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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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Pulvirenti F, Giufrè M, Pentimalli TM, Camilli R, Milito C, Villa A, Sculco E, Cerquetti M, Pantosti A, Quinti I. Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency. Front Immunol 2024; 15:1371118. [PMID: 38873612 PMCID: PMC11169596 DOI: 10.3389/fimmu.2024.1371118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
Background The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited. Objective This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections. Methods Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients. Results Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months. Conclusions CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.
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Affiliation(s)
- Federica Pulvirenti
- Reference Center for Primary Immune Deficiencies, Azienda Ospedaliero Universitaria (AOU) Policlinico Umberto I, Rome, Italy
| | - Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tancredi M. Pentimalli
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin School of Integrative Oncology (BSIO), Berlin, Germany
| | - Romina Camilli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annalisa Villa
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Eleonora Sculco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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3
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Cheng ZX, Zhang J. Exploring the Role of Gut-Lung Interactions in COPD Pathogenesis: A Comprehensive Review on Microbiota Characteristics and Inflammation Modulation. CHRONIC OBSTRUCTIVE PULMONARY DISEASES (MIAMI, FLA.) 2024; 11:311-325. [PMID: 38563747 PMCID: PMC11216226 DOI: 10.15326/jcopdf.2023.0442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is a paramount contributor to global morbidity and mortality. Over the past decade, the concept of the "gut-lung axis" has emerged, offering a lens through which to examine the intricate interplay between the host, microbiome, and respiratory diseases, including COPD. An expanding body of evidence underscores that the composition of both the gastrointestinal and respiratory microbiome deviates in COPD patients compared to healthy individuals, leading to distinct host immune responses and clinical manifestations. The objective of this review is to provide a concise overview of the role both gut and respiratory microbiome play in the development of COPD. This was accomplished by compiling current literature on the microbiome profile in stable and exacerbated cases of COPD, as well as exploring the biological mechanisms through a discussion of relevant experiments conducted on murine models. Hallmark characteristics of the microbial profile in COPD encompass reduced Prevotella species in the respiratory microbiome, culminating in a loss of anti-inflammatory protection, and diminished Bacteroidetes in the gut microbiome, leading to a decrease in protective short-chain fatty acids. The proliferation of Proteobacteria, particularly the Haemophilus species, Moraxellaspecies, and Pseudomonas species contribute to COPD pathologies via recognition of proinflammatory lipopolysaccharide via Toll-like receptors. As a consequence, deteriorated pulmonary function, enhanced severity, increased onset of exacerbations, and elevated mortality were observed.
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Affiliation(s)
- Zi-Xuan Cheng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai, China
- *PhD candidate
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai, China
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4
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Kou Z, Liu K, Qiao Z, Wang Y, Li Y, Li Y, Yu X, Han W. The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis. Front Immunol 2024; 15:1407439. [PMID: 38779669 PMCID: PMC11109405 DOI: 10.3389/fimmu.2024.1407439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Background Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons. Methods A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC. Results A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, Prevotella, Streptococcus, Actinomyces, and Veillonella of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that Haemophilus, Lactobacillus, and Pseudomonas were increased, but Veillonella, Prevotella, Actinomyces, Porphyromonas, and Atopobium were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of Haemophilus, Lactobacillus and Pseudomonas genera exhibited an increase, whereas Actinomyces and Porphyromonas showed a decrease in the airway microbiota of AECOPD compared to HC. And Lachnospira of intestine microbiota in SCOPD was reduced at the genus level. Conclusion The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed. Systematic review registration PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.
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Affiliation(s)
- Ziwei Kou
- Department of Medicine, Qingdao University, Qingdao, China
| | - Kai Liu
- Department of Rehabilitation Medicine, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Zhengtong Qiao
- School of Rehabilitation Medical, Binzhou Medical University, Yantai, China
| | - Yaoyao Wang
- Department of Medicine, Qingdao University, Qingdao, China
| | - Yanmiao Li
- Department of Medicine, Qingdao University, Qingdao, China
| | - Yinan Li
- Department of Medicine, Qingdao University, Qingdao, China
| | - Xinjuan Yu
- Clinical Research Center, Qingdao Key Laboratory of Common Diseases, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Han
- Department of Respiratory and Critical Medicine, Qingdao Key Laboratory of Common Diseases, Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Qingdao, China
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Galeana-Cadena D, Gómez-García IA, Lopez-Salinas KG, Irineo-Moreno V, Jiménez-Juárez F, Tapia-García AR, Boyzo-Cortes CA, Matías-Martínez MB, Jiménez-Alvarez L, Zúñiga J, Camarena A. Winds of change a tale of: asthma and microbiome. Front Microbiol 2023; 14:1295215. [PMID: 38146448 PMCID: PMC10749662 DOI: 10.3389/fmicb.2023.1295215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023] Open
Abstract
The role of the microbiome in asthma is highlighted, considering its influence on immune responses and its connection to alterations in asthmatic patients. In this context, we review the variables influencing asthma phenotypes from a microbiome perspective and provide insights into the microbiome's role in asthma pathogenesis. Previous cohort studies in patients with asthma have shown that the presence of genera such as Bifidobacterium, Lactobacillus, Faecalibacterium, and Bacteroides in the gut microbiome has been associated with protection against the disease. While, the presence of other genera such as Haemophilus, Streptococcus, Staphylococcus, and Moraxella in the respiratory microbiome has been implicated in asthma pathogenesis, indicating a potential link between microbial dysbiosis and the development of asthma. Furthermore, respiratory infections have been demonstrated to impact the composition of the upper respiratory tract microbiota, increasing susceptibility to bacterial diseases and potentially triggering asthma exacerbations. By understanding the interplay between the microbiome and asthma, valuable insights into disease mechanisms can be gained, potentially leading to the development of novel therapeutic approaches.
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Affiliation(s)
- David Galeana-Cadena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Itzel Alejandra Gómez-García
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Karen Gabriel Lopez-Salinas
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Valeria Irineo-Moreno
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Fabiola Jiménez-Juárez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Alan Rodrigo Tapia-García
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Red de Medicina para la Educación, el Desarrollo y la Investigación Científica de Iztacala, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Alberto Boyzo-Cortes
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Melvin Barish Matías-Martínez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Luis Jiménez-Alvarez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Angel Camarena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
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6
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Mannion JM, McLoughlin RM, Lalor SJ. The Airway Microbiome-IL-17 Axis: a Critical Regulator of Chronic Inflammatory Disease. Clin Rev Allergy Immunol 2023; 64:161-178. [PMID: 35275333 PMCID: PMC10017631 DOI: 10.1007/s12016-022-08928-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 02/07/2023]
Abstract
The respiratory tract is home to a diverse microbial community whose influence on local and systemic immune responses is only beginning to be appreciated. Increasing reports have linked changes in this microbiome to a range of pulmonary and extrapulmonary disorders, including asthma, chronic obstructive pulmonary disease and rheumatoid arthritis. Central to many of these findings is the role of IL-17-type immunity as an important driver of inflammation. Despite the crucial role played by IL-17-mediated immune responses in protection against infection, overt Th17 cell responses have been implicated in the pathogenesis of several chronic inflammatory diseases. However, our knowledge of the influence of bacteria that commonly colonise the respiratory tract on IL-17-driven inflammatory responses remains sparse. In this article, we review the current knowledge on the role of specific members of the airway microbiota in the modulation of IL-17-type immunity and discuss how this line of research may support the testing of susceptible individuals and targeting of inflammation at its earliest stages in the hope of preventing the development of chronic disease.
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Affiliation(s)
- Jenny M Mannion
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Rachel M McLoughlin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Stephen J Lalor
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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7
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Kim JG, Zhang A, Rauseo AM, Goss CW, Mudd PA, O'Halloran JA, Wang L. The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity. J Med Virol 2023; 95:e28445. [PMID: 36583481 PMCID: PMC9880756 DOI: 10.1002/jmv.28445] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID-19), we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.
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Affiliation(s)
- Josh G. Kim
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Ai Zhang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Adriana M. Rauseo
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Charles W. Goss
- Division of BiostatisticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Philip A. Mudd
- Department of Emergency MedicineWashington University School of MedicineSt. LouisMissouriUSA
| | - Jane A. O'Halloran
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Leyao Wang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
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8
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Abushawish A, Haro K, Hoshina T, Kitajima N, Kusuhara K. Environmental factors related to differences in the microbiota in the upper respiratory tract in young children: Focusing on the impact of early nursery attendance. Front Pediatr 2023; 11:1015872. [PMID: 36798144 PMCID: PMC9927022 DOI: 10.3389/fped.2023.1015872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Microbial colonization of the upper respiratory tract (URT) during the first years of life differs significantly according to environmental factors. We investigated the association between early nursery attendance, URT infection (URTI) and drugs used for its treatment and the differences in the URT microbiota. METHODS This prospective study included 33 young children (11 and 22 with and without nursery attendance during their infancy, respectively). URT secretions were collected from the nasopharynx of these children at 2, 4, 6, 12, 18 and 24 months old. Clinical information after the latest sampling, including histories of URTI and the uses of antibiotics or cold medicines, was collected from all children. URT bacteria were identified by a clone library analysis of the 16S rRNA gene. RESULTS In the diversity of URT microbiota using the Shannon index, we did not detect any associations between variations in the URT microbiota and environmental factors (nursery attendance, development of URTIs, or the uses of antibiotics or cold medicines). However, in a clustering analysis, the proportion of the samples classified as Corynebacterium propinquum-dominant cluster was significantly lower in children ≥6 months old with nursery attendance than in those without nursery attendance. In addition, the URT microbiota was significantly different between samples from children ≥6 months old with and without a history of ≥3 URTI episodes after the first sampling. Furthermore, the URT microbiota was also significantly different between samples from these children with and without antibiotic use between the previous and present samplings. CONCLUSION Early nursery attendance and its related factors, including the frequency of URTI and antibiotic treatment, may be associated with the differences in the URT flora in young children.
