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Paciência I, Sharma N, Hugg TT, Rantala AK, Heibati B, Al-Delaimy WK, Jaakkola MS, Jaakkola JJ. The Role of Biodiversity in the Development of Asthma and Allergic Sensitization: A State-of-the-Science Review. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:66001. [PMID: 38935403 PMCID: PMC11218706 DOI: 10.1289/ehp13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Changes in land use and climate change have been reported to reduce biodiversity of both the environment and human microbiota. These reductions in biodiversity may lead to inadequate and unbalanced stimulation of immunoregulatory circuits and, ultimately, to clinical diseases, such as asthma and allergies. OBJECTIVE We summarized available empirical evidence on the role of inner (gut, skin, and airways) and outer (air, soil, natural waters, plants, and animals) layers of biodiversity in the development of asthma, wheezing, and allergic sensitization. METHODS We conducted a systematic search in SciVerse Scopus, PubMed MEDLINE, and Web of Science up to 5 March 2024 to identify relevant human studies assessing the relationships between inner and outer layers of biodiversity and the risk of asthma, wheezing, or allergic sensitization. The protocol was registered in PROSPERO (CRD42022381725). RESULTS A total of 2,419 studies were screened and, after exclusions and a full-text review of 447 studies, 82 studies were included in the comprehensive, final review. Twenty-nine studies reported a protective effect of outer layer biodiversity in the development of asthma, wheezing, or allergic sensitization. There were also 16 studies suggesting an effect of outer layer biodiversity on increasing asthma, wheezing, or allergic sensitization. However, there was no clear evidence on the role of inner layer biodiversity in the development of asthma, wheezing, and allergic sensitization (13 studies reported a protective effect and 15 reported evidence of an increased risk). CONCLUSIONS Based on the reviewed literature, a future systematic review could focus more specifically on outer layer biodiversity and asthma. It is unlikely that association with inner layer biodiversity would have enough evidence for systematic review. Based on this comprehensive review, there is a need for population-based longitudinal studies to identify critical periods of exposure in the life course into adulthood and to better understand mechanisms linking environmental exposures and changes in microbiome composition, diversity, and/or function to development of asthma and allergic sensitization. https://doi.org/10.1289/EHP13948.
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Affiliation(s)
- Inês Paciência
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Needhi Sharma
- University of California, San Diego, San Diego, California, USA
| | - Timo T. Hugg
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aino K. Rantala
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Behzad Heibati
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Maritta S. Jaakkola
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jouni J.K. Jaakkola
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Finnish Meteorological Institute, Helsinki, Finland
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2
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Sinha S, Kumar S, Narwaria M, Singh A, Haque M. Severe Acute Bronchial Asthma with Sepsis: Determining the Status of Biomarkers in the Diagnosis of the Disease. Diagnostics (Basel) 2023; 13:2691. [PMID: 37627950 PMCID: PMC10453001 DOI: 10.3390/diagnostics13162691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/04/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Bronchial asthma is a widely prevalent illness that substantially impacts an individual's health standard worldwide and has a significant financial impact on society. Global guidelines for managing asthma do not recommend the routine use of antimicrobial agents because most episodes of the condition are linked to viral respiratory tract infections (RTI), and bacterial infection appears to have an insignificant impact. However, antibiotics are recommended when there is a high-grade fever, a consolidation on the chest radiograph, and purulent sputum that contains polymorphs rather than eosinophils. Managing acute bronchial asthma with sepsis, specifically the choice of whether or not to initiate antimicrobial treatment, remains difficult since there are currently no practical clinical or radiological markers that allow for a simple distinction between viral and bacterial infections. Researchers found that serum procalcitonin (PCT) values can efficiently and safely minimize antibiotic usage in individuals with severe acute asthma. Again, the clinical manifestations of acute asthma and bacterial RTI are similar, as are frequently used test values, like C-reactive protein (CRP) and white blood cell (WBC) count, making it harder for doctors to differentiate between viral and bacterial infections in asthma patients. The role and scope of each biomarker have not been precisely defined yet, although they have all been established to aid healthcare professionals in their diagnostics and treatment strategies.
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Affiliation(s)
- Susmita Sinha
- Department of Physiology, Khulna City Medical College and Hospital, 33 KDA Avenue, Hotel Royal Crossing, Khulna Sadar, Khulna 9100, Bangladesh
| | - Santosh Kumar
- Department of Periodontology, Karnavati School of Dentistry, Karnavati University, Gandhinagar 382422, Gujarat, India
| | - Mahendra Narwaria
- Asian Bariatrics Plus Hospital, V Wing-Mondeal Business Park, SG Highways, Ahmedabad 380054, Gujarat, India
| | - Arya Singh
- Asian Bariatrics Plus Hospital, V Wing-Mondeal Business Park, SG Highways, Ahmedabad 380054, Gujarat, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia, Kuala Lumpur 57000, Malaysia
- Department of Scientific Research Center (KSRC), Karnavati School of Dentistry, Karnavati University, Gandhinagar 382422, Gujarat, India
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Asai N, Ethridge AD, Fonseca W, Yagi K, Rasky AJ, Morris SB, Falkowski NR, Huang YJ, Huffnagle GB, Lukacs NW. A steroid-resistant cockroach allergen model is associated with lung and cecal microbiome changes. Physiol Rep 2023; 11:e15761. [PMID: 37403414 PMCID: PMC10320043 DOI: 10.14814/phy2.15761] [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: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
The pathogenesis of asthma has been partially linked to lung and gut microbiome. We utilized a steroid-resistant chronic model of cockroach antigen-induced (CRA) asthma with corticosteroid (fluticasone) treatment to examine lung and gut microbiome during disease. The pathophysiology assessment demonstrated that mucus and airway hyperresponsiveness were increased in the chronic CRA with no alteration in the fluticasone (Flut)-treated group, demonstrating steroid resistance. Analysis of mRNA from lungs showed no decrease of MUC5AC or Gob5 in the Flut-treated group. Furthermore, flow-cytometry in lung tissue showed eosinophils and neutrophils were not significantly reduced in the Flut-treated group compared to the chronic CRA group. When the microbiome profiles were assessed, data showed that only the Flut-treated animals were significantly different in the gut microbiome. Finally, a functional analysis of cecal microbiome metabolites using PiCRUSt showed several biosynthetic pathways were significantly enriched in the Flut-treated group, with tryptophan pathway verified by ELISA with increased kynurenine in homogenized cecum samples. While the implications of these data are unclear, they may suggest a significant impact of steroid treatment on future disease pathogenesis through microbiome and associated metabolite pathway changes.
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Affiliation(s)
- Nobuhiro Asai
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
| | - Alexander D. Ethridge
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
- Immunology Graduate ProgramUniversity of MichiganAnn ArborMichiganUSA
| | - Wendy Fonseca
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
| | - Kazuma Yagi
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
| | - Andrew J. Rasky
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
| | - Susan B. Morris
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
| | - Nicole R. Falkowski
- Division of Pulmonary and Critical Medicine, Department of MedicineUniversity of MichiganAnn ArborMichiganUSA
| | - Yvonne J. Huang
- Division of Pulmonary and Critical Medicine, Department of MedicineUniversity of MichiganAnn ArborMichiganUSA
| | - Gary B. Huffnagle
- Immunology Graduate ProgramUniversity of MichiganAnn ArborMichiganUSA
- Division of Pulmonary and Critical Medicine, Department of MedicineUniversity of MichiganAnn ArborMichiganUSA
- Mary H. Weiser Food Allergy CenterUniversity of MichiganAnn ArborMichiganUSA
- Department of Molecular, Cellular and Developmental BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Nicholas W. Lukacs
- Department of PathologyUniversity of MichiganAnn ArborMichiganUSA
- Immunology Graduate ProgramUniversity of MichiganAnn ArborMichiganUSA
- Mary H. Weiser Food Allergy CenterUniversity of MichiganAnn ArborMichiganUSA
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Britt RD, Ruwanpathirana A, Ford ML, Lewis BW. Macrophages Orchestrate Airway Inflammation, Remodeling, and Resolution in Asthma. Int J Mol Sci 2023; 24:10451. [PMID: 37445635 PMCID: PMC10341920 DOI: 10.3390/ijms241310451] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Asthma is a heterogenous chronic inflammatory lung disease with endotypes that manifest different immune system profiles, severity, and responses to current therapies. Regardless of endotype, asthma features increased immune cell infiltration, inflammatory cytokine release, and airway remodeling. Lung macrophages are also heterogenous in that there are separate subsets and, depending on the environment, different effector functions. Lung macrophages are important in recruitment of immune cells such as eosinophils, neutrophils, and monocytes that enhance allergic inflammation and initiate T helper cell responses. Persistent lung remodeling including mucus hypersecretion, increased airway smooth muscle mass, and airway fibrosis contributes to progressive lung function decline that is insensitive to current asthma treatments. Macrophages secrete inflammatory mediators that induce airway inflammation and remodeling. Additionally, lung macrophages are instrumental in protecting against pathogens and play a critical role in resolution of inflammation and return to homeostasis. This review summarizes current literature detailing the roles and existing knowledge gaps for macrophages as key inflammatory orchestrators in asthma pathogenesis. We also raise the idea that modulating inflammatory responses in lung macrophages is important for alleviating asthma.
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Affiliation(s)
- Rodney D. Britt
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Anushka Ruwanpathirana
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Maria L. Ford
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Brandon W. Lewis
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA; (R.D.B.J.); (A.R.); (M.L.F.)
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Bloodworth JC, Hoji A, Wolff G, Mandal RK, Schmidt NW, Deshane JS, Morrow CD, Kloepfer KM, Cook-Mills JM. Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen. FRONTIERS IN ALLERGY 2023; 4:1135412. [PMID: 36970065 PMCID: PMC10036811 DOI: 10.3389/falgy.2023.1135412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.
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Affiliation(s)
- Jeffery C. Bloodworth
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Aki Hoji
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Garen Wolff
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rabindra K. Mandal
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nathan W. Schmidt
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kirsten M. Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Joan M. Cook-Mills
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Valverde-Molina J, García-Marcos L. Microbiome and Asthma: Microbial Dysbiosis and the Origins, Phenotypes, Persistence, and Severity of Asthma. Nutrients 2023; 15:nu15030486. [PMID: 36771193 PMCID: PMC9921812 DOI: 10.3390/nu15030486] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The importance of the microbiome, and of the gut-lung axis in the origin and persistence of asthma, is an ongoing field of investigation. The process of microbial colonisation in the first three years of life is fundamental for health, with the first hundred days of life being critical. Different factors are associated with early microbial dysbiosis, such as caesarean delivery, artificial lactation and antibiotic therapy, among others. Longitudinal cohort studies on gut and airway microbiome in children have found an association between microbial dysbiosis and asthma at later ages of life. A low α-diversity and relative abundance of certain commensal gut bacterial genera in the first year of life are associated with the development of asthma. Gut microbial dysbiosis, with a lower abundance of Phylum Firmicutes, could be related with increased risk of asthma. Upper airway microbial dysbiosis, especially early colonisation by Moraxella spp., is associated with recurrent viral infections and the development of asthma. Moreover, the bacteria in the respiratory system produce metabolites that may modify the inception of asthma and is progression. The role of the lung microbiome in asthma development has yet to be fully elucidated. Nevertheless, the most consistent finding in studies on lung microbiome is the increased bacterial load and the predominance of proteobacteria, especially Haemophilus spp. and Moraxella catarrhalis. In this review we shall update the knowledge on the association between microbial dysbiosis and the origins of asthma, as well as its persistence, phenotypes, and severity.
