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He S, Zhuo Y, Cui L, Zhang S, Tu Z, Wang M, Lv X, Ge L, Lin J, Yang L, Wang X. Naringin dihydrochalcone alleviates sepsis-induced acute lung injury via improving gut microbial homeostasis and activating GPR18 receptor. Int Immunopharmacol 2024; 137:112418. [PMID: 38901244 DOI: 10.1016/j.intimp.2024.112418] [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: 03/22/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
Acute lung injury (ALI) is a life-threatening disease characterized by severe lung inflammation and intestinal microbiota disorder. The GPR18 receptor has been demonstrated to be a potential therapeutic target against ALI. Extracting Naringin dihydrochalcone (NDC) from the life-sustaining orange peel is known for its diverse anti-inflammatory properties, yet the specific action target remains uncertain. In the present study, we identified NDC as a potential agonist of the GPR18 receptor using virtual screening and investigated the pharmacological effects of NDC on sepsis-induced acute lung injury in rats and explored underlying mechanisms. In in vivo experiments, CLP-induced ALI model was established by cecum puncture and treated with NDC gavage one hour prior to drug administration, lung histopathology and inflammatory cytokines were evaluated, and feces were subjected to 16s rRNA sequencing and untargeted metabolomics analysis. In in vitro experiments, the anti-inflammatory properties were exerted by evaluating NDC targeting the GPR18 receptor to inhibit lipopolysaccharide (LPS)-induced secretion of TNF-α, IL-6, IL-1β and activation of inflammatory signaling pathways in MH-S cells. Our findings showed that NDC significantly ameliorated lung damage and pro-inflammatory cytokine levels (TNF-α, IL-6, IL-1β) in both cells and lung tissues via inhibiting the activation of STAT3, NF-κB, and NLRP3 inflammatory signaling pathways through GRP18 receptor activation. In addition, NDC can also partly reverse the imbalance of gut microbiota composition caused by CLP via increasing the proportion of Firmicutes/Bacteroidetes and Lactobacillus and decreasing the relative abundance of Proteobacteria. Meanwhile, the fecal metabolites in the NDC treatment group also significantly were changed, including decreased secretion of Phenylalanin, Glycine, and bile secretion, and increased secretion of Lysine. In conclusion, these findings suggest that NDC can alleviate sepsis-induced ALI via improving gut microbial homeostasis and metabolism and mitigate inflammation via activating GPR18 receptor. In conclusion, the results indicate that NDC, derived from the typical orange peel of food, could significantly contribute to development by enhancing intestinal microbial balance and metabolic processes, and reducing inflammation by activating the GPR18 receptor, thus mitigating sepsis-induced ALI and expanding the range of functional foods.
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Affiliation(s)
- Siqi He
- Graduate School, Tianjin Medical University, Tianjin 300270, China
| | - Yuzhen Zhuo
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin NanKai Hospital Tianjin Medical University, Tianjin 300100, China
| | - Lingzhi Cui
- Graduate School, Tianjin Medical University, Tianjin 300270, China
| | - Sijia Zhang
- Graduate School, Tianjin Medical University, Tianjin 300270, China
| | - Zhengwei Tu
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin NanKai Hospital Tianjin Medical University, Tianjin 300100, China
| | - Mukuo Wang
- College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Xinyue Lv
- College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Lixiu Ge
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin NanKai Hospital Tianjin Medical University, Tianjin 300100, China
| | - Jianping Lin
- College of Pharmacy, Nankai University, Tianjin 300071, China.
| | - Lei Yang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin NanKai Hospital Tianjin Medical University, Tianjin 300100, China.
| | - Ximo Wang
- Graduate School, Tianjin Medical University, Tianjin 300270, China; Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Artificial Cell Engineering Technology Research Center, Tianjin Institute of Hepatobiliary Disease, Tianjin Medical University Third Center Clinical College, Tianjin 300170, China.
