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Bai X, Nielsen SD, Kunisaki KM, Trøseid M. Pulmonary comorbidities in people with HIV- the microbiome connection. Curr Opin HIV AIDS 2024; 19:246-252. [PMID: 38935049 DOI: 10.1097/coh.0000000000000871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW To report recent evidence on associations between human microbiome, particularly airway and gut, and pulmonary comorbidities in people with HIV (PWH). Furthermore, we explore how changes in the microbiome may contribute to pulmonary immune dysregulation and higher rates of pulmonary comorbidities among PWH. Finally, we propose future directions in the field. RECENT FINDINGS Increased risk of pulmonary comorbidities and rapid lung function decline have been reported in even well treated PWH. Altered microbiota profiles have been reported in PWH with pulmonary comorbidities and rapid lung function decline as compared to those without. The most consistent data have been the association between HIV-related pulmonary comorbidities, lung and oral microbiota dysbiosis, which has been also associated with distinct respiratory mucosal inflammatory profiles and short-term mortality. However, a possible causal link remains to be elucidated. SUMMARY Associations between the lung and oral microbiome, HIV-associated pulmonary comorbidities and rapid lung function decline have been reported in recent studies. Yet the underlying mechanism underpinning the observed associations is largely unknown and substantial knowledge gaps remain. Future research is warranted to unveil the role and mechanism of human microbiome from different anatomical compartments in relation to pulmonary comorbidities in PWH.
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Affiliation(s)
- Xiangning Bai
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Dam Nielsen
- Viro-Immunology Research Unit, Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen
- Department of Surgical Gastroenterology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ken M Kunisaki
- Minneapolis Veterans Affairs Healthcare System
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Marius Trøseid
- Institute of Clinical Medicine, University of Oslo
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation
- Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
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Assefa A, Woldemariam M, Aklilu A, Alelign D, Zakir A, Manilal A, Mohammed T, M. Alahmadi R, Raman G, Idhayadhulla A. Typical pneumonia among human immunodeficiency virus-infected patients in public hospitals in southern Ethiopia. PLoS One 2024; 19:e0307780. [PMID: 39078837 PMCID: PMC11288459 DOI: 10.1371/journal.pone.0307780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Typical pneumonia is a pressing issue in the treatment of human immunodeficiency virus (HIV) patients, especially in Sub-Saharan Africa, where it remains a significant menace. Addressing this problem is crucial in improving health outcomes and the reduction of the burden of diseases in this vulnerable category of patients. OBJECTIVE To determine the prevalence of community-acquired typical pneumonia among HIV patients in Public Hospitals in southern Ethiopia. METHODS A cross-sectional study was done among 386 HIV patients clinically suspected of typical pneumonia attending the anti-retroviral therapy (ART) clinics of two hospitals from March to September 2022. A pretested structured questionnaire was employed to collect the demographic, clinical, and behavioral data. Sputum samples were collected and inspected for bacteria following standard procedures, and antimicrobial susceptibility testing was performed employing the Kirby-Bauer disk diffusion method. Besides, extended-spectrum β-lactamase (ESβL) and carbapenemase-producing Gram-negative bacteria were inspected by the double disk synergy test and modified carbapenem inactivation method. Descriptive and inferential statistical analyses were also done. RESULTS Overall, 39.1% (151/386) of sputum cultures (95% Confidence Interval: 32.4-44) were bacteriologically positive. A total of 151 bacteria were identified, comprising 72.8% (n = 110) of Gram-negative bacteria. The predominant isolate was Klebsiella pneumoniae (25.8%, n = 39), followed by Staphylococcus aureus (17.9%, n = 27); 59.6% (n = 90) of the entire isolates were multidrug-resistant (MDR). Forty percent (11/27) of S. aureus were methicillin-resistant S. aureus (MRSA), and 28.1% (n = 31) and 20.9% (n = 23) of Gram-negative bacteria were extended-spectrum beta-lactamases (ESBL) and carbapenemase producers, respectively. Occupational status, alcohol consumption, cluster of differentiation4 (CD4) Thymocyte cell count < 350, interruption of trimethoprim-sulfamethoxazole prophylaxis and antiretroviral treatment, and recent viral load ≥ 150 were found statistically significant. CONCLUSION The higher rates of MDR, MRSA, ESBL, and carbapenem-resistant Enterobacterales (CRE) indicate that bacterial pneumonia is a vexing problem among HIV patients and therefore it is advisable to implement an antimicrobial stewardship program in the study area.
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Affiliation(s)
- Ayele Assefa
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Melat Woldemariam
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Addis Aklilu
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Dagninet Alelign
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Abdurezak Zakir
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Aseer Manilal
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Temesgen Mohammed
- School of Public Health, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Reham M. Alahmadi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk-Do, South Korea
| | - Akbar Idhayadhulla
- Research Department of Chemistry, Nehru Memorial College (Affiliated to Bharathidasan University), Puthanampatti, Tiruchirappalli District, Tamil Nadu
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Yang J, Li J, Zhang L, Shen Z, Xiao Y, Zhang G, Chen M, Chen F, Liu L, Wang Y, Chen L, Wang X, Zhang L, Wang L, Wang Z, Wang J, Li M, Ren L. Highly diverse sputum microbiota correlates with the disease severity in patients with community-acquired pneumonia: a longitudinal cohort study. Respir Res 2024; 25:223. [PMID: 38811936 PMCID: PMC11137881 DOI: 10.1186/s12931-024-02821-2] [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: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a common and serious condition that can be caused by a variety of pathogens. However, much remains unknown about how these pathogens interact with the lower respiratory commensals, and whether any correlation exists between the dysbiosis of the lower respiratory microbiota and disease severity and prognosis. METHODS We conducted a retrospective cohort study to investigate the composition and dynamics of sputum microbiota in patients diagnosed with CAP. In total, 917 sputum specimens were collected consecutively from 350 CAP inpatients enrolled in six hospitals following admission. The V3-V4 region of the 16 S rRNA gene was then sequenced. RESULTS The sputum microbiota in 71% of the samples were predominately composed of respiratory commensals. Conversely, 15% of the samples demonstrated dominance by five opportunistic pathogens. Additionally, 5% of the samples exhibited sterility, resembling the composition of negative controls. Compared to non-severe CAP patients, severe cases exhibited a more disrupted sputum microbiota, characterized by the highly dominant presence of potential pathogens, greater deviation from a healthy state, more significant alterations during hospitalization, and sparser bacterial interactions. The sputum microbiota on admission demonstrated a moderate prediction of disease severity (AUC = 0.74). Furthermore, different pathogenic infections were associated with specific microbiota alterations. Acinetobacter and Pseudomonas were more abundant in influenza A infections, with Acinetobacter was also enriched in Klebsiella pneumoniae infections. CONCLUSION Collectively, our study demonstrated that pneumonia may not consistently correlate with severe dysbiosis of the respiratory microbiota. Instead, the degree of microbiota dysbiosis was correlated with disease severity in CAP patients.
