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Zhang W, Li L, Zhang Y, Dai J, Qiu C, Chen R, Shi F. Perturbations in the airway microbiome are associated with type 2 asthma phenotype and severity. Ann Allergy Asthma Immunol 2025; 134:296-305.e9. [PMID: 39549985 DOI: 10.1016/j.anai.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/14/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024]
Abstract
BACKGROUND Airway microbiome has been linked to asthma heterogeneity, yet little is known about the associations between airway microbiota and type 2 (T2) asthma phenotype and severity. OBJECTIVE To determine the relationship of nasopharyngeal (NP) and induced sputum (IS) microbiota to the phenotypic features of T2 asthma. METHODS NP and IS samples from subjects with T2 mild-to-moderate asthma (n = 23), subjects with severe asthma (n = 21), and healthy controls (n = 16) were analyzed. Bacterial microbiota and functional profiles were compared. The correlation between microbial communities and clinical and inflammatory features was evaluated in individuals with asthma of 2 statuses. RESULTS Differences in NP and IS microbiota were associated with T2 asthma phenotype. Alterations in NP microbiota were more reflective of T2 inflammation and severity, with additional stratification of a subgroup characterized by significant elevations in T2 inflammatory biomarkers and reductions in bacterial richness and diversity (P < .05). Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, and Rhodococcus were identified as hub taxa within NP microbial network in T2 severe asthma, which were prevalent in the entire airway and involved in bacterial functions including inflammatory and steroid responses (P < .05). The composition and diversity of IS microbiota were complex, with Veillonella as the most altered genus, having an increase with increasing asthma severity. CONCLUSION Our work revealed the significant associations of microbiota perturbations throughout the entire respiratory tract to the extent of T2 inflammation, phenotype and severity in T2 asthma. The specific taxa identified invite further mechanistic investigations to unravel their possibility as biomarkers and therapeutic targets for T2 severe asthma.
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Affiliation(s)
- Wei Zhang
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Lifei Li
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Yu Zhang
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Junjie Dai
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Chen Qiu
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Rongchang Chen
- Key Laboratory of Shenzhen Respiratory Diseases, Institute of Shenzhen Respiratory Diseases, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, People's Republic of China
| | - Fei Shi
- Department of Infectious Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China.
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Huang YJ. The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations. Immunol Rev 2025; 330:e70015. [PMID: 40072031 PMCID: PMC11899502 DOI: 10.1111/imr.70015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 02/13/2025] [Accepted: 02/28/2025] [Indexed: 03/15/2025]
Abstract
Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.
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Affiliation(s)
- Yvonne J. Huang
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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3
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Huang D, Ren Q, Xie L, Chen Y, Li C, Su X, Lin L, Liu L, Zhao H, Luo T, Wu J, Cai S, Dong H. Association between airway microbiota and systemic inflammation markers in non-small cell lung cancer patients. Sci Rep 2025; 15:3539. [PMID: 39875410 PMCID: PMC11775180 DOI: 10.1038/s41598-025-86231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 01/09/2025] [Indexed: 01/30/2025] Open
Abstract
Growing evidences have suggested the airway microbiota may participate in lung cancer progression. However, little was known about the relationship between airway microbiota and lung cancer associated systemic inflammation. Here we aimed to explore the association between sputum microbiota and systemic inflammation in lung cancer. The microbiota of spontaneous sputum samples from 51 non-small cell lung cancer (NSCLC) patients and 6 patients with lung benign nodules were sequenced via 16 S rRNA sequencing. Neutrophil-lymphocyte ratio (NLR), platelet-lymphocyte ratio (PLR) and C reactive protein (CRP) were used to represent systemic inflammation. Patients were divided into 2 groups based on level of inflammatory biomarkers respectively (CRP_low versus CRP_high; NLR_low versus NLR_high; PLR_low versus PLR_high). α-diversity was significantly decreased in CRP_high and NLR_high patients. β diversity analysis based on weighted unifrac distance indicated that microbial community structure differed significantly between patients with different inflammation status. Lefse identified genera Porphyromonas, Selenomonas, Moryella, Megasphaera, Corynebacterium were enriched in CRP_low group. Compared with NLR_high, genera Veillonella, Neisseria, Bulleidia, Moryella were enriched in NLR_low group. For patients with different PLR level, genera Veillonella, Prevotella, Moryella, Selenomonas were increased in PLR_ low patients. Function analysis identified propionate metabolism pathway was significantly enriched in CRP_low and PLR_low groups. Moreover, RDA analysis showed that compared with PLR, NLR and CRP had strongest association with microbial community. Airway microbial structure differed between lung cancer with different systemic inflammation status. Patients with relative high inflammation status were associated with alteration of specific airway genera and microbial metabolic function.
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Affiliation(s)
- DanHui Huang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - QianNan Ren
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - LingYan Xie
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - YueHua Chen
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cui Li
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - XiaoFang Su
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - LiShan Lin
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - LaiYu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Haijin Zhao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Tingyue Luo
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - JianHua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shaoxi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Hangming Dong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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4
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Utembe W, Kamng'ona AW. Inhalation exposure to chemicals, microbiota dysbiosis and adverse effects on humans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176938. [PMID: 39414049 DOI: 10.1016/j.scitotenv.2024.176938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 09/21/2024] [Accepted: 10/12/2024] [Indexed: 10/18/2024]
Abstract
As revealed by culture-independent methodologies, disruption of the normal lung microbiota (LM) configuration (LM dysbiosis) is a potential mediator of adverse effects from inhaled chemicals. LM, which consists of microbiota in the upper and lower respiratory tract, is influenced by various factors, including inter alia environmental exposures. LM dysbiosis has been associated with multiple respiratory pathologies such as asthma, lung cancer, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Chemically-induced LM dysbiosis appears to play significant roles in human respiratory diseases, as has been shown for some air pollutants, cigarette smoke and some inhalable chemical antibiotics. Lung microbiota are also linked with the central nervous system (CNS) in the so-called lung-brain axis. Inhaled chemicals that undergo mucociliary clearance may be linked to respiratory conditions through gut microbiota (GM) dysbiosis in the so-called Gut-Lung axis. However, current linkages of various disease states to LM appears to be associative, with causal linkages requiring further studies using more robust approaches, methods and techniques that are different from those applied in studies involving (GM). Most importantly, the sampling techniques determine the level of risk of cross contamination. Furthermore, the development of continuous or semi-continuous systems designed to replicate the lung microbiome will go a long way to further LM dysbiosis studies. These challenges notwithstanding, the preponderance of evidence points to the significant role of LM-mediated chemical toxicity in human disease and conditions.
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Affiliation(s)
- W Utembe
- Toxicology and Biochemistry Department, National Institute for Occupational Health, National Health Laboratory Services, Johannesburg 2000, South Africa; Environmental Health Division, School of Public Health and Family Medicine, University of Cape Town, Cape Town 7925, South Africa.
| | - A W Kamng'ona
- School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre Campus, Mahatma Gandhi Road, Blantyre 312224, Malawi
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Campbell S, Gerasimidis K, Milling S, Dicker AJ, Hansen R, Langley RJ. The lower airway microbiome in paediatric health and chronic disease. Paediatr Respir Rev 2024; 52:31-43. [PMID: 38538377 DOI: 10.1016/j.prrv.2024.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 12/16/2024]
Abstract
The advent of next generation sequencing has rapidly challenged the paediatric respiratory physician's understanding of lung microbiology and the role of the lung microbiome in host health and disease. In particular, the role of "microbial key players" in paediatric respiratory disease is yet to be fully explained. Accurate profiling of the lung microbiome in children is challenging since the ability to obtain lower airway samples coupled with processing "low-biomass specimens" are both technically difficult. Many studies provide conflicting results. Early microbiota-host relationships may be predictive of the development of chronic respiratory disease but attempts to correlate lower airway microbiota in premature infants and risk of developing bronchopulmonary dysplasia (BPD) have produced mixed results. There are differences in lung microbiota in asthma and cystic fibrosis (CF). The increased abundance of oral taxa in the lungs may (or may not) promote disease processes in asthma and CF. In CF, correlation between microbiota diversity and respiratory decline is commonly observed. When one considers other pathogens beyond the bacterial kingdom, the contribution and interplay of fungi and viruses within the lung microbiome further increase complexity. Similarly, the interaction between microbial communities in different body sites, such as the gut-lung axis, and the influence of environmental factors, including diet, make the co-existence of host and microbes ever more complicated. Future, multi-omics approaches may help uncover novel microbiome-based biomarkers and therapeutic targets in respiratory disease and explain how we can live in harmony with our microbial companions.
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Affiliation(s)
- S Campbell
- School of Medicine, Dentistry and Nursing, University of Glasgow
| | - K Gerasimidis
- School of Medicine, Dentistry and Nursing, University of Glasgow
| | - S Milling
- School of Infection & Immunity, University of Glasgow
| | - A J Dicker
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee
| | - R Hansen
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee
| | - R J Langley
- Department of Paediatric Respiratory & Sleep Medicine, Royal Hospital for Children, Glasgow; Department of Maternal and Child Health, School of Medicine, Dentistry and Nursing, University of Glasgow.
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6
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Jabeen MF, Sanderson ND, Tinè M, Donachie G, Barber C, Azim A, Lau LCK, Brown T, Pavord ID, Chauhan A, Klenerman P, Street TL, Marchi E, Howarth PH, Hinks TSC. Species-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma. Allergy 2024; 79:2966-2980. [PMID: 39127908 DOI: 10.1111/all.16269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses. METHODS Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link. RESULTS The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type-1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL-10. R. mucilaginosa associated positively with IL-6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type-1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways. CONCLUSIONS This species-level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma.