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2
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Long MB, Chotirmall SH, Shteinberg M, Chalmers JD. Rethinking bronchiectasis as an inflammatory disease. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00176-0. [PMID: 38971168 DOI: 10.1016/s2213-2600(24)00176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 07/08/2024]
Abstract
Bronchiectasis is understood to be the result of a complex interaction between infection, impaired mucociliary clearance, inflammation, and lung damage. Current therapeutic approaches to bronchiectasis are heavily focused on management of infection along with enhancing mucus clearance. Long-term antibiotics have had limited success in clinical trials, suggesting a need to re-evaluate the concept of bronchiectasis as an infective disorder. We invoke the example of asthma, for which treatment paradigms shifted away from targeting smooth muscle constriction, towards permanently suppressing airway inflammation, reducing risk and ultimately inducing remission with precision anti-inflammatory treatments. In this Review, we argue that bronchiectasis is primarily a chronic inflammatory disease, requiring early identification of at-risk individuals, and we introduce a novel concept of disease activity with important implications for clinical practice and future research. A new generation of novel anti-inflammatory treatments are under development and repurposing of anti-inflammatory agents from other diseases could revolutionise patient care.
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Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel; The Technion, Israel Institute of Technology, The B Rappaport Faculty of Medicine, Haifa, Israel
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK.
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3
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De Angelis A, Johnson ED, Sutharsan S, Aliberti S. Exacerbations of bronchiectasis. Eur Respir Rev 2024; 33:240085. [PMID: 39048130 PMCID: PMC11267293 DOI: 10.1183/16000617.0085-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Bronchiectasis presents a significant challenge due to its rising prevalence, associated economic burden and clinical heterogeneity. This review synthesises contemporary understanding and literature of bronchiectasis exacerbations, addressing the transition from stable state to exacerbations, underlining the importance of early and precise recognition, rigorous severity assessment, prompt treatment, and prevention measures, as well as emphasising the need for strategies to assess and improve early and long-term patient outcomes. The review highlights the interplay between stable state phases and exacerbations in bronchiectasis, introducing the concept of "exogenous and endogenous changes in airways homeostasis" and the "adapted island model" with a particular focus on "frequent exacerbators", a group of patients associated with specific clinical characteristics and worse outcomes. The pathophysiology of exacerbations is explored through the lens of microbial and nonmicrobial triggers and the presence and the activity of comorbidities, elaborating on the impact of both exogenous insults, such as infections and pollution, and endogenous factors such as inflammatory endotypes. Finally, the review proposes a multidisciplinary approach to care, integrating advancements in precision medicine and biomarker research, paving the way for tailored treatments that challenge the traditional antibiotic paradigm.
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Affiliation(s)
- Alessandro De Angelis
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy
| | - Emma D Johnson
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Sivagurunathan Sutharsan
- Division of Cystic Fibrosis, Department of Pulmonary Medicine, University Medicine Essen -Ruhrlandklinik, University of Duisburg-Essen, Essen, Germany
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy
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4
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Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 PMCID: PMC11220622 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
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Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
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5
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Mac Aogáin M, Xaverius Ivan F, Jaggi TK, Richardson H, Shoemark A, Narayana JK, Dicker AJ, Koh MS, Lee KCH, Thun How O, Poh ME, Chin KK, Hou ALY, Ser Hon P, Low TB, Abisheganaden JA, Dimakou K, Digalaki A, Kosti C, Gkousiou A, Hansbro PM, Blasi F, Aliberti S, Chalmers JD, Chotirmall SH. Airway "Resistotypes" and Clinical Outcomes in Bronchiectasis. Am J Respir Crit Care Med 2024; 210:47-62. [PMID: 38271608 PMCID: PMC11197066 DOI: 10.1164/rccm.202306-1059oc] [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: 06/19/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Rationale: Chronic infection and inflammation shapes the airway microbiome in bronchiectasis. Utilizing whole-genome shotgun metagenomics to analyze the airway resistome