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Affiliation(s)
- Jing Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Changping Laboratory, Beijing, 102206, China
| | - Jinman Li
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Linfeng Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijie Shen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guoliang Zhang
- Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Mingwei Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fuhui Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ling Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lan Chen
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Lu Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Zhang Wang
- Institute of Ecological Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, 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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Byanova KL, Abelman R, North CM, Christenson SA, Huang L. COPD in People with HIV: Epidemiology, Pathogenesis, Management, and Prevention Strategies. Int J Chron Obstruct Pulmon Dis 2023; 18:2795-2817. [PMID: 38050482 PMCID: PMC10693779 DOI: 10.2147/copd.s388142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive respiratory disorder characterized by airflow limitation and persistent respiratory symptoms. People with HIV (PWH) are particularly vulnerable to COPD development; PWH have demonstrated both higher rates of COPD and an earlier and more rapid decline in lung function than their seronegative counterparts, even after accounting for differences in cigarette smoking. Factors contributing to this HIV-associated difference include chronic immune activation and inflammation, accelerated aging, a predilection for pulmonary infections, alterations in the lung microbiome, and the interplay between HIV and inhalational toxins. In this review, we discuss what is known about the epidemiology and pathobiology of COPD among PWH and outline screening, diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Katerina L Byanova
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Abelman
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Crystal M North
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie A Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laurence Huang
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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Liu Y, Zhang J, Leng G, Hu J, Wang W, Deng G, Ma Y, Sha S. Mycobacterium tuberculosis Rv1987 protein attenuates inflammatory response and consequently alters microbiota in mouse lung. Front Cell Infect Microbiol 2023; 13:1256866. [PMID: 38029253 PMCID: PMC10646435 DOI: 10.3389/fcimb.2023.1256866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Healthy lung microbiota plays an important role in preventing Mycobacterium tuberculosis (Mtb) infections by activating immune cells and stimulating production of T-helper cell type 1 cytokines. The dynamic stability of lung microbiota relies mostly on lung homeostasis. In our previous studies, we found that Mtb virulence factor, Rv1987 protein, can mediate host immune response and enhance mycobacterial survival in host lung. However, the alteration of lung microbiota and the contribution of lung microbiota dysbiosis to mycobacterial evasion in this process are not clear so far. Methods M. smegmatis which does not contain the ortholog of Rv1987 protein was selected as a model strain to study the effects of Rv1987 on host lung microbiota. The lung microbiota, immune state and metabolites of mice infected by M. smegmatis overexpressing Rv1987 protein (MS1987) were detected and analyzed. Results The results showed that Rv1987 inhibited inflammatory response in mouse lung and anaerobic bacteria and Proteobacteria, Bacteroidota, Actinobacteriota and Acidobacteriota bacteria were enriched in the lung tissues correspondingly. The immune alterations and microbiota dysbiosis affected host metabolic profiles, and some of significantly altered bacteria in MS1987-infected mouse lung, such as Delftia acidovorans, Ralstonia pickettii and Escherichia coli, led to anti-inflammatory responses in mouse lung. The secretory metabolites of these altered bacteria also influenced mycobacterial growth and biofilm formation directly. Conclusion All these results suggested that Rv1987 can attenuate inflammatory response and alter microbiota in the lung, which in turn facilitates mycobacterial survival in the host.
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Affiliation(s)
- Yingying Liu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Jiaqi Zhang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Guangxian Leng
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Junxing Hu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Wenzhen Wang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Guoying Deng
- Department of Microbiology, Dalian Medical University, Dalian, Liaoning, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
- Department of Microbiology, Dalian Medical University, Dalian, Liaoning, China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
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Abelman RA, Fitzpatrick J, Zawedde J, Sanyu I, Byanyima P, Kaswabuli S, Musisi E, Hsieh J, Gardner K, Zhang M, Byanova KL, Sessolo A, Hunt PW, Lalitha R, Davis JL, Crothers K, Worodria W, Huang L. Sex modifies the risk of HIV-associated obstructive lung disease in Ugandans postpneumonia. AIDS 2023; 37:1683-1692. [PMID: 37352494 PMCID: PMC10527596 DOI: 10.1097/qad.0000000000003626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
OBJECTIVES Spirometric abnormalities are frequent, and obstructive lung disease (OLD) is a common comorbidity among people with HIV (PWH). HIV increases the risk of many comorbidities to a greater degree in women than in men. Few studies have evaluated whether sex modifies the HIV-associated risk of OLD. DESIGN AND METHODS To evaluate the associations between sex and HIV with abnormal lung function, women and men with and without HIV underwent spirometric testing after completing therapy for pneumonia, including tuberculosis (TB), in Kampala, Uganda. OLD was defined as a postbronchodilator forced expiratory volume in the first second to forced vital capacity (FEV 1 /FVC) ratio less than 0.70. Associations between sex, HIV, and lung function were evaluated using multivariable regression models including sex-by-HIV interaction terms after adjusting for age, BMI, smoking status, and TB status. RESULTS Among 348 participants, 147 (42%) were women and 135 (39%) were HIV-positive. Sixteen (11%) women and 23 men (11%) had OLD. The HIV-sex interaction was significant for obstructive lung disease ( P = 0.04). In the adjusted stratified analysis, women with HIV had 3.44 (95% CI 1.11-12.0; P = 0.04) increased odds of having OLD compared with men with HIV. Women without HIV did not have increased odds of having OLD compared with men without HIV. CONCLUSION HIV appears to increase the risk of OLD to a greater degree in women than in men in an urban Ugandan setting. The mechanistic explanation for this interaction by sex remains unclear and warrants further study.