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Affiliation(s)
- Asmaa Abushawish
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaoru Haro
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan.,Department of Pediatrics, Sato Children's Clinic, Kitakyushu, Japan
| | - Takayuki Hoshina
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Naoko Kitajima
- Department of Pediatrics, Onga Nakama Medical Association, Onga Hospital, Onga, Japan
| | - Koichi Kusuhara
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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9
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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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10
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Könönen E, Gursoy UK. Oral Prevotella Species and Their Connection to Events of Clinical Relevance in Gastrointestinal and Respiratory Tracts. Front Microbiol 2022; 12:798763. [PMID: 35069501 PMCID: PMC8770924 DOI: 10.3389/fmicb.2021.798763] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 12/19/2022] Open
Abstract
Prevotella is recognized as one of the core anaerobic genera in the oral microbiome. In addition, members of this genus belong to microbial communities of the gastrointestinal and respiratory tracts. Several novel Prevotella species, most of them of oral origin, have been described, but limited knowledge is still available of their clinical relevance. Prevotella melaninogenica is among the anaerobic commensals on oral mucosae from early months of life onward, and other early colonizing Prevotella species in the oral cavity include Prevotella nigrescens and Prevotella pallens. Oral Prevotella species get constant access to the gastrointestinal tract via saliva swallowing and to lower airways via microaspiration. At these extra-oral sites, they play a role as commensals but also as potentially harmful agents on mucosal surfaces. The aim of this narrative review is to give an updated overview on the involvement of oral Prevotella species in gastrointestinal and respiratory health and disease.
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Affiliation(s)
- Eija Könönen
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi K Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
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11
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Losol P, Park HS, Song WJ, Hwang YK, Kim SH, Holloway JW, Chang YS. Association of upper airway bacterial microbiota and asthma: systematic review. Asia Pac Allergy 2022; 12:e32. [PMID: 35966153 PMCID: PMC9353206 DOI: 10.5415/apallergy.2022.12.e32] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/31/2022] Open
Abstract
Individual studies have suggested that upper airway dysbiosis may be associated with asthma or its severity. We aimed to systematically review studies that evaluated upper airway bacterial microbiota in relation to asthma, compared to nonasthmatic controls. Searches used MEDLINE, Embase, and Web of Science Core Collection. Eligible studies included association between asthma and upper airway dysbiosis; assessment of composition and diversity of upper airway microbiota using 16S rRNA or metagenomic sequencing; upper airway samples from nose, nasopharynx, oropharynx or hypopharynx. Study quality was assessed and rated using the Newcastle-Ottawa scale. A total of 249 publications were identified; 17 in the final analysis (13 childhood asthma and 4 adult asthma). Microbiome richness was measured in 6 studies, species diversity in 12, and bacterial composition in 17. The quality of evidence was good and fair. The alpha-diversity was found to be higher in younger children with wheezing and asthma, while it was lower when asthmatic children had rhinitis or mite sensitization. In children, Proteobacteria and Firmicutes were higher in asthmatics compared to controls (7 studies), and Moraxella, Streptococcus, and Haemophilus were predominant in the bacterial community. In pooled analysis, nasal Streptococcus colonization was associated with the presence of wheezing at age 5 (p = 0.04). In adult patients with asthma, the abundance of Proteobacteria was elevated in the upper respiratory tract (3 studies). Nasal colonization of Corynebacterium was lower in asthmatics (2 studies). This study demonstrates the potential relationships between asthma and specific bacterial colonization in the upper airway in adult and children with asthma.
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Affiliation(s)
- Purevsuren Losol
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
| | - Hee-Sun Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Woo-Jung Song
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yu-Kyoung Hwang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Institute of Allergy and Clinical Immunology, Medical Research Center, Seoul National University, Seoul, Korea
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12
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Antibacterial, Immunomodulatory, and Lung Protective Effects of Boswelliadalzielii Oleoresin Ethanol Extract in Pulmonary Diseases: In Vitro and In Vivo Studies. Antibiotics (Basel) 2021; 10:antibiotics10121444. [PMID: 34943656 PMCID: PMC8698344 DOI: 10.3390/antibiotics10121444] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Lung diseases such as asthma, chronic obstructive pulmonary diseases, and pneumonia are causing many global health problems. The COVID-19 pandemic has directed the scientific community's attention toward performing more research to explore novel therapeutic drugs for pulmonary diseases. Herein, gas chromatography coupled with mass spectrometry tentatively identified 44 compounds in frankincense ethanol extract (FEE). We investigated the antibacterial and antibiofilm effects of FEE against Pseudomonas aeruginosa bacteria, isolated from patients with respiratory infections. In addition, its in vitro immunomodulatory activity was explored by the detection of the gene expression of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), nitric oxide synthase (iNOS), cycloxygenase-2 (COX-2), and nuclear factor kappa-B (NF-κB) in lipopolysaccharide (LPS)-induced peripheral blood mononuclear cells (PBMC). In addition, its anticancer activity against the A549 lung cancer cell line and human skin fibroblast (HSF) normal cell line was studied. Moreover, the in vivo lung protective potential of FEE was explored histologically and immunohistochemically in mice using a benzo(a)pyrene induced lung damage model. FEE exhibited antibacterial and antibiofilm activities besides the significant inhibition of gene expression of TNFα, IL-6, and NF-κB. FEE also exerted a cytotoxic effect against A549 cell line. Histological and immunohistochemical investigations with morphometric analysis of the mean area percentage and color intensity of positive TNF-α, COX-2, and NF-κB and Bcl-2 reactions revealed the lung protective activity of FEE. This study outlined the promising therapeutic activity of oleoresin obtained from B. dalzielii in the treatment of different pulmonary diseases.
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13
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Fabbrizzi A, Nannini G, Lavorini F, Tomassetti S, Amedei A. Microbiota and IPF: hidden and detected relationships. SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES 2021; 38:e2021028. [PMID: 34744424 PMCID: PMC8552575 DOI: 10.36141/svdld.v38i3.11365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Lung microbiota (LM) is an interesting new way to consider and redesign pathogenesis and possible therapeutic approach to many lung diseases, such as idiopathic pulmonary fibrosis (IPF), which is an interstitial pneumonia with bad prognosis. Chronic inflammation is the basis but probably not the only cause of lung fibrosis and although the risk factors are not completely clear, endogenous factors (e.g. gastroesophageal reflux) and environmental factors like cigarette smoking, industrial dusts, and precisely microbial agents could contribute to the IPF development. It is well demonstrated that many bacteria can cause epithelial cell injuries in the airways through induction of a host immune response or by activating flogosis mediators following a chronic, low-level antigenic stimulus. This persistent host response could influence fibroblast responsiveness suggesting that LM may play a role in repetitive alveolar injury in IPF. We reviewed literature regarding not only bacteria but also the role of virome and mycobiome in IPF. In fact, some viruses such as hepatitis C virus or certain fungi could be etiological agents or co-factors in the IPF progress. We aim to illustrate how the cross-talk between different local microbiotas throughout specific axis and immune modulation governed by microorganisms could be at the basis of lung dysfunctions and IPF development. Finally, since the future direction of medicine will be personalized, we suggest that the analysis of LM could be a goal to research new therapies also in IPF.
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Affiliation(s)
- Alessio Fabbrizzi
- Department of Respiratory Physiopathology, Palagi Hospital, Florence, Italy
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Federico Lavorini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy.,SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Florence, Italy
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14
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Li H, Wang Y, Zhang Z, Tan Y, Chen Z, Wang X, Pei T, Wang L. Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2502-2513. [PMID: 32305935 DOI: 10.1109/tcbb.2020.2986459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the years, numerous evidences have demonstrated that microbes living in the human body are closely related to human life activities and human diseases. However, traditional biological experiments are time-consuming and expensive, so it has become a research topic in bioinformatics to predict potential microbe-disease associations by adopting computational methods. In this study, a novel calculative method called BPNNHMDA is proposed to identify potential microbe-disease associations. In BPNNHMDA, a novel neural network model is first designed to infer potential microbe-disease associations, its input signal is a matrix of known microbe-disease associations, and its output signal is matrix of potential microbe-disease associations probabilities. And moreover, in the novel neural network model, a new activation function is designed to activate the hidden layer and the output layer based on the hyperbolic tangent function, and its initial connection weights are optimized by adopting Gaussian Interaction Profile kernel (GIP) similarity for microbes, which can improve the training speed of BPNNHMDA efficiently. Finally, in order to verify the performance of our prediction model, different frameworks such as the Leave-One-Out Cross Validation (LOOCV) and k-Fold Cross Validation ( k-Fold CV) are implemented on BPNNHMDA respectively. Simulation results illustrate that BPNNHMDA can achieve reliable AUCs of 0.9242, 0.9127 ± 0.0009 and 0.8955 ± 0.0018 in LOOCV, 5-Fold CV and 2-Fold CV separately, which are superior to previous state-of-the-art methods. Furthermore, case studies of inflammatory bowel disease (IBD), asthma and obesity demonstrate that BPNNHMDA has excellent prediction ability in practical applications as well.
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15
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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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16
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Stavropoulou E, Kantartzi K, Tsigalou C, Konstantinidis T, Voidarou C, Konstantinidis T, Bezirtzoglou E. Unraveling the Interconnection Patterns Across Lung Microbiome, Respiratory Diseases, and COVID-19. Front Cell Infect Microbiol 2021; 10:619075. [PMID: 33585285 PMCID: PMC7876344 DOI: 10.3389/fcimb.2020.619075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023] Open
Abstract
Albeit the lungs were thought to be sterile, recent scientific data reported a microbial microbiota in the lungs of healthy individuals. Apparently, new developments in technological approachesincluding genome sequencing methodologies contributed in the identification of the microbiota and shed light on the role of the gut and lung microbiomes in the development of respiratory diseases. Moreover, knowledge of the human microbiome in health may act as a tool for evaluating characteristic shifts in the case of disease. This review paper discusses the development of respiratory disease linked to the intestinal dysbiosis which influences the lung immunity and microbiome. The gastrointestinal-lung dialogue provides interesting aspects in the pathogenesis of the respiratory diseases. Lastly, we were further interested on the role of this interconnection in the progression and physiopathology of newly emergedCOVID-19.