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Affiliation(s)
- José Valverde-Molina
- Department of Paediatrics, Santa Lucía General University Hospital, 30202 Cartagena, Spain
| | - Luis García-Marcos
- Paediatric Allergy and Pulmonology Units, Virgen de la Arrixaca University Children’s Hospital, University of Murcia and IMIB Biomedical Research Institute, 20120 Murcia, Spain
- Correspondence:
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Marathe SJ, Snider MA, Flores-Torres AS, Dubin PJ, Samarasinghe AE. Human matters in asthma: Considering the microbiome in pulmonary health. Front Pharmacol 2022; 13:1020133. [PMID: 36532717 PMCID: PMC9755222 DOI: 10.3389/fphar.2022.1020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/15/2022] [Indexed: 07/25/2023] Open
Abstract
Microbial communities form an important symbiotic ecosystem within humans and have direct effects on health and well-being. Numerous exogenous factors including airborne triggers, diet, and drugs impact these established, but fragile communities across the human lifespan. Crosstalk between the mucosal microbiota and the immune system as well as the gut-lung axis have direct correlations to immune bias that may promote chronic diseases like asthma. Asthma initiation and pathogenesis are multifaceted and complex with input from genetic, epigenetic, and environmental components. In this review, we summarize and discuss the role of the airway microbiome in asthma, and how the environment, diet and therapeutics impact this low biomass community of microorganisms. We also focus this review on the pediatric and Black populations as high-risk groups requiring special attention, emphasizing that the whole patient must be considered during treatment. Although new culture-independent techniques have been developed and are more accessible to researchers, the exact contribution the airway microbiome makes in asthma pathogenesis is not well understood. Understanding how the airway microbiome, as a living entity in the respiratory tract, participates in lung immunity during the development and progression of asthma may lead to critical new treatments for asthma, including population-targeted interventions, or even more effective administration of currently available therapeutics.
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Affiliation(s)
- Sandesh J. Marathe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Mark A. Snider
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Emergency Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Armando S. Flores-Torres
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Patricia J. Dubin
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
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The Changes in Bacterial Microbiome Associated with Immune Disorder in Allergic Respiratory Disease. Microorganisms 2022; 10:microorganisms10102066. [PMID: 36296340 PMCID: PMC9610723 DOI: 10.3390/microorganisms10102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/05/2022] [Accepted: 10/16/2022] [Indexed: 12/02/2022] Open
Abstract
Allergic respiratory disease is a worldwide and increasingly prevalent health problem. Many researchers have identified complex changes in the microbiota of the respiratory and intestinal tracts in patients with allergic respiratory diseases. These affect immune response and influence the progression of disease. However, the diversity of bacterial changes in such cases make it difficult to identify a specific microorganism to target for adjustment. Recent research evidence suggests that common bacterial variations present in allergic respiratory disease are associated with immune disorders. This finding could lead to the discovery of potential therapeutic targets in cases of allergic respiratory disease. In this review, we summarize current knowledge of bacteria changes in cases of allergic respiratory disease, to identify changes commonly associated with immune disorders, and thus provide a theoretical basis for targeting therapies of allergic respiratory disease through effective modulation of key bacteria.
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Immunosenescence, Inflammaging, and Lung Senescence in Asthma in the Elderly. Biomolecules 2022; 12:biom12101456. [PMID: 36291665 PMCID: PMC9599177 DOI: 10.3390/biom12101456] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Prevalence of asthma in older adults is growing along with increasing global life expectancy. Due to poor clinical consequences such as high mortality, advancement in understanding the pathophysiology of asthma in older patients has been sought to provide prompt treatment for them. Age-related alterations of functions in the immune system and lung parenchyma occur throughout life. Alterations with advancing age are promoted by various stimuli, including pathobionts, fungi, viruses, pollutants, and damage-associated molecular patterns derived from impaired cells, abandoned cell debris, and senescent cells. Age-related changes in the innate and adaptive immune response, termed immunosenescence, includes impairment of phagocytosis and antigen presentation, enhancement of proinflammatory mediator generation, and production of senescence-associated secretory phenotype. Immnunosenescence could promote inflammaging (chronic low-grade inflammation) and contribute to late-onset adult asthma and asthma in the elderly, along with age-related pulmonary disease, such as chronic obstructive pulmonary disease and pulmonary fibrosis, due to lung parenchyma senescence. Aged patients with asthma exhibit local and systemic type 2 and non-type 2 inflammation, associated with clinical manifestations. Here, we discuss immunosenescence’s contribution to the immune response and the combination of type 2 inflammation and inflammaging in asthma in the elderly and present an overview of age-related features in the immune system and lung structure.
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Avalos-Fernandez M, Alin T, Métayer C, Thiébaut R, Enaud R, Delhaes L. The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis. Respir Res 2022; 23:214. [PMID: 35999634 PMCID: PMC9396807 DOI: 10.1186/s12931-022-02132-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/17/2022] [Indexed: 11/26/2022] Open
Abstract
Background While there seems to be a consensus that a decrease in gut microbiome diversity is related to a decline in health status, the associations between respiratory microbiome diversity and chronic lung disease remain a matter of debate. We provide a systematic review and meta-analysis of studies examining lung microbiota alpha-diversity in patients with asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) or bronchiectasis (NCFB), in which a control group based on disease status or healthy subjects is provided for comparison. Results We reviewed 351 articles on title and abstract, of which 27 met our inclusion criteria for systematic review. Data from 24 of these studies were used in the meta-analysis. We observed a trend that CF patients have a less diverse respiratory microbiota than healthy individuals. However, substantial heterogeneity was present and detailed using random-effects models, which limits the comparison between studies. Conclusions Knowledge on respiratory microbiota is under construction, and for the moment, it seems that alpha-diversity measurements are not enough documented to fully understand the link between microbiota and health, excepted in CF context which represents the most studied chronic respiratory disease with consistent published data to link alpha-diversity and lung function. Whether differences in respiratory microbiota profiles have an impact on chronic respiratory disease symptoms and/or evolution deserves further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02132-4.
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Affiliation(s)
- Marta Avalos-Fernandez
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France. .,SISTM team Inria BSO, F-33405, Talence, France.
| | - Thibaud Alin
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Clémence Métayer
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France.,Pole of Public Health, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Raphaël Enaud
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,University of Bordeaux, Bordeaux Cardio-Thoracic Research Center, U1045, INSERM, F-33000, Bordeaux, France
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12
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Zheng J, Wu Q, Zhang L, Zou Y, Wang M, He L, Guo S. Anti-inflammatory activities of Qingfei oral liquid and its influence on respiratory microbiota in mice with ovalbumin-induced asthma. Front Pharmacol 2022; 13:911667. [PMID: 36081945 PMCID: PMC9445488 DOI: 10.3389/fphar.2022.911667] [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: 04/03/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Dysbiosis of respiratory microbiota is closely related to the pathophysiological processes of asthma, including airway inflammation. Previous studies have shown that Qingfei oral liquid (QF) can alleviate airway inflammation and airway hyper-responsiveness in respiratory syncytial virus-infected asthmatic mice, but its effect on the respiratory microbiota is unknown. We therefore aimed to observe the effects of QF on airway inflammation and respiratory microbiota in ovalbumin (OVA)-induced asthmatic mice. We also explored the potential mechanism of QF in reducing airway inflammation by regulating respiratory microbiota. Hematoxylin and eosin as well as periodic acid-Schiff staining were performed to observe the effects of QF on lung pathology in asthmatic mice. Cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were also measured. Changes in respiratory microbiota were analyzed using 16S rRNA gene sequencing, followed by taxonomical analysis. In order to verify the metagenomic function prediction results, the expression of key proteins related to the MAPK and NOD-like receptor signaling pathways in the lung tissues were detected by immunohistochemistry. The current study found that QF had a significant anti-inflammatory effect in the airways of asthmatic mice. This is mainly attributed to a reduction in lung pathology changes and regulating cytokine levels in BALF. Analysis of the respiratory microbiota in asthmatic mice showed that the abundance of Proteobacteria at the phylum level and Pseudomonas at the genus level increased significantly and QF could significantly regulate the dysbiosis of respiratory microbiota in asthmatic mice. Metagenomic functional prediction showed that QF can downregulate the MAPK and Nod-like receptor signaling pathways. Immunohistochemical results showed that QF could downregulate the expression of p-JNK, p-P38, NLRP3, Caspase-1, and IL-1β, which are all key proteins in the signaling pathway of lung tissue. Our study therefore concluded that QF may reduce airway inflammation in asthmatic mice by regulating respiratory microbiota, and to the possibly downregulate MAPK and Nod-like receptor signaling pathways as its underlying mechanism.
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Affiliation(s)
- Jun Zheng
- Department of Traditional Chinese Medicine, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Wu
- Department of Traditional Chinese Medicine, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Zhang
- Department of Traditional Chinese Medicine, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Zou
- Department of Emergency Medicine, Putuo Hospital, Shanghai University of Traditional Medicine, Shanghai, China
| | - Meifen Wang
- Department of Pediatrics, Sanmen People’s Hospital, Taizhou, Zhejiang, China
| | - Li He
- Department of Traditional Chinese Medicine, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Li He, ; Sheng Guo,
| | - Sheng Guo
- Department of Endocrine, Genetics and Metabolism, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Li He, ; Sheng Guo,
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13
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Liu X, Sun W, Ma W, Wang H, Xu K, Zhao L, He Y. Smoking related environmental microbes affecting the pulmonary microbiome in Chinese population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154652. [PMID: 35307427 DOI: 10.1016/j.scitotenv.2022.154652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Smoking is a serious public health problem that affects human health conditions. Although there is evidence that microorganisms are associated with smoking-related lung diseases, the relationship between the rich lung microbiome of upper respiratory tract groups and smoking has not been studied. OBJECTIVE In this study, we investigated the effects of smoking on environmental microbes and lung microbiome in the Chinese population and provided clues for the role of smoking in the development of respiratory disease. METHODS Bronchoalveolar lavage fluid samples were collected from 55 individuals with a history of smoking. Microbial gene sequencing was carried out through NGS technology. We analyzed and compared the diversity, community structure, and species abundance of bronchoalveolar lavage microbiome between smokers and nonsmokers, to speculate the effects of smoking on the lung microbiome. RESULTS Smoking hardly affected the α diversity of microbial groups of bronchoalveolar lavage, but it had a huge influence on the microbiome composition. The relative abundance of Rothia, Actinomycetes, Haemophilus, Porphyrins, Neisseria, Acinetobacter, and Streptococcus genera had a remarkable increase in the smoking group. On the other hand, the relative abundance of Plusella and Veronella decreased significantly. CONCLUSION Smoking may change the environmental microbes and then alter the structure of the lung microbiome, which may lead to smoking-related diseases.