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Affiliation(s)
- Rebecca A Abelman
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jessica Fitzpatrick
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Jenny Hsieh
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
| | - Kendall Gardner
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Michelle Zhang
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rejani Lalitha
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut
| | - Kristina Crothers
- Division of Pulmonary, Critical Care and Sleep, Department of Medicine, Veterans Affairs (VA) Puget Sound Healthcare System and University of Washington, Seattle, Washington, USA
| | - William Worodria
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
- Division of Pulmonary Medicine, Department of Medicine, Mulago Hospital and Complex, Kampala, Uganda
| | - Laurence Huang
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
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Zhang L, Lu F, Wang Y, Ji J, Xu Y, Huang Y, Zhang M, Li M, Xia J, Wang B. Methodological comparison of bronchoalveolar lavage fluid-based detection of respiratory pathogens in diagnosis of bacterium/fungus-associated pneumonia in critically ill patients. Front Public Health 2023; 11:1168812. [PMID: 37255757 PMCID: PMC10225631 DOI: 10.3389/fpubh.2023.1168812] [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: 02/18/2023] [Accepted: 04/12/2023] [Indexed: 06/01/2023] Open
Abstract
Background Bacterium/fungus-associated pneumonia (BAP/FAP) is the prominent cause of high mortality and morbidity with important clinical impacts globally. Effective diagnostic methods and proper specimen types hopefully facilitate early diagnosis of pneumonia and prevent spread of drug-resistant bacteria/fungi among critically ill patients. Methods In the present study, 342 bronchoalveolar lavage fluid (BALF) samples were collected from critically ill patients with pulmonary infections between November 2020 and March 2021. The BALF materials were comparatively employed to screen BAP/FAP through microscopy, culture, antigenic marker and PCR-based methods. The limit of detection (LOD) of cultures and PCR for bacteria/fungi was determined by serial dilution assays. Specimen slides were prepared with Gram staining for microscopic examinations. Microbial cultures and identifications underwent routine clinical protocols with the aid of mass spectrometry. (1,3)-β-D-glucan and galactomannan tests with BALF were carried out accordingly. Direct detection of pathogens in BALF was achieved through PCR, followed by sequencing and BLAST in GenBank database for pathogenic identification. The subjects' demographic and clinical characteristics were well evaluated. Results BAP/FAP was identified in approximately 47% of the subjects by the BALF-based PCR. The PCR-based diagnostic methods showed improved detection performance for fungi with good LOD, but performed similarly for bacteria, when compared to the cultures. There was poor agreement among traditional microscopy, culture and PCR assays for bacterial detections (kappa value, 0.184 to 0.277). For overall bacterial/fungal detections, the microscopy showed the lowest detecting rate, followed by the cultures, which displayed a slightly higher sensitivity than the microscopy did. The sensitivity of PCR was much higher than that of the other means of interest. However, the traditional cultures rather than antigenic marker-based approaches were moderately consistent with the PCR-based methods in fungal species identification, particularly for Candida and Aspergillus spp. Our findings further revealed that the age, length of hospital stay, invasive procedures and cerebral diseases were likely considered as main risk factors for BAP/FAP. Conclusion Screening for BALF in critically ill patients with suspected pneumonia pertaining high risk factors using combined PCR-based molecular detection strategies would hopefully contribute to early diagnosis of BAP/FAP and improved prognosis of the patients.
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Affiliation(s)
- Luwen Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Fanbo Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuerong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juanjuan Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Min Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Moyan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jinxing Xia
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Wood SJ, Kuzel TM, Shafikhani SH. Pseudomonas aeruginosa: Infections, Animal Modeling, and Therapeutics. Cells 2023; 12:199. [PMID: 36611992 PMCID: PMC9818774 DOI: 10.3390/cells12010199] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is an important Gram-negative opportunistic pathogen which causes many severe acute and chronic infections with high morbidity, and mortality rates as high as 40%. What makes P. aeruginosa a particularly challenging pathogen is its high intrinsic and acquired resistance to many of the available antibiotics. In this review, we review the important acute and chronic infections caused by this pathogen. We next discuss various animal models which have been developed to evaluate P. aeruginosa pathogenesis and assess therapeutics against this pathogen. Next, we review current treatments (antibiotics and vaccines) and provide an overview of their efficacies and their limitations. Finally, we highlight exciting literature on novel antibiotic-free strategies to control P. aeruginosa infections.
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Affiliation(s)
- Stephen J. Wood
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Timothy M. Kuzel
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Cancer Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sasha H. Shafikhani
- Department of Medicine, Division of Hematology, Oncology, & Cell Therapy, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
- Cancer Center, Rush University Medical Center, Chicago, IL 60612, USA
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10
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Xia X, Chen J, Cheng Y, Chen F, Lu H, Liu J, Wang L, Pu F, Wang Y, Liu H, Cao D, Zhang Z, Xia Z, Fan M, Ling Z, Zhao L. Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study. Front Cell Infect Microbiol 2022; 12:1024867. [PMID: 36389135 PMCID: PMC9663837 DOI: 10.3389/fcimb.2022.1024867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022] Open
Abstract
Recent evidence suggests that lung microbiota can be recognized as one of the ecological determinants of various respiratory diseases. However, alterations in the lung microbiota and associated lung immunity in these respiratory diseases remain unclear. To compare the lung microbiota and lung immune profiles in common respiratory diseases, a total of 78 patients were enrolled in the present study, including 21 patients with primary pulmonary tuberculosis (PTB), eight patients with newly diagnosed lung cancer (LC), and 49 patients with community-acquired pneumonia (CAP). Bronchoalveolar lavage fluid (BALF) was collected for microbiota and cytokine analyses. With MiSeq sequencing system, increased bacterial alpha-diversity and richness were observed in patients with LC than in those with PTB and CAP. Linear discriminant analysis effect size revealed that CAP-associated pulmonary microbiota were significantly different between the PTB and LC groups. More key functionally different genera were found in the PTB and LC groups than in the CAP group. The interaction network revealed stronger positive and negative correlations among these genera in the LC group than in the other two groups. However, increased BALF cytokine profiles were observed in the PTB group than in the other two groups, while BALF cytokines were correlated with key functional bacteria. This comparative study provides evidence for the associations among altered lung microbiota, BALF inflammation, and different respiratory disorders, which provides insight into the possible roles and mechanisms of pulmonary microbiota in the progression of respiratory disorders.