provides insight into interplay between microbes, resistance genes, and clinical outcomes. Objectives: To apply whole-genome shotgun metagenomics to the airway microbiome in bronchiectasis to highlight a diverse pool of antimicrobial resistance genes: the "resistome," the clinical significance of which remains unclear. Methods: Individuals with bronchiectasis were prospectively recruited into cross-sectional and longitudinal cohorts (n = 280), including the international multicenter cross-sectional Cohort of Asian and Matched European Bronchiectasis 2 (CAMEB 2) study (n = 251) and two independent cohorts, one describing patients experiencing acute exacerbation and a further cohort of patients undergoing Pseudomonas aeruginosa eradication treatment. Sputum was subjected to metagenomic sequencing, and the bronchiectasis resistome was evaluated in association with clinical outcomes and underlying host microbiomes. Measurements and Main Results: The bronchiectasis resistome features a unique resistance gene profile and increased counts of aminoglycoside, bicyclomycin, phenicol, triclosan, and multidrug resistance genes. Longitudinally, it exhibits within-patient stability over time and during exacerbations despite between-patient heterogeneity. Proportional differences in baseline resistome profiles, including increased macrolide and multidrug resistance genes, associate with shorter intervals to the next exacerbation, whereas distinct resistome archetypes associate with frequent exacerbations, poorer lung function, geographic origin, and the host microbiome. Unsupervised analysis of resistome profiles identified two clinically relevant "resistotypes," RT1 and RT2, the latter characterized by poor clinical outcomes, increased multidrug resistance, and P. aeruginosa. Successful targeted eradication in P. aeruginosa-colonized individuals mediated reversion from RT2 to RT1, a more clinically favorable resistome profile demonstrating reduced resistance gene diversity. Conclusions: The bronchiectasis resistome associates with clinical outcomes, geographic origin, and the underlying host microbiome. Bronchiectasis resistotypes link to clinical disease and are modifiable through targeted antimicrobial therapy.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Hollian Richardson
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Amelia Shoemark
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | | | - Alison J. Dicker
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Ken Cheah Hooi Lee
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Ong Thun How
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Mau Ern Poh
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Ka Kiat Chin
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Albert Lim Yick Hou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Puah Ser Hon
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Teck Boon Low
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | - John Arputhan Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Katerina Dimakou
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Antonia Digalaki
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Chrysavgi Kosti
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Anna Gkousiou
- 5th Respiratory Medicine Department, General Hospital for Chest Diseases of Athens “Sotiria”, Athens, Greece
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Francesco Blasi
- Respiratory Unit and Cystic Fibrosis Center, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; and
- IRCCS Humanitas Research Hospital, Respiratory Unit, Rozzano, Milan, Italy
| | - James D. Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - 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
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6
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Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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7
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Chotirmall SH, Chalmers JD. The Precision Medicine Era of Bronchiectasis. Am J Respir Crit Care Med 2024; 210:24-34. [PMID: 38949497 PMCID: PMC11197062 DOI: 10.1164/rccm.202403-0473pp] [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: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 07/02/2024] Open
Affiliation(s)
- 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; and
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
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8
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Shteinberg M, Chalmers JD, Narayana JK, Dicker AJ, Rahat MA, Simanovitch E, Bidgood L, Cohen S, Stein N, Abo-Hilu N, Abbott J, Avital S, Fireman-Klein E, Richardson H, Muhammad E, Jrbashyan J, Schneer S, Nasrallah N, Eisenberg I, Chotirmall SH, Adir Y. Bronchiectasis with Chronic Rhinosinusitis Is Associated with Eosinophilic Airway Inflammation and Is Distinct from Asthma. Ann Am Thorac Soc 2024; 21:748-758. [PMID: 38194593 DOI: 10.1513/annalsats.202306-551oc] [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: 06/20/2023] [Accepted: 01/09/2024] [Indexed: 01/11/2024] Open
Abstract
