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Ochayon DE, DeVore SB, Chang WC, Krishnamurthy D, Seelamneni H, Grashel B, Spagna D, Andorf S, Martin LJ, Biagini JM, Waggoner SN, Khurana Hershey GK. Progressive accumulation of hyperinflammatory NKG2D low NK cells in early childhood severe atopic dermatitis. Sci Immunol 2024; 9:eadd3085. [PMID: 38335270 PMCID: PMC11107477 DOI: 10.1126/sciimmunol.add3085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disease that often precedes the development of food allergy, asthma, and allergic rhinitis. The prevailing paradigm holds that a reduced frequency and function of natural killer (NK) cell contributes to AD pathogenesis, yet the underlying mechanisms and contributions of NK cells to allergic comorbidities remain ill-defined. Here, analysis of circulating NK cells in a longitudinal early life cohort of children with AD revealed a progressive accumulation of NK cells with low expression of the activating receptor NKG2D, which was linked to more severe AD and sensitivity to allergens. This was most notable in children co-sensitized to food and aeroallergens, a risk factor for development of asthma. Individual-level longitudinal analysis in a subset of children revealed coincident reduction of NKG2D on NK cells with acquired or persistent sensitization, and this was associated with impaired skin barrier function assessed by transepidermal water loss. Low expression of NKG2D on NK cells was paradoxically associated with depressed cytolytic function but exaggerated release of the proinflammatory cytokine tumor necrosis factor-α. These observations provide important insights into a potential mechanism underlying the development of allergic comorbidity in early life in children with AD, which involves altered NK cell functional responses, and define an endotype of severe AD.
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Affiliation(s)
- David E. Ochayon
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
| | - Stanley B. DeVore
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
- Medical Scientist Training Program, University of Cincinnati College of Medicine
- Cancer and Cell Biology Program, University of Cincinnati College of Medicine
| | - Wan-Chi Chang
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
| | - Durga Krishnamurthy
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center
| | - Harsha Seelamneni
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center
| | - Brittany Grashel
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
| | - Daniel Spagna
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
| | - Sandra Andorf
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Jocelyn M. Biagini
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Stephen N. Waggoner
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center
- Medical Scientist Training Program, University of Cincinnati College of Medicine
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Gurjit K. Khurana Hershey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center
- Medical Scientist Training Program, University of Cincinnati College of Medicine
- Cancer and Cell Biology Program, University of Cincinnati College of Medicine
- Department of Pediatrics, University of Cincinnati College of Medicine
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Du X, Li Y, Xu Y, Yang Y, Li C, Chen Y, Lv Z, Corrigan CJ, Zhang D, Zhang L, Ying S, Wang W. Airways epithelial exposure to Streptococcus pneumoniae in the presence of the alarmin IL-33 induces a novel subset of pro-inflammatory ILC2s promoting a mixed inflammatory response. Inflamm Res 2024; 73:1239-1252. [PMID: 38844678 DOI: 10.1007/s00011-024-01896-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND We have previously shown that asthma-like airways inflammation may be induced by topical exposure to respiratory tract pathogens such as S. pneumoniae (SP) in concert with epithelial alarmins such as IL-33. Details of the pathogenesis of this murine surrogate remain however unexplored. METHODS Airways inflammation was induced by repeated, intranasal exposure of Il-4-/-, Rag1-/- and Rag2-/-Il2rg-/- mice (in which B lymphocyte IgE switching, adaptive and innate immunity are respectively ablated) as well as wild type mice to inactivated SP, IL-33 or both. Airways pathological changes were analysed, and the subsets and functions of locally accumulated ILC2s investigated by single cell RNA sequencing and flow cytometry. RESULTS In the presence of IL-33, repeated exposure of the airways to inactivated SP caused marked eosinophil- and neutrophil-rich inflammation and local accumulation of ILC2s, which was retained in the Il-4-/- and Rag1-/- deficient mice but abolished in the Rag2-/-Il2rg-/- mice, an effect partly reversed by adoptive transfer of ILC2s. Single cell sequencing analysis of ILC2s recruited following SP and IL-33 exposure revealed a Klrg1+Ly6a+subset, expressing particularly elevated quantities of the pro-inflammatory cytokine IL-6, type 2 cytokines (IL-5 and IL-13) and MHC class II molecules, promoting type 2 inflammation as well as involved in neutrophil-mediated inflammatory responses. CONCLUSION Local accumulation of KLRG1+Ly6a+ ILC2s in the lung tissue is a critical aspect of the pathogenesis of airways eosinophilic and neutrophil-rich inflammation induced by repeated exposure to SP in the presence of the epithelial alarmin IL-33.
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Affiliation(s)
- Xiaonan Du
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Yan Li
- Department of Otorhinolaryngology Head and Neck Surgery, Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Institute of Otolaryngology, Beijing Key Laboratory of Nasal Disease, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, 100005, China
- Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing, 100069, China
- Research Unit, Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Yingjie Xu
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Yiran Yang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Chenduo Li
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Yan Chen
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Zhe Lv
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China
| | - Chris J Corrigan
- King's Centre for Lung Health, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Dong Zhang
- Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Luo Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Institute of Otolaryngology, Beijing Key Laboratory of Nasal Disease, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, 100005, China
- Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing, 100069, China
- Research Unit, Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Sun Ying
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China.
- Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing, 100069, China.
| | - Wei Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, 10 Xi TouTiao, You An Men Wai, Fengtai District, Beijing, 100069, China.
- Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing, 100069, China.
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Wang S, Zheng X, Ye J, Sun Z, Chen Z, Cao G, Zhang Y, Shen F, Gao CX, Qian H. Impact of climate zones and seasons on indoor airborne microbial communities: Insights from a comprehensive analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171879. [PMID: 38521271 DOI: 10.1016/j.scitotenv.2024.171879] [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: 10/10/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Bacteria and fungi are ubiquitous throughout built environments and are suspended in the air, potentially affecting human health. However, the impacts of climate zones on the diversity, structure, and stochastic assembly of indoor airborne microbes remain unknown. This study comprehensively analyzed indoor airborne microbes across five climate zones in China during the summer and winter using high-throughput sequencing. The diversity and structure of indoor airborne communities vary across climatic zones. A random forest model was used to identify biomarkers in different climate zones. The results showed no relationship between the biomarkers and their rankings in mean relative abundance. The Sloan neutral model fitting results indicated that the impact of climate zones on the stochastic process in the assembly of indoor airborne microbes was considerably more important than that of seasons. Additionally, the influence of seasons on the diversity, structure, and stochastic assembly process of indoor airborne microbes differed among different climate zones. The diversity, structure, and stochastic assembly processes of bacteria present distinctive outcomes in climate zones and seasons compared with those of fungi. Overall, these findings indicate that customized strategies are necessary to manage indoor airborne microbial communities in each climate zone, season, and for specific microbial species.
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Affiliation(s)
- Shengqi Wang
- School of Energy and Environment, Southeast University, Nanjing 210096, China; Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia; Orygen, 35 Poplar Road, Parkville, VIC, Australia
| | - Xiaohong Zheng
- School of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Jin Ye
- School of Energy and Power, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Zongke Sun
- Department of Environmental Microbiology, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Ziguang Chen
- Institute of Building Environmental and Energy Efficiency, China Academy of Building Research, Beijing 100013, China
| | - Guoqing Cao
- Institute of Building Environmental and Energy Efficiency, China Academy of Building Research, Beijing 100013, China
| | - Yin Zhang
- School of Space and Environment, Beihang University, Beijing 100191, China
| | - Fangxia Shen
- School of Space and Environment, Beihang University, Beijing 100191, China
| | - Caroline X Gao
- Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia; Orygen, 35 Poplar Road, Parkville, VIC, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Hua Qian
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
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Song X, Liang J, Lin S, Xie Y, Ke C, Ao D, Lu J, Chen X, He Y, Liu X, Li W. Gut-lung axis and asthma: A historical review on mechanism and future perspective. Clin Transl Allergy 2024; 14:e12356. [PMID: 38687096 PMCID: PMC11060082 DOI: 10.1002/clt2.12356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/24/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Gut microbiota are closely related to the development and regulation of the host immune system by regulating the maturation of immune cells and the resistance to pathogens, which affects the host immunity. Early use of antibiotics disrupts the homeostasis of gut microbiota and increases the risk of asthma. Gut microbiota actively interact with the host immune system via the gut-lung axis, a bidirectional communication pathway between the gut and lung. The manipulation of gut microbiota through probiotics, helminth therapy, and fecal microbiota transplantation (FMT) to combat asthma has become a hot research topic. BODY: This review mainly describes the current immune pathogenesis of asthma, gut microbiota and the role of the gut-lung axis in asthma. Moreover, the potential of manipulating the gut microbiota and its metabolites as a treatment strategy for asthma has been discussed. CONCLUSION The gut-lung axis has a bidirectional effect on asthma. Gut microecology imbalance contributes to asthma through bacterial structural components and metabolites. Asthma, in turn, can also cause intestinal damage through inflammation throughout the body. The manipulation of gut microbiota through probiotics, helminth therapy, and FMT can inform the treatment strategies for asthma by regulating the maturation of immune cells and the resistance to pathogens.