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Affiliation(s)
- Xiaoxue Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Jiang Chen
- Department of Neurosurgery, Changxing People’s Hospital, Huzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Feng Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huoquan Lu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Jianfeng Liu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Ling Wang
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Fengxia Pu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Ying Wang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Hua Liu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Daxing Cao
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zhengye Zhang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zeping Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Meili Fan
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
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11
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Abstract
Until recently, bacteria have been studied in terms of their roles in infectious diseases and mainly by using isolation and culture methods. However, in practice, many bacteria existing on the earth are difficult to isolate and culture, and thus only a limited number of them have been studied to date. On the other hand, in 2005, the next-generation sequencing technology became generally available, and since then genomic analysis of bacterial flora has become widespread. As a result, it has been revealed that the lower respiratory tract, which was previously thought to be sterile, in fact has bacterial flora (a microbiome) with a high level of biodiversity. In addition, it has been found that various diseases develop and worsen depending on the balance of the bacterial flora, and in recent years, a relationship has been established between various disorders. Recent research on cancer-associated microbial communities has elucidated the reciprocal interactions among bacteria, tumors and immune cells, the bacterial pathways associated with induction of oncogenesis, and their translational significance. Nevertheless, despite the increasing evidence showing that dysbiosis is associated with lung oncogenesis, the detailed mechanisms remain to be fully elucidated. Microorganisms seem to trigger tumor initiation and progression, presumably through the production of bacterio-toxins and other pro-inflammatory factors. The purpose of this review is to present a context for the basic mechanisms and molecular functions of the airway microbiome in oncogenesis, in an effort to prevent cancer by strategies utilizing the airway microbiota, as well as summarizing the mechanisms wherein the microbiome acts as a modulator of immunotherapies in lung cancer.
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12
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The lung microbiome in HIV-positive patients with active pulmonary tuberculosis. Sci Rep 2022; 12:8975. [PMID: 35643931 PMCID: PMC9148312 DOI: 10.1038/s41598-022-12970-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.
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13
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Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. THE LANCET. MICROBE 2022; 3:e357-e365. [PMID: 35544096 DOI: 10.1016/s2666-5247(21)00357-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda. METHODS We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population. FINDINGS We consecutively enrolled 217 patients during the study period. A potential microbial cause for pneumonia was identified in 211 (97%) patients. At least one microorganism of established respiratory pathogenicity was identified in 113 (52%) patients, and a microbe of possible pathogenicity was identified in an additional 98 (45%). M tuberculosis was the most commonly identified established pathogen (35 [16%] patients; in whom bacterial or viral co-infections were identified in 13 [37%]). Streptococcus mitis, although not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (37 [17%] patients). Haemophilus influenzae was the most commonly identified established bacterial pathogen (20 [9%] patients). Pneumocystis jirovecii was only identified in patients with a CD4 count of less than 200 cells per mL. INTERPRETATION We show the feasibility of using metatranscriptomics for epidemiologic surveillance of pneumonia by describing the spectrum of respiratory pathogens in adults with HIV in Uganda. Applying these methods to a contemporary cohort could enable broad assessment of changes in pneumonia aetiology following the emergence of SARS-CoV-2. FUNDING US National Institutes of Health, Chan Zuckerberg Biohub.
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Affiliation(s)
- Natasha Spottiswoode
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Bloomstein
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abdul Sessolo
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Kathryn McCauley
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick Byanyima
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | | | | | - Sylvia Kaswabuli
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Rachel L Rutishauser
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica K Lieng
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Julia Moore
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Jan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shoko Iwai
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Meera Shenoy
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Ingvar Sanyu
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Joseph L DeRisi
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - William Worodria
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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14
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Shen J, Hu Y, Lv J, Zhao H, Wang B, Yang S, Du A, Liu S, An Y. Lung Microbiota Signature and Corticosteroid Responses in Pneumonia-Associated Acute Respiratory Distress Syndrome in Hematological Patients. J Inflamm Res 2022; 15:1317-1329. [PMID: 35237062 PMCID: PMC8884712 DOI: 10.2147/jir.s353662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jiawei Shen
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Yan Hu
- Department of Respiratory and Critical Care Medicine, Peking University International Hospital, Beijing, People’s Republic of China
| | - Jie Lv
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Huiying Zhao
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Bin Wang
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Shuguang Yang
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Anqi Du
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Shuang Liu
- Department of Respiratory and Critical Care Medicine, Peking University International Hospital, Beijing, People’s Republic of China
| | - Youzhong An
- Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China
- Correspondence: Youzhong An, Department of Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China, Email
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15
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Yano C, Tominaga M, Naito Y, Tokunaga Y, Kinoshita T, Sasaki J, Okamoto M, Yaita K, Obara H, Kakuma T, Hoshino T, Kawayama T. Airway hyperresponsiveness and inflammation in Japanese patients with human immunodeficiency virus 1 infection. J Infect Chemother 2021; 28:426-433. [PMID: 34933786 DOI: 10.1016/j.jiac.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Despite the growing population of long-term survivors with human immunodeficiency virus 1 (HIV) exhibiting asthma-like features worldwide, the pathogenesis underlying airway hyperresponsiveness (AHR) and airway inflammation remains unclear. We aimed to investigate AHR and airway inflammation in an HIV-infected Japanese population. METHODS Of 94 Japanese participants, 10 HIV-infected participants with asthma were excluded from the study. We compared the characteristics of HIV-infected (n = 34) and non-HIV-infected participants (n = 50). Eosinophilic, neutrophilic, mixed (eosinophilic and neutrophilic), and paucigranulocytic airway inflammatory phenotypes were classified based on induced sputum characteristics. RESULTS The prevalence of AHR in HIV-infected participants (32.4%) was significantly higher than that in their non-HIV-infected counterparts (10.0%) (P = 0.0213). The multivariate nominal logistic regression analysis revealed HIV as an independent risk factor for AHR. HIV-infected participants were significantly more likely to have a neutrophilic airway inflammatory phenotype than non-HIV-infected participants (P = 0.0358). Furthermore, HIV-infected participants with AHR demonstrated a significant correlation between AHR levels and the percentage of sputum neutrophils (r = -0.65, P = 0.0316). The percentage of sputum neutrophils was negatively associated with the blood CD4 cell count (r = -0.66, P = 0.0266). CONCLUSIONS We observed the high prevalence of AHR and neutrophilic airway inflammatory phenotype in Japanese participants with stable HIV infection. Our findings provide insight into the mechanisms of AHR and may facilitate the development of novel treatment for individuals with AHR and HIV infection.