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Affiliation(s)
- Elisavet Stavropoulou
- CHUV (Centre HospitalierUniversitaire Vaudois), Lausanne, Switzerland,Department of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland,*Correspondence: Elisavet Stavropoulou,
| | - Konstantia Kantartzi
- Nephrology Clinic, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Tsigalou
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theocharis Konstantinidis
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Theodoros Konstantinidis
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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17
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Tiew PY, Jaggi TK, Chan LLY, Chotirmall SH. The airway microbiome in COPD, bronchiectasis and bronchiectasis-COPD overlap. CLINICAL RESPIRATORY JOURNAL 2020; 15:123-133. [PMID: 33063421 DOI: 10.1111/crj.13294] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To review the airway microbiome in chronic obstructive pulmonary disease (COPD), bronchiectasis and bronchiectasis-COPD overlap (BCO). DATA SOURCE AND STUDY SELECTION Relevant studies were selected from PubMed, Google scholar, EMBASE and Web of Science. All studies involving human microbiomes, published in the English language, and using the search terms "COPD", "Chronic Obstructive Pulmonary Disease", "Bronchiectasis", "BCO" or "Bronchiectasis and COPD overlap", AND "microbiome", "mycobiome" or "metagenomics" were included. RESULTS Despite variability in sampling methods and specimen types used, microbiome composition remains relatively comparable in COPD and bronchiectasis with prominence of Proteobacteria, Firmicutes and Bacteroidetes. Alterations to airway microbiomes occur in association to disease severity and/or exacerbations in COPD and bronchiectasis. Decreased alpha diversity and Haemophilus-predominant microbiomes are associated with poorer survival in COPD, while, in bronchiectasis, Pseudomonas-predominant microbiomes demonstrate high exacerbation frequency and greater symptom burden while Aspergillus-dominant mycobiome profiles associate with exacerbations. The role of the microbiome in BCO remains understudied. CONCLUSION Use of next-generation sequencing has revolutionised our detection and understanding of the airway microbiome in chronic respiratory diseases such as COPD and bronchiectasis. Targeted amplicon sequencing reveals important associations between the respiratory microbiome and disease outcome while metagenomics may elucidate functional pathways. How best to apply this information into patient care, monitoring and treatment, however, remains challenging and necessitates further study.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Tavleen K Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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18
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Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant. Ann Am Thorac Soc 2020; 16:1383-1391. [PMID: 31415219 DOI: 10.1513/annalsats.201904-299oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rationale: The oropharyngeal microbiome is a primary source of lung microbiota, contributes to lower respiratory infection, and is also a driver of oral health.Objectives: We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics after lung transplantation, and ecological features of dysbiosis.Methods: Oropharyngeal wash samples were obtained from individuals with end-stage disease awaiting transplantation (n = 22) and longitudinally from individuals at 6 weeks, 3 months, and 6 months after transplantation (n = 33), along with healthy control subjects (n = 14). Bacterial 16S and fungal internal transcribed spacer rRNA regions were deep-sequenced, and bacterial community respiratory patterns were imputed from taxonomic composition.Results: Healthy subjects' oropharyngeal microbiomes showed a gradient of community types reflecting relative enrichment of strictly anaerobic, aerobic, or facultative anaerobic bacteria. Patients with end-stage lung disease showed severe dysbiosis by both taxonomic composition and respiration phenotypes, with reduced richness and diversity, increased facultative and decreased aerobic bacteria, and absence of communities characterized by obligate aerobes. In patients at 6 weeks and 3 months post-transplant, richness and diversity were intermediate between healthy and pretransplant subjects, with near-normal distribution of community types. However, by 6 months post-transplant, oropharyngeal wash resembled the low-diversity facultative-dominated profile of pretransplant subjects. Community ecotype correlated with Candida abundance.Conclusions: End-stage lung disease is associated with marked upper respiratory tract dysbiosis involving both community structure and respiratory metabolism profiles of constituent bacteria. Dynamic changes occur after lung transplantation, with partial normalization early but later appearance of severe dysbiosis similar to pretransplant patients. Aberrant oropharyngeal communities may predispose to abnormal lung microbiota and infection risk both in advanced lung disease and after transplantation.
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19
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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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20
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Mammen MJ, Scannapieco FA, Sethi S. Oral-lung microbiome interactions in lung diseases. Periodontol 2000 2020; 83:234-241. [PMID: 32385873 DOI: 10.1111/prd.12301] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The proximity and continuity of the oral cavity and the lower respiratory tract allows the oropharyngeal microbiome to be a major determinant of the lung microbiome. In addition, host-pathogen interactions related to the oropharyngeal microbiome or its metabolites could propagate systemic inflammation or modulate host defense mechanisms that could affect other organs, including the lung. There is increasing appreciation of the pathophysiologic significance of the lung microbiome, not only in the classical infection-related diseases, pneumonia, bronchiectasis, and cystic fibrosis, but also in chronic noninfectious lung diseases, such as chronic obstructive pulmonary disease, asthma, and pulmonary fibrosis. In this review, we will explore the relationship of the oral microbiome with lung diseases, such as pneumonia, chronic obstructive pulmonary disease, asthma, and cystic fibrosis.
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Affiliation(s)
- Manoj J Mammen
- Division of Pulmonary, Critical Care, and Sleep Medicine, Jacobs School of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Frank A Scannapieco
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Sanjay Sethi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Jacobs School of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA.,Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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21
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Abdel-Aziz MI, Neerincx AH, Vijverberg SJ, Kraneveld AD, Maitland-van der Zee AH. Omics for the future in asthma. Semin Immunopathol 2020; 42:111-126. [PMID: 31942640 DOI: 10.1007/s00281-019-00776-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/22/2019] [Indexed: 12/31/2022]
Abstract
Asthma is a common, complex, multifaceted disease. It comprises multiple phenotypes, which might benefit from treatment with different types of innovative targeted therapies. Refining these phenotypes and understanding their underlying biological structure would help to apply precision medicine approaches. Using different omics methods, such as (epi)genomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, allowed to view and investigate asthma from diverse angles. Technological advancement led to a large increase in the application of omics studies in the asthma field. Although the use of omics technologies has reduced the gap between bench to bedside, several design and methodological challenges still need to be tackled before omics can be applied in asthma patient care. Collaborating under a centralized harmonized work frame (such as in consortia, under consistent methodologies) could help worldwide research teams to tackle these challenges. In this review, we discuss the transition of single biomarker research to multi-omics studies. In addition, we deliberate challenges such as the lack of standardization of sampling and analytical methodologies and validation of findings, which comes in between omics and personalized patient care. The future of omics in asthma is encouraging but not completely clear with some unanswered questions, which have not been adequately addressed before. Therefore, we highlight these questions and emphasize on the importance of fulfilling them.
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Affiliation(s)
- Mahmoud I Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands.,Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Anne H Neerincx
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands. .,Department of Pediatric Respiratory Medicine, Emma Children's Hospital, Amsterdam UMC, Amsterdam, Netherlands.
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22
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Son JH, Kim JH, Chang HS, Park JS, Park CS. Relationship of Microbial Profile With Airway Immune Response in Eosinophilic or Neutrophilic Inflammation of Asthmatics. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:412-429. [PMID: 32141256 PMCID: PMC7061157 DOI: 10.4168/aair.2020.12.3.412] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/12/2019] [Accepted: 12/07/2019] [Indexed: 01/24/2023]
Abstract
PURPOSE Different characteristics of airway microbiome in asthmatics may lead to differential immune responses, which in turn cause eosinophilic or neutrophilic airway inflammation. However, the relationships among these factors have yet to be fully elucidated. METHODS Microbes in induced sputum samples were subjected to sequence analysis of 16S rRNA. Airway inflammatory phenotypes were defined as neutrophils (>60%) and eosinophils (>3%), and inflammation endotypes were defined by levels of T helper (Th) 1 (interferon-γ), Th2 (interleukin [IL]-5 and IL-13), Th-17 (IL-17), and innate Th2 (IL-25, IL-33, and thymic stromal lymphopoietin) cytokines, inflammasomes (IL-1β), epithelial activation markers (granulocyte-macrophage colony-stimulating factor and IL-8), and Inflammation (IL-6 and tumor necrosis factor-α) cytokines in sputum supernatants was assessed by enzyme-linked immunosorbent assay. RESULTS The numbers of operational taxonomic units were significantly higher in the mixed (n = 21) and neutrophilic (n = 23) inflammation groups than in the paucigranulocytic inflammation group (n = 19; p < 0.05). At the species level, Granulicatella adiacens, Streptococcus parasanguinis, Streptococcus pneumoniae, Veillonella rogosae, Haemophilus parainfluenzae, and Neisseria perflava levels were significantly higher in the eosinophilic inflammation group (n = 20), whereas JYGU_s levels were significantly higher in the neutrophilic inflammation group compared to the other subtypes (p < 0.05). Additionally, IL-5 and IL-13 concentrations were correlated with the percentage of eosinophils (p < 0.05) and IL-13 levels were positively correlated with the read counts of Porphyromonas pasteri and V. rogosae (p < 0.05). IL-1β concentrations were correlated with the percentage of neutrophils (p < 0.05). had a tendency to be positively correlated with the read count of JYGU_s (p = 0.095), and was negatively correlated with that of S. pneumoniae (p < 0.05). CONCLUSIONS Difference of microbial patterns in airways may induce distinctive endotypes of asthma, which is responsible for the neutrophilic or eosinophilic inflammation in asthma.
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Affiliation(s)
- Ji Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan, Korea
| | - Jung Hyun Kim
- Department of Internal Medicine, Korean Armed Forces Capital Hospital, Seongnam, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan, Korea.
| | - Jong Sook Park
- Genome Research Center and Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
| | - Choon Sik Park
- Genome Research Center and Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
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McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ, Lynch SV. Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma. J Allergy Clin Immunol 2019; 144:1187-1197. [PMID: 31201890 PMCID: PMC6842413 DOI: 10.1016/j.jaci.2019.05.035] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND In infants, distinct nasopharyngeal bacterial microbiotas differentially associate with the incidence and severity of acute respiratory tract infection and childhood asthma development. OBJECTIVE We hypothesized that distinct nasal airway microbiota structures also exist in children with asthma and relate to clinical outcomes. METHODS Nasal secretion samples (n = 3122) collected after randomization during the fall season from children with asthma (6-17 years, n = 413) enrolled in a trial of omalizumab (anti-IgE) underwent 16S rRNA profiling. Statistical analyses with exacerbation as the primary outcome and rhinovirus infection and respiratory illnesses as secondary outcomes were performed. Using A549 epithelial cells, we assessed nasal isolates of Moraxella, Staphylococcus, and Corynebacterium species for their capacity to induce epithelial damage and inflammatory responses. RESULTS Six nasal airway microbiota assemblages, each dominated by Moraxella, Staphylococcus, Corynebacterium, Streptococcus, Alloiococcus, or Haemophilus species, were observed. Moraxella and Staphylococcus species-dominated microbiotas were most frequently detected and exhibited temporal stability. Nasal microbiotas dominated by Moraxella species were associated with increased exacerbation risk and eosinophil activation. Staphylococcus or Corynebacterium species-dominated microbiotas were associated with reduced respiratory illness and exacerbation events, whereas Streptococcus species-dominated assemblages increased the risk of rhinovirus infection. Nasal microbiota composition remained relatively stable despite viral infection or exacerbation; only a few taxa belonging to the dominant genera exhibited relative abundance fluctuations during these events. In vitro, Moraxella catarrhalis induced significantly greater epithelial damage and inflammatory cytokine expression (IL-33 and IL-8) compared with other dominant nasal bacterial isolates tested. CONCLUSION Distinct nasal airway microbiotas of children with asthma relate to the likelihood of exacerbation, rhinovirus infection, and respiratory illnesses during the fall season.