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Affiliation(s)
- Xiu‐Ling Song
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Juan Liang
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Shao‐Zhu Lin
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Yu‐Wei Xie
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Chuang‐Hong Ke
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Dang Ao
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Jun Lu
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Xue‐Mei Chen
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Ying‐Zhi He
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Xiao‐Hua Liu
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Wen Li
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [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: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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Dou C, Hu L, Ding X, Chen F, Li X, Wei G, Yan Z. Microbiota Alterations in Lung, Ileum, and Colon of Guinea Pigs with Cough Variant Asthma. Int J Mol Sci 2024; 25:2449. [PMID: 38397126 PMCID: PMC10889264 DOI: 10.3390/ijms25042449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Alterations in the microbiota composition, or ecological dysbiosis, have been implicated in the development of various diseases, including allergic diseases and asthma. Examining the relationship between microbiota alterations in the host and cough variant asthma (CVA) may facilitate the discovery of novel therapeutic strategies. To elucidate the diversity and difference of microbiota across three ecological niches, we performed 16S rDNA amplicon sequencing on lung, ileum, and colon samples. We assessed the levels of interleukin-12 (IL-12) and interleukin-13 (IL-13) in guinea pig bronchoalveolar lavage fluid using the enzyme-linked immunosorbent assay (ELISA). We applied Spearman's analytical method to evaluate the correlation between microbiota and cytokines. The results demonstrated that the relative abundance, α-diversity, and β-diversity of the microbial composition of the lung, ileum, and colon varied considerably. The ELISA results indicated a substantial increase in the level of IL-13 and a decreasing trend in the level of IL-12 in the CVA guinea pigs. The Spearman analysis identified a correlation between Mycoplasma, Faecalibaculum, and Ruminococcus and the inflammatory factors in the CVA guinea pigs. Our guinea pig model showed that core microorganisms, such as Mycoplasma in the lung, Faecalibaculum in the ileum, and Ruminococcus in the colon, may play a crucial role in the pathogenesis of CVA. The most conspicuous changes in the ecological niche were observed in the guinea pig ileum, followed by the lung, while relatively minor changes were observed in the colon. Notably, the microbial structure of the ileum niche approximated that of the colon niche. Therefore, the results of this study suggest that CVA development is closely related to the dysregulation of ileal, lung, and colon microbiota and the ensuing inflammatory changes in the lung.
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Affiliation(s)
| | | | | | | | | | - Guihua Wei
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China; (C.D.); (L.H.); (X.D.); (F.C.); (X.L.)
| | - Zhiyong Yan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China; (C.D.); (L.H.); (X.D.); (F.C.); (X.L.)
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Morimoto C, Matsumoto H, Nomura N, Sunadome H, Nagasaki T, Sato S, Sato A, Oguma T, Ito I, Kogo M, Tomii K, Tajiri T, Ohashi K, Tsukahara T, Hirai T. Sputum microbiota and inflammatory subtypes in asthma, COPD, and its overlap. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100194. [PMID: 38155860 PMCID: PMC10753087 DOI: 10.1016/j.jacig.2023.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 12/30/2023]
Abstract
Background Airway microbiota in asthma-chronic obstructive pulmonary disease (COPD) overlap (ACO) remains unknown. Objective This study with ACO-enriched population aimed to clarify airway microbiota in ACO and in mixed granulocytic inflammation, often detected in ACO and chronic airway diseases. Methods This is an observational cross-sectional study. Patients with asthma with airflow limitation, ACO, and COPD were enrolled. Blood tests, pulmonary function, exhaled nitric oxide, and sputum tests were conducted. Sputum microbiota was evaluated using the 16S rRNA gene sequencing technique. Results A total of 112 patients (13 asthma, 67 ACO, and 32 COPD) were examined. There were no significant differences in α-diversity among the 3 diseases. The relative abundances of phylum Bacteroidetes, class Bacteroidia, and genus Porphyromonas were associated with decreased eosinophilic inflammation, and were significantly lower in ACO than in COPD. In a comparison of sputum inflammatory subtypes, the proportion of Haemophilus was numerically highest in the mixed granulocytic subtype, followed by the neutrophilic subtype. Likewise, the proportion of Haemophilus was the highest in the intermediate-high (2%-8%) sputum eosinophil group and lowest in the severe (≥8%) eosinophil group. Clinically, Haemophilus proportion was associated with sputum symptoms. Finally, the proportion of Streptococcus was associated with higher blood eosinophil counts and most severe airflow limitation. Conclusions Bacteroidia and Porphyromonas abundances in sputum are associated with the eosinophil-low phenotype, and ACO may be characterized by a decrease in these taxa. A mild elevation in sputum eosinophil does not preclude the presence of Haemophilus, which should be noted in the management of obstructive airway diseases.
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Affiliation(s)
- Chie Morimoto
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisako Matsumoto
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Medicine and Allergology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Natsuko Nomura
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironobu Sunadome
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Care and Sleep Control Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tadao Nagasaki
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Care and Sleep Control Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Susumu Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Care and Sleep Control Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsuyasu Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Oguma
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Isao Ito
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mariko Kogo
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Keisuke Tomii
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Tomoko Tajiri
- Department of Respiratory Medicine, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Kai Ohashi
- Kyoto Institute of Nutrition & Pathology, Inc, Kyoto, Japan
| | | | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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8
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Guo Z, Huang L, Lai S. Global knowledge mapping and emerging research trends in the microbiome and asthma: A bibliometric and visualized analysis using VOSviewer and CiteSpace. Heliyon 2024; 10:e24528. [PMID: 38304829 PMCID: PMC10831755 DOI: 10.1016/j.heliyon.2024.e24528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Background Numerous prior studies have extensively highlighted the significance of the microbiome in association with asthma. While several studies have concentrated on the asthma microbiome in previous research, there is currently a lack of publications that employ bibliometric methods to assess this area. Methods In this study, the Web of Science Core Collection database was utilized as the data source, and the SCI-EXPANDED index was employed to ensure that the retrieved data were comprehensive and accurate. All original research articles and review articles related to the correlation between asthma and the microbiome were systematically searched from the inception of the database until June 20, 2023. These articles were subsequently visualized and analyzed using VOSviewer and CiteSpace software. Results A total of 1366 relevant publications were acquired, indicating a consistent annual increase in global publications in the field. The United States and China emerged as the top two contributors to international publications. Among prolific authors, Susan V. Lynch achieved the highest publication record, with Hans Bisgaard and Jakob Stokholm sharing the second position. The majority of publications concentrated on allergy-related and microbiome areas, with a few comprehensive journals standing out. Journals with 40 or more publications included the Journal of Allergy and Clinical Immunology, Allergy, Frontiers in Immunology, and PLOS One. The top 5 cited journals were the Journal of Allergy and Clinical Immunology, PLOS One, American Journal of Respiratory and Critical Care Medicine, Clinical and Experimental Allergy, and Nature. Upon analyzing keywords, high-frequency terms, such as asthma, gut microbiota, microbiome, children, childhood asthma, allergy, risk, exposure, inflammation, diversity, and chain fatty acids emerged as representative terms in the field. Conclusion This study systematically presented a comprehensive overview of the literature regarding the association between asthma and the microbiome over the last two decades. Through a bibliometric perspective, the findings may assist researchers with a better understanding of the essential information in the field.
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Affiliation(s)
- ZhiFeng Guo
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - LingHong Huang
- Department of Endocrinology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
| | - SuMei Lai
- Stem Cell Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, China
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Naughten S, Ecklu-Mensah G, Constantino G, Quaranta A, Schulkers Escalante K, Bai-Tong S, Gilbert J, Leibel S, Wheelock CE, Leibel S. The re-emerging role of linoleic acid in paediatric asthma. Eur Respir Rev 2023; 32:230063. [PMID: 37914192 PMCID: PMC10618909 DOI: 10.1183/16000617.0063-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/04/2023] [Indexed: 11/03/2023] Open
Abstract
Asthma is the most common chronic disease within the paediatric population. Although it is multifactorial, its onset may be linked to early-life exposures with subsequent impact on immune system development. Microbial and dietary metabolic products have been implicated in the development and exacerbation of paediatric asthma. Linoleic acid is the most common omega-6 polyunsaturated fatty acid in the Western diet. In this review, we summarise the literature regarding the involvement of linoleic acid in the development of and its impact on existing paediatric asthma. First, we summarise the existing knowledge surrounding the relationship between human microbial metabolism and allergic diseases in children. Next, we examine cellular or animal model-based mechanistic studies that investigated the impact of dietary- and microbial-derived linoleic acid metabolites on asthma. Finally, we review the literature investigating the impact of linoleic acid metabolites on the development and exacerbation of childhood asthma. While there is conflicting evidence, there is growing support for a role of linoleic acid in the onset and pathophysiology of asthma. We recommend that additional cellular, animal, and longitudinal studies are performed that target linoleic acid and its metabolites.
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Affiliation(s)
- Sarah Naughten
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | - Alessandro Quaranta
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Shiyu Bai-Tong
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sandra Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Sydney Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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11
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Cochran SJ, Acosta L, Divjan A, Lemons AR, Rundle AG, Miller RL, Sobek E, Green BJ, Perzanowski MS, Dannemiller KC. Fungal diversity in homes and asthma morbidity among school-age children in New York City. ENVIRONMENTAL RESEARCH 2023; 239:117296. [PMID: 37806477 PMCID: PMC10842248 DOI: 10.1016/j.envres.2023.117296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 09/15/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Asthma development has been inversely associated with exposure to fungal diversity. However, the influence of fungi on measures of asthma morbidity is not well understood. OBJECTIVES This study aimed to test the hypothesis that fungal diversity is inversely associated with neighborhood asthma prevalence and identify specific fungal species associated with asthma morbidity. METHODS Children aged 7-8 years (n = 347) living in higher (11-18%) and lower (3-9%) asthma prevalence neighborhoods were recruited within an asthma case-control study. Fungal communities were analyzed from floor dust using high-throughput DNA sequencing. A subset of asthmatic children (n = 140) was followed to age 10-11 to determine asthma persistence. RESULTS Neighborhood asthma prevalence was inversely associated with fungal species richness (P = 0.010) and Shannon diversity (P = 0.059). Associations between neighborhood asthma prevalence and diversity indices were driven by differences in building type and presence of bedroom carpet. Among children with asthma at age 7-8 years, Shannon fungal diversity was inversely associated with frequent asthma symptoms at that age (OR 0.57, P = 0.025) and with asthma persistence to age 10-11 (OR 0.48, P = 0.043). Analyses of individual fungal species did not show significant associations with asthma outcomes when adjusted for false discovery rates. DISCUSSION Lower fungal diversity was associated with asthma symptoms in this urban setting. Individual fungal species associated with asthma morbidity were not detected. Further research is warranted into building type, carpeting, and other environmental characteristics which influence fungal exposures in homes.