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Affiliation(s)
- Chiyo Yano
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Masaki Tominaga
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Yoshiko Naito
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Yoshihisa Tokunaga
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Takashi Kinoshita
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Jun Sasaki
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Masaki Okamoto
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Kenichiro Yaita
- Department of Infection Control and Prevention, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Hitoshi Obara
- Biostatisctics Center, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Tatsuyuki Kakuma
- Biostatisctics Center, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Tomoaki Hoshino
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
| | - Tomotaka Kawayama
- Division of Respirology, Neurology and Rheumatology, Department of Medicine, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan.
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16
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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17
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The role of microbiota in respiratory health and diseases, particularly in tuberculosis. Biomed Pharmacother 2021; 143:112108. [PMID: 34560539 DOI: 10.1016/j.biopha.2021.112108] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.
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18
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Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, Segal LN. Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. Eur Respir J 2021; 58:13993003.03434-2020. [PMID: 33446604 DOI: 10.1183/13993003.03434-2020] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary. METHODS Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed. RESULTS Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing. CONCLUSIONS Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jun-Chieh Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya Sauthoff
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Kun Ji
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Dept of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael Weiden
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Drew Jones
- Dept of Biochemistry and Molecular Pharmacology and Dept of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen A Stringer
- Dept of Clinical Pharmacy, College of Pharmacy, and Division of Pulmonary and Critical Care Medicine, Dept of Medicine, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lingdi Zhang
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Stephanie Banakis
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Laura Tipton
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA.,Dept of Epidemiology, School of Global Public Health, New York University, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
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19
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Gu X, Hua YH, Zhang YD, Bao DI, Lv J, Hu HF. The Pathogenesis of Aspergillus fumigatus, Host Defense Mechanisms, and the Development of AFMP4 Antigen as a Vaccine. Pol J Microbiol 2021; 70:3-11. [PMID: 33815522 PMCID: PMC8008755 DOI: 10.33073/pjm-2021-003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Aspergillus fumigatus is one of the ubiquitous fungi with airborne conidia, which accounts for most aspergillosis cases. In immunocompetent hosts, the inhaled conidia are rapidly eliminated. However, immunocompromised or immunodeficient hosts are particularly vulnerable to most Aspergillus infections and invasive aspergillosis (IA), with mortality from 50% to 95%. Despite the improvement of antifungal drugs over the last few decades, the therapeutic effect for IA patients is still limited and does not provide significant survival benefits. The drawbacks of antifungal drugs such as side effects, antifungal drug resistance, and the high cost of antifungal drugs highlight the importance of finding novel therapeutic and preventive approaches to fight against IA. In this article, we systemically addressed the pathogenic mechanisms, defense mechanisms against A. fumigatus, the immune response, molecular aspects of host evasion, and vaccines' current development against aspergillosis, particularly those based on AFMP4 protein, which might be a promising antigen for the development of anti-A. fumigatus vaccines.
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Affiliation(s)
- Xiang Gu
- College of Law and Political Science, Nanjing University of Information Science and Technology, Nanjing, China.,The University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yan-Hong Hua
- The University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yang-Dong Zhang
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - D I Bao
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Jin Lv
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Hong-Fang Hu
- The PLA Rocket Force Characteristic Medical Center, Beijing, China
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20
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Chen J, Xi Z, Shi Y, Liu L, Wang L, Qian L, Lu A. Highly homogeneous microbial communities dominated by Mycoplasma pneumoniae instead of increased resistance to macrolide antibiotics is the characteristic of lower respiratory tract microbiome of children with refractory Mycoplasma pneumoniae pneumonia. Transl Pediatr 2021; 10:604-615. [PMID: 33850819 PMCID: PMC8039789 DOI: 10.21037/tp-20-404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Although researchers have found that the microbiota changed during the lower respiratory tract (LRT) infection, little was known about the association between LRT microbiome and refractory M. pneumoniae pneumonia (RMPP). METHODS From June 28th, 2019 to March 23rd, 2020, we enrolled fifty-two children diagnosed with RMPP or non-refractory M. pneumoniae pneumonia (NRMPP), and characterized the structure and function of microbiota in the bronchoalveolar lavage fluid (BALF) by metagenomic next generation sequencing (mNGS). RESULTS Based on Bray-Curtis distance between samples, samples in RMPP group were highly homogeneous, and Shannon index in the RMPP group was much lower than NRMPP group while Simpson index, which presents the degree of dominance, was higher in RMPP group. The dominant taxon with relative abundance greater than 50% was merely Mycoplasma among RMPP and NRMPP patients, but the proportions of other taxonomic distribution were different. M. pneumoniae was the dominant species and occupied almost all niches in the vast majority of RMPP patients, whereas the other genera were dramatically lower. The NRMPP group was more enriched in antibiotic resistance genes (ARGs) than the RMPP group, and also exhibited a greater relative abundance of macrolide antibiotics resistance gene (macB) and fluoroquinolone antibiotic resistance genes (patA-B) in M. pneumoniae genome. In RMPP patients, higher relative abundance of Streptococcus pneumoniae had a strong correlation with increased hospitalization days while higher relative abundance of Streptococcus pneumoniae had a negative correlation with hospitalization days among NRMPP patients. CONCLUSIONS The microbiota of LRT in children with RMPP was much more homogeneous and simpler than that of the NRMPP group and with lower relative abundance of macrolide antibiotics resistance gene in M. pneumoniae genome. M. pneumoniae was absolutely dominant in the vast majority of RMPP patients. Prolonged hospitalization days was associated with relative abundance of M. pneumoniae in NRMPP patients while it was related with other pathogens' relative abundance (e.g., Streptococcus pneumoniae) in RMPP patients.