Rationale: Bronchiectasis is an airway inflammatory disease that is frequently associated with chronic rhinosinusitis (CRS). An eosinophilic endotype of bronchiectasis has recently been described, but detailed testing to differentiate eosinophilic bronchiectasis from asthma has not been performed. Objectives: This prospective observational study aimed to test the hypotheses that bronchiectasis with CRS is enriched for the eosinophilic phenotype in comparison with bronchiectasis alone and that the eosinophilic bronchiectasis phenotype exists as a separate entity from bronchiectasis associated with asthma. Methods: People with idiopathic or postinfectious bronchiectasis were assessed for concomitant CRS. We excluded people with asthma or primary ciliary dyskinesia and smokers. We assessed sputum and blood cell counts, nasal NO and fractional excreted NO, methacholine reactivity, skin allergy testing and total and specific immunoglobulin (Ig) E, cytokines in the sputum and serum, and the microbiome in the sputum and nasopharynx. Results: A total of 22 people with CRS (BE + CRS) and 17 without CRS (BE - CRS) were included. Sex, age, Reiff score, and bronchiectasis severity were similar. Median sputum eosinophil percentages were 0% (IQR, 0-1.5%) in BE - CRS and 3% (1-12%) in BE + CRS (P = 0.012). Blood eosinophil counts were predictive of sputum eosinophilia (counts ⩾3%; area under the receiver operating characteristic curve, 0.68; 95% confidence interval, 0.50-0.85). Inclusion of CRS improved the prediction of sputum eosinophilia by blood eosinophil counts (area under the receiver operating characteristic curve, 0.79; 95% confidence interval, 0.65-0.94). Methacholine tests were negative in 85.7% of patients in the BE - CRS group and 85.2% of patients in the BE + CRS group (P > 0.99). Specific IgE and skin testing were similar between the groups, but total IgE levels were increased in people with increased sputum eosinophils. Microbiome analysis demonstrated distinct microbiota in nasopharyngeal and airway samples in the BE + CRS and BE - CRS groups, without significant differences between groups. However, interactome analysis revealed altered interactomes in individuals with high sputum eosinophil counts and CRS. Conclusions: Bronchiectasis with CRS is associated with an eosinophilic airway inflammation that is distinct from asthma.
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Affiliation(s)
- Michal Shteinberg
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Jayanth K Narayana
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
| | - Alison J Dicker
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Michal A Rahat
- Immunotherapy Laboratory
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | | | - Lucy Bidgood
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Shai Cohen
- Allergy and Immunology Unit
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - Nili Stein
- Community Medicine and Epidemiology Department
| | | | - James Abbott
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | | | - Einat Fireman-Klein
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | | | | | - Sonia Schneer
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | | | - Iya Eisenberg
- Radiology Department, Carmel Medical Center, Haifa, Israel
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Yochai Adir
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
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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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Rosenboom I, Thavarasa A, Richardson H, Long MB, Wiehlmann L, Davenport CF, Shoemark A, Chalmers JD, Tümmler B. Sputum metagenomics of people with bronchiectasis. ERJ Open Res 2024; 10:01008-2023. [PMID: 38444657 PMCID: PMC10910388 DOI: 10.1183/23120541.01008-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/07/2024] Open
Abstract
Background The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease. Methods The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing. Results Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci. Conclusion The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.
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Affiliation(s)
- Ilona Rosenboom
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ajith Thavarasa
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Merete B. Long
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | | | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Burkhard Tümmler
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Centre for Lung Research, Hannover, Germany
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11
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Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN, Chotirmall SH. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024; 18:111-125. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.
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Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ. Christensenella minuta interacts with multiple gut bacteria. Front Microbiol 2024; 15:1301073. [PMID: 38440147 PMCID: PMC10910051 DOI: 10.3389/fmicb.2024.1301073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.