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Affiliation(s)
- Samuel J Cochran
- Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, Ohio State University, Columbus, OH, 43210, USA
| | - Luis Acosta
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Adnan Divjan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Angela R Lemons
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, 26505, USA
| | - Andrew G Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, 10032, NY, USA
| | - Rachel L Miller
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Edward Sobek
- Assured Bio Laboratories, Oak Ridge, TN, 37830, USA
| | - Brett J Green
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, 26505, USA
| | - Matthew S Perzanowski
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA.
| | - Karen C Dannemiller
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH, 43210, USA; Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA; Sustainability Institute, Ohio State University, Columbus, OH, 43210, USA
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12
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Glatthardt T, van Tilburg Bernardes E, Arrieta MC. The mycobiome in atopic diseases: Inducers and triggers. J Allergy Clin Immunol 2023; 152:1368-1375. [PMID: 37865199 DOI: 10.1016/j.jaci.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
Abstract
Atopic diseases are characterized by type 2 inflammation, with high levels of allergen-specific TH2 cell immune responses and elevated production of IgE. These common disorders have increased in incidence around the world, which is partly explained by detrimental disturbances to the early-life intestinal microbiome. Although most studies have focused exclusively on bacterial members of the microbiome, intestinal fungi have started to be recognized for their impact on host immune development and atopy pathogenesis. From this perspective, we review recent findings demonstrating the strong interactions between members of the mycobiome and the host immune system early in life, leading to immune tolerance during eubiosis or inducing sensitization and overt TH2 cell responses during dysbiosis. Current evidence places intestinal fungi as central players in the development of allergic diseases and potential targets for atopy prevention and treatments.
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Affiliation(s)
- Thais Glatthardt
- the Department of Physiology and Pharmacology, University of Calgary, Calgary; the International Microbiome Centre, Snyder Institute for Chronic Diseases, University of Calgary, Calgary; the Department of Pediatrics, Alberta Children Hospital Research Institute, University of Calgary, Calgary
| | - Erik van Tilburg Bernardes
- the Department of Physiology and Pharmacology, University of Calgary, Calgary; the International Microbiome Centre, Snyder Institute for Chronic Diseases, University of Calgary, Calgary; the Department of Pediatrics, Alberta Children Hospital Research Institute, University of Calgary, Calgary
| | - Marie-Claire Arrieta
- the Department of Physiology and Pharmacology, University of Calgary, Calgary; the International Microbiome Centre, Snyder Institute for Chronic Diseases, University of Calgary, Calgary; the Department of Pediatrics, Alberta Children Hospital Research Institute, University of Calgary, Calgary.
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13
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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14
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Li Y, Zou C, Li J, Wang W, Wang F, Guo Y. Airway Microbiome Composition and Co-Occurrence Network Are Associated with Inflammatory Phenotypes of Asthma. Int Arch Allergy Immunol 2023; 184:1254-1263. [PMID: 37690443 PMCID: PMC10733928 DOI: 10.1159/000533315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/27/2023] [Indexed: 09/12/2023] Open
Abstract
INTRODUCTION The composition and co-occurrence network of the airway microbiome might influence the asthma inflammatory phenotype. Airway microbiota change with asthma phenotypes, and the structure of the bacterial community in the airway might differ between different asthma inflammatory phenotypes and may also influence therapy results. Identifying airway microbiota can help to investigate the role that microbiota play in the asthma inflammatory process. METHODS Induced sputum from 55 subjects and 12 healthy subjects from Beijing, China, was collected and analyzed for bacterial microbiota. Microbiome diversity, composition, co-occurrence networks, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were predicted and compared between the study groups. RESULTS Significant differences in the sputum microbiome composition, co-occurrence network, and predicted functional pathways were observed between the two inflammatory phenotypes. Asthmatics in the low FeNO group exhibited lower α-diversity in the sputum microbiota and had higher abundance of the phylum Proteobacteria compared with that of the high FeNO group. The network in the high FeNO group was more "closed" and "connected" compared with that of the low FeNO group, and an alteration in the abundance of keystone species T. socranskii was found. Significantly different predicted metabolic subfunctions including nucleotide metabolism, lipid metabolism, energy metabolism, replication and repair, and drug resistance antimicrobial and carbohydrate metabolism between the two studied phenotypes were also observed. CONCLUSION Our findings confirm that the airway microbiota is associated with the asthma inflammation process. The differences in the airway microbiome composition and co-occurrence network may affect distinct asthma inflammatory phenotypes, suggesting the possibility that more targeted therapies could be applied based on the airway bacterial genera.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Severe Weather of CMA, Chinese Academy of Meteorological Sciences, Beijing, China
| | - Congying Zou
- Department of Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jieying Li
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Feiran Wang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Yue Guo
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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15
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Ochayon DE, DeVore SB, Chang WC, Krishnamurthy D, Seelamneni H, Grashel B, Spagna D, Andorf S, Martin LJ, Biagini JM, Waggoner S, Hershey GKK. Progressive accumulation of hyperinflammatory NKG2D low NK cells in early childhood severe atopic dermatitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.02.23290884. [PMID: 37333102 PMCID: PMC10274972 DOI: 10.1101/2023.06.02.23290884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disease that often precedes the development of food allergy, asthma, and allergic rhinitis. The prevailing paradigm holds that a reduced frequency and function of natural killer (NK) cell contributes to AD pathogenesis, yet the underlying mechanisms and contributions of NK cells to allergic co-morbidities remain ill-defined. Herein, analysis of circulating NK cells in a longitudinal early life cohort of children with AD revealed a progressive accumulation of NK cells with low expression of the activating receptor NKG2D, which was linked to more severe AD and sensitivity to allergens. This was most notable in children co-sensitized to food and aero allergens, a risk factor for development of asthma. Individual-level longitudinal analysis in a subset of children revealed co-incident reduction of NKG2D on NK cells with acquired or persistent sensitization, and this was associated with impaired skin barrier function assessed by transepidermal water loss. Low expression of NKG2D on NK cells was paradoxically associated with depressed cytolytic function but exaggerated release of the proinflammatory cytokine TNF-α. These observations provide important insights into a potential mechanism underlying the development of allergic co-morbidity in early life in children with AD which involves altered NK-cell functional responses, and define an endotype of severe AD.
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16
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Shibata R, Zhu Z, Kyo M, Ooka T, Freishtat RJ, Mansbach JM, Pérez-Losada M, Camargo CA, Hasegawa K. Nasopharyngeal fungal subtypes of infant bronchiolitis and disease severity risk. EBioMedicine 2023; 95:104742. [PMID: 37536062 PMCID: PMC10415709 DOI: 10.1016/j.ebiom.2023.104742] [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: 04/25/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Bronchiolitis is a leading cause of infant hospitalization. Recent research suggests the heterogeneity within bronchiolitis and the relationship of airway viruses and bacteria with bronchiolitis severity. However, little is known about the pathobiological role of fungi. We aimed to identify bronchiolitis mycotypes by integrating fungus and virus data, and determine their association with bronchiolitis severity and biological characteristics. METHODS In a multicentre prospective cohort study of 398 infants (age <1 year, male 59%) hospitalized for bronchiolitis, we applied clustering approaches to identify mycotypes by integrating nasopharyngeal fungus (detected in RNA-sequencing data) and virus data (respiratory syncytial virus [RSV], rhinovirus [RV]) at hospitalization. We examined their association with bronchiolitis severity-defined by positive pressure ventilation (PPV) use and biological characteristics by nasopharyngeal metatranscriptome and transcriptome data. RESULTS In infants hospitalized for bronchiolitis, we identified four mycotypes: A) fungiM.restrictavirusRSV/RV, B) fungiM.restrictavirusRSV, C) fungiM.globosavirusRSV/RV, D) funginot-detectedvirusRSV/RV mycotypes. Compared to mycotype A infants (the largest subtype, n = 211), mycotype C infants (n = 85) had a significantly lower risk of PPV use (7% vs. 1%, adjOR, 0.21; 95% CI, 0.02-0.90; p = 0.033), while the risk of PPV use was not significantly different in mycotype B or D. In the metatranscriptome and transcriptome data, mycotype C had similar bacterial composition and microbial functions yet dysregulated pathways (e.g., Fc γ receptor-mediated phagocytosis pathway and chemokine signaling pathway; FDR <0.05). INTERPRETATION In this multicentre cohort, fungus-virus clustering identified distinct mycotypes of infant bronchiolitis with differential severity risks and unique biological characteristics. FUNDING This study was supported by the National Institutes of Health.
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Affiliation(s)
- Ryohei Shibata
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michihito Kyo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tadao Ooka
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Health Science, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA; Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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17
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Yuan H, Liu Z, Dong J, Bacharier LB, Jackson D, Mauger D, Boushey H, Castro M, Durack J, Huang YJ, Lemanske RF, Storch GA, Weinstock GM, Wylie K, Covar R, Fitzpatrick AM, Phipatanakul W, Robison RG, Beigelman A, Zhou Y. The Fungal Microbiome of the Upper Airway Is Associated With Future Loss of Asthma Control and Exacerbation Among Children With Asthma. Chest 2023; 164:302-313. [PMID: 37003356 PMCID: PMC10477953 DOI: 10.1016/j.chest.2023.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/10/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that the upper airway bacterial microbiota is implicated in asthma inception, severity, and exacerbation. Unlike bacterial microbiota, the role of the upper airway fungal microbiome (mycobiome) in asthma control is poorly understood. RESEARCH QUESTION What are the upper airway fungal colonization patterns among children with asthma and their relationship with subsequent loss of asthma control and exacerbation of asthma? STUDY DESIGN AND METHODS The study was coupled with the Step Up Yellow Zone Inhaled Corticosteroids to Prevent Exacerbations (ClinicalTrials.gov Identifier: NCT02066129) clinical trial. The upper airway mycobiome was investigated using Internal transcribed spacer 1 (ITS1) sequencing of nasal blow samples collected from children with asthma when asthma was well controlled (baseline, n = 194) and during early signs of loss of asthma control (yellow zone [YZ], n = 107). RESULTS At baseline, 499 fungal genera were detected in the upper airway samples, with two commensal fungal species, Malassezia globosa and Malassezia restricta, being most dominant. The relative abundance of Malassezia species varies by age, BMI, and race. Higher relative abundance of M globosa at baseline was associated with lower risk of future YZ episodes (P = .038) and longer time to development of first YZ episode (P = .022). Higher relative abundance of M globosa at YZ episode was associated with lower risk of progression from YZ episode to severe asthma exacerbation (P = .04). The upper airway mycobiome underwent significant changes from baseline to YZ episode, and increased fungal diversity was correlated highly with increased bacterial diversity (ρ = 0.41). INTERPRETATION The upper airway commensal mycobiome is associated with future asthma control. This work highlights the importance of the mycobiota in asthma control and may contribute to the development of fungi-based markers to predict asthma exacerbation.