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Affiliation(s)
- Kathryn McCauley
- Department of Medicine, University of California, San Francisco, Calif
| | - Juliana Durack
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Douglas W Fadrosh
- Department of Medicine, University of California, San Francisco, Calif
| | - Din L Lin
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | | | - Kei E Fujimura
- Department of Medicine, University of California, San Francisco, Calif
| | - Brandon LaMere
- Department of Medicine, University of California, San Francisco, Calif
| | - Geil Merana
- Department of Medicine, University of California, San Francisco, Calif
| | - Kole Lynch
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | | | - Carolyn M Kercsmar
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Michelle Gill
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Andrew H Liu
- Department of Pedatrics and Pulmonology Medicine, National Jewish Health, Denver, Colo; Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Haejin Kim
- Department of Internal Medicine, Division of Allergy and Immunology, Henry Ford Health System, Detroit, Mich
| | - Meyer Kattan
- College of Physicians and Surgeons, Columbia University, New York, NY
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, Calif
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis.
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, Calif.
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24
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Gomes S, Cavadas B, Ferreira JC, Marques PI, Monteiro C, Sucena M, Sousa C, Vaz Rodrigues L, Teixeira G, Pinto P, Tavares de Abreu T, Bárbara C, Semedo J, Mota L, Carvalho AS, Matthiesen R, Pereira L, Seixas S. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma. Sci Rep 2019; 9:12838. [PMID: 31492894 PMCID: PMC6731246 DOI: 10.1038/s41598-019-49195-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/19/2019] [Indexed: 12/31/2022] Open
Abstract
The lung is a complex ecosystem of host cells and microbes often disrupted in pathological conditions. Although bacteria have been hypothesized as agents of carcinogenesis, little is known about microbiota profile of the most prevalent cancer subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). To characterize lung cancer (LC) microbiota a first a screening was performed through a pooled sequencing approach of 16S ribosomal RNA gene (V3-V6) using a total of 103 bronchoalveaolar lavage fluid samples. Then, identified taxa were used to inspect 1009 cases from The Cancer Genome Atlas and to annotate tumor unmapped RNAseq reads. Microbial diversity was analyzed per cancer subtype, history of cigarette smoking and airflow obstruction, among other clinical data. We show that LC microbiota is enriched in Proteobacteria and more diverse in SCC than ADC, particularly in males and heavier smokers. High frequencies of Proteobacteria were found to discriminate a major cluster, further subdivided into well-defined communities’ associated with either ADC or SCC. Here, a SCC subcluster differing from other cases by a worse survival was correlated with several Enterobacteriaceae. Overall, this study provides first evidence for a correlation between lung microbiota and cancer subtype and for its influence on patient life expectancy.
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Affiliation(s)
- Sílvia Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Joana Catarina Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Catarina Monteiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Maria Sucena
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Catarina Sousa
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Luís Vaz Rodrigues
- Department of Pneumology, Unidade Local de Saúde da Guarda (USLG), Guarda, Portugal
| | - Gilberto Teixeira
- Department of Pneumology; Centro Hospitalar do Baixo Vouga (CHBV), Aveiro, Portugal
| | - Paula Pinto
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Tiago Tavares de Abreu
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Cristina Bárbara
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Júlio Semedo
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Leonor Mota
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
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25
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Lopes MP, Cruz ÁA, Xavier MT, Stöcker A, Carvalho-Filho P, Miranda PM, Meyer RJ, Soledade KR, Gomes-Filho IS, Trindade SC. Prevotella intermedia and periodontitis are associated with severe asthma. J Periodontol 2019; 91:46-54. [PMID: 31342509 DOI: 10.1002/jper.19-0065] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Periodontitis, an inflammatory disease of multibacterial etiology that affects the protective and supporting tissues surrounding teeth, can influence the course of respiratory diseases, such as asthma, due to epithelial alterations arising from inflammatory and immunological processes, bronchial remodeling, or by the aspiration of pathogenic colonizers found in periodontal pockets. This study evaluated the levels of periodontal pathogens Prevotella intermedia, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans in the subgingival biofilm of individuals with and without severe asthma. METHODS A case-control study enrolling 457 individuals (220 with asthma and 237 without asthma) was conducted at the Program for Control of Asthma in Bahia (ProAR) Clinic located in Salvador, Bahia, Brazil. A structured questionnaire was used to obtain data on sociodemographic, health status, and lifestyle habits. A clinical periodontal assessment was performed, including bleeding on probing, probing depth, and clinical attachment level. Subgingival biofilm was collected at the deepest site of each sextant, and bacterial DNA was extracted. Quantitative real-time PCR analysis was performed to detect and relatively quantify periodontopathogens in the biofilm. RESULTS Statistically significant positive associations were found between periodontitis and severe asthma, (odds ratio [OR]adjusted] : 4.00; 95% confidence interval [CI]: 2.26 to 7.10). High levels of P. intermedia were found in association with the presence of severe asthma (ORadjusted : 2.64; 95% CI: 1.62 to 4.39; P < 0.01). CONCLUSIONS The present results suggest that periodontitis and P. intermedia are associated with severe asthma. However, the functional consequences of this dysbiosis upon asthma susceptibility and its phenotypes remain unclear.
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Affiliation(s)
- Mabel P Lopes
- Post-Graduation Program, Federal University of Bahia, Salvador, Brazil
| | - Álvaro A Cruz
- Faculty of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Márcia T Xavier
- Department of Biointeraction, Federal University of Bahia, Salvador, Brazil
| | - Andreas Stöcker
- Universitary Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | | | | | - Roberto J Meyer
- Department of Biointeraction, Federal University of Bahia, Salvador, Brazil
| | - Kaliane R Soledade
- Department of Biointeraction, Federal University of Bahia, Salvador, Brazil
| | - Isaac S Gomes-Filho
- Department of Health, Feira de Santana State University, Feira de Santana, Brazil
| | - Soraya C Trindade
- Post-Graduation Program, Federal University of Bahia, Salvador, Brazil.,Department of Health, Feira de Santana State University, Feira de Santana, Brazil
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26
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Abdel-Aziz MI, Vijverberg SJH, Neerincx AH, Kraneveld AD, Maitland-van der Zee AH. The crosstalk between microbiome and asthma: Exploring associations and challenges. Clin Exp Allergy 2019; 49:1067-1086. [PMID: 31148278 PMCID: PMC6852296 DOI: 10.1111/cea.13444] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
With the advancement of high‐throughput DNA/RNA sequencing and computational analysis techniques, commensal bacteria are now considered almost as important as pathological ones. Understanding the interaction between these bacterial microbiota, host and asthma is crucial to reveal their role in asthma pathophysiology. Several airway and/or gut microbiome studies have shown associations between certain bacterial taxa and asthma. However, challenges remain before gained knowledge from these studies can be implemented into clinical practice, such as inconsistency between studies in choosing sampling compartments and/or sequencing approaches, variability of results in asthma studies, and not taking into account medication intake and diet composition especially when investigating gut microbiome. Overcoming those challenges will help to better understand the complex asthma disease process. The therapeutic potential of using pro‐ and prebiotics to prevent or reduce risk of asthma exacerbations requires further investigation. This review will focus on methodological issues regarding setting up a microbiome study, recent developments in asthma bacterial microbiome studies, challenges and future therapeutic potential.
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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
| | - 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
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Institute for Risk Assessment Sciences, 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, Amsterdam UMC, Emma Children's Hospital, Amsterdam, The Netherlands
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27
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Multi-Method Molecular Characterisation of Human Dust-Mite-associated Allergic Asthma. Sci Rep 2019; 9:8912. [PMID: 31221987 PMCID: PMC6586825 DOI: 10.1038/s41598-019-45257-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
Asthma is a chronic inflammatory disorder of the airways. Disease presentation varies greatly in terms of cause, development, severity, and response to medication, and thus the condition has been subdivided into a number of asthma phenotypes. There is still an unmet need for the identification of phenotype-specific markers and accompanying molecular tools that facilitate the classification of asthma phenotype. To this end, we utilised a range of molecular tools to characterise a well-defined group of female adults with poorly controlled atopic asthma associated with house dust mite (HDM) allergy, relative to non-asthmatic control subjects. Circulating messenger RNA (mRNA) and microRNA (miRNA) were sequenced and quantified, and a differential expression analysis of the two RNA populations performed to determine how gene expression and regulation varied in the disease state. Further, a number of circulating proteins (IL-4, 5, 10, 13, 17 A, Eotaxin, GM-CSF, IFNy, MCP-1, TARC, TNFα, Total IgE, and Endotoxin) were quantified to determine whether the protein profiles differed significantly dependent on disease state. Finally, we utilised a previously published assessment of the circulating “blood microbiome” performed using 16S rRNA amplification and sequencing. Asthmatic subjects displayed a range of significant alterations to circulating gene expression and regulation, relative to healthy control subjects, that may influence systemic immune activity. Notably, several circulating mRNAs were detected in just the asthma group or just in the control group, and many more were observed to be expressed at significantly different levels in the asthma group compared to the control group. Proteomic analysis revealed increased levels of inflammatory proteins within the serum, and decreased levels of the bacterial endotoxin protein in the asthmatic state. Comparison of blood microbiome composition revealed a significant increase in the Firmicutes phylum with asthma that was associated with a concomitant reduction in the Proteobacteria phylum. This study provides a valuable insight into the systemic changes evident in the HDM-associated asthma, identifies a range of molecules that are present in the circulation in a condition-specific manner (with clear biomarker potential), and highlights a range of hypotheses for further study.