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Affiliation(s)
- Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Li-Juan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Lin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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13
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van der Bie S, Haaksma ME, Vermin B, van Assema H, van Gorp ECM, Langerak T, Endeman H, Snijders D, van den Akker JPC, van Houten MA, van Lelyveld SFL, Goeijenbier M. A Systematic Review of the Pulmonary Microbiome in Patients with Acute Exacerbation COPD Requiring ICU Admission. J Clin Med 2024; 13:472. [PMID: 38256606 PMCID: PMC10816170 DOI: 10.3390/jcm13020472] [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: 11/30/2023] [Revised: 01/03/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a major health concern. Acute exacerbations (AECOPD) may require intensive care unit (ICU) admission and mechanical ventilation. Acute infections and chronic colonization of the respiratory system are known to precipitate AECOPD. Detailed knowledge of the respiratory microbiome could lead to effective treatment and prevention of exacerbations. Objective: The aim of this review is to summarize the available evidence on the respiratory microbiome of patients with a severe AECOPD requiring mechanical ventilation and intensive care admission. Methods: A systematic literature search was conducted to identify the published papers until January 2023. The collected data were then subjected to qualitative analysis. After the first analysis, a secondary focused review of the most recent publications studying the relationship between microbiome and mortality in AECOPD was performed. Results: Out of 120 screened articles six articles were included in this review. Potentially pathogenic microorganisms (PPMs) were identified in 30% to 72% of the patients with community-acquired bacteria, gram-negative enteric bacilli, Stenotrophomonas and Pseudomonas being the most frequently isolated. During hospitalization, 21% of patients experienced colonization by PPMs. Adequate antimicrobial therapy resulted in the eradication of 77% of the identified PPMs. However, 24% of the bacteria displayed multi-drug resistance leading to prolonged or failure of eradication. Conclusion: PPMs are prevalent in a significant proportion of patients experiencing an AECOPD. The most identified PPMs include community-acquired pathogens and gram-negative enteric bacilli. Notably, no differences in mortality or duration of ventilation were observed between patients with and without isolated PPMs. However, the included studies did not investigate the virome of the patients, which may influence the microbiome and the outcome of infection. Therefore, further research is essential to comprehensively investigate the complete microbial and viral composition of the lower respiratory system in COPD patients admitted to the ICU.
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Affiliation(s)
- Sjoerd van der Bie
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Mark E. Haaksma
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Ben Vermin
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Hidde van Assema
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Eric C. M. van Gorp
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Thomas Langerak
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Henrik Endeman
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
| | - Dominic Snijders
- Department of Pulmonology, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marlies A. van Houten
- Department of Pediatric Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marco Goeijenbier
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
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14
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McDaneld TG, Eicher SD, Dickey A, Kritchevsky JE, Bryan KA, Chitko-McKown CG. Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves. Front Microbiol 2024; 14:1298570. [PMID: 38249465 PMCID: PMC10797021 DOI: 10.3389/fmicb.2023.1298570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Probiotics have been investigated for their many health benefits and impact on the microbiota of the gut. Recent data have also supported a gut-lung axis regarding the bacterial populations (microbiomes) of the two locations; however, little research has been performed to determine the effects of oral probiotics on the microbiome of the bovine respiratory tract. We hypothesized that probiotic treatment would result in changes in the lung microbiome as measured in lung lavage fluid. Our overall goal was to characterize bacterial populations in the lungs of calves fed probiotics in milk replacer and dry rations from birth to weaning. Methods A group of 20 dairy calves was split into two treatment groups: probiotic (TRT; N = 10, milk replacer +5 g/d probiotics; Bovamine Dairy, Chr. Hansen, Inc., Milwaukee, WI) and control (CON; N = 10, milk replacer only). On day 0, birth weight was obtained, and calves were provided colostrum as per the dairy SOP. On day 2, probiotics were added to the milk replacer of the treated group and then included in their dry ration. Lung lavages were performed on day 52 on five random calves selected from each treatment group. DNA was extracted from lavage fluid, and 16S ribosomal RNA (rRNA) gene hypervariable regions 1-3 were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for the identification of the bacterial taxa present. Taxa were classified into both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs). Results Overall, the evaluation of these samples revealed that the bacterial genera identified in the lung lavage samples of probiotic-fed calves as compared to the control calves were significantly different based on the OTU dataset (p < 0.05) and approached significance for the ASV dataset (p < 0.06). Additionally, when comparing the diversity of taxa in lung lavage samples to nasal and tonsil samples, taxa diversity of lung samples was significantly lower (p < 0.05). Discussion In conclusion, analysis of the respiratory microbiome in lung lavage samples after probiotic treatment provides insight into the distribution of bacterial populations in response to oral probiotics and demonstrates that oral probiotics affect more than the gut microbiome.