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Affiliation(s)
- Hanshu Yuan
- Department of Medicine, University of Connecticut Health Center, Farmington, CT
| | - Zhongmao Liu
- Department of Statistics, University of Connecticut, Storrs, CT
| | - Jinhong Dong
- Department of Medicine, University of Connecticut Health Center, Farmington, CT
| | - Leonard B Bacharier
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Daniel Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - David Mauger
- Department of Public Health Sciences, Penn State University, Hershey, PA
| | - Homer Boushey
- Department of Medicine, University of California, San Francisco, CA
| | - Mario Castro
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS
| | | | - Yvonne J Huang
- Department of Medicine and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | - Robert F Lemanske
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO
| | | | - Kristine Wylie
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO
| | | | | | - Wanda Phipatanakul
- Asthma, Allergy and Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rachel G Robison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Avraham Beigelman
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO; Kipper Institute of Allergy and Immunology, Schneider Children's Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT.
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18
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Ramos-Tapia I, Reynaldos-Grandón KL, Pérez-Losada M, Castro-Nallar E. Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences. FRONTIERS IN ALLERGY 2023; 4:1223306. [PMID: 37577334 PMCID: PMC10419220 DOI: 10.3389/falgy.2023.1223306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
Around 155 million people worldwide suffer from asthma. In Chile, the prevalence of this disease in children is around 15% and has a high impact in the health system. Studies suggest that asthma is caused by multiple factors, including host genetics, antibiotic use, and the development of the airway microbiota. Here, we used 16S rRNA high-throughput sequencing to characterize the nasal and oral mucosae of 63 asthmatic and 89 healthy children (152 samples) from Santiago, Chile. We found that the nasal mucosa was dominated by a high abundance of Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, and Staphylococcus. In turn, the oral mucosa was characterized by a high abundance of Streptococcus, Haemophilus, Gemella, Veillonella, Neisseria, and Porphyromonas. Our results showed significantly (P < 0.001) lower alpha diversity and an over-abundance of Streptococcus (P < 0.01) in nasal samples from asthmatics compared to samples from healthy subjects. Community structure, as revealed by co-occurrence networks, showed different microbial interactions in asthmatic and healthy subjects, particularly in the nasal microbiota. The networks revealed keystone genera in each body site, including Prevotella, Leptotrichia, and Porphyromonas in the nasal microbiota, and Streptococcus, Granulicatella, and Veillonella in the oral microbiota. We also detected 51 functional pathways differentially abundant on the nasal mucosa of asthmatic subjects, although only 13 pathways were overrepresented in the asthmatic subjects (P < 0.05). We did not find any significant differences in microbial taxonomic (composition and structure) and functional diversity between the oral mucosa of asthmatic and healthy subjects. This study explores for the first time the relationships between the upper respiratory airways bacteriome and asthma in Chile. It demonstrates that the nasal cavity of children from Santiago harbors unique bacterial communities and identifies potential taxonomic and functional biomarkers of pediatric asthma.
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Affiliation(s)
- Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, United States
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
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19
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Ricciardolo FLM, Guida G, Bertolini F, Di Stefano A, Carriero V. Phenotype overlap in the natural history of asthma. Eur Respir Rev 2023; 32:32/168/220201. [PMID: 37197769 DOI: 10.1183/16000617.0201-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/23/2023] [Indexed: 05/19/2023] Open
Abstract
The heterogeneity of asthma makes it challenging to unravel the pathophysiologic mechanisms of the disease. Despite the wealth of research identifying diverse phenotypes, many gaps still remain in our knowledge of the disease's complexity. A crucial aspect is the impact of airborne factors over a lifetime, which often results in a complex overlap of phenotypes associated with type 2 (T2), non-T2 and mixed inflammation. Evidence now shows overlaps between the phenotypes associated with T2, non-T2 and mixed T2/non-T2 inflammation. These interconnections could be induced by different determinants such as recurrent infections, environmental factors, T-helper plasticity and comorbidities, collectively resulting in a complex network of distinct pathways generally considered as mutually exclusive. In this scenario, we need to abandon the concept of asthma as a disease characterised by distinct traits grouped into static segregated categories. It is now evident that there are multiple interplays between the various physiologic, cellular and molecular features of asthma, and the overlap of phenotypes cannot be ignored.
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Affiliation(s)
- Fabio L M Ricciardolo
- Department of Clinical and Biological Sciences, Severe Asthma and Rare Lung Disease Unit, San Luigi Gonzaga University Hospital, University of Turin, Turin, Italy
- Institute of Translational Pharmacology, National Research Council (IFT-CNR), section of Palermo, Palermo, Italy
| | - Giuseppe Guida
- Department of Clinical and Biological Sciences, Severe Asthma and Rare Lung Disease Unit, San Luigi Gonzaga University Hospital, University of Turin, Turin, Italy
| | - Francesca Bertolini
- Department of Clinical and Biological Sciences, Severe Asthma and Rare Lung Disease Unit, San Luigi Gonzaga University Hospital, University of Turin, Turin, Italy
| | - Antonino Di Stefano
- Department of Pneumology and Laboratory of Cytoimmunopathology of the Heart and Lung, Istituti Clinici Scientifici Maugeri SpA, IRCCS, Novara, Italy
| | - Vitina Carriero
- Department of Clinical and Biological Sciences, Severe Asthma and Rare Lung Disease Unit, San Luigi Gonzaga University Hospital, University of Turin, Turin, Italy
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20
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Pérez-Losada M, Castro-Nallar E, Laerte Boechat J, Delgado L, Azenha Rama T, Berrios-Farías V, Oliveira M. The oral bacteriomes of patients with allergic rhinitis and asthma differ from that of healthy controls. Front Microbiol 2023; 14:1197135. [PMID: 37440882 PMCID: PMC10335798 DOI: 10.3389/fmicb.2023.1197135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/15/2023] [Indexed: 07/15/2023] Open
Abstract
Allergic rhinitis and asthma are two of the most common chronic respiratory diseases in developed countries and have become a major public health concern. Substantial evidence has suggested a strong link between respiratory allergy and upper airway dysbacteriosis, but the role of the oral bacteriota is still poorly understood. Here we used 16S rRNA massive parallel sequencing to characterize the oral bacteriome of 344 individuals with allergic rhinitis (AR), allergic rhinitis with asthma (ARAS), asthma (AS) and healthy controls (CT). Four of the most abundant (>2%) phyla (Actinobacteriota, Firmicutes, Fusobacteriota, and Proteobacteria) and 10 of the dominant genera (Actinomyces, Fusobacterium, Gemella, Haemophilus, Leptotrichia, Neisseria, Porphyromonas, Prevotella, Streptococcus, and Veillonella) in the oral cavity differed significantly (p ≤ 0.03) between AR, ARAS or AS and CT groups. The oral bacteriome of ARAS patients showed the highest intra-group diversity, while CT showed the lowest. All alpha-diversity indices of microbial richness and evenness varied significantly (p ≤ 0.022) in ARAS vs. CT and ARAS vs. AR, but they were not significantly different in AR vs. CT. All beta-diversity indices of microbial structure (Unifrac, Bray-Curtis, and Jaccard distances) differed significantly (p ≤ 0.049) between each respiratory disease group and controls. Bacteriomes of AR and ARAS patients showed 15 and 28 upregulated metabolic pathways (PICRUSt2) mainly related to degradation and biosynthesis (p < 0.05). A network analysis (SPIEC-EASI) of AR and ARAS bacteriomes depicted simpler webs of interactions among their members than those observed in the bacteriome of CT, suggesting chronic respiratory allergic diseases may disrupt bacterial connectivity in the oral cavity. This study, therefore, expands our understanding of the relationships between the oral bacteriome and allergy-related conditions. It demonstrates for the first time that the mouth harbors distinct bacteriotas during health and allergic rhinitis (with and without comorbid asthma) and identifies potential taxonomic and functional microbial biomarkers of chronic airway disease.
