.1038/s41590-023-01550-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Respiratory infections are common in infants and young children. However, the immune system develops and matures as the child grows, thus the effects of infection during this time of dynamic change may have long-term consequences. The infant immune system develops in conjunction with the seeding of the microbiome at the respiratory mucosal surface, at a time that the lungs themselves are maturing. We are now recognizing that any disturbance of this developmental trajectory can have implications for lifelong lung health. Here, we outline our current understanding of the molecular mechanisms underlying relationships between immune and structural cells in the lung with the local microorganisms. We highlight the importance of gaining greater clarity as to what constitutes a healthy respiratory ecosystem and how environmental exposures influencing this network will aid efforts to mitigate harmful effects and restore lung immune health.
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Affiliation(s)
- Clare M Lloyd
- National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
| | - Sejal Saglani
- National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
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Abdel-Aziz MI, Thorsen J, Hashimoto S, Vijverberg SJH, Neerincx AH, Brinkman P, van Aalderen W, Stokholm J, Rasmussen MA, Roggenbuck-Wedemeyer M, Vissing NH, Mortensen MS, Brejnrod AD, Fleming LJ, Murray CS, Fowler SJ, Frey U, Bush A, Singer F, Hedlin G, Nordlund B, Shaw DE, Chung KF, Adcock IM, Djukanovic R, Auffray C, Bansal AT, Sousa AR, Wagers SS, Chawes BL, Bønnelykke K, Sørensen SJ, Kraneveld AD, Sterk PJ, Roberts G, Bisgaard H, Maitland-van der Zee AH. Oropharyngeal Microbiota Clusters in Children with Asthma or Wheeze Associate with Allergy, Blood Transcriptomic Immune Pathways, and Exacerbation Risk. Am J Respir Crit Care Med 2023; 208:142-154. [PMID: 37163754 DOI: 10.1164/rccm.202211-2107oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
Rationale: Children with preschool wheezing or school-age asthma are reported to have airway microbial imbalances. Objectives: To identify clusters in children with asthma or wheezing using oropharyngeal microbiota profiles. Methods: Oropharyngeal swabs from the U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes) pediatric asthma or wheezing cohort were characterized using 16S ribosomal RNA gene sequencing, and unsupervised hierarchical clustering was performed on the Bray-Curtis β-diversity. Enrichment scores of the Molecular Signatures Database hallmark gene sets were computed from the blood transcriptome using gene set variation analysis. Children with severe asthma or severe wheezing were followed up for 12-18 months, with assessment of the frequency of exacerbations. Measurements and Main Results: Oropharyngeal samples from 241 children (age range, 1-17 years; 40% female) revealed four taxa-driven clusters dominated by Streptococcus, Veillonella, Rothia, and Haemophilus. The clusters showed significant differences in atopic dermatitis, grass pollen sensitization, FEV1% predicted after salbutamol, and annual asthma exacerbation frequency during follow-up. The Veillonella cluster was the most allergic and included the highest percentage of children with two or more exacerbations per year during follow-up. The oropharyngeal clusters were different in the enrichment scores of TGF-β (transforming growth factor-β) (highest in the Veillonella cluster) and Wnt/β-catenin signaling (highest in the Haemophilus cluster) transcriptomic pathways in blood (all q values <0.05). Conclusions: Analysis of the oropharyngeal microbiota of children with asthma or wheezing identified four clusters with distinct clinical characteristics (phenotypes) that associate with risk for exacerbation and transcriptomic pathways involved in airway remodeling. This suggests that further exploration of the oropharyngeal microbiota may lead to novel pathophysiologic insights and potentially new treatment approaches.
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Affiliation(s)
- Mahmoud I Abdel-Aziz
- Department of Pulmonary Medicine and
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
- Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, and
| | - Simone Hashimoto
- Department of Pulmonary Medicine and
- Department of Paediatric Pulmonary Medicine, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Susanne J H Vijverberg
- Department of Pulmonary Medicine and
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Anne H Neerincx
- Department of Pulmonary Medicine and
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Paul Brinkman
- Department of Pulmonary Medicine and
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
| | - Wim van Aalderen
- Department of Paediatric Pulmonary Medicine, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Morten Arendt Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Michael Roggenbuck-Wedemeyer
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novozymes, Bagsvaerd, Denmark
| | - Nadja H Vissing
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
| | - Martin Steen Mortensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Asker Daniel Brejnrod
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Louise J Fleming
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Clare S Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Academic Health Science Centre and National Institute for Health and Care Research Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Manchester Academic Health Science Centre and National Institute for Health and Care Research Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Urs Frey
- University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Florian Singer
- Division of Paediatric Pulmonology and Allergology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
- Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Björn Nordlund
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Dominick E Shaw
- National Institute for Health and Care Research Respiratory Biomedical Research Unit, University of Nottingham, Nottingham, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ratko Djukanovic
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences and Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Lyon, France
| | - Aruna T Bansal
- Acclarogen Ltd., St. John's Innovation Centre, Cambridge, United Kingdom
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | | | - Bo Lund Chawes
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, and
| | - Klaus Bønnelykke
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, and
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Peter J Sterk
- Department of Pulmonary Medicine and
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Graham Roberts
- National Institute for Health and Care Research Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences and Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital
| | - Anke H Maitland-van der Zee
- Department of Pulmonary Medicine and
- Department of Paediatric Pulmonary Medicine, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam, the Netherlands
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Bustos IG, Martín-Loeches I, Acosta-González A, Chotirmall SH, Dickson RP, Reyes LF. Exploring the complex relationship between the lung microbiome and ventilator-associated pneumonia. Expert Rev Respir Med 2023; 17:889-901. [PMID: 37872770 DOI: 10.1080/17476348.2023.2273424] [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: 06/14/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
INTRODUCTION Understanding the presence and function of a diverse lung microbiome in acute lung infections, particularly ventilator-associated pneumonia (VAP), is still limited, evidencing significant gaps in our knowledge. AREAS COVERED In this comprehensive narrative review, we aim to elucidate the contribution of the respiratory microbiome in the development of VAP by examining the current knowledge on the interactions among microorganisms. By exploring these intricate connections, we endeavor to enhance our understanding of the disease's pathophysiology and pave the way for novel ideas and interventions in studying the respiratory tract microbiome. EXPERT OPINION The conventional perception of lungs as sterile is deprecated since it is currently recognized the existence of a diverse microbial community within them. However, despite extensive research on the role of the respiratory microbiome in healthy lungs, respiratory chronic diseases and acute lung infections such as pneumonia are not fully understood. It is crucial to investigate further the relationship between the pathophysiology of VAP and the pulmonary microbiome, elucidating the mechanisms underlying the interactions between the microbiome, host immune response and mechanical ventilation for the development of VAP.