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Affiliation(s)
- Maisha F Jabeen
- Nuffield Department of Medicine, Experimental Medicine Division, Respiratory Medicine Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicholas D Sanderson
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Mariaenrica Tinè
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Gillian Donachie
- Nuffield Department of Medicine, Experimental Medicine Division, Respiratory Medicine Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Clair Barber
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories and NIHR Southampton Respiratory Biomedical Research Unit, Southampton University, Southampton, UK
| | - Adnan Azim
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories and NIHR Southampton Respiratory Biomedical Research Unit, Southampton University, Southampton, UK
| | - Laurie C K Lau
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories and NIHR Southampton Respiratory Biomedical Research Unit, Southampton University, Southampton, UK
| | | | - Ian D Pavord
- Nuffield Department of Medicine, Experimental Medicine Division, Respiratory Medicine Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | | | - Paul Klenerman
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Teresa L Street
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Emanuele Marchi
- Nuffield Department of Medicine, Experimental Medicine Division, Respiratory Medicine Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Peter H Howarth
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories and NIHR Southampton Respiratory Biomedical Research Unit, Southampton University, Southampton, UK
| | - Timothy S C Hinks
- Nuffield Department of Medicine, Experimental Medicine Division, Respiratory Medicine Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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Liu L, He X, Wang J, Li M, Wei X, Yang J, Cheng G, Du W, Liu Z, Xiao X. Exploring the associations between gut microbiota composition and SARS-CoV-2 inactivated vaccine response in mice with type 2 diabetes mellitus. mSphere 2024; 9:e0038024. [PMID: 39189780 PMCID: PMC11423585 DOI: 10.1128/msphere.00380-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is crucial for protecting vulnerable individuals, yet individuals with type 2 diabetes mellitus (T2DM) often exhibit impaired vaccine responses. Emerging evidence suggests that the composition of the host microbiota, crucial in immune regulation and development, influences vaccine efficacy. This study aimed to characterize the relationships between the SARS-CoV-2 inactivated vaccine and the host microbiota (specifically, gut and lung microbiota) of C57BL/6 mice with T2DM. Employing 16S rRNA metagenomic sequencing and ultra-high-performance liquid chromatography-mass spectrometry, we observed lower alpha diversity and distinct beta diversity in fecal microbiota before vaccination and in gut microbiota 28 days post-vaccination between T2DM mice and healthy mice. Compared with healthy mice, T2DM mice showed a higher Firmicutes/Bacteroidetes ratio 28 days post-vaccination. Significant alterations in gut microbiota composition were detected following vaccination, while lung microbiota remained unchanged. T2DM was associated with a diminished initial IgG antibody response against the spike protein, which subsequently normalized after 28 days. Notably, the initial IgG response positively correlated with fecal microbiota alpha diversity pre-vaccination. Furthermore, after 28 days, increased relative abundance of gut probiotics (Bifidobacterium and Lactobacillus) and higher levels of the gut bacterial tryptophan metabolite, indole acrylic acid, were positively associated with IgG levels. These findings suggest a potential link between vaccine efficacy and gut microbiota composition. Nonetheless, further research is warranted to elucidate the precise mechanisms underlying the impact of the gut microbiome on vaccine response. Overall, this study enhances our understanding of the intricate relationships among host microbiota, SARS-CoV-2 vaccination, and T2DM, with potential implications for improving vaccine efficacy. IMPORTANCE Over 7 million deaths attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 6 May 2024 underscore the urgent need for effective vaccination strategies. However, individuals with type 2 diabetes mellitus (T2DM) have been identified as particularly vulnerable and display compromised immune responses to vaccines. Concurrently, increasing evidence suggests that the composition and diversity of gut microbiota, crucial regulators of immune function, may influence the efficacy of vaccines. Against this backdrop, our study explores the complex interplay among SARS-CoV-2 inactivated vaccination, T2DM, and host microbiota. We discover that T2DM compromises the initial immune response to the SARS-CoV-2 inactivated vaccine, and this response is positively correlated with specific features of the gut microbiota, such as alpha diversity. We also demonstrate that the vaccination itself induces alterations in the composition and structure of the gut microbiota. These findings illuminate potential links between the gut microbiota and vaccine efficacy in individuals with T2DM, offering valuable insights that could enhance vaccine responses in this high-risk population.
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Affiliation(s)
- Long Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Xianzhen He
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Department of Children's Medical Center, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Jiaqi Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Moran Li
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Xiuli Wei
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Jing Yang
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Weixing Du
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Xiao Xiao
- Department of Pathogen Biology, School of Basic Medical Sciences, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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Park YC, Choi SY, Cha Y, Yoon HW, Son YM. Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression. J Microbiol 2024; 62:709-725. [PMID: 39240507 DOI: 10.1007/s12275-024-00167-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/08/2024] [Accepted: 08/11/2024] [Indexed: 09/07/2024]
Abstract
The importance of the complex interplay between the microbiome and mucosal immunity, particularly within the respiratory tract, has gained significant attention due to its potential implications for the severity and progression of lung diseases. Therefore, this review summarizes the specific interactions through which the respiratory tract-specific microbiome influences mucosal immunity and ultimately impacts respiratory health. Furthermore, we discuss how the microbiome affects mucosal immunity, considering tissue-specific variations, and its capacity in respiratory diseases containing asthma, chronic obstructive pulmonary disease, and lung cancer. Additionally, we investigate the external factors which affect the relationship between respiratory microbiome and mucosal immune responses. By exploring these intricate interactions, this review provides valuable insights into the potential for microbiome-based interventions to modulate mucosal immunity and alleviate the severity of respiratory diseases.
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Affiliation(s)
- Young Chae Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Soo Yeon Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yunah Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hyeong Won Yoon
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Young Min Son
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Chiyaka TL, Nyawo GR, Naidoo CC, Moodley S, Clemente JC, Malherbe ST, Warren RM, Ku DN, Segal LN, Theron G. PneumoniaCheck, a novel aerosol collection device, permits capture of airborne Mycobacterium tuberculosis and characterisation of the cough aeromicrobiome in people with tuberculosis. Ann Clin Microbiol Antimicrob 2024; 23:74. [PMID: 39175010 PMCID: PMC11342687 DOI: 10.1186/s12941-024-00735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB. METHODS PMC was done in sputum culture-positive people (≥ 30 forced coughs each, n = 16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n = 6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF). FINDINGS 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum. INTERPRETATION PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes.
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Affiliation(s)
- Tinaye L Chiyaka
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Georgina R Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Charissa C Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stephanus T Malherbe
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - David N Ku
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa.
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa.
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10
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Opron K, Begley LA, Erb-Downward JR, Li G, Alexis NE, Barjaktarevic I, Barr RG, Bleecker ER, Boucher R, Bowler RP, Christenson SA, Comellas AP, Criner G, Cooper CB, Couper D, Galban CJ, Han MK, Hastie A, Hatt C, Hoffman EA, Kaner RJ, Kesimer M, Krishnan JA, LaFon DC, Martinez FJ, Ortega VE, Peters SP, Paine R, Putcha N, Woodruff PG, Huffnagle GB, Kozik AJ, Curtis JL, Huang YJ. Loss of Airway Phylogenetic Diversity Is Associated with Clinical and Pathobiological Markers of Disease Development in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 210:186-200. [PMID: 38261629 PMCID: PMC11273318 DOI: 10.1164/rccm.202303-0489oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024] Open
Abstract
Rationale: The airway microbiome has the potential to shape chronic obstructive pulmonary disease (COPD) pathogenesis, but its relationship to outcomes in milder disease is unestablished. Objectives: To identify sputum microbiome characteristics associated with markers of COPD in participants of the Subpopulations and Intermediate Outcome Measures of COPD Study (SPIROMICS). Methods: Sputum DNA from 877 participants was analyzed using 16S ribosomal RNA gene sequencing. Relationships between baseline airway microbiota composition and clinical, radiographic, and mucoinflammatory markers, including longitudinal lung function trajectory, were examined. Measurements and Main Results: Participant data represented predominantly milder disease (Global Initiative for Chronic Obstructive Lung Disease stage 0-2 obstruction in 732 of 877 participants). Phylogenetic diversity (i.e., range of different species within a sample) correlated positively with baseline lung function, decreased with higher Global Initiative for Chronic Obstructive Lung Disease stage, and correlated negatively with symptom burden, radiographic markers of airway disease, and total mucin concentrations (P < 0.001). In covariate-adjusted regression models, organisms robustly associated with better lung function included Alloprevotella, Oribacterium, and Veillonella species. Conversely, lower lung function, greater symptoms, and radiographic measures of small airway disease were associated with enrichment in members of Streptococcus, Actinobacillus, Actinomyces, and other genera. Baseline sputum microbiota features were also associated with lung function trajectory during SPIROMICS follow-up (stable/improved, decline, or rapid decline groups). The stable/improved group (slope of FEV1 regression ⩾66th percentile) had greater bacterial diversity at baseline associated with enrichment in Prevotella, Leptotrichia, and Neisseria species. In contrast, the rapid decline group (FEV1 slope ⩽33rd percentile) had significantly lower baseline diversity associated with enrichment in Streptococcus species. Conclusions: In SPIROMICS, baseline airway microbiota features demonstrate divergent associations with better or worse COPD-related outcomes.
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Affiliation(s)
- Kristopher Opron
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Lesa A. Begley
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | - Gen Li
- Department of Biostatistics, School of Public Health
| | - Neil E. Alexis
- Center for Environmental Medicine, Asthma, and Lung Biology, Division of Allergy and Immunology
| | | | - R. Graham Barr
- Department of Medicine, Division of General Medicine and
- Department of Epidemiology, Columbia University Medical Center, New York, New York
| | | | - Richard Boucher
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | | | | | - Alejandro P. Comellas
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | | | | | - David Couper
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - MeiLan K. Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Annette Hastie
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | - Eric A. Hoffman
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J. Kaner
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | - Mehmet Kesimer
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | - Jerry A. Krishnan
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Breathe Chicago Center, University of Illinois Chicago, Chicago, Illinois
| | - David C. LaFon
- Division of Pulmonary, Allergy and Critical Care, University of Alabama at Birmingham, Alabama
| | - Fernando J. Martinez
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | | | | | - Robert Paine
- Division of Respiratory, Critical Care, Occupational Pulmonary Medicine, University of Utah, Salt Lake City, Utah
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | - Prescott G. Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Gary B. Huffnagle
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Ariangela J. Kozik
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Jeffrey L. Curtis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Yvonne J. Huang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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11
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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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12
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McCauley KE, Durack J, Lynch KV, Fadrosh DW, Fujimura KE, Vundla F, Özçam M, LeBeau P, Caltroni A, Burns P, Tran HT, Bacharier LB, Kattan M, O'Connor GT, Wood RA, Togias A, Boushey HA, Jackson DJ, Gern JE, Lynch SV. Early-life nasal microbiota dynamics relate to longitudinal respiratory phenotypes in urban children. J Allergy Clin Immunol 2024; 153:1563-1573. [PMID: 38423369 PMCID: PMC11162315 DOI: 10.1016/j.jaci.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND Five distinct respiratory phenotypes based on latent classes of longitudinal patterns of wheezing, allergic sensitization. and pulmonary function measured in urban children from ages from 0 to 7 years have previously been described. OBJECTIVE Our aim was to determine whether distinct respiratory phenotypes are associated with early-life upper respiratory microbiota development and environmental microbial exposures. METHODS Microbiota profiling was performed using 16S ribosomal RNA-based sequencing of nasal samples collected at age 12 months (n = 120) or age 36 months (n = 142) and paired house dust samples collected at 3 months (12-month, n = 73; 36-month, n = 90) from all 4 centers in the Urban Environment and Childhood Asthma (URECA) cohort. RESULTS In these high-risk urban children, nasal microbiota increased in diversity between ages 12 and 36 months (ß = 2.04; P = .006). Age-related changes in microbiota evenness differed significantly by respiratory phenotypes (interaction P = .0007), increasing most in the transient wheeze group. At age 12 months, respiratory illness (R2 = 0.055; P = .0001) and dominant bacterial genus (R2 = 0.59; P = .0001) explained variance in nasal microbiota composition, and enrichment of Moraxella and Haemophilus members was associated with both transient and high-wheeze respiratory phenotypes. By age 36 months, nasal microbiota was significantly associated with respiratory phenotypes (R2 = 0.019; P = .0376), and Moraxella-dominated microbiota was associated specifically with atopy-associated phenotypes. Analysis of paired house dust and nasal samples indicated that 12 month olds with low wheeze and atopy incidence exhibited the largest number of shared bacterial taxa with their environment. CONCLUSION Nasal microbiota development over the course of early childhood and composition at age 3 years are associated with longitudinal respiratory phenotypes. These data provide evidence supporting an early-life window of airway microbiota development that is influenced by environmental microbial exposures in infancy and associates with wheeze- and atopy-associated respiratory phenotypes through age 7 years.