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Affiliation(s)
- Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca, Chile
| | - José Laerte Boechat
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Luís Delgado
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Serviço de Imunoalergologia, Centro Hospitalar Universitário São João (CHUSJ), Porto, Portugal
| | - Tiago Azenha Rama
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Serviço de Imunoalergologia, Centro Hospitalar Universitário São João (CHUSJ), Porto, Portugal
| | - Valentín Berrios-Farías
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca, Chile
| | - Manuela Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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22
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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: 2.0] [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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23
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Pérez-Losada M, Castro-Nallar E, Laerte Boechat J, Delgado L, Azenha Rama T, Berrios-Farías V, Oliveira M. Nasal Bacteriomes of Patients with Asthma and Allergic Rhinitis Show Unique Composition, Structure, Function and Interactions. Microorganisms 2023; 11:microorganisms11030683. [PMID: 36985258 PMCID: PMC10056468 DOI: 10.3390/microorganisms11030683] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Allergic rhinitis and asthma are major public health concerns and economic burdens worldwide. However, little is known about nasal bacteriome dysbiosis during allergic rhinitis, alone or associated with asthma comorbidity. To address this knowledge gap we applied 16S rRNA high-throughput sequencing to 347 nasal samples from participants with asthma (AS = 12), allergic rhinitis (AR = 53), allergic rhinitis with asthma (ARAS = 183) and healthy controls (CT = 99). One to three of the most abundant phyla, and five to seven of the dominant genera differed significantly (p < 0.021) between AS, AR or ARAS and CT groups. All alpha-diversity indices of microbial richness and evenness changed significantly (p < 0.01) between AR or ARAS and CT, while all beta-diversity indices of microbial structure differed significantly (p < 0.011) between each of the respiratory disease groups and controls. Bacteriomes of rhinitic and healthy participants showed 72 differentially expressed (p < 0.05) metabolic pathways each related mainly to degradation and biosynthesis processes. A network analysis of the AR and ARAS bacteriomes depicted more complex webs of interactions among their members than among those of healthy controls. This study demonstrates that the nose harbors distinct bacteriotas during health and respiratory disease and identifies potential taxonomic and functional biomarkers for diagnostics and therapeutics in asthma and rhinitis.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3460000, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3460000, Chile
| | - José Laerte Boechat
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Luis Delgado
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Serviço de Imunoalergologia, Centro Hospitalar Universitário São João (CHUSJ), 4200-319 Porto, Portugal
| | - Tiago Azenha Rama
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Valentín Berrios-Farías
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3460000, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3460000, Chile
| | - Manuela Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
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24
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Association Between Blood Eosinophils and Neutrophils With Clinical Features in Adult-Onset Asthma. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:811-821.e5. [PMID: 36473624 DOI: 10.1016/j.jaip.2022.11.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 10/20/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Asthma is a disease that can be separated into different phenotypes and endotypes based on the clinical characteristics and the molecular mechanisms of the condition, respectively. OBJECTIVE To assess the association between blood eosinophil and neutrophil counts with clinical and molecular features in patients with adult-onset asthma. METHODS Blood eosinophil and neutrophil counts were measured from 203 patients who took part in the Seinäjoki Adult Asthma Study and attended the 12-year follow-up visit. The patients were then divided into four groups (paucigranulocytic [n = 108], neutrophilic [n = 60], eosinophilic [n = 21], and mixed granulocytic [n = 14]), according to eosinophil and neutrophil levels. The cutoff values used to define the groups were 0.30 × 109 · L-1 for blood eosinophils and 4.4 × 109 · L-1 for blood neutrophils. RESULTS The neutrophilic group had highest body mass index. It was dispensed the highest doses of inhaled corticosteroids during the 12-year follow-up and made the most unplanned respiratory visits. The neutrophilic, eosinophilic, and mixed granulocytic groups had more severe asthma compared with the paucigranulocytic group. The neutrophilic and eosinophilic groups were associated with higher dispensed antibiotics. The eosinophilic group had more nasal polyps, more suspected sinusitis, a greater decline in lung function, and increased levels of periostin, FeNO, and IgE. The neutrophilic group had increased high-sensitivity C-reactive protein, matrix metalloproteinase-9, IL-6, leptin, and soluble urokinase plasminogen activator receptor levels. The mixed granulocytic group showed increased resistin levels together with the neutrophilic group. CONCLUSIONS In addition to blood eosinophils, the blood neutrophil count reflects underlying inflammatory patterns and indicates important differences in asthma clinical features and outcomes.
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25
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Losol P, Sokolowska M, Chang YS. Interactions between microbiome and underlying mechanisms in asthma. Respir Med 2023; 208:107118. [PMID: 36641058 DOI: 10.1016/j.rmed.2023.107118] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Microbiome primes host innate immunity in utero and play fundamental roles in the development, training, and function of the immune system throughout the life. Interplay between the microbiome and immune system maintains mucosal homeostasis, while alterations of microbial community dysregulate immune responses, leading to distinct phenotypic features of immune-mediated diseases including asthma. Microbial imbalance within the mucosal environments, including upper and lower airways, skin, and gut, has consistently been observed in asthma patients and linked to increased asthma exacerbations and severity. Microbiome research has increased to uncover hidden microbial members, function, and immunoregulatory effects of bacterial metabolites within the mucosa. This review provides an overview of environmental and genetic factors that modulate the composition and function of the microbiome, and the impacts of microbiome metabolites and skin microbiota on immune regulation in asthma.
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Affiliation(s)
- Purevsuren Losol
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea; Medical Research Center, Seoul National University, Seoul, South Korea; Department of Molecular Biology and Genetics, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Herman-Burchard Strasse 9, CH7265, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea; Medical Research Center, Seoul National University, Seoul, South Korea.
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26
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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27
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Ahmad JG, Marino MJ, Luong AU. Unified Airway Disease. Otolaryngol Clin North Am 2023; 56:181-195. [DOI: 10.1016/j.otc.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Marathe SJ, Snider MA, Flores-Torres AS, Dubin PJ, Samarasinghe AE. Human matters in asthma: Considering the microbiome in pulmonary health. Front Pharmacol 2022; 13:1020133. [PMID: 36532717 PMCID: PMC9755222 DOI: 10.3389/fphar.2022.1020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/15/2022] [Indexed: 07/25/2023] Open
Abstract
Microbial communities form an important symbiotic ecosystem within humans and have direct effects on health and well-being. Numerous exogenous factors including airborne triggers, diet, and drugs impact these established, but fragile communities across the human lifespan. Crosstalk between the mucosal microbiota and the immune system as well as the gut-lung axis have direct correlations to immune bias that may promote chronic diseases like asthma. Asthma initiation and pathogenesis are multifaceted and complex with input from genetic, epigenetic, and environmental components. In this review, we summarize and discuss the role of the airway microbiome in asthma, and how the environment, diet and therapeutics impact this low biomass community of microorganisms. We also focus this review on the pediatric and Black populations as high-risk groups requiring special attention, emphasizing that the whole patient must be considered during treatment. Although new culture-independent techniques have been developed and are more accessible to researchers, the exact contribution the airway microbiome makes in asthma pathogenesis is not well understood. Understanding how the airway microbiome, as a living entity in the respiratory tract, participates in lung immunity during the development and progression of asthma may lead to critical new treatments for asthma, including population-targeted interventions, or even more effective administration of currently available therapeutics.
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Affiliation(s)
- Sandesh J. Marathe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Mark A. Snider
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Emergency Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Armando S. Flores-Torres
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Patricia J. Dubin
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
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29
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Diver S, Haldar K, McDowell PJ, Busby J, Mistry V, Micieli C, Brown V, Cox C, Yang F, Borg C, Shrimanker R, Ramsheh MY, Hardman T, Arron J, Bradding P, Cowan D, Mansur AH, Fowler SJ, Lordan J, Menzies-Gow A, Robinson D, Matthews J, Pavord ID, Chaudhuri R, Heaney LG, Barer MR, Brightling C. Relationship between inflammatory status and microbial composition in severe asthma and during exacerbation. Allergy 2022; 77:3362-3376. [PMID: 35778780 DOI: 10.1111/all.15425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND In T2-mediated severe asthma, biologic therapies, such as mepolizumab, are increasingly used to control disease. Current biomarkers can indicate adequate suppression of T2 inflammation, but it is unclear whether they provide information about airway microbial composition. We investigated the relationships between current T2 biomarkers and microbial profiles, characteristics associated with a ProteobacteriaHIGH microbial profile and the effects of mepolizumab on airway ecology. METHODS Microbiota sequencing was performed on sputum samples obtained at stable and exacerbation state from 140 subjects with severe asthma participating in two clinical trials. Inflammatory subgroups were compared on the basis of biomarkers, including FeNO and sputum and blood eosinophils. ProteobacteriaHIGH subjects were identified by Proteobacteria to Firmicutes ratio ≥0.485. Where paired sputum from stable visits was available, we compared microbial composition at baseline and following ≥12 weeks of mepolizumab. RESULTS Microbial composition was not related to inflammatory subgroup based on sputum or blood eosinophils. FeNO ≥50 ppb when stable and at exacerbation indicated a group with less dispersed microbial profiles characterised by high alpha-diversity and low Proteobacteria. ProteobacteriaHIGH subjects were neutrophilic and had a longer time from asthma diagnosis than ProteobacteriaLOW subjects. In those studied, mepolizumab did not alter airway bacterial load or lead to increased Proteobacteria. CONCLUSION High FeNO could indicate a subgroup of severe asthma less likely to benefit from antimicrobial strategies at exacerbation or in the context of poor control. Where FeNO is <50 ppb, biomarkers of microbial composition are required to identify those likely to respond to microbiome-directed strategies. We found no evidence that mepolizumab alters airway microbial composition.