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Affiliation(s)
- Xinyue Liu
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Wenwen Sun
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Weiqi Ma
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Wang
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Kandi Xu
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lishu Zhao
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yayi He
- School of Medicine, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China.
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14
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Miao Z, Du W, Xiao C, Su C, Gou W, Shen L, Zhang J, Fu Y, Jiang Z, Wang Z, Jia X, Zheng JS, Wang H. Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study. BMC Med 2022; 20:204. [PMID: 35701845 PMCID: PMC9199182 DOI: 10.1186/s12916-022-02402-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/11/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The interplay among the plant-based dietary pattern, gut microbiota, and cardiometabolic health is still unclear, and evidence from large prospective cohorts is rare. We aimed to examine the association of long-term and short-term plant-based dietary patterns with gut microbiota and to assess the prospective association of the identified microbial features with cardiometabolic biomarkers. METHODS Using a population-based prospective cohort study: the China Health and Nutrition Survey, we included 3096 participants from 15 provinces/megacities across China. We created an overall plant-based diet index (PDI), a healthful plant-based diet index (hPDI), and an unhealthful plant-based diet index (uPDI). The average PDIs were calculated using repeat food frequency questionnaires collected in 2011 and 2015 to represent a long-term dietary pattern. Short-term dietary pattern was estimated using 3-day 24-h dietary recalls collected in 2015. Fecal samples were collected in 2015 and measured using 16S rRNA sequencing. We investigated the association of long-term and short-term plant-based dietary patterns with gut microbial diversity, taxonomies, and functional pathways using linear mixed models. Furthermore, we assessed the prospective associations between the identified gut microbiome signatures and cardiometabolic biomarkers (measured in 2018) using linear regression. RESULTS We found a significant association of short-term hPDI with microbial alpha-diversity. Both long-term and short-term plant-based diet indices were correlated with microbial overall structure, whereas long-term estimates explained more variance. Long-term and short-term PDIs were differently associated with microbial taxonomic composition, yet only microbes related to long-term estimates showed association with future cardiometabolic biomarkers. Higher long-term PDI was associated with the lower relative abundance of Peptostreptococcus, while this microbe was positively correlated with the high-sensitivity C-reactive protein and inversely associated with high-density lipoprotein cholesterol. CONCLUSIONS We found shared and distinct gut microbial signatures of long-term and short-term plant-based dietary patterns. The identified microbial genera may provide insights into the protective role of long-term plant-based dietary pattern for cardiometabolic health, and replication in large independent cohorts is needed.
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Affiliation(s)
- Zelei Miao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
| | - Wenwen Du
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China
| | - Congmei Xiao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Chang Su
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China
| | - Wanglong Gou
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Luqi Shen
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jiguo Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zengliang Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zhihong Wang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China
| | - Xiaofang Jia
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China
| | - Ju-Sheng Zheng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Rd, Cloud Town, Hangzhou, China.
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Huijun Wang
- Chinese Center for Disease Control and Prevention, National Institute for Nutrition and Health, Beijing, China.
- Key Laboratory of Trace Element Nutrition, National Health Commission, Beijing, China.
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15
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Huang C, Ni Y, Du W, Shi G. Effect of inhaled corticosteroids on microbiome and microbial correlations in asthma over a nine-month period. Clin Transl Sci 2022; 15:1723-1736. [PMID: 35514165 PMCID: PMC9283747 DOI: 10.1111/cts.13288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
The effect of inhaled corticosteroids (ICS) on airway microbiome requires longitudinal research to be corroborated. Asthma patients, not undergoing ICS treatment (baseline), were enrolled and prescribed with ICS; all of these patients were followed up with regular visits at 3 months (visit 1) and 9 months (visit 2). Induced sputum was collected, fungal microbiota (mycobiome) and bacterial microbiota (bacteriome) were estimated using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing. Bacterial α diversity indices were not significantly different among the baseline, visit 1 and visit 2. Visit 1 showed lower fungal evenness than the baseline, visit 2 showed lower fungal diversity and evenness than the baseline. Fungal, but not bacterial, community compositions differed significantly among the baseline, visit 1 and visit 2. The most abundant bacterial phyla and genera did not differ significantly among the baseline, visit 1 and visit 2. Compared with the baseline, visit 1 showed significantly increased frequency of fungal phylum Ascomycota and lower frequency of Basidiomycota. We found sharply decreased fungal genera Wallemia, Cladosporium, Penicillium, and Alternaria in visit 1 and visit 2 compared with the baseline, although the differences were not statistically significant. We also found the proportion of Basidiomycota was positively correlated with percentages of sputum eosinophils and neutrophils. The proportions of Saccharomyces, Wallemia, and Aplosporella were positively correlated with percentage of sputum eosinophils. Moreover, we identified distinct inter- and intra-kingdom interactions in baseline, visit 1 and visit 2. Therefore, ICS use altered the airway microbial diversity, evenness, community composition and microbial connections.
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Affiliation(s)
- Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yingmeng Ni
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Wei Du
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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16
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Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques. Cell Rep 2022; 39:110725. [PMID: 35443183 PMCID: PMC9096119 DOI: 10.1016/j.celrep.2022.110725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/09/2022] [Accepted: 03/30/2022] [Indexed: 01/04/2023] Open
Abstract
Older individuals are at increased risk of developing severe respiratory infections. However, our understanding of the impact of aging on the respiratory tract remains limited as samples from healthy humans are challenging to obtain and results can be confounded by variables such as smoking and diet. Here, we carry out a comprehensive cross-sectional study (n = 34 adult, n = 49 aged) to define the consequences of aging on the lung using the rhesus macaque model. Pulmonary function testing establishes similar age and sex differences as humans. Additionally, we report increased abundance of alveolar and infiltrating macrophages and a concomitant decrease in T cells were in aged animals. scRNAseq reveals shifts from GRZMB to IFN expressing CD8+ T cells in the lungs. These data provide insight into age-related changes in the lungs’ functional, microbial, and immunological landscape that explain increased prevalence and severity of respiratory diseases in the elderly. Rhoades et al. describe age-associated functional, microbial, and immunological changes in the lung using the rhesus macaque model. These data will support further studies aimed at designing and testing interventions to mitigate the impact of age-associated shifts in the lung environment to reduce age-related pulmonary disease in the elderly.
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17
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Mancabelli L, Milani C, Fontana F, Lugli GA, Tarracchini C, Turroni F, van Sinderen D, Ventura M. Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome. J Oral Microbiol 2022; 14:2051336. [PMID: 35309410 PMCID: PMC8933033 DOI: 10.1080/20002297.2022.2051336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background The Human Respiratory Tract (HRT) is colonized by various microbial taxa, known as HRT microbiota, in a manner that is indicative of mutualistic interaction between such microorganisms and their host. Aim To investigate the microbial composition of the HRT and its possible correlation with the different compartments of the respiratory tract. Methods In the current study, we performed an in-depth meta‐analysis of 849 HRT samples from public shotgun metagenomic datasets obtained through several distinct collection methods. Results The statistical robustness provided by this meta-analysis allowed the identification of 13 possible HRT-specific Community State Types (CSTs), which appear to be specific to each anatomical region of the respiratory tract. Furthermore, functional characterization of the metagenomic datasets revealed specific microbial metabolic features correlating with the different compartments of the respiratory tract. Conclusion The meta-analysis here performed suggested that the variable presence of certain bacterial species seems to be linked to a location-related abundance gradient in the HRT and seems to be characterized by a specific microbial metabolic capability.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
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18
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19
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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20
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Yin G, Wu X, Wu Y, Li H, Gao L, Zhu X, Jiang Y, Wang W, Shen Y, He Y, Chen C, Niu Y, Zhang Y, Mao R, Zeng Y, Kan H, Chen Z, Chen R. Evaluating carbon content in airway macrophages as a biomarker of personal exposure to fine particulate matter and its acute respiratory effects. CHEMOSPHERE 2021; 283:131179. [PMID: 34146873 DOI: 10.1016/j.chemosphere.2021.131179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
It remains unclear whether carbon content in airway macrophages (AM) can predict personal short-term exposure to fine particulate matter (PM2.5) air pollution and its respiratory health effects. We aimed to evaluate the pathway from personal PM2.5 exposure to adverse respiratory outcomes through AM carbon content. We designed a longitudinal panel study with 3 scheduled follow-ups among 113 non-smoking patients of chronic obstructive pulmonary disease in Shanghai, China, from April 2017 to January 2019. We quantified AM carbon content from induced sputum by image analysis, tested lung function and measured sputum levels of 4 pro-inflammatory cytokines and 2 anti-inflammatory cytokines. We applied the "meet in the middle" approach incorporating linear mixed-effect models to evaluate the associations from external PM2.5 exposure to respiratory outcomes through AM carbon content. Our results indicated that personal exposure to PM2.5 within 24 h was significantly associated with decreased forced expiratory volume in 1s and anti-inflammatory cytokines, as well as increased macrophages and pro-inflammatory cytokines. These changes were accompanied by increased areas of AM carbon and higher percentage of AM area occupied by carbon, both of which were associated with increased levels of pro-inflammatory cytokines and decreased levels of anti-inflammatory cytokines. Exposure to ambient black carbon and organic carbon in PM2.5 within 2 days was significantly associated with increased AM carbon area and percentage of AM area occupied by carbon. Our findings reinforced the causality in respiratory health effects of PM2.5 in which increased AM carbon content might serve as a valid exposure biomarker.
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Affiliation(s)
- Guanjin Yin
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Xiaodan Wu
- Respiratory Division of Zhongshan Hospital, Shanghai Institute of Respiratory Disease, Fudan University, Shanghai, 200032, China
| | - Yihan Wu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Hongjin Li
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Lei Gao
- Respiratory Division of Zhongshan Hospital, Shanghai Institute of Respiratory Disease, Fudan University, Shanghai, 200032, China
| | - Xinlei Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Yixuan Jiang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Weidong Wang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Yanling Shen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Yu He
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Chen Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Yi Zhang
- Air Liquide (China) Holding Co., Ltd., Shanghai, 200233, China
| | - Ruolin Mao
- Respiratory Division of Zhongshan Hospital, Shanghai Institute of Respiratory Disease, Fudan University, Shanghai, 200032, China
| | - Yuzhen Zeng
- Respiratory Division of Zhongshan Hospital, Shanghai Institute of Respiratory Disease, Fudan University, Shanghai, 200032, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China
| | - Zhihong Chen
- Respiratory Division of Zhongshan Hospital, Shanghai Institute of Respiratory Disease, Fudan University, Shanghai, 200032, China.