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Affiliation(s)
- Ingrid G Bustos
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Doctorado de Biociencias, Department of Engineering, Universidad de la Sabana, Chia, Colombia
| | - Ignacio Martín-Loeches
- Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Dublin, Ireland
| | - Alejandro Acosta-González
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Bioprospection Research Group (GIBP), Department of Engineering, Universidad de La Sabana, Chia, Colombia
| | - 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
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Critical Care Department, Clinica Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
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20
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Mesfin N, Sangani R, Shankar DA, Reardon C. New Frontiers in Therapeutics for Interstitial Lung Diseases. Am J Respir Crit Care Med 2023; 207:1089-1091. [PMID: 36735934 PMCID: PMC10112432 DOI: 10.1164/rccm.202206-1035rr] [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: 06/02/2022] [Accepted: 02/03/2023] [Indexed: 02/05/2023] Open
Affiliation(s)
- Nathan Mesfin
- The Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Ruchika Sangani
- The Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Divya A Shankar
- The Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Christine Reardon
- The Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
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Abstract
The human microbiome is vast and is present in spaces previously thought to be sterile such as the lungs. A healthy microbiome is diverse and functions in an adaptive way to support local as well as organism health and function. Furthermore, a normal microbiome is essential for normal immune system development rendering the array of microbes that live in and on the human body key components of homeostasis. A wide array of clinical conditions and interventions including anesthesia, analgesia, and surgical intervention may derange the human microbiome in a maladaptive fashion with bacterial responses spanning decreased diversity to transformation to a pathogenic phenotype. Herein, we explore the normal microbiome of the skin, gastrointestinal tract, and the lungs as prototype sites to describe the influence of the microbiomes in each of those locations on health, and how care may derange those relations.
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22
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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.
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Abdelgawad A, Nicola T, Martin I, Halloran BA, Tanaka K, Adegboye CY, Jain P, Ren C, Lal CV, Ambalavanan N, O'Connell AE, Jilling T, Willis KA. Antimicrobial peptides modulate lung injury by altering the intestinal microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.529700. [PMID: 36993189 PMCID: PMC10054967 DOI: 10.1101/2023.03.14.529700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mammalian mucosal barriers secrete antimicrobial peptides (AMPs) as critical host-derived regulators of the microbiota. However, mechanisms that support homeostasis of the microbiota in response to inflammatory stimuli such as supraphysiologic oxygen remain unclear. Here, we show that neonatal mice breathing supraphysiologic oxygen or direct exposure of intestinal organoids to supraphysiologic oxygen suppress the intestinal expression of AMPs and alters the composition of the intestinal microbiota. Oral supplementation of the prototypical AMP lysozyme to hyperoxia exposed neonatal mice reduced hyperoxia-induced alterations in their microbiota and was associated with decreased lung injury. Our results identify a gut-lung axis driven by intestinal AMP expression and mediated by the intestinal microbiota that is linked to lung injury. Together, these data support that intestinal AMPs modulate lung injury and repair. In Brief Using a combination of murine models and organoids, Abdelgawad and Nicola et al. find that suppression of antimicrobial peptide release by the neonatal intestine in response to supra-physiological oxygen influences the progression of lung injury likely via modulation of the ileal microbiota. Highlights Supraphysiologic oxygen exposure alters intestinal antimicrobial peptides (AMPs).Intestinal AMP expression has an inverse relationship with the severity of lung injury.AMP-driven alterations in the intestinal microbiota form a gut-lung axis that modulates lung injury.AMPs may mediate a gut-lung axis that modulates lung injury.
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Tiew PY, Meldrum OW, Chotirmall SH. Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2023; 24:ijms24032955. [PMID: 36769278 PMCID: PMC9918109 DOI: 10.3390/ijms24032955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 169608, Singapore
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Oliver W. Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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Vieceli T, Tejada S, Martinez-Reviejo R, Pumarola T, Schrenzel J, Waterer GW, Rello J. Impact of air pollution on respiratory microbiome: A narrative review. Intensive Crit Care Nurs 2022. [DOI: 10.1016/j.iccn.2022.103336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [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] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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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.
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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.
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