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Affiliation(s)
- Sarah Diver
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Koirobi Haldar
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Pamela Jane McDowell
- Wellcome-Wolfson Centre for Experimental Medicine, School of Medicine, Dentistry, and Biological Sciences, Belfast, UK
- Queen's University Belfast, Belfast, UK
| | - John Busby
- Wellcome-Wolfson Centre for Experimental Medicine, School of Medicine, Dentistry, and Biological Sciences, Belfast, UK
- Queen's University Belfast, Belfast, UK
| | - Vijay Mistry
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Claudia Micieli
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Vanessa Brown
- Wellcome-Wolfson Centre for Experimental Medicine, School of Medicine, Dentistry, and Biological Sciences, Belfast, UK
- Queen's University Belfast, Belfast, UK
| | - Ciara Cox
- Regional Virus Laboratory, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Freda Yang
- Division of Immunology, Infection and Inflammation, University of Glasgow, Glasgow, UK
| | - Catherine Borg
- Oxford Respiratory NIHR BRC, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rahul Shrimanker
- Oxford Respiratory NIHR BRC, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mohammadali Yavari Ramsheh
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Tim Hardman
- Niche Science & Technology Ltd., Unit 26, Falstaff House, Richmond, UK
| | - Joseph Arron
- Genentech Inc., South San Francisco, California, USA
| | - Peter Bradding
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Douglas Cowan
- NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | - Adel Hasan Mansur
- University of Birmingham and Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Jim Lordan
- The Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - John Matthews
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
- 23andMe, Sunnyvale, California, USA
| | - Ian D Pavord
- Oxford Respiratory NIHR BRC, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rekha Chaudhuri
- Division of Immunology, Infection and Inflammation, University of Glasgow, Glasgow, UK
| | - Liam G Heaney
- Wellcome-Wolfson Centre for Experimental Medicine, School of Medicine, Dentistry, and Biological Sciences, Belfast, UK
- Queen's University Belfast, Belfast, UK
| | - Michael R Barer
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Christopher Brightling
- Department of Respiratory Sciences, Leicester NIHR BRC, Institute for Lung Health, University of Leicester, Leicester, UK
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30
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Sesé L, Mahay G, Barnig C, Guibert N, Leroy S, Guilleminault L. [Markers of severity and predictors of response to treatment in severe asthma]. Rev Mal Respir 2022; 39:740-757. [PMID: 36115752 DOI: 10.1016/j.rmr.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/19/2022] [Indexed: 10/14/2022]
Abstract
Asthma is a multifactorial disease with complex pathophysiology. Knowledge of its immunopathology and inflammatory mechanisms is progressing and has led to the development over recent years of increasingly targeted therapeutic strategies. The objective of this review is to pinpoint the different predictive markers of asthma severity and therapeutic response. Obesity, nasal polyposis, gastroesophageal reflux disease and intolerance to aspirin have all been considered as clinical markers associated with asthma severity, as have functional markers such as bronchial obstruction, low FEV1, small daily variations in FEV1, and high FeNO. While sinonasal polyposis and allergic comorbidities are associated with better response to omalizumab, nasal polyposis or long-term systemic steroid use are associated with better response to antibodies targeting the IL5 pathway. Elevated total IgE concentrations and eosinophil counts are classic biological markers regularly found in severe asthma. Blood eosinophils are predictive biomarkers of response to anti-IgE, anti-IL5, anti-IL5R and anti-IL4R biotherapies. Dupilumab is particularly effective in a subgroup of patients with marked type 2 inflammation (long-term systemic corticosteroid therapy, eosinophilia≥150/μl or FENO>20 ppb). Chest imaging may help to identify severe patients by seeking out bronchial wall thickening and bronchial dilation. Study of the patient's environment is crucial insofar as exposure to tobacco, dust mites and molds, as well as outdoor and indoor air pollutants (cleaning products), can trigger asthma exacerbation. Wider and more systematic use of markers of severity or response to treatment could foster increasingly targeted and tailored approaches to severe asthma.
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Affiliation(s)
- L Sesé
- AP-HP, service de physiologie, hôpital Avicenne, Bobigny, France
| | - G Mahay
- Service de pneumologie, oncologie thoracique et soins intensifs respiratoires, CHU Rouen, Rouen, France
| | - C Barnig
- INSERM, EFS BFC, LabEx LipSTIC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, University Bourgogne Franche-Comté, Besançon, France; Service de pneumologie, oncologie thoracique et allergologie respiratoire, CHRU Besançon, Besançon, France
| | - N Guibert
- AP-HP, service de physiologie, hôpital Avicenne, Bobigny, France
| | - S Leroy
- Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, CNRS UMR 7275-FHU OncoAge, service de pneumologie oncologie thoracique et soins intensifs respiratoires, CHU de Nice, hôpital Pasteur, Nice, France
| | - L Guilleminault
- AP-HP, service de physiologie, hôpital Avicenne, Bobigny, France; Institut Toulousain des maladies infectieuses et inflammatoires (Infinity) inserm UMR1291-CNRS UMR5051-université Toulouse III, CRISALIS F-CRIN, Toulouse, France.
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31
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Tang X, Rönnberg E, Säfholm J, Thulasingam M, Trauelsen M, Schwartz TW, Wheelock CE, Dahlén S, Nilsson G, Haeggström JZ. Activation of succinate receptor 1 boosts human mast cell reactivity and allergic bronchoconstriction. Allergy 2022; 77:2677-2687. [PMID: 35122266 PMCID: PMC9545225 DOI: 10.1111/all.15245] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/31/2021] [Accepted: 01/23/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND SUCNR1 is a sensor of extracellular succinate, a Krebs cycle intermediate generated in excess during oxidative stress and has been linked to metabolic regulation and inflammation. While mast cells express SUCNR1, its role in mast cell reactivity and allergic conditions such as asthma remains to be elucidated. METHODS Cord blood-derived mast cells and human mast cell line LAD-2 challenged by SUCNR1 ligands were analyzed for the activation and mediator release. Effects on mast cell-dependent bronchoconstriction were assessed in guinea pig trachea and isolated human small bronchi challenged with antigen and anti-IgE, respectively. RESULTS SUCNR1 is abundantly expressed on human mast cells. Challenge with succinate, or the synthetic non-metabolite agonist cis-epoxysuccinate, renders mast cells hypersensitive to IgE-dependent activation, resulting in augmented degranulation and histamine release, de novo biosynthesis of eicosanoids and cytokine secretion. The succinate-potentiated mast cell reactivity was attenuated by SUCNR1 knockdown and selective SUCNR1 antagonists and could be tuned by pharmacologically targeting protein kinase C and extracellular signal-regulated kinase. Both succinate and cis-epoxysuccinate dose-dependently potentiated antigen-induced contraction in a mast cell-dependent guinea pig airway model, associated with increased generation of cysteinyl-leukotrienes and histamine in trachea. Similarly, cis-epoxysuccinate aggravated IgE-receptor-induced contraction of human bronchi, which was blocked by SUCNR1 antagonism. CONCLUSION SUCNR1 amplifies IgE-receptor-induced mast cell activation and allergic bronchoconstriction, suggesting a role for this pathway in aggravation of allergic asthma, thus linking metabolic perturbations to mast cell-dependent inflammation.
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Affiliation(s)
- Xiao Tang
- Division of Physiological Chemistry IIDepartment of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Elin Rönnberg
- Division of Immunology and AllergyDepartment of Medicine SolnaKarolinska Institutet, and Karolinska University HospitalSolnaSweden
| | - Jesper Säfholm
- Unit of Experimental Asthma and Allergy ResearchInstitute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | - Madhuranayaki Thulasingam
- Division of Physiological Chemistry IIDepartment of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Mette Trauelsen
- Novo Nordisk Foundation Center for Basic Metabolic ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Thue W. Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Craig E. Wheelock
- Division of Physiological Chemistry IIDepartment of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Sven‐Erik Dahlén
- Unit of Experimental Asthma and Allergy ResearchInstitute of Environmental MedicineKarolinska InstitutetStockholmSweden,Department of Respiratory MedicineKarolinska University Hospital HuddingeStockholmSweden
| | - Gunnar Nilsson
- Division of Immunology and AllergyDepartment of Medicine SolnaKarolinska Institutet, and Karolinska University HospitalSolnaSweden,Department of Medical SciencesUppsala UniversityUppsalaSweden
| | - Jesper Z. Haeggström
- Division of Physiological Chemistry IIDepartment of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
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32
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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: 10] [Impact Index Per Article: 5.0] [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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33
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Sood U, Dhingra GG, Anand S, Hira P, Kumar R, Kaur J, Verma M, Singhvi N, Lal S, Rawat CD, Singh VK, Kaur J, Verma H, Tripathi C, Singh P, Dua A, Saxena A, Phartyal R, Jayaraj P, Makhija S, Gupta R, Sahni S, Nayyar N, Abraham JS, Somasundaram S, Lata P, Solanki R, Mahato NK, Prakash O, Bala K, Kumari R, Toteja R, Kalia VC, Lal R. Microbial Journey: Mount Everest to Mars. Indian J Microbiol 2022; 62:323-337. [PMID: 35974919 PMCID: PMC9375815 DOI: 10.1007/s12088-022-01029-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022] Open
Abstract
A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | | | - Shailly Anand
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Princy Hira
- Maitreyi College, University of Delhi, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar India
| | | | - Mansi Verma
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | - Sukanya Lal
- Ramjas College, University of Delhi, Delhi, India
| | | | | | - Jaspreet Kaur
- Maitreyi College, University of Delhi, New Delhi, India
| | | | | | - Priya Singh
- Maitreyi College, University of Delhi, New Delhi, India
| | - Ankita Dua
- Shivaji College, University of Delhi, New Delhi, India
| | - Anjali Saxena
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | | | - Perumal Jayaraj
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, India
| | - Sumit Sahni
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Namita Nayyar
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | | | - Pushp Lata
- Ramjas College, University of Delhi, Delhi, India
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Nitish Kumar Mahato
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra India
| | - Kiran Bala
- Deshbandhu College, University of Delhi, New Delhi, India
| | - Rashmi Kumari
- College of Commerce, Arts and Science, Patliputra University, Patna, Bihar India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | | | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
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34
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [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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35
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DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma. Proc Natl Acad Sci U S A 2022; 119:e2116467119. [PMID: 35666868 PMCID: PMC9214527 DOI: 10.1073/pnas.2116467119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Maternal asthma is one of the most replicated risk factors for childhood-onset asthma. However, the underlying mechanisms are unknown. We identified DNA methylation signatures in bronchial epithelial cells from adults with asthma that were specific to those with a mother with asthma. These maternal asthma-associated methylation signatures were correlated with distinct gene regulatory pathways and clinical features. Genes in 16 pathways discriminated cases with and without maternal asthma and suggested impaired T cell signaling and responses to viral and bacterial pathogens in asthmatic children of an asthmatic mother. Our findings suggest that the prenatal environment in pregnancies of mothers with asthma alters epigenetically mediated developmental programs that may lead to severe asthma in their children through diverse gene regulatory pathways. Maternal asthma (MA) is among the most consistent risk factors for asthma in children. Possible mechanisms for this observation are epigenetic modifications in utero that have lasting effects on developmental programs in children of mothers with asthma. To test this hypothesis, we performed differential DNA methylation analyses of 398,186 individual CpG sites in primary bronchial epithelial cells (BECs) from 42 nonasthma controls and 88 asthma cases, including 56 without MA (NMA) and 32 with MA. We used weighted gene coexpression network analysis (WGCNA) of 69 and 554 differentially methylated CpGs (DMCs) that were specific to NMA and MA cases, respectively, compared with controls. WGCNA grouped 66 NMA-DMCs and 203 MA-DMCs into two and five comethylation modules, respectively. The eigenvector of one MA-associated module (turquoise) was uniquely correlated with 85 genes expressed in BECs and enriched for 36 pathways, 16 of which discriminated between NMA and MA using machine learning. Genes in all 16 pathways were decreased in MA compared with NMA cases (P = 7.1 × 10−3), a finding that replicated in nasal epithelial cells from an independent cohort (P = 0.02). Functional interpretation of these pathways suggested impaired T cell signaling and responses to viral and bacterial pathogens. The MA-associated turquoise module eigenvector was additionally correlated with clinical features of severe asthma and reflective of type 2 (T2)-low asthma (i.e., low total serum immunoglobulin E, fractional exhaled nitric oxide, and eosinophilia). Overall, these data suggest that MA alters diverse epigenetically mediated pathways that lead to distinct subtypes of severe asthma in adults, including hard-to-treat T2-low asthma.