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Affiliation(s)
- Kathryn E McCauley
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Juliana Durack
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Kole V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Douglas W Fadrosh
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Kei E Fujimura
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Faith Vundla
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Mustafa Özçam
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | | | | | | | | | - Leonard B Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in St Louis, St Louis, Mo
| | - Meyer Kattan
- Department of Pediatrics, Columbia University, New York, NY
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Robert A Wood
- Departments of Pediatrics and Allergy and Immunology, Johns Hopkins University, Baltimore, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Homer A Boushey
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis.
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, Calif.
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13
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Quinn-Bohmann N, Freixas-Coutin JA, Seo J, Simmons R, Diener C, Gibbons SM. Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC Biol 2024; 22:93. [PMID: 38654335 PMCID: PMC11040984 DOI: 10.1186/s12915-024-01887-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult. RESULTS In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex, and geographic location, in order to isolate these associations from health and disease states. CONCLUSIONS We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.
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Affiliation(s)
- Nick Quinn-Bohmann
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, 98195, USA.
| | | | - Jin Seo
- Reckitt Health US LLC, 1 Philips Pkwy, Montvale, NJ, 07645, USA
| | - Ruth Simmons
- Reckitt Benckiser Healthcare Ltd, 105 Bath Road, Slough, Berkshire, SL1 3UH, UK
| | | | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, 98195, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- eScience Institute, University of Washington, Seattle, WA, 98195, USA.
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14
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Chiyaka TL, Nyawo GR, Naidoo C, Moodley S, Clemente JC, Malherbe ST, Warren R, Ku D, Segal LN, Theron G. A novel aerosol collection method shows the cough aeromicrobiome of people with tuberculosis is phylogenetically distinct from respiratory tract specimens. RESEARCH SQUARE 2024:rs.3.rs-4106141. [PMID: 38659922 PMCID: PMC11042404 DOI: 10.21203/rs.3.rs-4106141/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB. Methods PMC was done in sputum culture-positive people (≥30 forced coughs each, n=16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n=6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF). Findings 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum. Interpretation PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes.
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15
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 PMCID: PMC10791971 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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16
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Barosova R, Baranovicova E, Hanusrichterova J, Mokra D. Metabolomics in Animal Models of Bronchial Asthma and Its Translational Importance for Clinics. Int J Mol Sci 2023; 25:459. [PMID: 38203630 PMCID: PMC10779398 DOI: 10.3390/ijms25010459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Bronchial asthma is an extremely heterogenous chronic respiratory disorder with several distinct endotypes and phenotypes. These subtypes differ not only in the pathophysiological changes and/or clinical features but also in their response to the treatment. Therefore, precise diagnostics represent a fundamental condition for effective therapy. In the diagnostic process, metabolomic approaches have been increasingly used, providing detailed information on the metabolic alterations associated with human asthma. Further information is brought by metabolomic analysis of samples obtained from animal models. This article summarizes the current knowledge on metabolomic changes in human and animal studies of asthma and reveals that alterations in lipid metabolism, amino acid metabolism, purine metabolism, glycolysis and the tricarboxylic acid cycle found in the animal studies resemble, to a large extent, the changes found in human patients with asthma. The findings indicate that, despite the limitations of animal modeling in asthma, pre-clinical testing and metabolomic analysis of animal samples may, together with metabolomic analysis of human samples, contribute to a novel way of personalized treatment of asthma patients.
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Affiliation(s)
- Romana Barosova
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; (R.B.); (J.H.)
| | - Eva Baranovicova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Juliana Hanusrichterova
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; (R.B.); (J.H.)
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Daniela Mokra
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; (R.B.); (J.H.)
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17
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Clemente-Suárez VJ, Mielgo-Ayuso J, Ramos-Campo DJ, Beltran-Velasco AI, Martínez-Guardado I, Navarro Jimenez E, Redondo-Flórez L, Yáñez-Sepúlveda R, Tornero-Aguilera JF. Basis of preventive and non-pharmacological interventions in asthma. Front Public Health 2023; 11:1172391. [PMID: 37920579 PMCID: PMC10619920 DOI: 10.3389/fpubh.2023.1172391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023] Open
Abstract
Asthma is one of the most common atopic disorders in all stages of life. Its etiology is likely due to a complex interaction between genetic, environmental, and lifestyle factors. Due to this, different non-pharmacological interventions can be implemented to reduce or alleviate the symptoms caused by this disease. Thus, the present narrative review aimed to analyze the preventive and non-pharmacological interventions such as physical exercise, physiotherapy, nutritional, ergonutritional, and psychological strategies in asthma treatment. To reach these aims, an extensive narrative review was conducted. The databases used were MedLine (PubMed), Cochrane (Wiley), Embase, PsychINFO, and CinAhl. Asthma is an immune-mediated inflammatory condition characterized by increased responsiveness to bronchoconstrictor stimuli. Different factors have been shown to play an important role in the pathogenesis of asthma, however, the treatments used to reduce its incidence are more controversial. Physical activity is focused on the benefits that aerobic training can provide, while physiotherapy interventions recommend breathing exercises to improve the quality of life of patients. Nutritional interventions are targeted on implement diets that prioritize the consumption of fruits and vegetables and supplementation with antioxidants. Psychological interventions have been proposed as an essential non-pharmacological tool to reduce the emotional problems associated with asthma.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Madrid, Spain
- Studies Centre in Applied Combat (CESCA), Toledo, Spain
| | - Juan Mielgo-Ayuso
- Department of Health Sciences, Faculty of Health Sciences, University of Burgos, Burgos, Spain
| | - Domingo Jesús Ramos-Campo
- LFE Research Group, Department of Health and Human Performance, Faculty of Physical Activity and Sport Science-INEF, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Ismael Martínez-Guardado
- BRABE Group, Department of Psychology, Faculty of Life and Natural Sciences, Universidad Camilo José Cela, Madrid, Spain
| | | | - Laura Redondo-Flórez
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | | | - Jose Francisco Tornero-Aguilera
- Faculty of Sports Sciences, Universidad Europea de Madrid, Madrid, Spain
- Studies Centre in Applied Combat (CESCA), Toledo, Spain
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18
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Ng WZJ, van Hasselt J, Aggarwal B, Manoharan A. Association Between Adult Antibiotic Use, Microbial Dysbiosis and Atopic Conditions - A Systematic Review. J Asthma Allergy 2023; 16:1115-1132. [PMID: 37822520 PMCID: PMC10564082 DOI: 10.2147/jaa.s401755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
Background Strong associations between early antibiotic exposure and increased risk of childhood allergies have been established. Antibiotics have the potential to induce microbial dysbiosis that may be linked to allergic conditions. This review examines the limited available evidence on the associations between adult antibiotic use, microbial dysbiosis and atopic conditions. Methods A systematic literature search was conducted using PubMed and Embase for relevant studies, published between 01-01-2000 and 08-17-2022. We searched for associations between antibiotic use, microbial dysbiosis, and allergic conditions in adults, defined as over 13 years of age for the purposes of this review. Results Twenty-one studies were analyzed, with the inclusion of four narrative reviews as scarce relevant literature was found when stricter selection criteria were employed. Relevant studies predominantly focused on asthma. Significant microbial differences were observed in most measures between healthy subjects and subjects with allergic conditions. However, no system-wise and strain-wise associations were evident. Notably, at the phyla level, the Bacillota and Pseudomonadota phyla were associated with asthmatics, while the Actinobacteria phylum was linked to healthy controls. Asthmatics tends to reflect upregulation in the Bacillota and Pseudomonadota phyla in both airway and gut microbiomes. Conclusion No compelling evidence could be found between adult antibiotic exposure, consequent microbial dysbiosis, and allergic conditions in adults. Our review is limited by scarce literature and therefore remains inconclusive. However, potential implications of antibiotic use impacting on allergic conditions justify additional research and heightened pharmacovigilance in this area.
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Affiliation(s)
- Wan Zhen Janice Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Bhumika Aggarwal
- Regional Respiratory Medical Affairs, GSK Plc, Singapore, Singapore
| | - Anand Manoharan
- Infectious Diseases Medical & Scientific Affairs, GSK, Mumbai, India
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19
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Chen IL, Huang F, Li SC, Huang HC. Salivary microbiome and asthma risk in children with orofacial defects. Pediatr Pulmonol 2023; 58:2777-2785. [PMID: 37470110 DOI: 10.1002/ppul.26582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Patients with congenital orofacial defects, cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP) have continuous exposure of the respiratory system to the microbiome from the oral environment, offering opportunities to develop mucosal immunity in the airway. This two-part study aims to analyze data on asthma occurrence in CL, CP, and CLP infants and the composition of the salivary microbiome, and to evaluate the oral microbiota and its association with the risk of developing childhood asthma. METHODS Patient data from the research database of Chang Gung Memorial Hospital from 2004 to 2015 were retrospectively analyzed by multivariable regression. Diseases diagnoses were defined by ICD codes. Asthma must also meet the criteria for receiving selective β2 agonistic or/and inhaled corticosteroid treatments twice within 1 year. Analysis of the saliva microbiome was performed prospectively from 2016 to 2020 in 10 healthy term infants and 10 CLP infants on postnatal 7th day, 1 month, and 6 months by next-generation sequencing. RESULTS Asthma and nonasthma groups included 988 and 3952 patients, respectively. The incidence of asthma development was higher in patients with CP than in CL and CLP groups (aOR: 5.644, CI: 1.423-22.376). The species composition of the microbiome at 1 and 6 months was significantly different between infants with CLP and healthy infants. CONCLUSION Children with orofacial defects have a higher risk of developing asthma with a possible contribution from oral microbiota in the early months of life.