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Affiliation(s)
- Tara G. McDaneld
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Susan D. Eicher
- Livestock Behavior Research Unit, USDA, ARS, West Lafayette, IN, United States
| | - Aaron Dickey
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Janice E. Kritchevsky
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
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15
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Tian Y, Xu P, Wu X, Gong Z, Yang X, Zhu H, Zhang J, Hu Y, Li G, Sang N, Yue H. Lung injuries induced by ozone exposure in female mice: Potential roles of the gut and lung microbes. ENVIRONMENT INTERNATIONAL 2024; 183:108422. [PMID: 38217903 DOI: 10.1016/j.envint.2024.108422] [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: 09/21/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Ozone (O3) is one of the most harmful pollutants affecting health. However, the potential effects of O3 exposure on microbes in the gut-lung axis related to lung injuries remain elusive. In this study, female mice were exposed to 0-, 0.5- and 1-ppm O3 for 28 days, followed by routine blood tests, lung function tests and histopathological examination of the colon, nasal cavity and lung. Mouse faeces and lungs were collected for 16s rRNA sequencing to assess the overall microbiological profile and screen for key differential enriched microbes (DEMs). The key DEMs in faecal samples were Butyricimonas, Rikenellaceae RC9 and Escherichia-Shigella, whereas those in lung samples were DNF00809, Fluviicola, Bryobacter, Family XII AD3011 group, Sharpea, MND1 and unclassified Phycisphaeraceae. After a search in microbe-disease databases, these key DEMs were found to be associated with lung diseases such as lung neoplasms, cystic fibrosis, pneumonia, chronic obstructive pulmonary disease, respiratory distress syndrome and bronchiectasis. Subsequently, we used transcriptomic data from Gene Expression Omnibus (GEO) with exposure conditions similar to those in this study to cross-reference with Comparative Toxicogenomic Database (CTD). Il-6 and Ccl2 were identified as the key causative genes and were validated. The findings of this study suggest that exposure to O3 leads to significant changes in the microbial composition of the gut and lungs. These changes are associated with increased levels of inflammatory factors in the lungs and impaired lung function, resulting in an increased risk of lung disease. Altogether, this study provides novel insights into the role of microbes present in the gut-lung axis in O3 exposure-induced lung injury.
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Affiliation(s)
- Yuchai Tian
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Pengchong Xu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Xiaoyun Wu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Zhihua Gong
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China; Department of Clinical Laboratory, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tong ji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi 030032, PR China; Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xiaowen Yang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Huizhen Zhu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Jiyue Zhang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Yangcheng Hu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Huifeng Yue
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
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16
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Zhang C, Li G, Lu T, Liu L, Sui Y, Bai R, Li L, Sun B. The Interaction of Microbiome and Pancreas in Acute Pancreatitis. Biomolecules 2023; 14:59. [PMID: 38254659 PMCID: PMC10813032 DOI: 10.3390/biom14010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Acute pancreatitis (AP) is a common acute abdomen disease characterized by the pathological activation of digestive enzymes and the self-digestion of pancreatic acinar cells. Secondary infection and sepsis are independent prognosticators for AP progression and increased mortality. Accumulating anatomical and epidemiological evidence suggests that the dysbiosis of gut microbiota affects the etiology and severity of AP through intestinal barrier disruption, local or systemic inflammatory response, bacterial translocation, and the regulatory role of microbial metabolites in AP patients and animal models. Recent studies discussing the interactions between gut microbiota and the pancreas have opened new scopes for AP, and new therapeutic interventions that target the bacteria community have received substantial attention. This review concentrates on the alterations of gut microbiota and its roles in modulating gut-pancreas axis in AP. The potential therapies of targeting microbes as well as the major challenges of applying those interventions are explored. We expect to understand the roles of microbes in AP diagnosis and treatment.