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, 200032, China; Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai, 200030, China.
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21
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Xiang L, Meng X. Emerging cellular and molecular interactions between the lung microbiota and lung diseases. Crit Rev Microbiol 2021; 48:577-610. [PMID: 34693852 DOI: 10.1080/1040841x.2021.1992345] [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: 12/24/2022]
Abstract
With the discovery of the lung microbiota, its study in both pulmonary health and disease has become a vibrant area of emerging research interest. Thus far, most studies have described the lung microbiota composition in lung disease quite well, and some of these studies indicated alterations in lung microbial communities related to the onset and development of lung disease and vice versa. However, the underlying mechanisms, particularly the cellular and molecular links, are still largely unknown. In this review, we highlight the current progress in the complex cellular and molecular mechanisms by which the lung microbiome interacts with immune homeostasis and pulmonary disease pathogenesis to advance our understanding of the elaborate function of the lung microbiota in lung disease. We hope that this work can attract more attention to this still-young yet very promising field to facilitate the identification of new therapeutic targets and provide more innovative therapies. Additional accurate standard-based methodologies and technological breakthroughs are critical to propel the field forward to ultimately achieve the goal of maintaining respiratory health.
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Affiliation(s)
- Li Xiang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianli Meng
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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22
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Zheng J, Wu Q, Zou Y, Wang M, He L, Guo S. Respiratory Microbiota Profiles Associated With the Progression From Airway Inflammation to Remodeling in Mice With OVA-Induced Asthma. Front Microbiol 2021; 12:723152. [PMID: 34526979 PMCID: PMC8435892 DOI: 10.3389/fmicb.2021.723152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/27/2021] [Indexed: 12/31/2022] Open
Abstract
Background The dysbiosis of respiratory microbiota plays an important role in asthma development. However, there is limited information on the changes in the respiratory microbiota and how these affect the host during the progression from acute allergic inflammation to airway remodeling in asthma. Objective An ovalbumin (OVA)-induced mouse model of chronic asthma was established to explore the dynamic changes in the respiratory microbiota in the different stages of asthma and their association with chronic asthma progression. Methods Hematoxylin and eosin (H&E), periodic acid-schiff (PAS), and Masson staining were performed to observe the pathological changes in the lung tissues of asthmatic mice. The respiratory microbiota was analyzed using 16S rRNA gene sequencing followed by taxonomical analysis. The cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were measured. The matrix metallopeptidase 9 (MMP-9) and vascular endothelial growth factor (VEGF-A) expression levels in lung tissues were measured to detect airway remodeling in OVA-challenged mice. Results Acute allergic inflammation was the major manifestation at weeks 1 and 2 after OVA atomization stimulation, whereas at week 6 after the stimulation, airway remodeling was the most prominent observation. In the acute inflammatory stage, Pseudomonas was more abundant, whereas Staphylococcus and Cupriavidus were more abundant at the airway remodeling stage. The microbial compositions of the upper and lower respiratory tracts were similar. However, the dominant respiratory microbiota in the acute inflammatory and airway remodeling phases were different. Metagenomic functional prediction showed that the pathways significantly upregulated in the acute inflammatory phase and airway remodeling phase were different. The cytokine levels in BALF and the expression patterns of proteins associated with airway remodeling in the lung tissue were consistent with the metagenomic function results. Conclusion The dynamic changes in respiratory microbiota are closely associated with the progression of chronic asthma. Metagenomic functional prediction indicated the changes associated with acute allergic inflammation and airway remodeling.
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Affiliation(s)
- Jun Zheng
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Wu
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Zou
- Department of Emergency Medicine, Putuo Hospital, Shanghai University of Traditional Medicine, Shanghai, China
| | - Meifen Wang
- Department of Pediatrics, Sanmen People's Hospital, Taizhou, China
| | - Li He
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng Guo
- Department of Endocrine, Genetics and Metabolism, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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23
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The Role of Respiratory Flora in the Pathogenesis of Chronic Respiratory Diseases. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6431862. [PMID: 34435047 PMCID: PMC8382525 DOI: 10.1155/2021/6431862] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/20/2021] [Accepted: 07/31/2021] [Indexed: 12/13/2022]
Abstract
Large quantities of bacteria, including Firmicutes, Actinobacteria, and Bacteroidetes, colonize the surface of the respiratory mucosa of healthy people. They interact and coexist with the local mucosal immune system of the human airway, maintaining the immune stability and balance of the respiratory system. While suffering from chronic respiratory diseases, the microbial population in the airway changes and the proportion of Proteobacteria is increased in patients with asthma. The abundance of the microbial population in patients with chronic obstructive pulmonary disease (COPD) is decreased, and conversely, the proportion of Firmicutes and Proteobacteria increased. The diversity of airway microorganisms in cystic fibrosis (CF) patients is decreased, while pathogenic bacteria and conditional pathogenic bacteria are proliferated in large numbers. The proportion of Firmicutes and Proteobacteria is increased in patients with upper airway cough syndrome (UACS), which replaces the dominance of Streptococcus and Neisseria in the pharynx of a normal population. Therefore, a clear understanding of the immune process of the airway flora and the immune dysfunction of the flora on the pathogenesis of chronic respiratory diseases can provide new ideas for the prevention and treatment of human respiratory diseases.
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24
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Wang Z, Lai Z, Zhang X, Huang P, Xie J, Jiang Q, Zhang Q, Chung KF. Altered gut microbiome compositions are associated with the severity of asthma. J Thorac Dis 2021; 13:4322-4338. [PMID: 34422359 PMCID: PMC8339736 DOI: 10.21037/jtd-20-2189] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/31/2021] [Indexed: 12/31/2022]
Abstract
Background Despite substantial evidence on the contribution of the diversity of the gut microbiome to the pathogenesis of asthma and allergic diseases, little is known about their relationship with asthma severity and/or clinical phenotypes. We analyzed the difference in composition of the gut microbiome between subjects with asthma and healthy subjects and explored its role in the development of asthma. Methods Fecal samples from 15 subjects with severe asthma (SA), 14 with non-severe asthma (NSA), and 15 healthy subjects were assessed by 16S ribosomal RNA gene sequencing methods to identify the gut bacterial composition. Results Compared with those in the NSA group, patients in the SA group had a higher dose of inhaled corticosteroids, and there were more atopic subjects (60% vs. 35.7%, respectively). No significant differences were found at the phylum level either in operational taxonomic unit numbers or in diversity scores among the SA, NSA, and healthy groups. However, at the family level, the relative abundance of Acidaminococcaceae in the SA group was remarkedly lower than that in the group with healthy subjects (P<0.05). Furthermore, Veillonellaceae and Prevotellaceae were significantly more common in samples from the SA group than in those from the NSA group (P<0.05). In the SA group, positive correlations were observed between the relative abundance of Veillonellaceae and mid-expiratory flow 25% (MEF25%) predicted (r=0.538, P=0.047), as well as between the relative abundance of Acidaminococcaceae and body mass index (r=0642, P=0.010). Principal component analysis suggested that the relative abundances of Acidaminococcaceae and Prevotellaceae were associated with severe asthma. Moreover, we found that class Betaproteobacteria, order Burkholderiales, and family Alcaligenaceae were significantly different among the groups defined by serum immunoglobulin E (IgE) levels. Conclusions Our findings suggest that altered gut microbiome compositions are involved in the severity of asthma and that there are specific bacteria related to different asthma phenotypes in terms of serum IgE levels.
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Affiliation(s)
- Zhiqiang Wang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Hexian Memorial Hospital of PanYu District, Guangzhou, China
| | - Zhengdao Lai
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Dongguan Institute of Respiratory and Critical Care Medicine, Afliated Dongguan People's Hospital, Southern Medicial University, Dongguan, China
| | - Xiaoxian Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peikai Huang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Respiration Medicine, Huizhou Municipal Central Hospital, Huizhou, China
| | - Jiaxing Xie
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian Jiang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qingling Zhang
- Pulmonary and Critical Care Medicine, Guangzhou Insitute of Respiratory Health, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- National Heart & Lung Institute, Imperial College London & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, UK
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25
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Zou XL, Wu JJ, Ye HX, Feng DY, Meng P, Yang HL, Wu WB, Li HT, He Z, Zhang TT. Associations Between Gut Microbiota and Asthma Endotypes: A Cross-Sectional Study in South China Based on Patients with Newly Diagnosed Asthma. J Asthma Allergy 2021; 14:981-992. [PMID: 34408443 PMCID: PMC8367087 DOI: 10.2147/jaa.s320088] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
Objective This study aimed to investigate the gut microbiome profile in different inflammatory phenotypes of treatment-naive newly diagnosed asthmatic adults, to gain insight on the associations between intestinal microbiota and phenotypic features that characterize asthma heterogeneity to develop new treatments for asthma. Methods Fresh stool samples were obtained from 20 healthy subjects and 47 newly diagnosed asthmatic patients prior to any interventions. The asthmatics were divided into allergic and non-allergic cohorts. Intestinal microbiota was analyzed by 16S rRNA next-generation sequencing. Demographic and clinical parameters were collected. Alpha and beta diversity analysis were calculated to detect differences within sample phylotype richness and evenness between controls and asthmatic patients. Statistically significant differences between samples were analyzed for all used metrics, and features of gut bacterial community structure were evaluated in relation to extensive clinical characteristics of asthmatic patients. Results Gut microbial compositions were significantly different between asthmatic and healthy groups. Alpha-diversity of the gut microbiome was significantly lower in asthmatics than in controls. The microbiome between allergic and non-allergic asthmatic patients were also different, and 28 differential species were identified. PPAR signaling pathway, carotenoid biosynthesis, and flavonoid biosynthesis were significantly positively correlated with allergy-associated clinical index, including FENO value, blood eosinophil counts, and serum IgE and IL-4 levels. A combination of Ruminococcus bromii, Brevundimonas vesicularis, and Clostridium disporicum showed an AUC of 0.743 in the specific allergic/non-allergic cohort. When integrating C. disporicum, flavone, flavonol biosynthesis, and serum IL-4 values, the AUC achieved 0.929 to classify asthmatics. At the same time, C. colinum and its associated functional pathway exhibited an AUC of 0.78 to distinguish allergic asthmatics from those without allergies. Conclusion We demonstrated a distinct taxonomic composition of gut microbiota in different asthmatic phenotypes, highlighting their significant relationships. Our study may support considerations of intestinal microbial signatures in delineating asthma phenotypes.