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Affiliation(s)
- I-Lun Chen
- Department of Pediatrics, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Faye Huang
- Department of Plastic Surgery, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Department of Medical Research, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
| | - Hsin-Chun Huang
- Department of Pediatrics, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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20
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Sardon-Prado O, Diaz-Garcia C, Corcuera-Elosegui P, Korta-Murua J, Valverde-Molina J, Sanchez-Solis M. Severe Asthma and Biological Therapies: Now and the Future. J Clin Med 2023; 12:5846. [PMID: 37762787 PMCID: PMC10532431 DOI: 10.3390/jcm12185846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Recognition of phenotypic variability in pediatric asthma allows for a more personalized therapeutic approach. Knowledge of the underlying pathophysiological and molecular mechanisms (endotypes) of corresponding biomarkers and new treatments enables this strategy to progress. Biologic therapies for children with severe asthma are becoming more relevant in this sense. The T2 phenotype is the most prevalent in childhood and adolescence, and non-T2 phenotypes are usually rare. This document aims to review the mechanism of action, efficacy, and potential predictive and monitoring biomarkers of biological drugs, focusing on the pediatric population. The drugs currently available are omalizumab, mepolizumab, benralizumab, dupilumab, and 1ezepelumab, with some differences in administrative approval prescription criteria between the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA). Previously, we described the characteristics of severe asthma in children and its diagnostic and therapeutic management.
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Affiliation(s)
- Olaia Sardon-Prado
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 20014 Leioa, Spain
| | - Carolina Diaz-Garcia
- Paediatric Pulmonology and Allergy Unit, Santa Lucia General University Hospital, 30202 Cartagena, Spain;
| | - Paula Corcuera-Elosegui
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
| | - Javier Korta-Murua
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
| | - Jose Valverde-Molina
- Department of Paediatrics, Santa Lucía General University Hospital, 30202 Cartagena, Spain
- IMIB Biomedical Research Institute, 20120 Murcia, Spain;
| | - Manuel Sanchez-Solis
- IMIB Biomedical Research Institute, 20120 Murcia, Spain;
- Department of Pediatrics, University of Murcia, 20120 Murcia, Spain
- Paediatric Allergy and Pulmonology Units, Virgen de la Arrixaca University Children’s Hospital, 20120 Murcia, Spain
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21
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Lin L, Yi X, Liu H, Meng R, Li S, Liu X, Yang J, Xu Y, Li C, Wang Y, Xiao N, Li H, Liu Z, Xiang Z, Shu W, Guan WJ, Zheng XY, Sun J, Wang Z. The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans. Nat Med 2023:10.1038/s41591-023-02424-2. [PMID: 37349537 DOI: 10.1038/s41591-023-02424-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.
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Affiliation(s)
- Lifeng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyue Liu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ruilin Meng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Saiqiang Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaomin Liu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junhao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yanjun Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chuan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ye Wang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ni Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zuheng Liu
- Xiamen Key Laboratory of Cardiac Electrophysiology, Department of Cardiology, Xiamen Institute of Cardiovascular Diseases, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiming Xiang
- Department of Radiology, Panyu Central Hospital, Guangzhou, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xue-Yan Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Jiufeng Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China.
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22
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Wong KK, Segal LN. Correcting dysbiosis in the lungs of COPD, one pathogen at a time. Cell Host Microbe 2023; 31:925-927. [PMID: 37321178 DOI: 10.1016/j.chom.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
In this issue of Cell Host & Microbe, Liang et al. demonstrate through genomic analysis of the sputum microbiome from COPD patients and preclinical models that Staphylococcus aureus promotes lung function decline via regulation of homocysteine levels. Homocysteine can promote lung injury by promoting neutrophil apoptosis-to-NETosis shift via AKT1-S100A8/A9 axis.
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Affiliation(s)
- Kendrew K Wong
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
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23
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Campbell CD, Gleeson M, Sulaiman I. The role of the respiratory microbiome in asthma. FRONTIERS IN ALLERGY 2023; 4:1120999. [PMID: 37324782 PMCID: PMC10262749 DOI: 10.3389/falgy.2023.1120999] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023] Open
Abstract
Asthma is a common airways disease and the human microbiome plays an increasingly recognised role in asthma pathogenesis. Furthermore, the respiratory microbiome varies with asthma phenotype, endotype and disease severity. Consequently, asthma therapies have a direct effect on the respiratory microbiome. Newer biological therapies have led to a significant paradigm shift in how we treat refractory Type 2 high asthma. While airway inflammation is the generally accepted mechanism of action of all asthma therapies, including both inhaled and systemic therapies, there is evidence to suggest that they may also alter the microbiome to create a more functionally balanced airway microenvironment while also influencing airway inflammation directly. This downregulated inflammatory cascade seen biochemically, and reflected in improved clinical outcomes, supports the hypothesis that biological therapies may in fact affect the microbiome-host immune system dynamic and thus represent a therapeutic target for exacerbations and disease control.
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Affiliation(s)
- Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Margaret Gleeson
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Imran Sulaiman
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
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24
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Che Y, Wang N, Ma Q, Liu J, Xu Z, Li Q, Wang J, Sun Y. Microbial characterization of the nasal cavity in patients with allergic rhinitis and non-allergic rhinitis. Front Cell Infect Microbiol 2023; 13:1166389. [PMID: 37180436 PMCID: PMC10166850 DOI: 10.3389/fcimb.2023.1166389] [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: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis. Method From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora. Results The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans. Conclusion In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.
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Affiliation(s)
| | | | | | | | | | | | | | - Yanan Sun
- *Correspondence: Jingting Wang, ; Yanan Sun,
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25
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Kozik AJ, Begley LA, Lugogo N, Baptist A, Erb-Downward J, Opron K, Huang YJ. Airway microbiota and immune mediator relationships differ in obesity and asthma. J Allergy Clin Immunol 2023; 151:931-942. [PMID: 36572355 PMCID: PMC10566565 DOI: 10.1016/j.jaci.2022.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Asthma and obesity are both complex conditions characterized by chronic inflammation, and obesity-related severe asthma has been associated with differences in the microbiome. However, whether the airway microbiome and microbiota-immune response relationships differ between obese persons with or without nonsevere asthma is unestablished. OBJECTIVE We compared the airway microbiome and microbiota-immune mediator relationships between obese and nonobese subjects, with and without mild-moderate asthma. METHODS We performed cross-sectional analyses of the airway (induced sputum) microbiome and cytokine profiles from blood and sputum using 16S ribosomal RNA gene and internal transcribed spacer region sequencing to profile bacteria and fungi, and multiplex immunoassays. Analysis tools included QIIME 2, linear discriminant analysis effect size (aka LEfSe), Piphillin, and Sparse inverse covariance estimation for ecological association inference (aka SPIEC-EASI). RESULTS Obesity, irrespective of asthma status, was associated with significant differences in sputum bacterial community structure and composition (unweighted UniFrac permutational analysis of variance, P = .02), including a higher relative abundance of Prevotella, Gemella, and Streptococcus species. Among subjects with asthma, additional differences in sputum bacterial composition and fungal richness were identified between obese and nonobese individuals. Correlation network analyses demonstrated differences between obese and nonobese asthma in relationships between cytokine mediators, and these together with specific airway bacteria involving blood PAI-1, sputum IL-1β, GM-CSF, IL-8, TNF-α, and several Prevotella species. CONCLUSION Obesity itself is associated with an altered sputum microbiome, which further differs in those with mild-moderate asthma. The distinct differences in airway microbiota and immune marker relationships in obese asthma suggest potential involvement of airway microbes that may affect mechanisms or outcomes of obese asthma.
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Affiliation(s)
- Ariangela J Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich.
| | - Lesa A Begley
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Njira Lugogo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Alan Baptist
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Ann Arbor, Mich
| | - John Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Kristopher Opron
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Mich.
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The upper-airway microbiome as a biomarker of asthma exacerbations despite inhaled corticosteroid treatment. J Allergy Clin Immunol 2023; 151:706-715. [PMID: 36343772 DOI: 10.1016/j.jaci.2022.09.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite receipt of ICS. METHODS Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Control/case subjects were defined by the absence/presence of asthma exacerbations in the past 6 months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data. RESULTS In nasal and saliva samples, case subjects had lower bacterial diversity (Richness, Shannon, and Faith indices) than control subjects (.007 ≤ P ≤ .037). Asthma exacerbations accounted for 8% to 9% of the interindividual variation of the salivary and nasal microbiomes (.003 ≤ P ≤ .046). Three, 4, and 11 bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09 × 10-12 ≤ FDR ≤ 0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite receipt of ICS (AUCtraining: 0.82 and AUCvalidation: 0.77). CONCLUSION The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite receipt of ICS.
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Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma. Microorganisms 2023; 11:microorganisms11030546. [PMID: 36985120 PMCID: PMC10059697 DOI: 10.3390/microorganisms11030546] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.