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Affiliation(s)
- Can Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Guanqun Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Tianqi Lu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Liwei Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Yuhang Sui
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Rui Bai
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
| | - Le Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
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17
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Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
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Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
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18
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Allinson JP, Vlies BH, Brill SE, Law M, Burnside G, Finney LJ, Alves-Moreira L, Calverley PMA, Walker PP, Wedzicha JA. Reply to Martinez-Garcia et al. and to Wang et al.. Am J Respir Crit Care Med 2023; 208:1144-1145. [PMID: 37734070 PMCID: PMC10867927 DOI: 10.1164/rccm.202309-1604le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
- James P. Allinson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton Hospital, London, United Kingdom
| | | | - Simon E. Brill
- Thoracic Medicine, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Martin Law
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom; and
| | | | | | - Luana Alves-Moreira
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | | | - Jadwiga A. Wedzicha
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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19
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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20
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Scialò F, Vitale M, D'Agnano V, Mariniello DF, Perrotta F, Castaldo A, Campbell SFM, Pastore L, Cazzola M, Bianco A. Lung Microbiome as a Treatable Trait in Chronic Respiratory Disorders. Lung 2023; 201:455-466. [PMID: 37752217 DOI: 10.1007/s00408-023-00645-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
Once thought to be a sterile environment, it is now established that lungs are populated by various microorganisms that participate in maintaining lung function and play an important role in shaping lung immune surveillance. Although our comprehension of the molecular and metabolic interactions between microbes and lung cells is still in its infancy, any event causing a persistent qualitative or quantitative variation in the composition of lung microbiome, termed "dysbiosis", has been virtually associated with many respiratory diseases. A deep understanding of the composition and function of the "healthy" lung microbiota and how dysbiosis can cause or participate in disease progression will be pivotal in finding specific therapies aimed at preventing diseases and restoring lung function. Here, we review lung microbiome dysbiosis in different lung pathologies and the mechanisms by which these bacteria can cause or contribute to the severity of the disease. Furthermore, we describe how different respiratory disorders can be caused by the same pathogen, and that the real pathogenetic mechanism is not only dependent by the presence and amount of the main pathogen but can be shaped by the interaction it can build with other bacteria, fungi, and viruses present in the lung. Understanding the nature of this bacteria crosstalk could further our understanding of each respiratory disease leading to the development of new therapeutic strategies.
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Affiliation(s)
- Filippo Scialò
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
| | - Maria Vitale
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
| | - Vito D'Agnano
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Fabio Perrotta
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Alice Castaldo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Susan F M Campbell
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Cazzola
- Dipartimento di Medicina Sperimentale, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Bianco
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy.