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Affiliation(s)
- Xiao-Ling Zou
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin-Jie Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hui-Xia Ye
- Department of Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ding-Yun Feng
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ping Meng
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hai-Ling Yang
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen-Bin Wu
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hong-Tao Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zhen He
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tian-Tuo Zhang
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Institute of Respiratory Diseases of Sun Yat-sen University, Guangzhou, People's Republic of China
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26
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Mahdavinia M, Greenfield LR, Moore D, Botha M, Engen P, Gray C, Lunjani N, Hlela C, Basera W, Hobane L, Watkins A, Mankahla A, Gaunt B, Facey-Thomas H, Landay A, Keshavarzian A, Levin ME. House dust microbiota and atopic dermatitis; effect of urbanization. Pediatr Allergy Immunol 2021; 32:1006-1012. [PMID: 33570236 DOI: 10.1111/pai.13471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Previous studies have shown that a child's risk of developing atopic disease is impacted by both genetic and environmental factors. Because small children spend the majority of their time in their homes, exposure to microbial factors in their home environment may be protective or risk factors for development of atopic diseases, such as atopic dermatitis. METHODS Dust samples from the homes of 86 Black South African children 12 to 36 months old were collected for analysis of the bacterial microbiome. This case-control study design included children with and without atopic dermatitis from rural and urban environments. RESULTS Significant differences in bacterial composition and diversity were found when comparing children with and without atopic dermatitis. Furthermore, house dust microbiota was significantly different in rural and urban areas. Differences were best accounted for by higher relative abundance of Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae families in rural compared with urban houses. Levels of Ruminococcaceae were also found to be significantly depleted in the house dust of rural children with atopic dermatitis as compared to control children. CONCLUSIONS House dust composition may be an important risk factor for the development of atopic disease, and this association may be driven in part by the gut microbiome. Low levels of the Ruminococcaceae family from Clostridia class in particular may explain the association between urban living and atopy. However, further research is needed to elucidate these links.
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Affiliation(s)
- Mahboobeh Mahdavinia
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA.,InVivo Planetary Health Network, Chicago, IL, USA
| | - Leah R Greenfield
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA.,Rush Medical College, Chicago, IL, USA
| | - Donyea Moore
- Department of Internal Medicine, Allergy and Immunology Division, Rush University Medical Center, Chicago, IL, USA
| | - Maresa Botha
- InVivo Planetary Health Network, Chicago, IL, USA.,Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | | | - Claudia Gray
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.,Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Nonhlanhla Lunjani
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Carol Hlela
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Wisdom Basera
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Lelani Hobane
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Alexandra Watkins
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Avumile Mankahla
- Eastern Cape Department of Health, Zithulele Hospital, Mqanduli, South Africa
| | - Ben Gaunt
- Division of Dermatology, Department of Medicine and Pharmacology, Walter Sisulu University, Mthatha, South Africa
| | - Heidi Facey-Thomas
- Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Alan Landay
- Geriatrics Division, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA
| | - Michael E Levin
- InVivo Planetary Health Network, Chicago, IL, USA.,Division of Allergy, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
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27
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Hartmann JE, Albrich WC, Dmitrijeva M, Kahlert CR. The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review. Front Med (Lausanne) 2021; 8:588584. [PMID: 33777968 PMCID: PMC7988087 DOI: 10.3389/fmed.2021.588584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Since its discovery, the respiratory microbiome has been implicated in the pathogenesis of multiple pulmonary diseases. Even though corticosteroid treatments are widely prescribed for pulmonary diseases, their effects on the respiratory microbiome are still poorly understood. This systematic review summarizes the current understanding of the effects of corticosteroids on the microbiome of the airways. Research Question: How does treatment with corticosteroids impact the respiratory microbiome? Study Design and Methods: According to the PRISMA guidelines, Embase, Medline, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were systematically searched for all observational or randomized-controlled studies comparing the microbiome parameters of patients receiving corticosteroids to those of controls. The primary outcomes of interest were changes in the diversity, composition and total burden of the respiratory microbiome as assessed by culture-independent molecular methods. Results: Out of 1,943 identified reports, five studies could be included: two on patients with asthma, two on patients with chronic obstructive pulmonary disease and one on patients with chronic rhinosinusitis. The studies were highly heterogeneous with regards to the methods used and the populations investigated. Microbiome diversity increased with corticosteroids at least transiently in three studies and decreased in one study. The effects of corticosteroids on the composition of the respiratory microbiome were significant but without a clear shared direction. A significant increase in microbial burden after corticosteroids was seen in one study. Interpretation: Data on the effect of corticosteroids on the respiratory microbiome are still limited, with considerable heterogeneity between studies. However, available data suggest that corticosteroid treatment may have significant effects on the composition and possibly the diversity of the respiratory microbiome. Further research is needed to better understand the influence of corticosteroids on the respiratory microbiome and thus better target its widespread therapeutic use.
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Affiliation(s)
- Julia E. Hartmann
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Werner C. Albrich
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christian R. Kahlert
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
- Division of Infectious Diseases/Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
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28
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Porto BN, Moraes TJ. The triad: respiratory microbiome - virus - immune response in the pathophysiology of pulmonary viral infections. Expert Rev Respir Med 2021; 15:635-648. [PMID: 33605840 DOI: 10.1080/17476348.2021.1893168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The longstanding dogma that the healthy lung is sterile has been refuted by recent advances in culture-independent analyses of airway samples. The respiratory microbiome comprises all airway and lung tissue-associated microbes. These micro-organisms occur throughout the upper and lower respiratory tracts, with different populations and distinct burdens at specific sites and can be classified as pathogenic or commensal. AREAS COVERED The majority of studies investigating the respiratory microbiome have focused on bacteria; however, emerging evidence has revealed the composition of the lung virome, the global viral communities present in the lung tissue. In this review, we searched PubMed and used keywords such as airway microbiome. We restricted outputs to English language and did not limit by any dates. We summarize the up-to-date knowledge on how the microbiome interacts with the host immune system and influences the pathogenesis of pulmonary viral infections. EXPERT OPINION The relationship between colonizing microbes and the host is complex and various factors need to be considered in order to appreciate its pathophysiological consequences. Understanding these intricate mechanisms of interaction among the respiratory microbiome, viruses and the immune response may lead to the development of better therapies to treat or prevent respiratory viral infections.
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Affiliation(s)
- Bárbara N Porto
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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29
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Yan C, Duan G, Wu FX, Pan Y, Wang J. MCHMDA:Predicting Microbe-Disease Associations Based on Similarities and Low-Rank Matrix Completion. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:611-620. [PMID: 31295117 DOI: 10.1109/tcbb.2019.2926716] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
With the development of high-through sequencing technology and microbiology, many studies have evidenced that microbes are associated with human diseases, such as obesity, liver cancer, and so on. Therefore, identifying the association between microbes and diseases has become an important study topic in current bioinformatics. The emergence of microbe-disease association database has provided an unprecedented opportunity to develop computational method for predicting microbe-disease associations. In the study, we propose a low-rank matrix completion method (called MCHMDA) to predict microbe-disease associations by integrating similarities of microbes and diseases and known microbe-disease associations into a heterogeneous network. The microbe similarity is computed from Gaussian Interaction Profile (GIP) kernel similarity based on the known microbe-disease associations. Then, we further improve the microbe similarity by taking into account the inhabiting organs of these microbes in human body. The disease similarity is computed by the average of disease GIP similarity, disease symptom-based similarity, and disease functional similarity. Then, we construct a heterogeneous microbe-disease association network by integrating the microbe similarity network, disease similarity network, and known microbe-disease association network. Finally, a matrix completion method is used to calculate the association scores of unknown microbe-disease pairs by the fast Singular Value Thresholding (SVT) algorithm. Via 5-fold Cross Validation (5CV) and Leave-One-Out Cross Validation (LOOCV), we evaluate the prediction performances of MCHMDA and other state-of-the-art methods which include BRWMDA, NGRHMDA, LRLSHMDA, and KATZHMDA. On benchmark dataset HMDAD, the experimental results show that MCHMDA outperforms other methods in terms of area under the receiver operating characteristic curve (AUC). MCHMDA achieves the AUC values of 0.9251 and 0.9495 in 5CV and LOOCV, respectively, which are the highest values among the competing methods. In addition, we also further indicate the prediction generality of MCHMDA on an expanded microbe-disease associations dataset (HMDAD-SUP). Finally, case studies prove the prediction ability in practical applications.
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30
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Yang R, Wang G, Li L, He H, Zheng M, Lu L, Wu S. Tespa1 plays a role in the modulation of airway hyperreactivity through the IL-4/STAT6 pathway. J Transl Med 2020; 18:444. [PMID: 33228696 PMCID: PMC7685668 DOI: 10.1186/s12967-020-02621-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/18/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Thymocyte-expressed, positive selection-associated 1 (Tespa1) is a critical signaling molecule in thymocyte development. This study aimed to investigate the regulatory effect of Tespa1 on mast cells in the pathogenesis of asthma and its relationship with the interleukin (IL)-4/signal transducers and activators of transcription 6 (STAT6) signaling pathway. METHODS Tespa1 mRNA expression analysis and IgE levels were carried out using the induced sputum of 33 adults with stable asthma and 36 healthy controls. Tespa1-knockout mice (Tespa1-/-, KO) and C57BL/6 background (wild-type, WT) mice were sensitized and treated with ovalbumin (OVA) to establish an asthma model. Pathological changes, number and activity of mast cells, and changes in activation of the IL-4/STAT6 pathway in lung tissue were detected. The changes of tryptase expression and STAT6 activation after mast cell gene knockout were analyzed in vitro. The changes of enzyme expression and STAT6 activation after mast cell gene knockout were analyzed in vitro. The association between the Tespa1 and p-STAT6 was analyzed by co-immunoprecipitation method. RESULTS Compared with the healthy controls, Tespa1 expression was decreased, and IgE levels were elevated in the sputum of asthmatic patients. Animal experiments showed that Tespa1-/- mice exhibited more severe inflammation, higher quantity of goblet cells and mast cells in the bronchium, and greater expression of mast cell tryptase, which is induced by ovalbumin, than WT mice. And IL-4, IL-13, phospho-Janus kinase 1, and p-STAT6 expressions presented a higher increase in the Tespa1-/- mouse model than in the WT mouse model. Further in vitro studies confirmed that IL-4 could more significantly promote tryptase and p-STAT6 activities in Tespa1-/- mast cells than their WT counterparts. Correlation analysis results showed a negative correlation between Tespa1 and p-STAT6. Co-immunoprecipitation results demonstrated an association between Tespa1 and p-STAT6. CONCLUSIONS Altogether, our results indicate that Tespa1 can negatively regulate mast cell activity, and this event is related to the mast cell IL-4/STAT6 signaling pathway and could be therapeutically exploited to treat asthma attacks.
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Affiliation(s)
- Ruhui Yang
- Department of Pharmacology, College of Medicine and Health, Lishui University, No. 1 Xueyuan Road, Liandu District, Lishui, 323000, China
| | - Guangli Wang
- College of Medicine and Health, Lishui University, No. 1 Xueyuan Road, Liandu District, Lishui, 323000, China
| | - Lingyun Li
- Clinical Laboratory, Lishui People's Hospital, Lishui, 323000, China
| | - Hanjiang He
- College of Medicine and Health, Lishui University, No. 1 Xueyuan Road, Liandu District, Lishui, 323000, China
| | - Mingzhu Zheng
- Program in Molecular and Cellular Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Linrong Lu
- Program in Molecular and Cellular Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Songquan Wu
- College of Medicine and Health, Lishui University, No. 1 Xueyuan Road, Liandu District, Lishui, 323000, China.