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28
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Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA, Nicol MP. Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease. MICROBIOME 2023; 11:29. [PMID: 36803868 PMCID: PMC9940396 DOI: 10.1186/s40168-023-01460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Long-term azithromycin (AZM) treatment reduces the frequency of acute respiratory exacerbation in children and adolescents with HIV-associated chronic lung disease (HCLD). However, the impact of this treatment on the respiratory bacteriome is unknown. METHOD African children with HCLD (defined as forced expiratory volume in 1 s z-score (FEV1z) less than - 1.0 with no reversibility) were enrolled in a placebo-controlled trial of once-weekly AZM given for 48-weeks (BREATHE trial). Sputum samples were collected at baseline, 48 weeks (end of treatment) and 72 weeks (6 months post-intervention in participants who reached this timepoint before trial conclusion). Sputum bacterial load and bacteriome profiles were determined using 16S rRNA gene qPCR and V4 region amplicon sequencing, respectively. The primary outcomes were within-participant and within-arm (AZM vs placebo) changes in the sputum bacteriome measured across baseline, 48 weeks and 72 weeks. Associations between clinical or socio-demographic factors and bacteriome profiles were also assessed using linear regression. RESULTS In total, 347 participants (median age: 15.3 years, interquartile range [12.7-17.7]) were enrolled and randomised to AZM (173) or placebo (174). After 48 weeks, participants in the AZM arm had reduced sputum bacterial load vs placebo arm (16S rRNA copies/µl in log10, mean difference and 95% confidence interval [CI] of AZM vs placebo - 0.54 [- 0.71; - 0.36]). Shannon alpha diversity remained stable in the AZM arm but declined in the placebo arm between baseline and 48 weeks (3.03 vs. 2.80, p = 0.04, Wilcoxon paired test). Bacterial community structure changed in the AZM arm at 48 weeks compared with baseline (PERMANOVA test p = 0.003) but resolved at 72 weeks. The relative abundances of genera previously associated with HCLD decreased in the AZM arm at 48 weeks compared with baseline, including Haemophilus (17.9% vs. 25.8%, p < 0.05, ANCOM ω = 32) and Moraxella (1% vs. 1.9%, p < 0.05, ANCOM ω = 47). This reduction was sustained at 72 weeks relative to baseline. Lung function (FEV1z) was negatively associated with bacterial load (coefficient, [CI]: - 0.09 [- 0.16; - 0.02]) and positively associated with Shannon diversity (0.19 [0.12; 0.27]). The relative abundance of Neisseria (coefficient, [standard error]: (2.85, [0.7], q = 0.01), and Haemophilus (- 6.1, [1.2], q < 0.001) were positively and negatively associated with FEV1z, respectively. An increase in the relative abundance of Streptococcus from baseline to 48 weeks was associated with improvement in FEV1z (3.2 [1.11], q = 0.01) whilst an increase in Moraxella was associated with decline in FEV1z (-2.74 [0.74], q = 0.002). CONCLUSIONS AZM treatment preserved sputum bacterial diversity and reduced the relative abundances of the HCLD-associated genera Haemophilus and Moraxella. These bacteriological effects were associated with improvement in lung function and may account for reduced respiratory exacerbations associated with AZM treatment of children with HCLD. Video Abstract.
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Affiliation(s)
- Regina E Abotsi
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Felix S Dube
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrea M Rehman
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Victoria Simms
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Kilaza S Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Stellenbosch University, Stellenbosch, South Africa
| | - Grace McHugh
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lucky G Ngwira
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Jon Ø Odland
- Department of Community Medicine, University of Tromsø, Tromsø, Norway
- International Research Laboratory for Reproductive Ecotoxicology (IL RET), The National Research University Higher School of Economics, Moscow, Russia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Rashida A Ferrand
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia.
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29
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Fraga-Silva TFDC, Boko MMM, Martins NS, Cetlin AA, Russo M, Vianna EO, Bonato VLD. Asthma-associated bacterial infections: Are they protective or deleterious? THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:14-22. [PMID: 37780109 PMCID: PMC10510013 DOI: 10.1016/j.jacig.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 10/03/2023]
Abstract
Eosinophilic, noneosinophilic, or mixed granulocytic inflammations are the hallmarks of asthma heterogeneity. Depending on the priming of lung immune and structural cells, subjects with asthma might generate immune responses that are TH2-prone or TH17-prone immune response. Bacterial infections caused by Haemophilus, Moraxella, or Streptococcus spp. induce the secretion of IL-17, which in turn recruit neutrophils into the airways. Clinical studies and experimental models of asthma indicated that neutrophil infiltration induces a specific phenotype of asthma, characterized by an impaired response to corticosteroid treatment. The understanding of pathways that regulate the TH17-neutrophils axis is critical to delineate and develop host-directed therapies that might control asthma and its exacerbation episodes that course with infectious comorbidities. In this review, we outline clinical and experimental studies on the role of airway epithelial cells, S100A9, and high mobility group box 1, which act in concert with the IL-17-neutrophil axis activated by bacterial infections, and are related with asthma that is difficult to treat. Furthermore, we report critically our view in the light of these findings in an attempt to stimulate further investigations and development of immunotherapies for the control of severe asthma.
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Affiliation(s)
| | - Mèdéton Mahoussi Michaël Boko
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Núbia Sabrina Martins
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Andrea Antunes Cetlin
- Pulmonary Division, Department of Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Momtchilo Russo
- Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Elcio Oliveira Vianna
- Pulmonary Division, Department of Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Vania Luiza Deperon Bonato
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
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30
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Bagnasco D, Caminati M. Editorial: Innate immunity and severe asthma: From microbiome to target therapy. Front Immunol 2022; 13:1114275. [PMID: 36643921 PMCID: PMC9834275 DOI: 10.3389/fimmu.2022.1114275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Affiliation(s)
- Diego Bagnasco
- Allergy and Respiratory Diseases, Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Martino, Genoa, Italy,Department of internal medicine (DIMI), University of Genoa, Genoa, Italy,*Correspondence: Diego Bagnasco,
| | - Marco Caminati
- Asthma, Allergy and Clinical Immunology Section, Department of Medicine, University of Verona, Verona, Italy
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31
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DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development. Allergy 2022; 77:3617-3628. [PMID: 35841380 PMCID: PMC9712226 DOI: 10.1111/all.15442] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/25/2022] [Accepted: 06/11/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The path to childhood asthma is thought to initiate in utero and be further promoted by postnatal exposures. However, the underlying mechanisms remain underexplored. We hypothesized that prenatal maternal immune dysfunction associated with increased childhood asthma risk (revealed by low IFN-γ:IL-13 secretion during the third trimester of pregnancy) alters neonatal immune training through epigenetic mechanisms and promotes early-life airway colonization by asthmagenic microbiota. METHODS We examined epigenetic, immunologic, and microbial features potentially related to maternal prenatal immunity (IFN-γ:IL-13 ratio) and childhood asthma in a birth cohort of mother-child dyads sampled pre-, peri-, and postnatally (N = 155). Epigenome-wide DNA methylation and cytokine production were assessed in cord blood mononuclear cells (CBMC) by array profiling and ELISA, respectively. Nasopharyngeal microbiome composition was characterized at age 2-36 months by 16S rRNA sequencing. RESULTS Maternal prenatal immune status related to methylome profiles in neonates born to non-asthmatic mothers. A module of differentially methylated CpG sites enriched for microbe-responsive elements was associated with childhood asthma. In vitro responsiveness to microbial products was impaired in CBMCs from neonates born to mothers with the lowest IFN-γ:IL-13 ratio, suggesting defective neonatal innate immunity in those who developed asthma during childhood. These infants exhibited a distinct pattern of upper airway microbiota development characterized by early-life colonization by Haemophilus that transitioned to a Moraxella-dominated microbiota by age 36 months. CONCLUSIONS Maternal prenatal immune status shapes asthma development in her child by altering the epigenome and trained innate immunity at birth, and is associated with pathologic upper airway microbial colonization in early life.
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Affiliation(s)
- Avery DeVries
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
| | - Kathryn McCauley
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Douglas Fadrosh
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Kei E. Fujimura
- Genetic Disease LabCalifornia Department of Public HealthRichmondCaliforniaUSA
| | - Debra A. Stern
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
| | - Susan V. Lynch
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Donata Vercelli
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
- Department of Cellular and Molecular MedicineThe University of ArizonaTucsonArizonaUSA
- Arizona Center for the Biology of Complex DiseasesThe University of ArizonaTucsonArizonaUSA
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32
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Zhao C, Hu X, Bao L, Wu K, Zhao Y, Xiang K, Li S, Wang Y, Qiu M, Feng L, Meng X, Zhang N, Fu Y. Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia. MICROBIOME 2022; 10:205. [PMID: 36451232 PMCID: PMC9714159 DOI: 10.1186/s40168-022-01402-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/24/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Mounting experimental evidence has shown that the gut microbiota plays a significant role in the pathogenesis of mastitis, and clinical investigations have found that the occurrence of mastitis is correlated with ruminal dysbiosis. However, the underlying mechanism by which the ruminal microbiota participates in the development of mastitis remains unknown. RESULTS In the present study, we found that cows with clinical mastitis had marked systemic inflammation, which was associated with significant ruminal dysbiosis, especially enriched Proteobacteria in the rumen. Ruminal microbiota transplantation from mastitis cows (M-RMT) to mice induced mastitis symptoms in recipient mice along with increased mammary proinflammatory signature activation of the TLR4-cGAS-STING-NF-κB/NLRP3 pathways. M-RMT also induced mucosal inflammation and impaired intestinal barrier integrity, leading to increased endotoxemia and systemic inflammation. Moreover, we showed that M-RMT mirrored ruminal microbiota disruption in the gut of recipient mice, as evidenced by enriched Proteobacteria and similar bacterial functions, which were correlated with most proinflammatory parameters and serum lipopolysaccharide (LPS) levels in mice. Recurrent low-grade LPS treatment mirrored gut dysbiosis-induced endotoxemia and caused severe mastitis in mice. Furthermore, we found that gut dysbiosis-derived LPS reduced host alkaline phosphatase activity by activating neuraminidase (Neu), which facilitates low-grade LPS exposure and E. coli-induced mastitis in mice. Conversely, treatment with calf intestinal alkaline phosphatase or the Neu inhibitor zanamivir alleviated low-grade LPS exposure and E. coli-induced mastitis in mice. CONCLUSIONS Our results suggest that ruminal dysbiosis-derived low-grade endotoxemia can cause mastitis and aggravate pathogen-induced mastitis by impairing host anti-inflammatory enzymes, which implies that regulating the ruminal or gut microbiota to prevent low-grade systemic inflammation is a potential strategy for mastitis intervention. Video Abstract.
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Affiliation(s)
- Caijun Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Xiaoyu Hu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Lijuan Bao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Keyi Wu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Yihong Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Kaihe Xiang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Shuang Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Ying Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Min Qiu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Lianjun Feng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Xiangyue Meng
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Naisheng Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Yunhe Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China.