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Affiliation(s)
- Jinglong Chen
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Zhimin Xi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Shi
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Liu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Aizhen Lu
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
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21
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Cyprian F, Sohail MU, Abdelhafez I, Salman S, Attique Z, Kamareddine L, Al-Asmakh M. SARS-CoV-2 and immune-microbiome interactions: Lessons from respiratory viral infections. Int J Infect Dis 2021; 105:540-550. [PMID: 33610778 PMCID: PMC7891052 DOI: 10.1016/j.ijid.2021.02.071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
By the beginning of 2020, infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had rapidly evolved into an emergent worldwide pandemic, an outbreak whose unprecedented consequences highlighted many existing flaws within public healthcare systems across the world. While coronavirus disease 2019 (COVID-19) is bestowed with a broad spectrum of clinical manifestations, involving the vital organs, the respiratory system transpires as the main route of entry for SARS-CoV-2, with the lungs being its primary target. Of those infected, up to 20% require hospitalization on account of severity, while the majority of patients are either asymptomatic or exhibit mild symptoms. Exacerbation in the disease severity and complications of COVID-19 infection have been associated with multiple comorbidities, including hypertension, diabetes mellitus, cardiovascular disorders, cancer, and chronic lung disease. Interestingly, a recent body of evidence indicated the pulmonary and gut microbiomes as potential modulators for altering the course of COVID-19, potentially via the microbiome-immune system axis. While the relative concordance between microbes and immunity has yet to be fully elucidated with regards to COVID-19, we present an overview of our current understanding of COVID-19-microbiome-immune cross talk and discuss the potential contributions of microbiome-related immunity to SARS-CoV-2 pathogenesis and COVID-19 disease progression.
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Affiliation(s)
- Farhan Cyprian
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Muhammad Umar Sohail
- Proteomics Core, Weill Cornell Medicine, Qatar Foundation-Education City, PO Box 24144, Doha, Qatar
| | | | - Salma Salman
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Zakria Attique
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Layla Kamareddine
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Maha Al-Asmakh
- Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar; Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Centre, Qatar University, Doha, Qatar.
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22
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Hu Y, Cheng M, Liu B, Dong J, Sun L, Yang J, Yang F, Chen X, Jin Q. Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study. Emerg Microbes Infect 2021; 9:1444-1452. [PMID: 32552447 PMCID: PMC7473061 DOI: 10.1080/22221751.2020.1783188] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB- group. There was a significant difference in beta diversity between the MTB+ and MTB- subjects. MTB+ lung samples were dominated by MTB, while MTB- samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB- communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB- subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.
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Affiliation(s)
- Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing, People's Republic of China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
| | - Xinchun Chen
- Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, People's Republic of China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, P. R. People's Republic of China
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23
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Affiliation(s)
- Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Windy Tanner
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anthony D Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore Maryland, USA
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24
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Xiang Z, Koo H, Chen Q, Zhou X, Liu Y, Simon-Soro A. Potential implications of SARS-CoV-2 oral infection in the host microbiota. J Oral Microbiol 2020; 13:1853451. [PMID: 33312449 PMCID: PMC7711743 DOI: 10.1080/20002297.2020.1853451] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The oral cavity, as the entry point to the body, may play a critical role in the pathogenesis of SARS-CoV-2 infection that has caused a global outbreak of the coronavirus disease 2019 (COVID-19). Available data indicate that the oral cavity may be an active site of infection and an important reservoir of SARS-CoV-2. Considering that the oral surfaces are colonized by a diverse microbial community, it is likely that viruses have interactions with the host microbiota. Patients infected by SARS-CoV-2 may have alterations in the oral and gut microbiota, while oral species have been found in the lung of COVID-19 patients. Furthermore, interactions between the oral, lung, and gut microbiomes appear to occur dynamically whereby a dysbiotic oral microbial community could influence respiratory and gastrointestinal diseases. However, it is unclear whether SARS-CoV-2 infection can alter the local homeostasis of the resident microbiota, actively cause dysbiosis, or influence cross-body sites interactions. Here, we provide a conceptual framework on the potential impact of SARS-CoV-2 oral infection on the local and distant microbiomes across the respiratory and gastrointestinal tracts ('oral-tract axes'), which remains largely unexplored. Studies in this area could further elucidate the pathogenic mechanism of SARS-CoV-2 and the course of infection as well as the clinical symptoms of COVID-19 across different sites in the human host.
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Affiliation(s)
- Zhenting Xiang
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics, Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,State Key Laboratory of Oral Disease & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hyun Koo
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics, Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Qianming Chen
- Stomatology Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xuedong Zhou
- State Key Laboratory of Oral Disease & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Liu
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics, Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aurea Simon-Soro
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics, Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Stomatology, School of Dentistry, University of Seville, Seville, Spain
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25
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Levy E, Delvin E, Marcil V, Spahis S. Can phytotherapy with polyphenols serve as a powerful approach for the prevention and therapy tool of novel coronavirus disease 2019 (COVID-19)? Am J Physiol Endocrinol Metab 2020; 319:E689-E708. [PMID: 32755302 PMCID: PMC7518070 DOI: 10.1152/ajpendo.00298.2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 02/08/2023]
Abstract
Much more serious than the previous severe acute respiratory syndrome (SARS) coronavirus (CoV) outbreaks, the novel SARS-CoV-2 infection has spread speedily, affecting 213 countries and causing ∼17,300,000 cases and ∼672,000 (∼+1,500/day) deaths globally (as of July 31, 2020). The potentially fatal coronavirus disease (COVID-19), caused by air droplets and airborne as the main transmission modes, clearly induces a spectrum of respiratory clinical manifestations, but it also affects the immune, gastrointestinal, hematological, nervous, and renal systems. The dramatic scale of disorders and complications arises from the inadequacy of current treatments and absence of a vaccine and specific anti-COVID-19 drugs to suppress viral replication, inflammation, and additional pathogenic conditions. This highlights the importance of understanding the SARS-CoV-2 mechanisms of actions and the urgent need of prospecting for new or alternative treatment options. The main objective of the present review is to discuss the challenging issue relative to the clinical utility of plants-derived polyphenols in fighting viral infections. Not only is the strong capacity of polyphenols highlighted in magnifying health benefits, but the underlying mechanisms are also stressed. Finally, emphasis is placed on the potential ability of polyphenols to combat SARS-CoV-2 infection via the regulation of its molecular targets of human cellular binding and replication, as well as through the resulting host inflammation, oxidative stress, and signaling pathways.