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31
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Huang C, Yu Y, Du W, Liu Y, Dai R, Tang W, Wang P, Zhang C, Shi G. Fungal and bacterial microbiome dysbiosis and imbalance of trans-kingdom network in asthma. Clin Transl Allergy 2020; 10:42. [PMID: 33110490 PMCID: PMC7583303 DOI: 10.1186/s13601-020-00345-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls. Methods Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome. Results 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment. Conclusion We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma.
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Affiliation(s)
- Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Youchao Yu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Wei Du
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Yahui Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Ranran Dai
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Wei Tang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800, Dongchuan Road, Shanghai, 200240 People's Republic of China
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025 People's Republic of China
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32
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Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M, Wang L. Sex effects in the association between airway microbiome and asthma. Ann Allergy Asthma Immunol 2020; 125:652-657.e3. [PMID: 32931909 DOI: 10.1016/j.anai.2020.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Sex differences exist in asthma susceptibility and severity. Accumulating evidence has linked airway microbiome dysbiosis to asthma, and airway microbial communities have been found to differ by sex. However, whether sex modifies the link between airway microbiome and asthma has not been investigated. OBJECTIVE To evaluate sex effects in the association between airway microbiome and asthma. METHODS We analyzed induced sputum samples from 47 subjects (n = 23 patients with asthma and n = 24 normal controls) using 16S ribosomal RNA gene sequencing methods. The bacterial composition was analyzed for sex differences. Bacterial associations with asthma were assessed for each sex at the core taxa and genus levels. RESULTS The microbiome in induced sputum differed in women vs men at the community level. A total of 5 core bacterial taxa were found in all samples. No sex-specific core taxa were detected. The most abundant core taxon, Streptococcus salivarius, was significantly enriched in women than in men (P = .02). Within each sex, individuals with relatively lower abundance of S salivarius were more likely to have asthma (P = .006). For both sexes, increased Lactobacillus species were found in sputum samples of patients with patients compared with normal controls (adjusted P = .01). Haemophilus species were associated with asthma in men and not in women. CONCLUSION The airway microbiome differed by sex, and sex effects exist in the association of airway microbial markers and asthma. Future airway microbiome studies may yield better resolution if the context of specific sex is considered. The airway microbiome is a potential mechanism driving sex differences in asthma.
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Affiliation(s)
- Renjin Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Leran Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Tammy Koch
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Vanessa Curtis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Huiqing Yin-DeClue
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Liang Shan
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Mario Castro
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas
| | - Leyao Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.
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33
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Vandenborght LE, Enaud R, Urien C, Coron N, Girodet PO, Ferreira S, Berger P, Delhaes L. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome. J Allergy Clin Immunol 2020; 147:1296-1305.e6. [PMID: 32926879 PMCID: PMC7486598 DOI: 10.1016/j.jaci.2020.08.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
Abstract
Background The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters. Objective The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). Methods A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during “stable” or pulmonary “exacerbation” periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. Results Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. Conclusion These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.
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Affiliation(s)
- Louise-Eva Vandenborght
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Raphaël Enaud
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Charlotte Urien
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Noémie Coron
- Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Pierre-Olivier Girodet
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Stéphanie Ferreira
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Patrick Berger
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Laurence Delhaes
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France.
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34
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Rick EM, Woolnough KF, Seear PJ, Fairs A, Satchwell J, Richardson M, Monteiro WR, Craner M, Bourne M, Wardlaw AJ, Pashley CH. The airway fungal microbiome in asthma. Clin Exp Allergy 2020; 50:1325-1341. [PMID: 32808353 DOI: 10.1111/cea.13722] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. OBJECTIVES To use high-throughput sequencing to describe the airway mycobiota in asthmatics with and without fungal sensitization and healthy controls; to compare samples representing different airway compartments; to determine whether the mycobiota was influenced by the fungal composition of outdoor air; and to compare findings with clinically relevant outcomes. METHODS We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety-seven subjects were recruited and provided sputum (83 asthmatics; 14 healthy subjects), with 29 also undergoing a bronchoscopy. A subset of airway samples were compared with matched outdoor air and mouthwash samples. RESULTS Two hundred and six taxa at the species level were identified in sputum, most at low relative abundance. Aspergillus fumigatus, Candida albicans and Mycosphaerella tassiana had the highest relative abundances and were the most prevalent species across all subjects. The airway mycobiota consisted of a complex community with high diversity between individuals. Notable shifts in the balance of fungi detected in the lung were associated with asthma status, asthma duration and biomarkers of inflammation. Aspergillus tubingensis, a member of the Aspergillus niger species complex, was most prevalent from bronchoscopic protected brush samples and significantly associated with a low sputum neutrophilia. Cryptococcus pseudolongus, from the Cryptococcus humicola species complex, was more abundant from bronchoscopy samples than sputum, and differentially more abundant in asthma than health. CONCLUSIONS AND CLINICAL RELEVANCE The airway mycobiota was dominated by a relatively small number of species, but was distinct from the oropharyngeal mycobiota and air samples. Members of the A. niger and C. humicola species complexes may play unexpected roles in the pathogenesis of asthma.
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Affiliation(s)
- Eva-Maria Rick
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Kerry F Woolnough
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Paul J Seear
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Abbie Fairs
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Jack Satchwell
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Matthew Richardson
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - William R Monteiro
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Craner
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Bourne
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Andrew J Wardlaw
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK.,Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Catherine H Pashley
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
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35
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Ye S, Yan F, Wang H, Mo X, Liu J, Zhang Y, Li H, Chen D. Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population. J Dermatol 2020; 48:158-167. [PMID: 32860635 DOI: 10.1111/1346-8138.15530] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022]
Abstract
An increasing body of evidence suggests that gut microbiota is involved in atopic dermatitis (AD). We aimed to use high-throughput sequencing to characterize the differences in the composition of the gut microbiota between healthy controls and patients with AD. Fecal samples from 93 volunteers were analyzed using 16S rRNA sequencing, including 44 patients with AD and 49 healthy control subjects, aged 6-22 years. Our data show that the operational taxonomic unit composition in patients with AD had greater component similarity than the healthy controls. Patients with AD had a lower alpha diversity than healthy control subjects. The relative abundance of Porphyromonadaceae, Blautia, Parabacteroides, Bacteroides ovatus, Bacteroides uniformis and Prevotella stercorea was significantly higher (P < 0.05) in patients with AD than healthy control subjects. Clostridium and P. stercorea were higher (P < 0.05) in healthy control subjects compared with patients with AD. The results of linear discriminant analysis effect size show that Bacteroidaceae and Porphyromonadaceae can act as possible biomarkers associated with diagnosis of AD. However, this needs further experimental verification. Taken together, these results demonstrate the changes in microbiota composition in AD compared with a healthy control group, opening the way to future diagnosis or intervention studies.
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Affiliation(s)
- Siqi Ye
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fenggen Yan
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, China
| | - Haiyan Wang
- Department of Dermatology, The First Affiliated Hospital of HeNan University of Chinese Medicine, Zhengzhou, China
| | - Xiumei Mo
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, China
| | - Junfeng Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, China
| | - Yu Zhang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongyi Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dacan Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, China
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36
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Long Y, Luo J, Zhang Y, Xia Y. Predicting human microbe-disease associations via graph attention networks with inductive matrix completion. Brief Bioinform 2020; 22:5876591. [PMID: 32725163 DOI: 10.1093/bib/bbaa146] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION human microbes play a critical role in an extensive range of complex human diseases and become a new target in precision medicine. In silico methods of identifying microbe-disease associations not only can provide a deep insight into understanding the pathogenic mechanism of complex human diseases but also assist pharmacologists to screen candidate targets for drug development. However, the majority of existing approaches are based on linear models or label propagation, which suffers from limitations in capturing nonlinear associations between microbes and diseases. Besides, it is still a great challenge for most previous methods to make predictions for new diseases (or new microbes) with few or without any observed associations. RESULTS in this work, we construct features for microbes and diseases by fully exploiting multiply sources of biomedical data, and then propose a novel deep learning framework of graph attention networks with inductive matrix completion for human microbe-disease association prediction, named GATMDA. To our knowledge, this is the first attempt to leverage graph attention networks for this important task. In particular, we develop an optimized graph attention network with talking-heads to learn representations for nodes (i.e. microbes and diseases). To focus on more important neighbours and filter out noises, we further design a bi-interaction aggregator to enforce representation aggregation of similar neighbours. In addition, we combine inductive matrix completion to reconstruct microbe-disease associations to capture the complicated associations between diseases and microbes. Comprehensive experiments on two data sets (i.e. HMDAD and Disbiome) demonstrated that our proposed model consistently outperformed baseline methods. Case studies on two diseases, i.e. asthma and inflammatory bowel disease, further confirmed the effectiveness of our proposed model of GATMDA. AVAILABILITY python codes and data set are available at: https://github.com/yahuilong/GATMDA. CONTACT luojiawei@hnu.edu.cn.
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Affiliation(s)
- Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China.,School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yan Xia
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China
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37
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Liu HY, Li CX, Liang ZY, Zhang SY, Yang WY, Ye YM, Lin YX, Chen RC, Zhou HW, Su J. The Interactions of Airway Bacterial and Fungal Communities in Clinically Stable Asthma. Front Microbiol 2020; 11:1647. [PMID: 32849339 PMCID: PMC7396634 DOI: 10.3389/fmicb.2020.01647] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/24/2020] [Indexed: 12/31/2022] Open
Abstract
Dysbiotic airway microbiota play important roles in the inflammatory progression of asthma, and exploration of airway microbial interactions further elucidates asthma pathogenesis. However, little is known regarding the airway bacterial-fungal interactions in asthma patients. We conducted a cross-sectional survey of the sputum bacterial and fungal microbiota from 116 clinically stable asthma patients and 29 healthy controls using 16S rRNA gene and ITS1 sequencing. Compared with healthy individuals, asthma patients exhibited a significantly altered microbiota and increased bacterial and fungal alpha diversities in the airway. Microbial genera Moraxella, Capnocytophaga, and Ralstonia (bacteria) and Schizophyllum, Candida, and Phialemoniopsis (fungi) were more abundant in the asthma airways, while Rothia, Veillonella and Leptotrichia (bacteria) and Meyerozyma (fungus) were increased in healthy controls. The Moraxellaceae family and their genus Moraxella were significantly enriched in asthma patients compared with healthy controls (80.5-fold, P = 0.007 and 314.7-fold, P = 0.027, respectively). Moreover, Moraxellaceae, along with Schizophyllum, Candida, and Aspergillus (fungal genera), were positively associated with fungal alpha diversity. Correlation networks revealed 3 fungal genera (Schizophyllum, Candida, and Aspergillus) as important airway microbes in asthma that showed positive correlations with each other and multiple co-exclusions with other common microbiota. Moraxellaceae members were positively associated with asthma-enriched fungal taxa but negatively related to several healthy-enriched bacterial taxa. Collectively, our findings revealed an altered microbiota and complex microbial interactions in the airways of asthma patients. The Moraxellaceae family and their genus Moraxella, along with 3 important fungal taxa, showed significant interactions with the airway microbiota, providing potential insights into the novel pathogenic mechanisms of asthma.