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36
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Zhang Y, Shen F, Yang Y, Niu M, Chen D, Chen L, Wang S, Zheng Y, Sun Y, Zhou F, Qian H, Wu Y, Zhu T. Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6282-6293. [PMID: 35512288 PMCID: PMC9113006 DOI: 10.1021/acs.est.2c00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 05/04/2023]
Abstract
Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents' exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation-maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.
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Affiliation(s)
- Yin Zhang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Fangxia Shen
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Yi Yang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Mutong Niu
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Da Chen
- School
of Environment and Guangdong Key Laboratory of Environmental Pollution
and Health, Jinan University, Guangzhou 510632, China
| | - Longfei Chen
- School
of Energy and Power Engineering, Beihang
University, Beijing 100191, China
| | - Shengqi Wang
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yunhao Zheng
- Institute
of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ye Sun
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Feng Zhou
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Hua Qian
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yan Wu
- School of
Environmental Science and Engineering, Shandong
University, Jinan 250100, China
| | - Tianle Zhu
- School
of Space and Environment, Beihang University, Beijing 100191, China
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37
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Huang C, Ni Y, Du W, Shi G. Effect of inhaled corticosteroids on microbiome and microbial correlations in asthma over a nine-month period. Clin Transl Sci 2022; 15:1723-1736. [PMID: 35514165 PMCID: PMC9283747 DOI: 10.1111/cts.13288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
The effect of inhaled corticosteroids (ICS) on airway microbiome requires longitudinal research to be corroborated. Asthma patients, not undergoing ICS treatment (baseline), were enrolled and prescribed with ICS; all of these patients were followed up with regular visits at 3 months (visit 1) and 9 months (visit 2). Induced sputum was collected, fungal microbiota (mycobiome) and bacterial microbiota (bacteriome) were estimated using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing. Bacterial α diversity indices were not significantly different among the baseline, visit 1 and visit 2. Visit 1 showed lower fungal evenness than the baseline, visit 2 showed lower fungal diversity and evenness than the baseline. Fungal, but not bacterial, community compositions differed significantly among the baseline, visit 1 and visit 2. The most abundant bacterial phyla and genera did not differ significantly among the baseline, visit 1 and visit 2. Compared with the baseline, visit 1 showed significantly increased frequency of fungal phylum Ascomycota and lower frequency of Basidiomycota. We found sharply decreased fungal genera Wallemia, Cladosporium, Penicillium, and Alternaria in visit 1 and visit 2 compared with the baseline, although the differences were not statistically significant. We also found the proportion of Basidiomycota was positively correlated with percentages of sputum eosinophils and neutrophils. The proportions of Saccharomyces, Wallemia, and Aplosporella were positively correlated with percentage of sputum eosinophils. Moreover, we identified distinct inter- and intra-kingdom interactions in baseline, visit 1 and visit 2. Therefore, ICS use altered the airway microbial diversity, evenness, community composition and microbial connections.
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Affiliation(s)
- Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yingmeng Ni
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Wei Du
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Institute of Respiratory Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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38
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Notarbartolo V, Giuffrè M, Montante C, Corsello G, Carta M. Composition of Human Breast Milk Microbiota and Its Role in Children's Health. Pediatr Gastroenterol Hepatol Nutr 2022; 25:194-210. [PMID: 35611376 PMCID: PMC9110848 DOI: 10.5223/pghn.2022.25.3.194] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/02/2022] [Indexed: 12/26/2022] Open
Abstract
Human milk contains a number of nutritional and bioactive molecules including microorganisms that constitute the so-called "Human Milk Microbiota (HMM)". Recent studies have shown that not only bacterial but also viral, fungal, and archaeal components are present in the HMM. Previous research has established, a "core" microbiome, consisting of Firmicutes (i.e., Streptococcus, Staphylococcus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas, Bradyrhizobium), and Actinobacteria (i.e., Propionibacterium, Corynebacterium). This review aims to summarize the main characteristics of HMM and the role it plays in shaping a child's health. We reviewed the most recent literature on the topic (2019-2021), using the PubMed database. The main sources of HMM origin were identified as the retrograde flow and the entero-mammary pathway. Several factors can influence its composition, such as maternal body mass index and diet, use of antibiotics, time and type of delivery, and mode of breastfeeding. The COVID-19 pandemic, by altering the mother-infant dyad and modifying many of our previous habits, has emerged as a new risk factor for the modification of HMM. HMM is an important contributor to gastrointestinal colonization in children and therefore, it is fundamental to avoid any form of perturbation in the HMM that can alter the microbial equilibrium, especially in the first 100 days of life. Microbial dysbiosis can be a trigger point for the development of necrotizing enterocolitis, especially in preterm infants, and for onset of chronic diseases, such as asthma and obesity, later in life.
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Affiliation(s)
- Veronica Notarbartolo
- Department of Health Promotion, Mather and Child Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
| | - Mario Giuffrè
- Department of Health Promotion, Mather and Child Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
| | - Claudio Montante
- Department of Health Promotion, Mather and Child Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
| | - Giovanni Corsello
- Department of Health Promotion, Mather and Child Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
| | - Maurizio Carta
- Department of Health Promotion, Mather and Child Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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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] [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,*Correspondence: Amali E. Samarasinghe
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Characterization of Distinct Microbiota Associated with Scalp Dermatitis in Patients with Atopic Dermatitis. J Clin Med 2022; 11:jcm11061735. [PMID: 35330061 PMCID: PMC8949928 DOI: 10.3390/jcm11061735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have focused on the role of skin microbiota in the pathogenesis of atopic dermatitis (AD). Among the various clinical phenotypes of AD, scalp dermatitis is a commonly observed clinical feature of AD. However, little is known about the pathogenesis of scalp dermatitis in AD. Hence, the aim of this study was to identify the distinct microbiota associated with scalp dermatitis in patients with AD. Using scalp swab samples from 10 patients with AD and 10 healthy controls, this study characterized the scalp microbiota in patients with AD via V3–V4 regions of the 16S rRNA gene sequencing for bacterial identification, and ITS2 gene sequencing for fungal identification. Among bacterial genera, Staphylococcus was the most abundant in AD than in healthy controls, whereas Cutibacterium was the most abundant species in the healthy controls. The most predominant scalp fungal microbiota was Malassezia both in AD and healthy controls, while a higher diversity of non-Malassezia fungi was observed in AD than in healthy controls. The study findings indicate the dysbiosis of scalp microbiota in AD and highlight the potential biomarker role of specific microbiota in AD on the scalp dermatitis.
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Different Airway Inflammatory Phenotypes Correlate with Specific Fungal and Bacterial Microbiota in Asthma and Chronic Obstructive Pulmonary Disease. J Immunol Res 2022; 2022:2177884. [PMID: 35310604 PMCID: PMC8933093 DOI: 10.1155/2022/2177884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/22/2022] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
Background Studies of chronic airway inflammatory diseases have increasingly focused on airway microbiota. However, the microbiota characteristics of asthma and chronic obstructive pulmonary disease (COPD) patients with different airway inflammatory phenotypes remain unclear. Objective We aimed to reveal the differences of fungal and bacterial microbiota between eosinophilic asthma (EA) and noneosinophilic asthma (NEA) patients and between eosinophilic COPD (EC) and noneosinophilic COPD (NEC) patients. Further, explore whether similarities exist in the airway microbiota of patients with the same phenotype. Methods Induced sputum samples were collected from 45 asthma subjects and 39 COPD subjects. The airway microbiota of the subjects was profiled by nearly full-length 16S rRNA and internal transcribed space (ITS) sequencing. Results Subjects with eosinophilic phenotype (EA and EC) showed significant differences in both fungal and bacterial microbiota compared to the corresponding subjects with noneosinophilic phenotype (NEA and NEC). In addition, no differences were observed between the fungal microbiota of subjects with the same phenotype (EA vs. EC, NEA vs. NEC). In bacterial microbiota, the greater relative abundance of Streptococcus thermophilus was observed in EA and EC subjects, while Ochrobactrum was enriched in NEA and NEC subjects. In fungal microbiota, the EA and EC subjects showed higher relative abundances of Aspergillus and Bjerkandera, while the NEA and NEC subjects were enriched in Rhodotorula and Papiliotrema. Conclusions Different airway inflammatory phenotypes were related to specific fungal and bacterial microbiota in both asthma and COPD, while the same airway inflammatory phenotype revealed a degree of similarity in airway microbiota, particularly in fungal microbiota.