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28
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Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status. mSystems 2018; 3:mSystems00199-18. [PMID: 30417108 PMCID: PMC6208642 DOI: 10.1128/msystems.00199-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 12/16/2022] Open
Abstract
Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases. Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease. Community structure analyses revealed three distinct microbial compositions, which were significantly correlated with bacterial biomass, human Th17 immune response, and COPD exacerbation frequency. Specifically, samples with transcriptionally active Streptococcus, Rothia, or Pseudomonas had bacterial loads 16 times higher than samples enriched for Escherichia and Ralstonia. These high-bacterial-load samples also tended to undergo a stronger Th17 immune response. Furthermore, an increased proportion of lymphocytes was found in samples with active Pseudomonas. In addition, COPD patients with active Streptococcus or Rothia infections tended to have lower rates of exacerbations than patients with active Pseudomonas and patients with lower bacterial biomass. Our results support the idea of a stratified structure of the active lung microbiome and a significant host-microbe interaction. We speculate that diverse lung microbiomes exist in the population and that their presence and activities could either influence or reflect different aspects of lung health. IMPORTANCE Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.
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29
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Choi J, Oh JY, Lee YS, Hur GY, Lee SY, Shim JJ, Kang KH, Min KH. Pseudomonas aeruginosa infection increases the readmission rate of COPD patients. Int J Chron Obstruct Pulmon Dis 2018; 13:3077-3083. [PMID: 30323578 PMCID: PMC6174684 DOI: 10.2147/copd.s173759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction Acute exacerbation of COPD (AECOPD) leads to rapid deterioration of pulmonary function and quality of life. It is unclear whether the prognosis for AECOPD differs depending on the bacterium or virus identified. The purpose of this study is to determine whether readmission of patients with severe AECOPD varies according to the bacterium or virus identified. Methods We performed a retrospective review of medical records of 704 severe AECOPD events at Korea University Guro Hospital from January 2011 to May 2017. We divided events into two groups, one in which patients were readmitted within 30 days after discharge and the other in which there was no readmission. Results Of the 704 events, 65 were followed by readmission within 30 days. Before propensity score matching, the readmission group showed a higher rate of bacterial identification with no viral identification and a higher rate of identification with the Pseudomonas aeruginosa (P=0.003 and P=0.007, respectively). Using propensity score matching, the readmission group still showed a higher P. aeruginosa identification rate (P=0.030), but there was no significant difference in the rate of bacterial identification, with no viral identification (P=0.210). In multivariate analysis, the readmission group showed a higher P. aeruginosa identification rate than the no-readmission group (odds ratio, 4.749; 95% confidence interval, 1.296-17.041; P=0.019). Conclusion P. aeruginosa identification is associated with a higher readmission rate in AECOPD patients.
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Affiliation(s)
- Juwhan Choi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Jee Youn Oh
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Young Seok Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Gyu Young Hur
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Sung Yong Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Jae Jeong Shim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Kyung Ho Kang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
| | - Kyung Hoon Min
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea,
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30
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van der Does AM, Amatngalim GD, Keijser B, Hiemstra PS, Villenave R. Contribution of Host Defence Proteins and Peptides to Host-Microbiota Interactions in Chronic Inflammatory Lung Diseases. Vaccines (Basel) 2018; 6:vaccines6030049. [PMID: 30060554 PMCID: PMC6161034 DOI: 10.3390/vaccines6030049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
The respiratory tract harbours a variety of microorganisms, collectively called the respiratory microbiota. Over the past few years, alterations in respiratory and gut microbiota composition have been associated with chronic inflammatory diseases of the lungs. How these changes influence disease development and progression is an active field of investigation. Identifying and understanding host-microbiota interactions and factors contributing to these interactions could promote the development of novel therapeutic strategies aimed at restoring host-microbiota homeostasis. In this review, we discuss recent literature on host-microbiota interactions in the respiratory tract, with a specific focus on the influence of endogenous host defence peptides and proteins (HDPs) on the composition of microbiota populations in vivo and explore possible HDPs-related therapeutic approaches targeting microbiota dysbiosis in chronic inflammatory lung diseases.
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Affiliation(s)
- Anne M van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
| | - Gimano D Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
| | - Bart Keijser
- Research Group Microbiology and Systems Biology, TNO (The Netherlands Organization for Applied Scientific Research), Zeist 3704 HE, The Netherlands.
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam, Amsterdam 1008 AA, The Netherlands.
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
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Jiang W, Ma Z, Zhang H, Lynn HS, Xu B, Zhang X, Bi R, Fu J, Chen Y, Xiao Z, Zhang Z, Lu Z. Efficacy of Jia Wei Yang He formula as an adjunctive therapy for asthma: study protocol for a randomized, double blinded, controlled trial. Trials 2018; 19:355. [PMID: 29973284 PMCID: PMC6032802 DOI: 10.1186/s13063-018-2739-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Over the past two or three decades, the prevalence of asthma has significantly increased worldwide; therefore, effective treatment without side effects is of utmost importance. Traditional Chinese medicine (TCM) plays a vital role in reducing symptoms and improving the quality of life in persistent-asthma patients. The aim of this study is to evaluate the efficacy of the Jia Wei Yang He (JWYH) formula in the treatment of asthma and to explore the relationship between the airway microbiome and TCM treatment in asthma patients. METHODS/DESIGN This multicenter, parallel-arm, randomized, double-blinded, placebo-controlled trial will assess the efficacy of JWYH in asthma patients with usual care. Persistent-asthma patients without life-threatening disease will be enrolled on a random basis and are equally assigned to a high- or a low-dose JWYH plus usual care group, or a placebo plus usual care group. Patients are followed up for 4 months. Accordingly, 240 patients will yield sufficient statistical power to determine a difference between groups. Based on modified intent-to-treat (mITT) analyses, the three groups will be compared at 4 weeks after the beginning of treatment. The primary efficacy measurement is the mean change in the Asthma Control Test (ACT) score from baseline to 4 weeks post treatment. Secondary outcomes include forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), peak expiratory flow (PEF), and asthma exacerbations. This trial also includes analyses of the associations between airway microbiome and asthma treatment. DISCUSSION In this study, a randomized clinical trial design is described. The results are based on several outcomes that estimate the efficacy of the JWYH formula and prospective links between the airway microbiome and asthma treatment. TRIAL REGISTRATION ClinicalTrials.gov, ID: NCT03299322 . Registered on 3 October 2017.
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Affiliation(s)
- Wenhan Jiang
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, People’s Republic of China
| | - Zifeng Ma
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Huiyong Zhang
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Henry S. Lynn
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, People’s Republic of China
| | - Beiqi Xu
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Xiao Zhang
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Rongrong Bi
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Jiyou Fu
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Yue Chen
- School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON Canada
| | - Zhen Xiao
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
| | - Zhijie Zhang
- Department of Epidemiology, School of Public Health, Fudan University, 130 Dongan Road, No.8 building, Xuhui District, Shanghai, People’s Republic of China
| | - Zhenhui Lu
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, No.725 South Wanping Road, No.1 building, Xuhui District, Shanghai, People’s Republic of China
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Novel human microbe-disease associations inference based on network consistency projection. Sci Rep 2018; 8:8034. [PMID: 29795313 PMCID: PMC5966389 DOI: 10.1038/s41598-018-26448-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/09/2018] [Indexed: 02/06/2023] Open
Abstract
Increasing evidence shows that microbes are closely related to various human diseases. Obtaining a comprehensive and detailed understanding of the relationships between microbes and diseases would not only be beneficial to disease prevention, diagnosis and prognosis, but also would lead to the discovery of new drugs. However, because of a lack of data, little effort has been made to predict novel microbe-disease associations. To date, few methods have been proposed to solve the problem. In this study, we developed a new computational model based on network consistency projection to infer novel human microbe-disease associations (NCPHMDA) by integrating Gaussian interaction profile kernel similarity of microbes and diseases, and symptom-based disease similarity. NCPHMDA is a non-parametric and global network based model that combines microbe space projection and disease space projection to achieve the final prediction. Experimental results demonstrated that the integrated space projection of microbes and diseases, and symptom-based disease similarity played roles in the model performance. Cross validation frameworks and case studies further illustrated the superior predictive performance over other methods.
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33
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Wu C, Gao R, Zhang D, Han S, Zhang Y. PRWHMDA: Human Microbe-Disease Association Prediction by Random Walk on the Heterogeneous Network with PSO. Int J Biol Sci 2018; 14:849-857. [PMID: 29989079 PMCID: PMC6036753 DOI: 10.7150/ijbs.24539] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
Microorganisms resided in human body play a vital role in metabolism, immune defense, nutrition absorption, cancer control and protection against pathogen colonization. The changes of microbial communities can cause human diseases. Based on the known microbe-disease association, we presented a novel computational model employing Random Walking with Restart optimized by Particle Swarm Optimization (PSO) on the heterogeneous interlinked network of Human Microbe-Disease Associations (PRWHMDA) (see Figure 1). Based on the known human microbe-disease associations, we constructed the heterogeneous interlinked network with Cosine similarity. The extended random walk with restart (RWR) method was derived to get the potential microbe-disease associations. PSO was utilized to get the optimal parameters of RWR. To evaluate the prediction effectiveness, we performed leave one out cross validation (LOOCV) and 5-fold cross validation (CV), which got the AUC (The area under ROC curve) of 0.915 (LOOCV) and the average AUCs of 0.8875 ± 0.0046 (5-fold CV). Moreover, we carried out three case studies of asthma, inflammatory bowel disease (IBD) and type 1 diabetes (T1D) for the further evaluation. The result showed that 10, 10 and 9 of top-10 predicted microbes were verified by previously published experimental results, respectively. It is anticipated that PRWHMDA can be effective to identify the disease-related microbes and maybe helpful to disclose the relationship between microorganisms and their human host.