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Affiliation(s)
- Hai-Yue Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.,State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chun-Xi Li
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen-Yu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shi-Yu Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wan-Ying Yang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Mei Ye
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Xia Lin
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong-Chang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Su
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Lira-Lucio JA, Falfán-Valencia R, Ramírez-Venegas A, Buendía-Roldán I, Rojas-Serrano J, Mejía M, Pérez-Rubio G. Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases. Microorganisms 2020; 8:E1059. [PMID: 32708647 PMCID: PMC7409050 DOI: 10.3390/microorganisms8071059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The lung microbiome composition has critical implications in the regulation of innate and adaptive immune responses. Next-generation sequencing techniques have revolutionized the understanding of pulmonary physiology and pathology. Currently, it is clear that the lung is not a sterile place; therefore, the investigation of the participation of the pulmonary microbiome in the presentation, severity, and prognosis of multiple pathologies, such as asthma, chronic obstructive pulmonary disease, and interstitial lung diseases, contributes to a better understanding of the pathophysiology. Dysregulation of microbiota components in the microbiome-host interaction is associated with multiple lung pathologies, severity, and prognosis, making microbiome study a useful tool for the identification of potential therapeutic strategies. This review integrates the findings regarding the activation and regulation of the innate and adaptive immune response pathways according to the microbiome, including microbial patterns that could be characteristic of certain diseases. Further studies are required to verify whether the microbial profile and its metabolites can be used as biomarkers of disease progression or poor prognosis and to identify new therapeutic targets that restore lung dysbiosis safely and effectively.
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Affiliation(s)
- Juan Alberto Lira-Lucio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Alejandra Ramírez-Venegas
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Jorge Rojas-Serrano
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Mayra Mejía
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
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Luo J, Long Y. NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1341-1351. [PMID: 30489271 DOI: 10.1109/tcbb.2018.2883041] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Accumulating clinic evidences have demonstrated that the microbes residing in human bodies play a significantly important role in the formation, development, and progression of various complex human diseases. Identifying latent related microbes for disease could provide insight into human disease mechanisms and promote disease prevention, diagnosis, and treatment. In this paper, we first construct a heterogeneous network by connecting the disease similarity network and the microbe similarity network through known microbe-disease association network, and then develop a novel computational model to predict human microbe-disease associations based on random walk by integrating network topological similarity (NTSHMDA). Specifically, each microbe-disease association pair is regarded as a distinct relationship level and, thus, assigned different weights based on network topological similarity. The experimental results show that NTSHMDA outperforms some state-of-the-art methods with average AUCs of 0.9070, 0.8896 ± 0.0038 in the frameworks of Leave-one-out cross validation and 5-fold cross validation, respectively. In case studies, 9, 18, 38 and 9, 18, 45 out of top-10, 20, 50 candidate microbes are verified by recently published literatures for asthma and inflammatory bowel disease, respectively. In conclusion, NTSHMDA has potential ability to identify novel disease-microbe associations and can also provide valuable information for drug discovery and biological researches.
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Wu R, Li X, Ma N, Jin X, Yuan X, Qu C, Tang H, Liu Z, Zhang Z. Bacterial Quorum Sensing Molecules Promote Allergic Airway Inflammation by Activating the Retinoic Acid Response. iScience 2020; 23:101288. [PMID: 32622265 PMCID: PMC7334417 DOI: 10.1016/j.isci.2020.101288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/24/2020] [Accepted: 06/14/2020] [Indexed: 12/14/2022] Open
Abstract
IgE and IgG1 production in the type 2 immune response is the characteristic feature of an allergic reaction. However, whether bacterial molecules modulate IgE and IgG1 production remains obscure. Here, we demonstrate that the bacterial quorum sensing molecules acyl homoserine lactones (AHLs) induce IgE and IgG1 production by activating the RARE (retinoic acid response element) response in dendritic cells (DCs) in vivo. DC-specific knockout of the retinoic acid transcriptional factor Rara diminished the AHL-stimulated type 2 immune response in vitro. AHLs altered DC phenotype, upregulated OX40L and IFN-I signature, and promoted T helper 2 cell differentiation in vitro. Finally, AHLs activated the RARE response by inhibiting AKT phosphorylation in vitro, as the AKT agonists IGF-1 and PDGF abolished the effect of AHLs on the RARE response. This study demonstrates a mechanism by which AHLs drive allergic airway inflammation through activating retinoic acid signaling in DCs. Acyl homoserine lactones (AHLs) exacerbate allergic airway inflammation AHLs induce IgE and IgG1 production AHLs activate the RARE response in dendritic cells AHLs inhibit AKT phosphorylation
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Affiliation(s)
- Renlan Wu
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Xingjie Li
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; The School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Ning Ma
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiufeng Jin
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiefang Yuan
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Chen Qu
- Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Hongmei Tang
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Zhigang Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen University School of Medicine, Shenzhen 518060, China
| | - Zongde Zhang
- Inflammation & Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; The School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, China; Model Animal Research Center, Nanjing University, Nanjing 210061, China.
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Abdel-Aziz MI, Brinkman P, Vijverberg SJH, Neerincx AH, Riley JH, Bates S, Hashimoto S, Kermani NZ, Chung KF, Djukanovic R, Dahlén SE, Adcock IM, Howarth PH, Sterk PJ, Kraneveld AD, Maitland-van der Zee AH. Sputum microbiome profiles identify severe asthma phenotypes of relative stability at 12 to 18 months. J Allergy Clin Immunol 2020; 147:123-134. [PMID: 32353491 DOI: 10.1016/j.jaci.2020.04.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Asthma is a heterogeneous disease characterized by distinct phenotypes with associated microbial dysbiosis. OBJECTIVES Our aim was to identify severe asthma phenotypes based on sputum microbiome profiles and assess their stability after 12 to 18 months. A further aim was to evaluate clusters' robustness after inclusion of an independent cohort of patients with mild-to-moderate asthma. METHODS In this longitudinal multicenter cohort study, sputum samples were collected for microbiome profiling from a subset of the Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes adult patient cohort at baseline and after 12 to 18 months of follow-up. Unsupervised hierarchical clustering was performed by using the Bray-Curtis β-diversity measure of microbial profiles. For internal validation, partitioning around medoids, consensus cluster distribution, bootstrapping, and topological data analysis were applied. Follow-up samples were studied to evaluate within-patient clustering stability in patients with severe asthma. Cluster robustness was evaluated by using an independent cohort of patients with mild-to-moderate asthma. RESULTS Data were available for 100 subjects with severe asthma (median age 55 years; 42% males). Two microbiome-driven clusters were identified; they were characterized by differences in asthma onset, smoking status, residential locations, percentage of blood and/or sputum neutrophils and macrophages, lung spirometry results, and concurrent asthma medications (all P values < .05). The cluster 2 patients displayed a commensal-deficient bacterial profile that was associated with worse asthma outcomes than those of the cluster 1 patients. Longitudinal clusters revealed high relative stability after 12 to 18 months in those with severe asthma. Further inclusion of an independent cohort of 24 patients with mild-to-moderate asthma was consistent with the clustering assignments. CONCLUSION Unbiased microbiome-driven clustering revealed 2 distinct robust phenotypes of severe asthma that exhibited relative overtime stability. This suggests that the sputum microbiome may serve as a biomarker for better characterizing asthma phenotypes.
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Affiliation(s)
- Mahmoud I Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Paul Brinkman
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J H Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne H Neerincx
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - John H Riley
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Stewart Bates
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Simone Hashimoto
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Pediatric Respiratory Medicine, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands
| | | | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, and Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ratko Djukanovic
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Sven-Erik Dahlén
- Centre for Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, and Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Peter H Howarth
- NIHR Southampton Respiratory Biomedical Research Unit, Clinical and Experimental Sciences and Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Peter J Sterk
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Pediatric Respiratory Medicine, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands.
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Lei X, Wang Y. Predicting Microbe-Disease Association by Learning Graph Representations and Rule-Based Inference on the Heterogeneous Network. Front Microbiol 2020; 11:579. [PMID: 32351464 PMCID: PMC7174569 DOI: 10.3389/fmicb.2020.00579] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
More and more clinical observations have implied that microbes have great effects on human diseases. Understanding the relations between microbes and diseases are of profound significance for disease prevention and therapy. In this paper, we propose a predictive model based on the known microbe-disease associations to discover potential microbe-disease associations through integrating Learning Graph Representations and a modified Scoring mechanism on the Heterogeneous network (called LGRSH). Firstly, the similarity networks for microbe and disease are obtained based on the similarity of Gaussian interaction profile kernel. Then, we construct a heterogeneous network including these two similarity networks and microbe-disease associations' network. After that, the embedding algorithm Node2vec is implemented to learn representations of nodes in the heterogeneous network. Finally, according to these low-dimensional vector representations, we calculate the relevance between each microbe and disease by utilizing a modified rule-based inference method. By comparison with three other methods including LRLSHMDA, KATZHMDA and BiRWHMDA, LGRSH performs better than others. Moreover, in case studies of asthma, Chronic Obstructive Pulmonary Disease and Inflammatory Bowel Disease, there are 8, 8, and 10 out of the top-10 discovered disease-related microbes were validated respectively, demonstrating that LGRSH performs well in predicting potential microbe-disease associations.
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Affiliation(s)
- Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yueyue Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
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Xu X, Wu L, Sheng Y, Liu J, Xu Z, Kong W, Tang L, Chen Z. Airway microbiota in children with bronchial mucus plugs caused by Mycoplasma pneumoniae pneumonia. Respir Med 2020; 170:105902. [PMID: 32843185 DOI: 10.1016/j.rmed.2020.105902] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/29/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND There is increasing evidence for a role of lung microbiota in the pathogenesis of Mycoplasma pneumoniae pneumonia (MPP). However, the alterations of lung microbiota in MPP with bronchial mucus plugs and its role in disease pathogenesis remain poorly understood. METHODS In this prospective observational study, we performed a longitudinal 16S rRNA-based microbiome survey on bronchoalveolar lavage (BAL) samples collected from 31 MPP with bronchial mucus plugs and 52 MPP without mucus plugs. RESULTS Our study showed a clear difference in airway microbiota between MPP children with and without bronchial mucus plugs. The MPP children with mucus plugs had lower abundances of Sphingomonas and Elizabethkingia, and a high abundance of Mycoplasma compared with MPP children without mucus plugs, subsequently contributing to increased ratios of Mycoplasma to Sphingomonas and Mycoplasma to Elizabethkingia. Children's age, fever time and serum cytokine levels were associated with airway microbiota alteration. Furthermore, significant correlations between bacterial genus abundances were found in MPP children with mucus plugs. CONCLUSIONS Our results suggest an impact of airway microbiota on the clinical course of MPP in children, deserving further investigations.