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Wang Y, Chen Y, Wu C, Yang X. Informatic analysis of the pulmonary microecology in non-cystic fibrosis bronchiectasis at three different stages. Open Life Sci 2022; 17:107-120. [PMID: 35291562 PMCID: PMC8886608 DOI: 10.1515/biol-2022-0014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
This study explored the impact of pulmonary microecological changes on disease progression in non-cystic fibrosis bronchiectasis (nCFB). A careful search of the NCBI BioProject database revealed the 16S rRNA-based microbiological testing results of 441 pulmonary sputum samples from patients in the relatively stable (baseline), acute exacerbation, or recovery stage. After preliminary analysis and screening, we selected 152 samples for further analyses, including determination of the operational taxonomic unit (OTU) distribution at the phylum, class, order, family and genus levels, community structure, alpha diversity, beta diversity, microbial multivariables, correlations, and community structure after the abundances of intragroup samples were averaged. The recovery group showed significant differences in pulmonary microbiological changes (P < 0.05) compared with the other groups. There were 30 differentially abundant OTUs, with 27 and 7 at the genus and phylum levels, respectively. The Chao1 value of the recovery group was comparable to that of the baseline group, and the Shannon and Simpson values of the recovery group were the highest. Rhodococcus in Actinobacteria was positively correlated with Ochrobactrum in Firmicutes. The differences in pulmonary microecological changes at different nCFB stages may serve as a biologically predictive indicator of nCFB progression.
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Affiliation(s)
- Yuchao Wang
- Graduate School, Xinjiang Medical University , 830001 Urumqi , China
| | - Ying Chen
- Department of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region , No. 91 Tianchi Road, Tianshan District , Urumqi 830001 , China
| | - Chao Wu
- Department of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region , No. 91 Tianchi Road, Tianshan District , Urumqi 830001 , China
| | - Xiaohong Yang
- Department of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region , No. 91 Tianchi Road, Tianshan District , Urumqi 830001 , China
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Gautam Y, Johansson E, Mersha TB. Multi-Omics Profiling Approach to Asthma: An Evolving Paradigm. J Pers Med 2022; 12:jpm12010066. [PMID: 35055381 PMCID: PMC8778153 DOI: 10.3390/jpm12010066] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Asthma is a complex multifactorial and heterogeneous respiratory disease. Although genetics is a strong risk factor of asthma, external and internal exposures and their interactions with genetic factors also play important roles in the pathophysiology of asthma. Over the past decades, the application of high-throughput omics approaches has emerged and been applied to the field of asthma research for screening biomarkers such as genes, transcript, proteins, and metabolites in an unbiased fashion. Leveraging large-scale studies representative of diverse population-based omics data and integrating with clinical data has led to better profiling of asthma risk. Yet, to date, no omic-driven endotypes have been translated into clinical practice and management of asthma. In this article, we provide an overview of the current status of omics studies of asthma, namely, genomics, transcriptomics, epigenomics, proteomics, exposomics, and metabolomics. The current development of the multi-omics integrations of asthma is also briefly discussed. Biomarker discovery following multi-omics profiling could be challenging but useful for better disease phenotyping and endotyping that can translate into advances in asthma management and clinical care, ultimately leading to successful precision medicine approaches.
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Abstract
Severe pneumonia is associated with high mortality (short and long term), as well as pulmonary and extrapulmonary complications. Appropriate diagnosis and early initiation of adequate antimicrobial treatment for severe pneumonia are crucial in improving survival among critically ill patients. Identifying the underlying causative pathogen is also critical for antimicrobial stewardship. However, establishing an etiological diagnosis is challenging in most patients, especially in those with chronic underlying disease; those who received previous antibiotic treatment; and those treated with mechanical ventilation. Furthermore, as antimicrobial therapy must be empiric, national and international guidelines recommend initial antimicrobial treatment according to the location's epidemiology; for patients admitted to the intensive care unit, specific recommendations on disease management are available. Adherence to pneumonia guidelines is associated with better outcomes in severe pneumonia. Yet, the continuing and necessary research on severe pneumonia is expansive, inviting different perspectives on host immunological responses, assessment of illness severity, microbial causes, risk factors for multidrug resistant pathogens, diagnostic tests, and therapeutic options.
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Affiliation(s)
- Catia Cillóniz
- Department of pneumology, Hospital Clinic of Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Centers in Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Antoni Torres
- Department of pneumology, Hospital Clinic of Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Centers in Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Michael S Niederman
- Weill Cornell Medical College, Department of Pulmonary Critical Care Medicine, New York, NY, USA
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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Clinical relevance of Alternaria alternata sensitization in patients within type 2-high and type 2-low asthma. Int Immunopharmacol 2021; 101:108333. [PMID: 34773759 DOI: 10.1016/j.intimp.2021.108333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/17/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022]
Abstract
Alternaria sensitization is correlated with persistent asthma. Type 2 (T2)-asthma endotypes are characterized by the release of eosinophils. However, the prevalence and sensitization patterns in patients with Alternaria asthma between T2-high and T2-low endotypes are unknown. We retrospectively reviewed 582 patients with Alternaria asthma and divided them into T2-high (n = 376) and T2-low (n = 206) groups with a threshold of 300 cells/µL in blood eosinophil counts. Data for basic information, skin test or IgE detection results, and blood eosinophil counts were collected. The age of patients in the T2-high group (13.66 ± 13.23) was lower than that of the T2-low group (18.02 ± 15.03). Patients with T2-high asthma had relatively higher rates of taking inhaled corticosteroids (ICS) and positive family history than the T2-low group. Pet keepers and allergen immunotherapy (AIT) patients were comparable between these groups, In the T2-high group, patients had higher levels of total serum IgE (T-IgE) and showed a significant positive correlation with eosinophil counts (r = 0.166, P = 0.001), followed by higher Alternaria-specific IgE (sIgE) levels (median, 13.7; range, 4.86-25.3). Compared to the T2-low group, the frequency of poly-sensitized patients and the rate of each allergen among the nine common allergens were all higher in the T2-high group; the statistical differences mainly focused on pollens such as birch (P = 0.005), firmiana (P = 0.004), and mugwort (P = 0.005). Young, male patients had a high prevalence of T2-high Alternaria asthma, along with higher rates of T-IgE, sIgE levels, and poly-sensitized patterns.
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Ackland J, Watson A, Wilkinson TMA, Staples KJ. Interrupting the Conversation: Implications for Crosstalk Between Viral and Bacterial Infections in the Asthmatic Airway. FRONTIERS IN ALLERGY 2021; 2:738987. [PMID: 35386999 PMCID: PMC8974750 DOI: 10.3389/falgy.2021.738987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Asthma is a heterogeneous, chronic respiratory disease affecting 300 million people and is thought to be driven by different inflammatory endotypes influenced by a myriad of genetic and environmental factors. The complexity of asthma has rendered it challenging to develop preventative and disease modifying therapies and it remains an unmet clinical need. Whilst many factors have been implicated in asthma pathogenesis and exacerbations, evidence indicates a prominent role for respiratory viruses. However, advances in culture-independent detection methods and extensive microbial profiling of the lung, have also demonstrated a role for respiratory bacteria in asthma. In particular, airway colonization by the Proteobacteria species Nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) is associated with increased risk of developing recurrent wheeze and asthma in early life, poor clinical outcomes in established adult asthma and the development of more severe inflammatory phenotypes. Furthermore, emerging evidence indicates that bacterial-viral interactions may influence exacerbation risk and disease severity, highlighting the need to consider the impact chronic airway colonization by respiratory bacteria has on influencing host responses to viral infection. In this review, we first outline the currently understood role of viral and bacterial infections in precipitating asthma exacerbations and discuss the underappreciated potential impact of bacteria-virus crosstalk in modulating host responses. We discuss the mechanisms by which early life infection may predispose to asthma development. Finally, we consider how infection and persistent airway colonization may drive different asthma phenotypes, with a view to identifying pathophysiological mechanisms that may prove tractable to new treatment modalities.
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Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tom M. A. Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Karl J. Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
- *Correspondence: Karl J. Staples
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Miller RL, Grayson MH, Strothman K. Advances in asthma: New understandings of asthma's natural history, risk factors, underlying mechanisms, and clinical management. J Allergy Clin Immunol 2021; 148:1430-1441. [PMID: 34655640 DOI: 10.1016/j.jaci.2021.10.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
The last 2 years yielded a proliferation of high-quality asthma research. These include new understandings of the incidence and natural history of asthma, findings on the effects of exposure to air pollution, allergens, and intake of acetaminophen, soy isoflavones, and polyunsaturated fatty acids, and exposure to microbial products. The past 2 years have benefited from great strides in determining potential mechanisms of asthma development and asthma exacerbations. These novel understandings led to identification and development of exciting new avenues for potential therapeutic intervention. Finally, there has been significant progress made in the development of tools to facilitate the diagnosis of asthma and measurement of airway physiology and in precision diagnostic approaches. Asthma guidelines were updated and new insights into the pharmacologic management of patients, including biologics, were reported. We review the most notable advances in the natural history of asthma, risk factors for the development of asthma, underlying mechanisms, diagnostic approaches, and treatments. Although greater knowledge of the mechanisms underlying responses and nonresponses to novel therapeutics and across asthma phenotypes would be beneficial, the progress over just the past 2 years has been immense and impactful.
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Affiliation(s)
- Rachel L Miller
- Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Mitchell H Grayson
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio; Center for Clinical and Translational Research, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kasey Strothman
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio
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Santiago-Rodriguez TM, Hollister EB. Multi 'omic data integration: A review of concepts, considerations, and approaches. Semin Perinatol 2021; 45:151456. [PMID: 34256961 DOI: 10.1016/j.semperi.2021.151456] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen, Inc, 3 Greenway Plaza, Suite 1575, Houston, TX 77046, USA.
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