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Wang H, Hu J, Wu J, Ji P, Shang A, Li D. The Function and Molecular Mechanism of Commensal Microbiome in Promoting Malignant Progression of Lung Cancer. Cancers (Basel) 2022; 14:5394. [PMID: 36358812 PMCID: PMC9658664 DOI: 10.3390/cancers14215394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/29/2022] [Accepted: 10/30/2022] [Indexed: 02/03/2024] Open
Abstract
The human commensal microbiome existing in an internal environment is relatively consistent with that of the host. The presence of bacterial dysbiosis, on the other hand, promptly results in the termination of this symbiotic association. The altered microbial structure in the lung may be responsible for the development of lung cancer by controlling the host's inflammatory response and influencing a variety of immunological pathways. More and more studies have pointed to the fact that the commensal microbiota plays a vital role in both the development of tumors and the body's response to lung cancer treatment. Microbiome dysbiosis, genotoxicity, virulence effect, and epigenetic dysregulations are some of the potential mechanisms that may lie behind the process of tumorigenesis that is mediated by microbiome. Other potential mechanisms include regulating host immune activity through a variety of pathogenic factors, dysregulating host metabolism as a result of microbiome alterations, and microbiome dysbiosis. In this historical overview, we go through some of the more recent mechanistic discoveries into the biological processes that are involved in lung cancer that are caused by bacteria. Without a question, obtaining a greater knowledge of the dynamic link between the lung microbiome and lung cancer has the potential to inspire the development of innovative early detection and customized treatment methods for lung cancer.
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Affiliation(s)
| | | | | | | | - Anquan Shang
- Department of Laboratory Medicine, Tongji Hospital of Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Dong Li
- Department of Laboratory Medicine, Tongji Hospital of Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
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34
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Zhang J, Wu Y, Liu J, Yang Y, Li H, Wu X, Zheng X, Liang Y, Tu C, Chen M, Tan C, Chang B, Huang Y, Wang Z, Tian G, Ding T. Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203115. [PMID: 36031410 PMCID: PMC9661847 DOI: 10.1002/advs.202203115] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Indexed: 05/09/2023]
Abstract
The oral and upper respiratory tracts are closely linked anatomically and physiologically with the lower respiratory tract and lungs, and the influence of oral and upper respiratory microbes on the lung microbiota is increasingly being recognized. However, the ecological process and individual heterogeneity of the oral and upper respiratory tract microbes shaping the lung microbiota remain unclear owing to the lack of controlled analyses with sufficient sample sizes. Here, the microbiomes of saliva, nasal cavity, oropharyngeal area, and bronchoalveolar lavage samples are profiled and the shaping process of multisource microbes on the lung microbiota is measured. It is found that oral and nasal microbial inputs jointly shape the lung microbiota by occupying different ecological niches. It is also observed that the spread of oral microbes to the lungs is heterogeneous, with more oral microbes entering the lungs being associated with decreased lung function and increased lung proinflammatory cytokines. These results depict the external shaping process of lung microbiota and indicate the great value of oral samples, such as saliva, in monitoring and assessing lung microbiota status in clinical settings.
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Affiliation(s)
- Jingxiang Zhang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiping Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Jing Liu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yongqiang Yang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Hui Li
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaorong Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaobin Zheng
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yingjian Liang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Changli Tu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Meizhu Chen
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Cuiyan Tan
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Bozhen Chang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiying Huang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Zhengguo Wang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Guo‐Bao Tian
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
- School of MedicineXizang Minzu UniversityXianyangShaanxi712082China
| | - Tao Ding
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
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Lin Z, Chen P, Yuan Z, Yang L, Miao L, Wang H, Xu D. Fine particulate matter, airway inflammation, stress response, non-specific immune function and buccal microbial diversity in young adults. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119692. [PMID: 35772617 DOI: 10.1016/j.envpol.2022.119692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/26/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Fine particulate matter (PM2.5) has been associated with risk of oral and respiratory diseases. However, the biological mechanisms of adverse oral and respiratory health response to PM2.5 fluctuation have not been well characterized. This study aims to explore the relationships of PM2.5 with airway inflammation, salivary biomarkers and buccal mucosa microbiota. We performed a panel study among 40 college students involving 4 follow-ups from August to October 2021 in Hefei, Anhui Province, China. Health outcomes included fractional exhaled nitric oxide (FeNO), salivary biomarkers [C-reactive protein (CRP), cortisol, lysozyme and alpha-amylase] and buccal mucosa microbial diversity. Linear mixed-effect models were applied to explore the cumulative impacts of PM2.5 on health indicators. PM2.5 was positively correlated with FeNO, CRP, cortisol and alpha-amylase, while negatively with lysozyme. Per 10-μg/m3 increase in PM2.5 was linked to maximum increments in FeNO of 10.71% (95%CI: 2.01%, 19.41%) at lag 0-24 h, in CRP of 7.10% (95%CI: 5.39%, 8.81%) at lag 0-24 h, in cortisol of 1.25% (95%CI: 0.44%, 2.07%) at lag 0-48 h, and in alpha-amylase of 2.12% (95%CI: 0.53%, 3.71%) at lag 0-24 h, while associated with maximum decrement in lysozyme of 0.53% (95%CI: 0.12%, 0.95%) at lag 0-72 h. Increased PM2.5 was linked to reduction in the richness and evenness of buccal microbe and o_Bacillales and o_Bacteroidales were identified as differential microbes after PM2.5 inhalation. Bio-information analysis indicated that immunity system pathway was the most important enriched abundant process altered by PM2.5 exposure. In summary, short-term PM2.5 exposure may impair oral and respiratory health by inducing inflammatory and stress responses, weakening immune function and altering buccal mucosa microbial diversity.
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Affiliation(s)
- Zhijing Lin
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Anhui Medical University, Hefei, 230032, China.
| | - Ping Chen
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Zhi Yuan
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Liyan Yang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Lin Miao
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Anhui Medical University, Hefei, 230032, China
| | - Dexiang Xu
- Department of Toxicology, School of Public Health, Anhui Medical University, Hefei, 230032, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, Anhui Medical University, Hefei, 230032, China
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36
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Huang YJ, Porsche C, Kozik AJ, Lynch SV. Microbiome-Immune Interactions in Allergy and Asthma. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:2244-2251. [PMID: 35724951 PMCID: PMC10566566 DOI: 10.1016/j.jaip.2022.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/13/2022] [Accepted: 05/28/2022] [Indexed: 06/13/2023]
Abstract
The human microbiota has been established as a key regulator of host health, in large part owing to its constant interaction with and impact on host immunity. A range of environmental exposures spanning from the prenatal period through adulthood are known to affect the composition and molecular productivity of microbiomes across mucosal and dermal tissues with short- and long-term consequences for host immune function. Here we review recent findings in the field that provide insights into how microbial-immune interactions promote and sustain immune dysfunction associated with allergy and asthma. We consider both early life microbiome perturbation and the molecular underpinnings of immune dysfunction associated with subsequent allergy and asthma development in childhood, as well as microbiome features that relate to phenotypic attributes of allergy and asthma in older patients with established disease.
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Affiliation(s)
- Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, Mich; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Mich.
| | - Cara Porsche
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Ariangela J Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, Mich
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, Calif.
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Yi X, Gao J, Wang Z. The human lung microbiome-A hidden link between microbes and human health and diseases. IMETA 2022; 1:e33. [PMID: 38868714 PMCID: PMC10989958 DOI: 10.1002/imt2.33] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome. The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
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38
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Hu YJ, Satten GA. A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome. Bioinformatics 2022; 38:3689-3697. [PMID: 35723568 PMCID: PMC9991891 DOI: 10.1093/bioinformatics/btac399] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION PERMANOVA is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence-absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias but at the potential costs of information loss and the introduction of a stochastic component into the analysis. RESULTS Here, we develop a non-stochastic approach to PERMANOVA presence-absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease in which samples from case participants have systematically smaller library sizes than samples from control participants. AVAILABILITY AND IMPLEMENTATION We have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Glen A Satten
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Tuazon JA, Kilburg-Basnyat B, Oldfield LM, Wiscovitch-Russo R, Dunigan-Russell K, Fedulov AV, Oestreich KJ, Gowdy KM. Emerging Insights into the Impact of Air Pollution on Immune-Mediated Asthma Pathogenesis. Curr Allergy Asthma Rep 2022; 22:77-92. [PMID: 35394608 PMCID: PMC9246904 DOI: 10.1007/s11882-022-01034-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Increases in ambient levels of air pollutants have been linked to lung inflammation and remodeling, processes that lead to the development and exacerbation of allergic asthma. Conventional research has focused on the role of CD4+ T helper 2 (TH2) cells in the pathogenesis of air pollution-induced asthma. However, much work in the past decade has uncovered an array of air pollution-induced non-TH2 immune mechanisms that contribute to allergic airway inflammation and disease. RECENT FINDINGS In this article, we review current research demonstrating the connection between common air pollutants and their downstream effects on non-TH2 immune responses emerging as key players in asthma, including PRRs, ILCs, and non-TH2 T cell subsets. We also discuss the proposed mechanisms by which air pollution increases immune-mediated asthma risk, including pre-existing genetic risk, epigenetic alterations in immune cells, and perturbation of the composition and function of the lung and gut microbiomes. Together, these studies reveal the multifaceted impacts of various air pollutants on innate and adaptive immune functions via genetic, epigenetic, and microbiome-based mechanisms that facilitate the induction and worsening of asthma.
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Affiliation(s)
- J A Tuazon
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, 43210, USA
| | - B Kilburg-Basnyat
- Department of Pharmacology and Toxicology, East Carolina University, Greenville, NC, 27858, USA
| | - L M Oldfield
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
- Department of Synthetic Genomics, Replay Holdings LLC, San Diego, 92121, USA
| | - R Wiscovitch-Russo
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - K Dunigan-Russell
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, OH, 43210, USA
| | - A V Fedulov
- Division of Surgical Research, Department of Surgery, Alpert Medical School, Brown University, Rhode Island Hospital, Providence, RI, 02903, USA
| | - K J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, The James Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - K M Gowdy
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, OH, 43210, USA.