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Affiliation(s)
- Emile Levy
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Edgard Delvin
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Valérie Marcil
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Schohraya Spahis
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
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26
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Bhadriraju S, Fadrosh DW, Shenoy MK, Lin DL, Lynch KV, McCauley K, Ferrand RA, Majonga ED, McHugh G, Huang L, Lynch SV, Metcalfe JZ. Distinct lung microbiota associate with HIV-associated chronic lung disease in children. Sci Rep 2020; 10:16186. [PMID: 32999331 PMCID: PMC7527458 DOI: 10.1038/s41598-020-73085-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
Chronic lung disease (CLD) is a common co-morbidity for HIV-positive children and adolescents on antiretroviral therapy (ART) in sub-Saharan Africa. In this population, distinct airway microbiota may differentially confer risk of CLD. In a cross-sectional study of 202 HIV-infected children aged 6-16 years in Harare, Zimbabwe, we determined the association of sputum microbiota composition (using 16S ribosomal RNA V4 gene region sequencing) with CLD defined using clinical, spirometric, or radiographic criteria. Forty-two percent of children were determined to have CLD according to our definition. Dirichlet multinomial mixtures identified four compositionally distinct sputum microbiota structures. Patients whose sputum microbiota was dominated by Haemophilus, Moraxella or Neisseria (HMN) were at 1.5 times higher risk of CLD than those with Streptococcus or Prevotella (SP)-dominated microbiota (RR = 1.48, p = 0.035). Cell-free products of HMN sputum microbiota induced features of epithelial disruption and inflammatory gene expression in vitro, indicating enhanced pathogenic potential of these CLD-associated microbiota. Thus, HIV-positive children harbor distinct sputum microbiota, with those dominated by Haemophilus, Moraxella or Neisseria associated with enhanced pathogenesis in vitro and clinical CLD.
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Affiliation(s)
- Sudha Bhadriraju
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and Trauma Center, University of California San Francisco, 1001 Potrero Avenue, Rm 5K1, San Francisco, CA, 94110-0111, USA
| | - Douglas W Fadrosh
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Meera K Shenoy
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Din L Lin
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Kole V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Kathryn McCauley
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - Rashida A Ferrand
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Edith D Majonga
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Grace McHugh
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and Trauma Center, University of California San Francisco, 1001 Potrero Avenue, Rm 5K1, San Francisco, CA, 94110-0111, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, USA
| | - John Z Metcalfe
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and Trauma Center, University of California San Francisco, 1001 Potrero Avenue, Rm 5K1, San Francisco, CA, 94110-0111, USA.
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27
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Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast. Sci Rep 2020; 10:12645. [PMID: 32724137 PMCID: PMC7387350 DOI: 10.1038/s41598-020-69602-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.
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28
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Lira-Lucio JA, Falfán-Valencia R, Ramírez-Venegas A, Buendía-Roldán I, Rojas-Serrano J, Mejía M, Pérez-Rubio G. Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases. Microorganisms 2020; 8:E1059. [PMID: 32708647 PMCID: PMC7409050 DOI: 10.3390/microorganisms8071059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The lung microbiome composition has critical implications in the regulation of innate and adaptive immune responses. Next-generation sequencing techniques have revolutionized the understanding of pulmonary physiology and pathology. Currently, it is clear that the lung is not a sterile place; therefore, the investigation of the participation of the pulmonary microbiome in the presentation, severity, and prognosis of multiple pathologies, such as asthma, chronic obstructive pulmonary disease, and interstitial lung diseases, contributes to a better understanding of the pathophysiology. Dysregulation of microbiota components in the microbiome-host interaction is associated with multiple lung pathologies, severity, and prognosis, making microbiome study a useful tool for the identification of potential therapeutic strategies. This review integrates the findings regarding the activation and regulation of the innate and adaptive immune response pathways according to the microbiome, including microbial patterns that could be characteristic of certain diseases. Further studies are required to verify whether the microbial profile and its metabolites can be used as biomarkers of disease progression or poor prognosis and to identify new therapeutic targets that restore lung dysbiosis safely and effectively.
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Affiliation(s)
- Juan Alberto Lira-Lucio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
| | - Alejandra Ramírez-Venegas
- Tobacco Smoking and COPD Research Department, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Jorge Rojas-Serrano
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Mayra Mejía
- Interstitial Lung Disease and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-S.); (M.M.)
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.L.-L.); (R.F.-V.)
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29
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Sommariva M, Le Noci V, Bianchi F, Camelliti S, Balsari A, Tagliabue E, Sfondrini L. The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy. Cell Mol Life Sci 2020; 77:2739-2749. [PMID: 31974656 PMCID: PMC7326824 DOI: 10.1007/s00018-020-03452-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/29/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022]
Abstract
Like other body districts, lungs present a complex bacteria community. An emerging function of lung microbiota is to promote and maintain a state of immune tolerance, to prevent uncontrolled and not desirable inflammatory response caused by inhalation of harmless environmental stimuli. This effect is mediated by a continuous dialog between commensal bacteria and immune cells resident in lungs, which express a repertoire of sensors able to detect microorganisms. The same receptors are also involved in the recognition of pathogens and in mounting a proper immune response. Due to its important role in preserving lung homeostasis, the lung microbiota can be also considered a mirror of lung health status. Indeed, several studies indicate that lung bacterial composition drastically changes during the occurrence of pulmonary pathologies, such as lung cancer, and the available data suggest that the modifications of lung microbiota can be part of the etiology of tumors in lungs and can influence their progression and response to therapy. These results provide the scientific rationale to analyze lung microbiota composition as biomarker for lung cancer and to consider lung microbiota a new potential target for therapeutic intervention to reprogram the antitumor immune microenvironment. In the present review, we discussed about the role of lung microbiota in lung physiology and summarized the most relevant data about the relationship between lung microbiota and cancer.
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Affiliation(s)
- Michele Sommariva
- Dipartimento Di Scienze Biomediche Per La Salute, Università Degli Studi Di Milano, via Mangiagalli 31, 20133, Milano, Italy
| | - Valentino Le Noci
- Dipartimento Di Scienze Biomediche Per La Salute, Università Degli Studi Di Milano, via Mangiagalli 31, 20133, Milano, Italy
| | - Francesca Bianchi
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS, Istituto Nazionale Dei Tumori, via Amadeo 42, 20133, Milano, Italy
| | - Simone Camelliti
- Dipartimento Di Scienze Biomediche Per La Salute, Università Degli Studi Di Milano, via Mangiagalli 31, 20133, Milano, Italy
| | - Andrea Balsari
- Dipartimento Di Scienze Biomediche Per La Salute, Università Degli Studi Di Milano, via Mangiagalli 31, 20133, Milano, Italy
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS, Istituto Nazionale Dei Tumori, via Amadeo 42, 20133, Milano, Italy
| | - Elda Tagliabue
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS, Istituto Nazionale Dei Tumori, via Amadeo 42, 20133, Milano, Italy
| | - Lucia Sfondrini
- Dipartimento Di Scienze Biomediche Per La Salute, Università Degli Studi Di Milano, via Mangiagalli 31, 20133, Milano, Italy.