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Affiliation(s)
- Chuanyan Wu
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Daoliang Zhang
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Shiyun Han
- General Clinic, The No. 2 People's Hospital of Tianqiao, Jinan, 250032, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
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Padilla-Galo A, Olveira C, Fernández de Rota-Garcia L, Marco-Galve I, Plata AJ, Alvarez A, Rivas-Ruiz F, Carmona-Olveira A, Cebrian-Gallardo JJ, Martinez-Garcia MA. Factors associated with bronchiectasis in patients with uncontrolled asthma; the NOPES score: a study in 398 patients. Respir Res 2018; 19:43. [PMID: 29548297 PMCID: PMC5857069 DOI: 10.1186/s12931-018-0746-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/09/2018] [Indexed: 02/04/2023] Open
Abstract
Background Some studies have reported a high prevalence of bronchiectasis in patients with uncontrolled asthma, but the factors associated with this condition are unknown. The objective of this study was to determine the prevalence of bronchiectasis in uncontrolled moderate-to-severe asthma and to identify risk factors and their correlation with bronchiectasis in these patients. Methods This is a prospective study of data from consecutive patients with uncontrolled moderate-to-severe asthma. Diagnosis of bronchiectasis was based on high-resolution computed tomography. A prognostic score was developed using a logistic regression model, which was used to determine the factors associated with bronchiectasis. Results A total of 398 patients (60% with severe asthma) were included. The prevalence of bronchiectasis was 28.4%. The presence of bronchiectasis was associated with a higher frequency of chronic expectoration (OR, 2.95; 95% CI, 1.49–5.84; p = 0.002), greater severity of asthma (OR, 2.43; 95% CI, 1.29–4.57; p = 0.006), at least one previous episode of pneumonia (OR, 2.42; 95% CI, 1.03–5.69; p = 0.044), and lower levels of FeNO (OR, 0.98; 95% CI, 0.97–0.99; p = 0.016). The NOPES score was developed on the basis of these variables (FeNO[cut off point 20.5 ppb], Pneumonia, Expectoration and asthma Severity), and it ranges from 0 to 4 points, where 0 means “no risk” and 4 corresponds to “high risk”. The NOPES score yielded an AUC-ROC of 70% for the diagnosis of bronchiectasis, with a specificity of 95%. Conclusions Almost a third of the patients with uncontrolled moderate-to-severe asthma had bronchiectasis. Bronchiectasis was related to the severity of asthma, the presence of chronic expectoration, a previous history of pneumonia, and lower levels of FeNO. The NOPES score is an easy-to-use scoring system with a high prognostic value for bronchiectasis in patients with uncontrolled moderate-to-severe asthma.
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Affiliation(s)
- A Padilla-Galo
- Pneumology Unit. Agencia Sanitaria Costa del Sol, Carretera Nacional 340, Km 187, 29603, Marbella, Málaga, Spain
| | - C Olveira
- Pneumology Department, IBIMA (Institute for biomedical research of Málaga), Hospital Regional Universitario de Málaga/ University of Málaga, Avenida Carlos Haya, 29010, Málaga, Spain.
| | - L Fernández de Rota-Garcia
- Pneumology Unit. Agencia Sanitaria Costa del Sol, Carretera Nacional 340, Km 187, 29603, Marbella, Málaga, Spain
| | - I Marco-Galve
- Radiology Deparment. Hospital de Alta Resolución de Benalmádena, Arroyo Hondo s/n, 29639, Benalmádena, Málaga, Spain
| | - A J Plata
- Infectious Diseases Department, Hospital Regional Universitario de Málaga, Avenida Carlos Haya, 29010, Málaga, Spain
| | - A Alvarez
- Radiology Deparment. Hospital de Alta Resolución de Benalmádena, Arroyo Hondo s/n, 29639, Benalmádena, Málaga, Spain
| | - F Rivas-Ruiz
- Research Unit. Red de Investigación en Servicios de Salud en Enfermedades Crónicas, REDISSEC (Spanish healthcare network for chronic diseases), Agencia Sanitaria Costa del Sol, Carretera Nacional 340, Km 187, 29603, Marbella, Málaga, Spain
| | | | - J J Cebrian-Gallardo
- Pneumology Unit. Agencia Sanitaria Costa del Sol, Carretera Nacional 340, Km 187, 29603, Marbella, Málaga, Spain
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Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. Mediators Inflamm 2017; 2017:5047403. [PMID: 29445257 PMCID: PMC5763206 DOI: 10.1155/2017/5047403] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/24/2017] [Accepted: 10/22/2017] [Indexed: 12/16/2022] Open
Abstract
A genuine microbiota resides in the lungs which emanates from the colonization by the oropharyngeal microbiota. Changes in the oropharyngeal microbiota might be the source of dysbiosis observed in the lower airways in patients suffering from asthma or cystic fibrosis (CF). To examine this hypothesis, we compared the throat microbiota from healthy children (n = 62) and that from children with asthma (n = 27) and CF (n = 57) aged 6 to 12 years using 16S rRNA amplicon sequencing. Our results show high levels of similarities between healthy controls and children with asthma and CF revealing the existence of a core microbiome represented by Prevotella, Streptococcus, Neisseria, Veillonella, and Haemophilus. However, in CF, the global diversity, the bacterial load, and abundances of 53 OTUs were significantly reduced, whereas abundances of 6 OTUs representing opportunistic pathogens such as Pseudomonas, Staphylococcus, and Streptococcus were increased compared to those in healthy controls controls and asthmatics. Our data reveal a core microbiome in the throat of healthy children that persists in asthma and CF indicating shared host regulation favoring growth of commensals. Furthermore, we provide evidence for dysbiosis with a decrease in diversity and biomass associated with the presence of known pathogens consistent with impaired host defense in children with CF.
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The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas? PLoS One 2017; 12:e0187852. [PMID: 29145477 PMCID: PMC5690629 DOI: 10.1371/journal.pone.0187852] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/29/2017] [Indexed: 01/01/2023] Open
Abstract
Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic “adverse toxin effect” paradigm and our novel “altered environmental microbiome” hypothesis.
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37
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Tian X, Shi Y, Geng L, Chu H, Zhang J, Song F, Duan J, Shu C. Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities. FRONTIERS IN PLANT SCIENCE 2017; 8:1623. [PMID: 29018461 PMCID: PMC5622981 DOI: 10.3389/fpls.2017.01623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/05/2017] [Indexed: 06/01/2023]
Abstract
Phyllosphere microbial communities are highly diverse and have important ecological implications; in that context, bacterial identification based on 16S rRNA genes is an important research issue. In studies of phyllosphere microbial communities, microporous filtration and centrifugation are used to collect microorganism samples, but it is unclear which one has a better collection efficiency. In this study, we compared these two microorganism collection methods and investigated the effects of the DNA extraction process on the estimation of microbial community composition and organization. The following four treatments were examined: (A) filtration, resuspension, and direct PCR; (B) filtration, DNA isolation, and PCR; (C) centrifugation, resuspension, and direct PCR; (D) centrifugation, DNA isolation, and PCR. Our results showed that the percentage of chloroplast sequence contaminants was affected by the DNA extraction process. The bacterial compositions clearly differed between treatments A and C, suggesting that the collection method has an influence on the determination of community structure. Compared with treatments B and D, treatments A and C resulted in higher Shannon index values, indicating that the DNA extraction process might reduce the observed phyllosphere microbial alpha diversity. However, with respect to community structure, treatments B and D yielded very similar results, suggesting that the DNA extraction process erases the effect of the collection method. Our findings provide key information to ensure accurate estimates of diversity and community composition in studies of phyllosphere microorganisms.
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Affiliation(s)
- Xiaoyan Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Life Sciences, Shaanxi Normal University, Linfen, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangyan Duan
- School of Life Sciences, Shaanxi Normal University, Linfen, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Zou S, Zhang J, Zhang Z. A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network. PLoS One 2017; 12:e0184394. [PMID: 28880967 PMCID: PMC5589230 DOI: 10.1371/journal.pone.0184394] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
Since the microbiome has a significant impact on human health and disease, microbe-disease associations can be utilized as a valuable resource for understanding disease pathogenesis and promoting disease diagnosis and prognosis. Accordingly, it is necessary for researchers to achieve a comprehensive and deep understanding of the associations between microbes and diseases. Nevertheless, to date, little work has been achieved in implementing novel human microbe-disease association prediction models. In this paper, we develop a novel computational model to predict potential microbe-disease associations by bi-random walk on the heterogeneous network (BiRWHMDA). The heterogeneous network was constructed by connecting the microbe similarity network and the disease similarity network via known microbe-disease associations. Microbe similarity and disease similarity were calculated by the Gaussian interaction profile kernel similarity measure; moreover, a logistic function was applied to regulate disease similarity. Additionally, leave-one-out cross validation and 5-fold cross validation were implemented to evaluate the predictive performance of our method; both cross validation methods performed well. The leave-one-out cross validation experiment results illustrate that our method outperforms other previously proposed methods. Furthermore, case studies on asthma and inflammatory bowel disease prove the favorable performance of our method. In conclusion, our method can be considered as an effective computational model for predicting novel microbe-disease associations.
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Affiliation(s)
- Shuai Zou
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
| | - Jingpu Zhang
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
| | - Zuping Zhang
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
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Agarwal D, Dhotre D, Patil R, Shouche Y, Juvekar S, Salvi S. Potential of Health and Demographic Surveillance System in Asthma and Chronic Obstructive Pulmonary Disease Microbiome Research. Front Public Health 2017; 5:196. [PMID: 28824902 PMCID: PMC5543077 DOI: 10.3389/fpubh.2017.00196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022] Open
Abstract
Health and demographic surveillance system (HDSS) is a population-based health and vital event registration system that monitors demographic and health events in a geographically defined population at regular intervals. Human microbiome research in the past decade has been the field of increasingly intense research much due to its demonstrated impact upon various health conditions including human chronic airway diseases such as asthma and chronic obstructive pulmonary disease (COPD). Many confounding factors have been revealed to play a role in shaping the microbiome in chronic airway diseases. Asthma and COPD follows a typical pattern of disease progression, which includes stable and exacerbation state in which the microbiota is known to vary. However, many such studies lack extensive and longitudinal sampling with inadequate metadata, which has resulted in the inconsistencies in the observations. HDSS provides such a platform, which can offer a deeper understanding of the role of the microbiome in human health. In this review, we highlight opportunities and limitations in microbiome research with the help of studies conducted on chronic airway diseases like asthma and COPD. In addition, we also emphasize on the benefits of HDSS and future directions in lung microbiome research.