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40
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Hou J, Song Y, Leung ASY, Tang MF, Shi M, Wang EY, Tsun JGS, Chan RWY, Wong GWK, Tsui SKW, Leung TF. Temporal Dynamics of the Nasopharyngeal Microbiome and its Relationship with Childhood Asthma Exacerbation. Microbiol Spectr 2022; 10:e0012922. [PMID: 35546575 PMCID: PMC9241764 DOI: 10.1128/spectrum.00129-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Despite distinct nasopharyngeal microbiome (NPM) profiles between asthmatics and healthy subjects, little is known about the NPM dynamics and its relation to childhood asthma exacerbation (AE). We investigated NPM changes by longitudinally collecting 135 flocked nasopharyngeal swabs (FNPSs) from 33 school-age asthmatic children at six time points (2 to 4-week intervals) from September to December 2017 in Hong Kong. Subjects were categorized into AE and stable asthma (AS) groups according to whether they experienced any exacerbation during follow-up. One-off FNPSs from nine nonasthmatic children were included as controls. Microbiota profiles were analyzed using 16S rRNA gene sequencing. All 144 NPMs were classified into six microbiome profile groups (MPGs), each dominated by Moraxella, Corynebacterium 1, Dolosigranulum, Staphylococcus, Streptococcus, or Anoxybacillus. The microbial diversity and compositions of NPM in exacerbation samples were different from both baseline samples and those from healthy controls. Moraxella and Dolosigranulum-dominated NPM exhibited high temporal stability revealed by MPG transition analysis. NPM diversity decreased whereas microbial composition remained similar over time. The relative abundances of Moraxella increased while Corynebacterium 1, Anoxybacillus, and Pseudomonas decreased longitudinally. However, these temporal patterns did not differ between AE and AS groups, suggesting that short-term dynamic patterns were not sufficient to predict AE occurrence. Asthmatic NPM underwent Moraxella expansion during AE and presented a high microbiome resilience (recovery potential) after AE resolution. Microbial pathways involved in methane, ketone bodies, and vitamin B3 metabolisms were enhanced during AE and primarily contributed by Moraxella. IMPORTANCE Evidence on the dynamic changes of NPM in asthmatic patients remains limited. Here, we present that asthmatic NPMs deviating from a healthy status still showed resilience after disturbance. Our data imply from a longitudinal perspective that Moraxella increase is closely related to AE occurrence. The finding of functional dysbiosis (imbalance) during AE offers a plausible explanation for the known association between nasopharyngeal Moraxella expansion and increased AE risk. This work serves as a basis for future long-term prospective studies leveraging multiomics approaches to elucidate the temporal association between NPM and pediatric AE.
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Affiliation(s)
- Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuping Song
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Agnes Sze Yin Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Man Fung Tang
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Evy Yiwei Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Gar Shun Tsun
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Renee Wan Yi Chan
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Gary Wing Kin Wong
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
- Center for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fan Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
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Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV. Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota. Dig Dis Sci 2022; 67:2433-2443. [PMID: 34059992 DOI: 10.1007/s10620-021-07045-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/08/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microscopic colitis (MC), an inflammatory disease of the colon, is characterized by chronic non-bloody diarrhea with characteristic inflammation and for some, collagen deposits in mucosal biopsies. The etiology of MC is unclear, although previous findings implicate luminal factors and thus the gut microbiome. However, the relationships between fecal microbiota and MC are relatively unexplored. METHODS Stool microbiota of MC (n = 15) and healthy controls (HC; n = 21) were assessed by 16S rRNA V4 amplicon sequencing and analysis performed in QIIME. Gut microbiota functions were predicted using Piphillin and inflammatory potential assessed using an in vitro HT29 colonocyte cell assay. RESULTS MC patient fecal microbiota were less diverse (Faiths index; p < 0.01) and compositionally distinct (PERMANOVA, weighted UniFrac, R2 = 0.08, p = 0.02) compared with HC subjects. MC microbiota were significantly depleted of members of the Clostridiales, enriched for Prevotella and more likely to be dominated by this genus (Chi2 = 0.03). Predicted pathways enriched in MC microbiota included those related to biosynthesis of antimicrobials, and sphingolipids, to glycan degradation, host defense evasion, and Th17 cell differentiation and activation. In vitro, exposure of cultured colonocytes to cell-free products of MC patient feces indicates reduced gene expression of IL-1B and occludin and increased GPR119 and the lymphocyte chemoattractant CCL20. CONCLUSION MC gut microbiota are distinct from HC and characterized by lower bacterial diversity and Prevotella enrichment and distinct predicted functional pathways. Limited in vitro experiments indicate that compared with cell-free products from healthy fecal microbiota, MC microbiota induce distinct responses when co-cultured with epithelial cells, implicating microbiota perturbation in MC-associated mucosal dysfunction.
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Affiliation(s)
- Sandra Hertz
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA. .,Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark.
| | - Juliana Durack
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Karina Frahm Kirk
- Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Mølleparkvej 10, 6th floor, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Din L Lin
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Douglas Fadrosh
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Kole Lynch
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Yvette Piceno
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
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Flores-Torres AS, Samarasinghe AE. Impact of Therapeutics on Unified Immunity During Allergic Asthma and Respiratory Infections. FRONTIERS IN ALLERGY 2022; 3:852067. [PMID: 35386652 PMCID: PMC8974821 DOI: 10.3389/falgy.2022.852067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/21/2022] [Indexed: 11/04/2022] Open
Abstract
Asthma is a common chronic respiratory disease that affects millions of people worldwide. Patients with allergic asthma, the most prevalent asthma endotype, are widely considered to possess a defective immune response against some respiratory infectious agents, including viruses, bacteria and fungi. Furthermore, respiratory pathogens are associated with asthma development and exacerbations. However, growing data suggest that the immune milieu in allergic asthma may be beneficial during certain respiratory infections. Immunomodulatory asthma treatments, although beneficial, should then be carefully prescribed to avoid misuse and overuse as they can also alter the host microbiome. In this review, we summarize and discuss recent evidence of the correlations between allergic asthma and the most significant respiratory infectious agents that have a role in asthma pathogenesis. We also discuss the implications of current asthma therapeutics beyond symptom prevention.
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Affiliation(s)
- Armando S. Flores-Torres
- Division of Pulmonology, Allergy-Immunology, and Sleep, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Division of Pulmonology, Allergy-Immunology, and Sleep, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States
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Chen M, He S, Miles P, Li C, Ge Y, Yu X, Wang L, Huang W, Kong X, Ma S, Li Y, Jiang Q, Zhang W, Cao C. Nasal Bacterial Microbiome Differs Between Healthy Controls and Those With Asthma and Allergic Rhinitis. Front Cell Infect Microbiol 2022; 12:841995. [PMID: 35310838 PMCID: PMC8928226 DOI: 10.3389/fcimb.2022.841995] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
Perturbation of the microbiome has numerous associations with the phenotypes and progression in chronic airways disease. However, the differences in the nasal microbiome in asthma and allergic rhinitis (AR) have not been defined. We examined whether the nasal microbiome would vary among different comorbidities in asthma and AR and that those differences may be associated with the severity of asthma. Nasal lavage fluid was collected from 110 participants, including 20 healthy controls, 30 subjects with AR, 30 subjects with asthma and 30 subjects with combined asthma + AR. The Asthma Control Questionnaire (ACQ-7) was used to evaluate asthma control status. Using 16S rRNA bacterial gene sequencing, we analyzed nasal microbiome in patients with asthma, AR, combined asthma + AR, and healthy controls. Bacterial diversity was analyzed in corresponding with α diversity indices (Chao and Shannon index). Compared with healthy controls, the Chao index tended to be lower in subjects with AR (P = 0.001), asthma (P = 0.001), and combined asthma + AR (P = 0.001) when compared with healthy controls. Furthermore, the Shannon index was significantly lower in subjects with asthma (P = 0.013) and comorbid asthma with AR (P = 0.004) than the control subjects. Disparity in the structure and composition of nasal bacteria were also observed among the four groups. Furthermore, patients with combined asthma + AR and isolated asthma were divided into two groups according to the level of disease control: partially or well-controlled and uncontrolled asthma. The mean relative abundance observed in the groups mentioned the genera of Pseudoflavonifractor were dominated in patients with well and partially controlled disease, in both isolated asthma and combined asthma + AR. In subjects with uncontrolled asthma and combined asthma + AR, a lower evenness and richness (Shannon index, P = 0.040) was observed in nasal microbiome composition. Importantly, lower evenness and richness in the nasal microbiome may be associated with poor disease control in combined asthma + AR. This study showed the upper airway microbiome is associated with airway inflammation disorders and the level of asthma control.
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Affiliation(s)
- Meiping Chen
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Shiyi He
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Phoebe Miles
- Faculty of Humanities and Social Sciences, University of Nottingham Ningbo, Ningbo, China
| | - Chunlin Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Ningbo First Hospital, Ningbo, China
| | - Yijun Ge
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Xuechan Yu
- School of Medicine, Ningbo University, Ningbo, China
| | - Linfeng Wang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Weina Huang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Xue Kong
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Shanni Ma
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Yiting Li
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Qingwen Jiang
- School of Medicine, Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Wen Zhang
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Care Medicine, Ningbo First Hospital, Ningbo, China
- *Correspondence: Chao Cao,
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Dong H, Tan R, Chen Z, Wang L, Song Y, Jin M, Yin J, Li H, Li J, Yang D. The Effects of Immunosuppression on the Lung Microbiome and Metabolites in Rats. Front Microbiol 2022; 13:817159. [PMID: 35237248 PMCID: PMC8882871 DOI: 10.3389/fmicb.2022.817159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Immunosuppressed patients are more likely to suffer from pneumonia, especially Streptococcus and Enterobacter pneumonia. Studies have demonstrated the existence of a complex and dynamic microbiota on the surface of human respiratory epithelial cells, both in healthy and diseased states. However, it is not clear whether the pneumonia in immunosuppressed patients is caused by inhaled oropharyngeal pathogens or abnormal proliferation of pulmonary proteobacteria. In this study, immunosuppressed model was made by intraperitoneal injection of cyclophosphamide and oropharyngeal saliva aspiration was simulated by oral and pharyngeal tracheal instillation of sterilized phosphate buffered saline (PBS). Furthermore, the effects of immunosuppression on the lung microbial community and its metabolism were investigated using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis. The 16S rRNA gene sequencing results showed that immunosuppression alone did not change the composition of pulmonary bacteria. Moreover, although the bacteria brought by sterilized PBS from oropharynx to lower respiratory tract changed the composition of the microflora in healthy and immunosuppressed rats, the change in the latter was more obvious. Metabolomic analysis revealed that the levels of pulmonary metabolites were disturbed in the immunosuppressed rats. The altered lung microbiota, including Streptococcaceae and Enterobacteriaceae, showed significant positive correlations with pulmonary metabolites. Our study suggested that the source of the pathogens of pneumonia in immunosuppressed rats was via inhalation and explored the relationship between lung microbiome and metabolites in immunosuppressed rats. Our results provide the basis for the development of prevention and treatment strategies for pneumonia.