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21
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Mac Aogáin M, Narayana JK, Chotirmall SH. Reply to Ward et al.. Am J Respir Crit Care Med 2023; 208:631-632. [PMID: 37348125 PMCID: PMC10492252 DOI: 10.1164/rccm.202305-0872le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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22
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Ward C, Al Momani H, McDonnell MJ, Murphy DM, Walsh L, Mac Sharry J, Griffin M, Forrest IA, Jones R, Krishnan A, Pearson J, Rutherford RM. The Potential Role of Gastric Microbiology in Respiratory Disease. Am J Respir Crit Care Med 2023; 208:630-631. [PMID: 37348122 PMCID: PMC10492259 DOI: 10.1164/rccm.202303-0366le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
- Chris Ward
- Translational and Clinical Research Institute and
- Biosciences Institute, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hafez Al Momani
- Translational and Clinical Research Institute and
- Biosciences Institute, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Microbiology, Pathology and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Melissa J. McDonnell
- Department of Respiratory Medicine, Galway University Hospitals, Galway, Ireland
| | - Desmond M. Murphy
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
- School of Microbiology and
- School of Medicine, APC Institute, University College Cork, Cork, Ireland
| | - Laura Walsh
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
- School of Microbiology and
- School of Medicine, APC Institute, University College Cork, Cork, Ireland
| | - John Mac Sharry
- School of Microbiology and
- School of Medicine, APC Institute, University College Cork, Cork, Ireland
| | - Mike Griffin
- The Royal College of Surgeons of Edinburgh, Edinburgh, United Kingdom
| | - Ian A. Forrest
- The Chest Clinic, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Rhys Jones
- The James Cook University Hospital, Middlesbrough, United Kingdom; and
| | - Amaran Krishnan
- Yorkshire and The Humber Strategic Health Authority, Leeds, United Kingdom
| | - Jeffrey Pearson
- Translational and Clinical Research Institute and
- Biosciences Institute, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert M. Rutherford
- Department of Respiratory Medicine, Galway University Hospitals, Galway, Ireland
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23
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Narayana JK, Aliberti S, Mac Aogáin M, Jaggi TK, Ali NABM, Ivan FX, Cheng HS, Yip YS, Vos MIG, Low ZS, Lee JXT, Amati F, Gramegna A, Wong SH, Sung JJY, Tan NS, Tsaneva-Atanasova K, Blasi F, Chotirmall SH. Microbial Dysregulation of the Gut-Lung Axis in Bronchiectasis. Am J Respir Crit Care Med 2023; 207:908-920. [PMID: 36288294 PMCID: PMC10111978 DOI: 10.1164/rccm.202205-0893oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Emerging data support the existence of a microbial "gut-lung" axis that remains unexplored in bronchiectasis. Methods: Prospective and concurrent sampling of gut (stool) and lung (sputum) was performed in a cohort of n = 57 individuals with bronchiectasis and subjected to bacteriome (16S rRNA) and mycobiome (18S Internal Transcribed Spacer) sequencing (total, 228 microbiomes). Shotgun metagenomics was performed in a subset (n = 15; 30 microbiomes). Data from gut and lung compartments were integrated by weighted similarity network fusion, clustered, and subjected to co-occurrence analysis to evaluate gut-lung networks. Murine experiments were undertaken to validate specific Pseudomonas-driven gut-lung interactions. Results: Microbial communities in stable bronchiectasis demonstrate a significant gut-lung interaction. Multibiome integration followed by unsupervised clustering reveals two patient clusters, differing by gut-lung interactions and with contrasting clinical phenotypes. A high gut-lung interaction cluster, characterized by lung Pseudomonas, gut Bacteroides, and gut Saccharomyces, is associated with increased exacerbations and greater radiological and overall bronchiectasis severity, whereas the low gut-lung interaction cluster demonstrates an overrepresentation of lung commensals, including Prevotella, Fusobacterium, and Porphyromonas with gut Candida. The lung Pseudomonas-gut Bacteroides relationship, observed in the high gut-lung interaction bronchiectasis cluster, was validated in a murine model of lung Pseudomonas aeruginosa infection. This interaction was abrogated after antibiotic (imipenem) pretreatment in mice confirming the relevance and therapeutic potential of targeting the gut microbiome to influence the gut-lung axis. Metagenomics in a subset of individuals with bronchiectasis corroborated our findings from targeted analyses. Conclusions: A dysregulated gut-lung axis, driven by lung Pseudomonas, associates with poorer clinical outcomes in bronchiectasis.
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Affiliation(s)
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | | | | | | | | | | | | | | | - Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Andrea Gramegna
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Sunny H. Wong
- Lee Kong Chian School of Medicine and
- Department of Gastroenterology and
| | - Joseph J. Y. Sung
- Lee Kong Chian School of Medicine and
- Department of Gastroenterology and
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine and
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Statistics and
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Francesco Blasi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore; and
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24
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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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