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Affiliation(s)
- Xuefeng Xu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China; Department of Rheumatology Immunology & Allergy, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Lei Wu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Yuanjian Sheng
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Jinling Liu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Zhufei Xu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Weixing Kong
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Lanfang Tang
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Zhimin Chen
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China.
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Louhaichi S, Mlika M, Hamdi B, Hamzaoui K, Hamzaoui A. Sputum IL-26 Is Overexpressed in Severe Asthma and Induces Proinflammatory Cytokine Production and Th17 Cell Generation: A Case-Control Study of Women. J Asthma Allergy 2020; 13:95-107. [PMID: 32099415 PMCID: PMC7006858 DOI: 10.2147/jaa.s229522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/12/2020] [Indexed: 12/16/2022] Open
Abstract
Objective Asthma inflammation is a complex pathway involving numerous mediators. Interleukin-26 (IL-26), a member of the IL-10 cytokine family, is abundant in human airways and induces the production of proinflammatory cytokines. Our aim was to investigate the possible role of IL-26 in severe asthma. We analysed the expression of IL-26 in severe asthma both in peripheral blood and induced sputum. Patients and Methods A total of 50 adult women with severe asthma were recruited and compared to 30 healthy controls (HC). Serum and sputum fluid (SF) levels of IL-26 and IL-17 were defined by ELISA. IL-26 mRNA expression and IL-26 protein were analysed using RT-PCR and Western blot. In vitro, we studied the effect of recombinant IL-26 (rIL-26) and SF-IL-26 on cultured CD4+ T cells and monocytes, comparing patients and controls. Results Concentrations of IL-26 are higher in serum and induced sputum of asthmatic patients than in HC. Moreover, IL-26 protein and mRNA expression were significantly elevated in asthma sputum cells compared to PBMCs. We observed a positive correlation between body mass index (BMI) and sputum fluid IL-26, while the correlation between IL-26 and lung function tests (FEV1% and FEV1/FVC ratio) was negative. IL-17A was highly expressed in SF and correlated positively with IL-26. In patients’ sputum IL-26 and IL-17A were significantly associated with neutrophils. Stimulation of cultured CD4+ T cells with monocytes by recombinant IL-26 promoted the generation of RORγt+ Th17+ cells inducing the production of IL-17A, IL-1β, IL-6 and TNF-α cytokines. IL-26 expressed in SF was biologically active and induced IL-17 secretion in the presence of IL-1β and IL-6 cytokines. Conclusion These findings show that IL-26 is highly produced in asthmatic sputum, induces pro-inflammatory cytokine secretion by monocytes/macrophages, and favours Th17 cell generation. IL-26 thereby appears as a novel pro-inflammatory cytokine, produced locally in the airways that may constitute a promising target to treat asthma inflammatory process.
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Affiliation(s)
- Sabrine Louhaichi
- Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Abderrahman Mami Hospital, Ariana, Tunisia.,Medicine Faculty of Tunis, Department of Basic Sciences, Tunis El Manar University, Tunis, Tunisia.,Department of Paediatric and Respiratory Diseases, Abderrahman Mami Hospital, Pavillon B, Ariana, Tunisia
| | - Mona Mlika
- Medicine Faculty of Tunis, Department of Basic Sciences, Tunis El Manar University, Tunis, Tunisia.,Pathology Department, Abderrahman Mami Hospital, Ariana, Tunisia
| | - Besma Hamdi
- Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Abderrahman Mami Hospital, Ariana, Tunisia.,Medicine Faculty of Tunis, Department of Basic Sciences, Tunis El Manar University, Tunis, Tunisia.,Department of Paediatric and Respiratory Diseases, Abderrahman Mami Hospital, Pavillon B, Ariana, Tunisia
| | - Kamel Hamzaoui
- Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Abderrahman Mami Hospital, Ariana, Tunisia.,Medicine Faculty of Tunis, Department of Basic Sciences, Tunis El Manar University, Tunis, Tunisia
| | - Agnès Hamzaoui
- Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Abderrahman Mami Hospital, Ariana, Tunisia.,Medicine Faculty of Tunis, Department of Basic Sciences, Tunis El Manar University, Tunis, Tunisia.,Department of Paediatric and Respiratory Diseases, Abderrahman Mami Hospital, Pavillon B, Ariana, Tunisia
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Cho YJ. Does the Difference in Microbial Patterns in the Airways Induce Distinct Endotypes of Asthma? ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:375-377. [PMID: 32141252 PMCID: PMC7061159 DOI: 10.4168/aair.2020.12.3.375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 11/20/2022]
Affiliation(s)
- Young Joo Cho
- Department of Allergy and Clinical Immunology, Ewha Womans University Mokdong Hospital, Ewha Womans University College of Medicine, Seoul, Korea.
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Lung Microbiome in Asthma: Current Perspectives. J Clin Med 2019; 8:jcm8111967. [PMID: 31739446 PMCID: PMC6912699 DOI: 10.3390/jcm8111967] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022] Open
Abstract
A growing body of evidence implicates the human microbiome as a potentially influential player actively engaged in shaping the pathogenetic processes underlying the endotypes and phenotypes of chronic respiratory diseases, particularly of the airways. In this article, we specifically review current evidence on the characteristics of lung microbiome, and specifically the bacteriome, the modes of interaction between lung microbiota and host immune system, the role of the “lung–gut axis”, and the functional effects thereof on asthma pathogenesis. We also attempt to explore the possibilities of therapeutic manipulation of the microbiome, aiming at the establishment of asthma prevention strategies and the optimization of asthma treatment.
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Banskar S, Detzner AA, Juarez-Rodriguez MD, Hozo I, Gupta D, Dziarski R. The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma. THE JOURNAL OF IMMUNOLOGY 2019; 203:3113-3125. [PMID: 31704882 DOI: 10.4049/jimmunol.1900711] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022]
Abstract
Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1 -/- mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1 -/- mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1 -/- mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1 -/- mice.
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Affiliation(s)
- Sunil Banskar
- Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Ashley A Detzner
- Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | | | - Iztok Hozo
- Department of Mathematics, Indiana University-Northwest, Gary, IN 46408
| | - Dipika Gupta
- Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Roman Dziarski
- Indiana University School of Medicine-Northwest, Gary, IN 46408; and
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Long Y, Luo J. WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network. BMC Bioinformatics 2019; 20:541. [PMID: 31675979 PMCID: PMC6824056 DOI: 10.1186/s12859-019-3066-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Inferring potential related microbes for diseases can not only promote disease prevention, diagnosis and treatment, but also provide valuable information for drug development. Considering that experimental methods are expensive and time-consuming, developing computational methods is an alternative choice. However, most of existing methods are biased towards well-characterized diseases and microbes. Furthermore, existing computational methods are limited in predicting potential microbes for new diseases. RESULTS Here, we developed a novel computational model to predict potential human microbe-disease associations (MDAs) based on Weighted Meta-Graph (WMGHMDA). We first constructed a heterogeneous information network (HIN) by combining the integrated microbe similarity network, the integrated disease similarity network and the known microbe-disease bipartite network. And then, we implemented iteratively pre-designed Weighted Meta-Graph search algorithm on the HIN to uncover possible microbe-disease pairs by cumulating the contribution values of weighted meta-graphs to the pairs as their probability scores. Depending on contribution potential, we described the contribution degree of different types of meta-graphs to a microbe-disease pair with bias rating. Meta-graph with higher bias rating will be assigned greater weight value when calculating probability scores. CONCLUSIONS The experimental results showed that WMGHMDA outperformed some state-of-the-art methods with average AUCs of 0.9288, 0.9068 ±0.0031 in global leave-one-out cross validation (LOOCV) and 5-fold cross validation (5-fold CV), respectively. In the case studies, 9, 19, 37 and 10, 20, 45 out of top-10, 20, 50 candidate microbes were manually verified by previous reports for asthma and inflammatory bowel disease (IBD), respectively. Furthermore, three common human diseases (Crohn's disease, Liver cirrhosis, Type 1 diabetes) were adopted to demonstrate that WMGHMDA could be efficiently applied to make predictions for new diseases. In summary, WMGHMDA has a high potential in predicting microbe-disease associations.
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Affiliation(s)
- Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
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Schoettler N, Strek ME. Recent Advances in Severe Asthma: From Phenotypes to Personalized Medicine. Chest 2019; 157:516-528. [PMID: 31678077 DOI: 10.1016/j.chest.2019.10.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/15/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
This review focuses on recent clinical and translational discoveries in severe and uncontrolled asthma that now enable phenotyping and personalized therapies in these patients. Although asthma is common in both children and adults and typically responds to standard therapies, a subset of individuals with asthma experience severe and/or persistent symptoms despite appropriate therapies. Airflow obstruction leading to frequent symptoms requiring higher levels of controller therapy is the cardinal feature of severe asthma, but the underlying molecular mechanisms, or endotypes, are diverse and variable between individuals. Two major risk factors that contribute to severe asthma are genetics and environmental exposures that modulate immune responses, and although these often interact in complex manners that are not fully understood, certain endotypes converge in severe asthma. A number of studies have evaluated various features of patients with severe asthma and classified patients into phenotypes with clinical relevance. This phenotyping is now incorporated into clinical practice and can be used to guide advanced biological therapies that target specific molecules and inflammatory pathways that contribute to asthma pathogenesis.
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Affiliation(s)
- Nathan Schoettler
- Department of Medicine, Section of Pulmonary and Critical Care, University of Chicago, Chicago, IL.
| | - Mary E Strek
- Department of Medicine, Section of Pulmonary and Critical Care, University of Chicago, Chicago, IL
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50
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Wypych TP, Wickramasinghe LC, Marsland BJ. The influence of the microbiome on respiratory health. Nat Immunol 2019; 20:1279-1290. [PMID: 31501577 DOI: 10.1038/s41590-019-0451-9] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Abstract
The revolution in microbiota research over the past decade has provided invaluable knowledge about the function of the microbial species that inhabit the human body. It has become widely accepted that these microorganisms, collectively called 'the microbiota', engage in networks of interactions with each other and with the host that aim to benefit both the microbial members and the mammalian members of this unique ecosystem. The lungs, previously thought to be sterile, are now known to harbor a unique microbiota and, additionally, to be influenced by microbial signals from distal body sites, such as the intestine. Here we review the role of the lung and gut microbiotas in respiratory health and disease and highlight the main pathways of communication that underlie the gut-lung axis.
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Affiliation(s)
- Tomasz P Wypych
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
| | - Lakshanie C Wickramasinghe
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
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