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Huang DH, He J, Su XF, Wen YN, Zhang SJ, Liu LY, Zhao H, Ye CP, Wu JH, Cai S, Dong H. The airway microbiota of non-small cell lung cancer patients and its relationship to tumor stage and EGFR gene mutation. Thorac Cancer 2022; 13:858-869. [PMID: 35142041 PMCID: PMC8930493 DOI: 10.1111/1759-7714.14340] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Accumulating studies have suggested the airway microbiota in lung cancer patients is significantly different from that of healthy controls. However, little is known about the relationship between airway microbiota and important clinical parameters of lung cancer. In this study, we aimed to explore the association between sputum microbiota and lung cancer stage, lymph node metastasis, intrathoracic metastasis, and epidermal growth factor receptor (EGFR) gene mutation. METHODS The microbiota of sputum samples from 85 newly-diagnosed NSCLC patients were sequenced via 16S rRNA sequencing of the V3-V4 region. Sequencing reads were filtered using QIIME2 and clustered against UPARSE. RESULTS Alpha- and β-diversity was significantly different between patients in stages I to II (early stage, ES) and patients in stages III to IV (advanced stage, AS). Linear discriminant analysis Effect Size (LEfSe) identified that genera Granulicatella and Actinobacillus were significantly enriched in ES, and the genus Actinomyces was significantly enriched in AS. PICRUSt2 identified that the NAD salvage pathway was significantly enriched in AS, which was positively associated with Granulicatella. Patients with intrathoracic metastasis were associated with increased genus Peptostreptococcus and incomplete reductive TCA cycle, which was associated with increased Peptostreptococcus. Genera Parvimonas, Pseudomona and L-valine biosynthesis were positively associated with lymph node metastasis. L-valine biosynthesis was related with increased Pseudomona. Finally, the genus Parvimonas was significantly enriched in adenocarcinoma patients with EGFR mutation. CONCLUSION The taxonomy structure differed between different lung cancer stages. The tumor stage, intrathoracic metastasis, lymph node metastasis, and EGFR mutation were associated with alteration of specific airway genera and metabolic function of sputum microbiota.
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Affiliation(s)
- Dan Hui Huang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing He
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiao Fang Su
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ya Na Wen
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shu Jia Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lai Yu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haijin Zhao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Cui Pin Ye
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Hua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shaoxi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hangming Dong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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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: 17] [Impact Index Per Article: 5.7] [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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Nielsen R, Xue Y, Jonassen I, Haaland I, Kommedal Ø, Wiker HG, Drengenes C, Bakke PS, Eagan TML. Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable? BMC Pulm Med 2021; 21:342. [PMID: 34727907 PMCID: PMC8561866 DOI: 10.1186/s12890-021-01687-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). METHODS 21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS. RESULTS A final table of 551 ASVs consisted of 19 × 106 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity. CONCLUSION The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.
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Affiliation(s)
- Rune Nielsen
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway.
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Yaxin Xue
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Ingvild Haaland
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Harald G Wiker
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Christine Drengenes
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Per S Bakke
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway
| | - Tomas M L Eagan
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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Hu T, Dong Y, Yang C, Zhao M, He Q. Pathogenesis of Children's Allergic Diseases: Refocusing the Role of the Gut Microbiota. Front Physiol 2021; 12:749544. [PMID: 34721073 PMCID: PMC8551706 DOI: 10.3389/fphys.2021.749544] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Allergic diseases comprise a genetically heterogeneous cluster of immunologically mediated diseases, including asthma, food allergy (FA), allergic rhinitis (AR) and eczema, that have become major worldwide health problems. Over the past few decades, the spread of allergic diseases has displayed an increasing trend, and it has been reported that 22% of 1.39 billion people in 30 countries have a type of allergic disease. Undoubtedly, allergic diseases, which can be chronic, with significant morbidity, mortality and dynamic progression, impose major economic burdens on society and families; thus, exploring the cause of allergic diseases and reducing their prevalence is a top priority. Recently, it has been reported that the gastrointestinal (GI) microbiota can provide vital signals for the development, function, and regulation of the immune system, and the above-mentioned contributions make the GI microbiota a key player in allergic diseases. Notably, the GI microbiota is highly influenced by the mode of delivery, infant diet, environment, antibiotic use and so on. Specifically, changes in the environment can result in the dysbiosis of the GI microbiota. The proper function of the GI microbiota depends on a stable cellular composition which in the case of the human microbiota consists mainly of bacteria. Large shifts in the ratio between these phyla or the expansion of new bacterial groups lead to a disease-promoting imbalance, which is often referred to as dysbiosis. And the dysbiosis can lead to alterations of the composition of the microbiota and subsequent changes in metabolism. Further, the GI microbiota can affect the physiological characteristics of the human host and modulate the immune response of the host. The objectives of this review are to evaluate the development of the GI microbiota, the main drivers of the colonization of the GI tract, and the potential role of the GI microbiota in allergic diseases and provide a theoretical basis as well as molecular strategies for clinical practice.
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Affiliation(s)
- Tingting Hu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yinmiao Dong
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Chenghao Yang
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingnan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
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49
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Kim YH, Jang H, Kim SY, Jung JH, Kim GE, Park MR, Hong JY, Kim MN, Kim EG, Kim MJ, Kim KW, Sohn MH. Gram-negative microbiota is related to acute exacerbation in children with asthma. Clin Transl Allergy 2021; 11:e12069. [PMID: 34667591 PMCID: PMC8507365 DOI: 10.1002/clt2.12069] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The upper-airway microbiota may be associated with the pathogenesis of asthma and useful for predicting acute exacerbation. However, the relationship between the lower-airway microbiota and acute exacerbation in children with asthma is not well understood. We evaluated the characteristics of the airway microbiome using induced sputum from children with asthma exacerbation and compared the microbiota-related differences of inflammatory cytokines with those in children with asthma. METHODS We analysed the microbiome using induced sputum during acute exacerbation of asthma in children. We identified microbial candidates that were prominent in children with asthma exacerbation and compared them with those in children with stable asthma using various analytical methods. The microbial candidates were analysed to determine their association with inflammatory cytokines. We also developed a predictive functional profile using PICRUSt. RESULTS A total of 95 children with allergic sensitisation including 22 with asthma exacerbation, 67 with stable asthma, and 6 controls were evaluated. We selected 26 microbial candidates whose abundances were significantly increased, decreased, or correlated during acute exacerbation in children with asthma. Among the microbial candidates, Campylobacter, Capnocytophaga, Haemophilus, and Porphyromonas were associated with inflammatory cytokines including macrophage inflammatory protein (MIP)-1β, programmed death-ligand 1, and granzyme B. Both Campylobacter and MIP-1β levels were correlated with sputum eosinophils. Increased lipopolysaccharide biosynthesis and decreased glycan degradation were observed in children with asthma exacerbation. CONCLUSION Gram-negative microbes in the lower airway were related to acute exacerbation in children with asthma. These microbes and associated cytokines may play a role in exacerbating asthma in children.
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Affiliation(s)
- Yoon Hee Kim
- Department of PediatricsGangnam Severance HospitalSeoulKorea
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
| | - Haerin Jang
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Soo Yeon Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Jae Hwa Jung
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Ga Eun Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Mi Reu Park
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Jung Yeon Hong
- Division of Cardiovascular Disease ResearchDepartment for Chronic Disease Convergence ResearchKorea National Institute of HealthCheongjuKorea
| | - Mi Na Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Eun Gyul Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Min Jung Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsYongin Severance HospitalYonginKorea
| | - Kyung Won Kim
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
| | - Myung Hyun Sohn
- Institute of AllergySeverance Biomedical Science InstituteBrain Korea 21 Project for Medical ScienceYonsei University College of MedicineSeoulKorea
- Department of PediatricsSeverance HospitalSeoulKorea
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50
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Zheng J, Wu Q, Zou Y, Wang M, He L, Guo S. Respiratory Microbiota Profiles Associated With the Progression From Airway Inflammation to Remodeling in Mice With OVA-Induced Asthma. Front Microbiol 2021; 12:723152. [PMID: 34526979 PMCID: PMC8435892 DOI: 10.3389/fmicb.2021.723152] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/27/2021] [Indexed: 12/31/2022] Open
Abstract
Background The dysbiosis of respiratory microbiota plays an important role in asthma development. However, there is limited information on the changes in the respiratory microbiota and how these affect the host during the progression from acute allergic inflammation to airway remodeling in asthma. Objective An ovalbumin (OVA)-induced mouse model of chronic asthma was established to explore the dynamic changes in the respiratory microbiota in the different stages of asthma and their association with chronic asthma progression. Methods Hematoxylin and eosin (H&E), periodic acid-schiff (PAS), and Masson staining were performed to observe the pathological changes in the lung tissues of asthmatic mice. The respiratory microbiota was analyzed using 16S rRNA gene sequencing followed by taxonomical analysis. The cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were measured. The matrix metallopeptidase 9 (MMP-9) and vascular endothelial growth factor (VEGF-A) expression levels in lung tissues were measured to detect airway remodeling in OVA-challenged mice. Results Acute allergic inflammation was the major manifestation at weeks 1 and 2 after OVA atomization stimulation, whereas at week 6 after the stimulation, airway remodeling was the most prominent observation. In the acute inflammatory stage, Pseudomonas was more abundant, whereas Staphylococcus and Cupriavidus were more abundant at the airway remodeling stage. The microbial compositions of the upper and lower respiratory tracts were similar. However, the dominant respiratory microbiota in the acute inflammatory and airway remodeling phases were different. Metagenomic functional prediction showed that the pathways significantly upregulated in the acute inflammatory phase and airway remodeling phase were different. The cytokine levels in BALF and the expression patterns of proteins associated with airway remodeling in the lung tissue were consistent with the metagenomic function results. Conclusion The dynamic changes in respiratory microbiota are closely associated with the progression of chronic asthma. Metagenomic functional prediction indicated the changes associated with acute allergic inflammation and airway remodeling.
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Affiliation(s)
- Jun Zheng
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Wu
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Zou
- Department of Emergency Medicine, Putuo Hospital, Shanghai University of Traditional Medicine, Shanghai, China
| | - Meifen Wang
- Department of Pediatrics, Sanmen People's Hospital, Taizhou, China
| | - Li He
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng Guo
- Department of Endocrine, Genetics and Metabolism, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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