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Affiliation(s)
- Dhiraj Agarwal
- Chest Research Foundation, Pune, India.,Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Dhiraj Dhotre
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, India.,INDEPTH Network, Accra, Ghana
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40
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Dahyot S, Lemee L, Pestel-Caron M. [Description and role of bacteriological techniques in the management of lung infections]. Rev Mal Respir 2017; 34:1098-1113. [PMID: 28688757 PMCID: PMC7134997 DOI: 10.1016/j.rmr.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/28/2016] [Indexed: 01/07/2023]
Abstract
Les pneumopathies aiguës recouvrent des contextes cliniques variés et les étiologies bactériennes impliquées le sont tout autant. Aucun outil microbiologique n’est 100 % sensible ni 100 % spécifique et malgré les investigations, plus de 30 % des pneumopathies restent sans étiologie identifiée. Si aucun prélèvement n’est indiqué pour les patients traités en ambulatoire, les prélèvements respiratoires non invasifs sont à privilégier pour les pneumopathies aiguës hospitalisées (communautaires ou associées aux soins), tandis que les prélèvements invasifs sont indiqués en seconde ligne pour les pneumopathies aiguës communautaires en réanimation, et en première ligne pour les pneumopathies aiguës de l’immunodéprimé. La culture microbiologique garde une place importante, à condition que le malade soit prélevé avant instauration de l’antibiothérapie. Certains contextes peuvent justifier le recours aux hémocultures, à la recherche d’antigènes urinaires ou aux sérologies. Les PCR rendent déjà service au quotidien mais l’avenir à court terme appartient probablement aux panels moléculaires multiplex capables de détecter de nombreux micro-organismes en quelques heures, surtout dans les pneumopathies communautaires sévères de réanimation et les pneumopathies aiguës de l’immunodéprimé. Le séquençage nucléotidique haut débit révolutionnera bientôt le diagnostic microbiologique, en pneumologie comme dans les autres domaines de l’infectiologie.
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Affiliation(s)
- S Dahyot
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France.
| | - L Lemee
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France
| | - M Pestel-Caron
- UNIROUEN, GRAM EA2656, laboratoire de bactériologie, CHU de Rouen, Normandie université, 76000 Rouen, France
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41
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Diao W, Shen N, Du Y, Qian K, He B. Characterization of throat microbial flora in smokers with or without COPD. Int J Chron Obstruct Pulmon Dis 2017; 12:1933-1946. [PMID: 28740374 PMCID: PMC5503495 DOI: 10.2147/copd.s140243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The study aimed to determine the relationship between throat microbiome and COPD. Sixty-five Chinese males (n=20, smokers without COPD; n=45 smokers with COPD) were included. Nonmetric multidimensional scaling indicated differences of microbiome between COPD and controls, but no difference was observed between COPD patients with differing degrees of lung function or disease severity. Rarefaction analyses suggested that operational taxonomic units (OTUs, species-level) richness decreased in COPD. The dominant taxa between COPD and controls were similar, but the proportions of taxonomic distribution were different. The dominant phyla were Bacteroidetes, Proteobacteria, Firmicutes and Fusobacteria. The dominant genera were Haemophilus, Leptotrichia, Porphyromonas, Fusobacterium, Veillonella, Streptococcus, Neisseria and Prevotella. Two dominant OTUs, otu3 (Veillonella_dispar) and otu4 (Streptococcus_unclassified), were identified. Otu3 and its father-level taxa, which were negatively correlated with predicted percent of forced expiratory volume in a second (FEV1%pred), were increased in COPD. By contrast, otu4 and its father-level taxa, which were positively correlated with FEV1%pred, were decreased in COPD. Otu4 also showed a slight potential as a COPD biomarker. To conclude, the throat microbiome was different between smokers with or without COPD, which is similar to findings from the lower respiratory tract. This study may strengthen our understanding of the relationship between microbiomes of different airway sites and COPD.
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Affiliation(s)
- Wenqi Diao
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
| | - Yipeng Du
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
| | - Ke Qian
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
| | - Bei He
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing, China
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42
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Dorn ES, Tress B, Suchodolski JS, Nisar T, Ravindran P, Weber K, Hartmann K, Schulz BS. Bacterial microbiome in the nose of healthy cats and in cats with nasal disease. PLoS One 2017; 12:e0180299. [PMID: 28662139 PMCID: PMC5491177 DOI: 10.1371/journal.pone.0180299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). Methodology/Principal findings DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed. Conclusion This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.
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Affiliation(s)
- Elisabeth S. Dorn
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Barbara Tress
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tariq Nisar
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Prajesh Ravindran
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karin Weber
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Bianka S. Schulz
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
- * E-mail:
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43
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Yadava K, Pattaroni C, Sichelstiel AK, Trompette A, Gollwitzer ES, Salami O, von Garnier C, Nicod LP, Marsland BJ. Microbiota Promotes Chronic Pulmonary Inflammation by Enhancing IL-17A and Autoantibodies. Am J Respir Crit Care Med 2017; 193:975-87. [PMID: 26630356 DOI: 10.1164/rccm.201504-0779oc] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RATIONALE Changes in the pulmonary microbiota are associated with progressive respiratory diseases including chronic obstructive pulmonary disease (COPD). Whether there is a causal relationship between these changes and disease progression remains unknown. OBJECTIVES To investigate the link between an altered microbiota and disease, we used a murine model of chronic lung inflammation that is characterized by key pathological features found in COPD and compared responses in specific pathogen-free (SPF) mice and mice depleted of microbiota by antibiotic treatment or devoid of a microbiota (axenic). METHODS Mice were challenged with LPS/elastase intranasally over 4 weeks, resulting in a chronically inflamed and damaged lung. The ensuing cellular infiltration, histological damage, and decline in lung function were quantified. MEASUREMENTS AND MAIN RESULTS Similar to human disease, the composition of the pulmonary microbiota was altered in diseased animals. We found that the microbiota richness and diversity were decreased in LPS/elastase-treated mice, with an increased representation of the genera Pseudomonas and Lactobacillus and a reduction in Prevotella. Moreover, the microbiota was implicated in disease development as mice depleted, or devoid, of microbiota exhibited an improvement in lung function, reduced inflammation, and lymphoid neogenesis. The absence of microbial cues markedly decreased the production of IL-17A, whereas intranasal transfer of fluid enriched with the pulmonary microbiota isolated from diseased mice enhanced IL-17A production in the lungs of antibiotic-treated or axenic recipients. Finally, in mice harboring a microbiota, neutralizing IL-17A dampened inflammation and restored lung function. CONCLUSIONS Collectively, our data indicate that host-microbial cross-talk promotes inflammation and could underlie the chronicity of inflammatory lung diseases.
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Affiliation(s)
- Koshika Yadava
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland.,2 Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Céline Pattaroni
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Anke K Sichelstiel
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Aurélien Trompette
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Eva S Gollwitzer
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Olawale Salami
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Christophe von Garnier
- 3 Department of Respiratory Medicine, Inselspital, Bern University Hospital, Bern, Switzerland; and.,4 Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Laurent P Nicod
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Benjamin J Marsland
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
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44
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Liu HY, Zhang SY, Yang WY, Su XF, He Y, Zhou HW, Su J. Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease. Front Microbiol 2017; 8:1163. [PMID: 28690603 PMCID: PMC5479893 DOI: 10.3389/fmicb.2017.01163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Growing evidence suggests that the airway microbiota might be involved in acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Understanding this relationship requires examination of a large-scale population for a long duration to accurately monitor changes in the microbiome. This type of longitudinal study requires an appropriate sampling strategy; two options are the collection of sputum or oropharyngeal swabs. Comparative analysis of the changes that occur in these two specimen types has not been previously performed. This observational study was conducted to explore oropharyngeal microbial community dynamics over time and to examine the relationship between oropharyngeal swabs and sputum. A total of 114 samples were collected from four patients suffering from severe AECOPD. Bacterial and fungal communities were evaluated using 16S rRNA and ITS sequencing. Inter-individual differences were found in bacterial community structure, but the core genera were shared by both sample types and included 32 lineages. Most of the core genera were members of the phyla Proteobacteria, Firmicutes and Ascomycota. Although the oropharyngeal samples showed higher bacterial alpha diversity, the two sample types generated rather similar taxonomic profiles. These results suggest that the sputum microbiome is remarkably similar to the oropharyngeal microbiome. Thus, oropharyngeal swabs can potentially be used instead of sputum samples for patients with exacerbation of COPD.
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Affiliation(s)
- Hai-Yue Liu
- Department of Environmental Health, School of Public Health, Southern Medical UniversityGuangzhou, China.,State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhou, China
| | - Shi-Yu Zhang
- Department of Environmental Health, School of Public Health, Southern Medical UniversityGuangzhou, China
| | - Wan-Ying Yang
- Department of Environmental Health, School of Public Health, Southern Medical UniversityGuangzhou, China
| | - Xiao-Fang Su
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical UniversityGuangzhou, China
| | - Yan He
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhou, China
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical UniversityGuangzhou, China
| | - Jin Su
- Department of Environmental Health, School of Public Health, Southern Medical UniversityGuangzhou, China.,Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical UniversityGuangzhou, China
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45
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Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 2017; 151:363-374. [PMID: 28542929 DOI: 10.1111/imm.12760] [Citation(s) in RCA: 714] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/10/2017] [Accepted: 05/15/2017] [Indexed: 02/07/2023] Open
Abstract
The microbiota plays a central role in human health and disease by shaping immune development, immune responses and metabolism, and by protecting from invading pathogens. Technical advances that allow comprehensive characterization of microbial communities by genetic sequencing have sparked the hunt for disease-modulating bacteria. Emerging studies in humans have linked the increased abundance of Prevotella species at mucosal sites to localized and systemic disease, including periodontitis, bacterial vaginosis, rheumatoid arthritis, metabolic disorders and low-grade systemic inflammation. Intriguingly, Prevotella abundance is reduced within the lung microbiota of patients with asthma and chronic obstructive pulmonary disease. Increased Prevotella abundance is associated with augmented T helper type 17 (Th17) -mediated mucosal inflammation, which is in line with the marked capacity of Prevotella in driving Th17 immune responses in vitro. Studies indicate that Prevotella predominantly activate Toll-like receptor 2, leading to production of Th17-polarizing cytokines by antigen-presenting cells, including interleukin-23 (IL-23) and IL-1. Furthermore, Prevotella stimulate epithelial cells to produce IL-8, IL-6 and CCL20, which can promote mucosal Th17 immune responses and neutrophil recruitment. Prevotella-mediated mucosal inflammation leads to systemic dissemination of inflammatory mediators, bacteria and bacterial products, which in turn may affect systemic disease outcomes. Studies in mice support a causal role of Prevotella as colonization experiments promote clinical and inflammatory features of human disease. When compared with strict commensal bacteria, Prevotella exhibit increased inflammatory properties, as demonstrated by augmented release of inflammatory mediators from immune cells and various stromal cells. These findings indicate that some Prevotella strains may be clinically important pathobionts that can participate in human disease by promoting chronic inflammation.
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Affiliation(s)
- Jeppe Madura Larsen
- Department of Technology, Faculty of Health and Technology, Metropolitan University College, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Lyngby, Denmark
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46
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Gilpin DF, Nixon KA, Bull M, McGrath SJ, Sherrard L, Rolain JM, Mahenthiralingam E, Elborn JS, Tunney MM. Evidence of persistence of Prevotella spp. in the cystic fibrosis lung. J Med Microbiol 2017; 66:825-832. [DOI: 10.1099/jmm.0.000500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- D. F. Gilpin
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - K. A. Nixon
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - M. Bull
- Cardiff School of Biosciences, Cardiff University, Wales, UK
| | - S. J. McGrath
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - L. Sherrard
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - J. M. Rolain
- Faculté de Médicine, Université de la Mediterranée, Marseilles, France
| | | | - J. S. Elborn
- School of Medicine, Dentistry and Biomedical Science, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - M. M. Tunney
- School of Pharmacy, Queen’s University of Belfast, Belfast, Northern Ireland, UK
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47
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Ploton MC, Abakka S, Amouyal E, Besnard C, Dufour L, El Harrif S, Kipnis C, Prim B, Vignot J, Houdouin V. [The lung microbiota. Review]. Arch Pediatr 2017; 24:667-674. [PMID: 28576586 DOI: 10.1016/j.arcped.2017.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 02/13/2017] [Accepted: 04/12/2017] [Indexed: 01/12/2023]
Abstract
In the last 20years, culture-independent DNA-based techniques ("shotgun sequencing") demonstrated that complex microbial communities reside on most epithelial surfaces, including the lower airways. Until the amniotic sac ruptures, a fetus is considered to be essentially sterile. Many factors affect the composition of the lung microbiota: inheritance, mode of delivery, diet, and age-related changes in adults. It interacts with the digestive and oropharyngeal microbiotas. Animal models show that these interactions play a role in innate pulmonary immunity and modulation of the inflammatory response. The microbial composition of the airway microbiota differs between healthy children and those with chronic lung disease. The advances in the comprehension of microbiome changes have resulted in new approaches concerning the microbiota for treatment and prevention of disease.
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Affiliation(s)
- M-C Ploton
- Service de pédiatrie générale, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France
| | - S Abakka
- Service de pédiatrie générale, hôpital Trousseau, 26, avenue du Dr-Arnold-Netter, 75012 Paris, France
| | - E Amouyal
- Service de génétique clinique, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France
| | - C Besnard
- Inserm UMR 1163, laboratoire d'immunogénétique des maladies auto-immunes pédiatriques, Paris, France
| | - L Dufour
- Interne, service de pédiatrie générale, centre hospitalier intercommunal de Créteil, 40, avenue de Verdun, 94000 Créteil, France
| | - S El Harrif
- Service des maladies digestives et respiratoires de l'enfant, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France
| | - C Kipnis
- Service de pédiatrie générale, hôpital Trousseau, 26, avenue du Dr-Arnold-Netter, 75012 Paris, France
| | - B Prim
- Service de néphrologie pédiatrique, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France
| | - J Vignot
- Service de cardiologie pédiatrique, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France
| | - V Houdouin
- Service des maladies digestives et respiratoires de l'enfant, hôpital Robert-Debré, 48, boulevard Serrurier, 75019 Paris, France.
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48
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Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF, Chung IF. Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood. Sci Rep 2017; 7:1820. [PMID: 28500319 PMCID: PMC5431806 DOI: 10.1038/s41598-017-02067-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/10/2017] [Indexed: 12/15/2022] Open
Abstract
Microbiota plays an important role in regulating immune responses associated with atopic diseases. We sought to evaluate relationships among airway microbiota, serum IgE levels, allergic sensitization and their relevance to rhinitis and asthma. Microbial characterization was performed using Illumina-based 16S rRNA gene sequencing of 87 throat swabs collected from children with asthma (n = 32) and rhinitis (n = 23), and from healthy controls (n = 32). Data analysis was performed using QIIME (Quantitative Insights Into Microbial Ecology) v1.8. Significantly higher abundance of Proteobacteria was found in children with rhinitis than in the healthy controls (20.1% vs. 16.1%, P = 0.009). Bacterial species richness (Chao1 index) and diversity (Shannon index) were significantly reduced in children with mite sensitization but not in those with food or IgE sensitization. Compared with healthy children without mite sensitization, the mite-sensitized children with rhinitis and asthma showed significantly lower Chao1 and Shannon indices. Moraxella and Leptotrichia species were significantly found in the interaction of mite sensitization with rhinitis and asthma respectively. Airway microbial diversity appears to be inversely associated with sensitization to house dust mites. A modulation between airway dysbiosis and responses to allergens may potentially cause susceptibility to rhinitis and asthma in early childhood.
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Affiliation(s)
- Chih-Yung Chiu
- Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, and Chang Gung University, Taoyuan, Taiwan. .,Division of Pediatric Pulmonology, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, Taiwan.
| | - Yi-Ling Chan
- Department of Emergency Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yu-Shuen Tsai
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ssu-An Chen
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Jung Wang
- Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, and Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Fu Chen
- Department of Emergency Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - I-Fang Chung
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. .,The Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan.
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49
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Lopes Dos Santos Santiago G, Brusselle G, Dauwe K, Deschaght P, Verhofstede C, Vaneechoutte D, Deschepper E, Jordens P, Joos G, Vaneechoutte M. Influence of chronic azithromycin treatment on the composition of the oropharyngeal microbial community in patients with severe asthma. BMC Microbiol 2017; 17:109. [PMID: 28486933 PMCID: PMC5424369 DOI: 10.1186/s12866-017-1022-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/03/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND This study of the oropharyngeal microbiome complements the previously published AZIthromycin in Severe ASThma (AZISAST) clinical trial, where the use of azithromycin was assessed in subjects with exacerbation-prone severe asthma. Here, we determined the composition of the oropharyngeal microbial community by means of deep sequencing of the amplified 16S rRNA gene in oropharyngeal swabs from patients with exacerbation-prone severe asthma, at baseline and during and after 6 months treatment with azithromycin or placebo. RESULTS A total of 1429 OTUs were observed, of which only 59 were represented by more than 0.02% of the reads. Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Streptococcus and Prevotella were the most abundant genera in all the samples. Thirteen species only accounted for two thirds of the reads and two species only, i.e. Prevotella melaninogenica and Streptococcus mitis/pneumoniae, accounted for one fourth of the reads. We found that the overall composition of the oropharyngeal microbiome in patients with severe asthma is comparable to that of the healthy population, confirming the results of previous studies. Long term treatment (6 months) with azithromycin increased the species Streptococcus salivarius approximately 5-fold and decreased the species Leptotrichia wadei approximately 5-fold. This was confirmed by Boruta feature selection, which also indicated a significant decrease of L. buccalis/L. hofstadtii and of Fusobacterium nucleatum. Four of the 8 treated patients regained their initial microbial composition within one month after cessation of treatment. CONCLUSIONS Despite large diversity of the oropharyngeal microbiome, only a few species predominate. We confirm the absence of significant differences between the oropharyngeal microbiomes of people with and without severe asthma. Possibly, long term azithromycin treatment may have long term effects on the composition of the oropharygeal microbiome in half of the patients.
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Affiliation(s)
- Guido Lopes Dos Santos Santiago
- Laboratory Bacteriology Research, Department Clinical Chemistry, Microbiology & Immunology, Faculty of Medicine & Health Sciences, University of Ghent, Ghent, Belgium
| | - Guy Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Kenny Dauwe
- AIDS Reference Laboratory, Ghent University, Ghent, Belgium
| | - Pieter Deschaght
- Laboratory Bacteriology Research, Department Clinical Chemistry, Microbiology & Immunology, Faculty of Medicine & Health Sciences, University of Ghent, Ghent, Belgium
| | | | - Dries Vaneechoutte
- Department of Plant Systems Biology (VIB), Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ellen Deschepper
- Biostatistics Unit, Department of Public Health, Ghent University Hospital, Ghent, Belgium
| | - Paul Jordens
- Department of Respiratory Medicine, OLV Ziekenhuis Aalst, Aalst, Belgium
| | - Guy Joos
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department Clinical Chemistry, Microbiology & Immunology, Faculty of Medicine & Health Sciences, University of Ghent, Ghent, Belgium.
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50
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Vientós-Plotts AI, Ericsson AC, Rindt H, Grobman ME, Graham A, Bishop K, Cohn LA, Reinero CR. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats. PLoS One 2017; 12:e0173818. [PMID: 28278278 PMCID: PMC5344508 DOI: 10.1371/journal.pone.0173818] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/27/2017] [Indexed: 12/15/2022] Open
Abstract
Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p < 0.001) with no significant difference (p = 0.180) in richness between time points. PCA revealed site-specific microbial communities in the feces, and upper and lower airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but shared more OTUs with feces. Samples clustered more by time than by individual, with OP swabs having subjectively greater variation than other samples. In summary, healthy cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be altered by factors such as age, environmental influences, and disease states. Further data are necessary to determine how the distinct feline microbiomes from the upper and lower airways, feces and blood are established and evolve. These data are relevant for comparisons between healthy cats and cats with respiratory disease.
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Affiliation(s)
- Aida I. Vientós-Plotts
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
| | - Hansjorg Rindt
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Megan E. Grobman
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Amber Graham
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Kaitlin Bishop
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Leah A. Cohn
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
| | - Carol R. Reinero
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
- Comparative Internal Medicine Laboratory, University of Missouri, Columbia, Missouri, United States of America
- * E-mail: (ACE); (CRR)
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