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30
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Vendl C, Ferrari BC, Thomas T, Slavich E, Zhang E, Nelson T, Rogers T. Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales. FEMS Microbiol Ecol 2020; 95:5526219. [PMID: 31260051 DOI: 10.1093/femsec/fiz102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023] Open
Abstract
Cetacean represent vulnerable species impacted by multiple stressors, including reduction in prey species, habitat destruction, whaling and infectious disease. The composition of blow microbiota has been claimed to provide a promising tool for non-invasive health monitoring aiming to inform conservation management. Still, little is known about the temporal stability and composition of blow microbiota in whales. We used East Australian humpback whales (Megaptera novaeangliae) as a model species and collected blow and control samples in August 2016 and 2017 for an interannual comparison. We analysed the blow by barcode tag sequencing of the bacterial 16S rRNA gene. We found that the microbial communities in 2016 and 2017 were statistically similar regarding alpha and beta diversity but distinct to seawater. Zero-radius operational taxonomic units (zOTUs) shared by both groups accounted for about 50% of all zOTUs present. Still, the large individual variability in the blow microbiota resulted in a small number of core taxa (defined as present in at least 60% of whales). We conclude that the blow microbiota of humpback whales is either generally limited and of transient nature or the reduced airway microbiota is the symptom of a compromised physiological state potentially due to the challenges of the whales' annual migration.
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Affiliation(s)
- C Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
| | - B C Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW 2052, Australia
| | - T Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
| | - E Slavich
- Stats Central, Mark Wainwright Analytical Centre, UNSW, Sydney, NSW 2052, Australia
| | - E Zhang
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW 2052, Australia
| | - T Nelson
- Queensland Facility for Advanced Bioinformatics, Griffith University, Gold Coast, Southport, QLD 4215, Australia
| | - T Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
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Le Noci V, Guglielmetti S, Arioli S, Camisaschi C, Bianchi F, Sommariva M, Storti C, Triulzi T, Castelli C, Balsari A, Tagliabue E, Sfondrini L. Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. Cell Rep 2019; 24:3528-3538. [PMID: 30257213 DOI: 10.1016/j.celrep.2018.08.090] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/04/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022] Open
Abstract
Pulmonary immunological tolerance to inhaled particulates might create a permissive milieu for lung metastasis. Lung microbiota contribute to pulmonary tolerance; here, we explored whether its manipulation via antibiotic or probiotic aerosolization favors immune response against melanoma metastasis. In lungs of vancomycin/neomycin-aerosolized mice, a decrease in bacterial load was associated with reduced regulatory T cells and enhanced T cell and NK cell activation that paralleled a significant reduction of melanoma B16 lung metastases. Reduction of metastases also occurred in lungs transplanted with bacterial isolates from antibiotic-treated lungs. Aerosolized Lactobacillus rhamnosus strongly promoted immunity against B16 lung metastases as well. Furthermore, probiotics or antibiotics improved chemotherapy activity against advanced B16 metastases. Thus, we identify a role for lung microbiota in metastasis and show that its targeting via aerosolization is a therapy that can prevent metastases and enhance responses to chemotherapy.
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Affiliation(s)
- Valentino Le Noci
- Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Simone Guglielmetti
- Dipartimento di Scienze degli Alimenti, Nutrizione e Ambiente (DeFENS), Università degli Studi di Milano, Milan 20133, Italy
| | - Stefania Arioli
- Dipartimento di Scienze degli Alimenti, Nutrizione e Ambiente (DeFENS), Università degli Studi di Milano, Milan 20133, Italy
| | - Chiara Camisaschi
- Immunotherapy Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Francesca Bianchi
- Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy; Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
| | - Michele Sommariva
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
| | - Chiara Storti
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
| | - Tiziana Triulzi
- Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Chiara Castelli
- Immunotherapy Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Andrea Balsari
- Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy; Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy.
| | - Elda Tagliabue
- Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan 20133, Italy
| | - Lucia Sfondrini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan 20133, Italy
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Cribbs SK, Crothers K, Morris A. Pathogenesis of HIV-Related Lung Disease: Immunity, Infection, and Inflammation. Physiol Rev 2019; 100:603-632. [PMID: 31600121 DOI: 10.1152/physrev.00039.2018] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite anti-retroviral therapy (ART), human immunodeficiency virus-1 (HIV)-related pulmonary disease continues to be a major cause of morbidity and mortality for people living with HIV (PLWH). The spectrum of lung diseases has changed from acute opportunistic infections resulting in death to chronic lung diseases for those with access to ART. Chronic immune activation and suppression can result in impairment of innate immunity and progressive loss of T cell and B cell functionality with aberrant cytokine and chemokine responses systemically as well as in the lung. HIV can be detected in the lungs of PLWH and has profound effects on cellular immune functions. In addition, HIV-related lung injury and disease can occur secondary to a number of mechanisms including altered pulmonary and systemic inflammatory pathways, viral persistence in the lung, oxidative stress with additive effects of smoke exposure, microbial translocation, and alterations in the lung and gut microbiome. Although ART has had profound effects on systemic viral suppression in HIV, the impact of ART on lung immunology still needs to be fully elucidated. Understanding of the mechanisms by which HIV-related lung diseases continue to occur is critical to the development of new preventive and therapeutic strategies to improve lung health in PLWH.
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Affiliation(s)
- Sushma K Cribbs
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristina Crothers
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Alison Morris
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G. The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. THE LANCET. RESPIRATORY MEDICINE 2019; 7:892-906. [PMID: 30910543 DOI: 10.1016/s2213-2600(18)30501-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023]
Abstract
The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.
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Affiliation(s)
- Charissa C Naidoo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Georgina R Nyawo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gerhard Walzl
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Grant Theron
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients. Am J Respir Crit Care Med 2019; 197:621-631. [PMID: 29035085 DOI: 10.1164/rccm.201702-0441oc] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE Cigarette smoking is associated with increased risk of acute respiratory distress syndrome (ARDS) in patients after severe trauma; however, the mechanisms underlying this association are unknown. OBJECTIVES To determine whether cigarette smoking contributes to ARDS development after trauma by altering community composition of the lung microbiota. METHODS We studied the lung microbiota of mechanically ventilated patients admitted to the ICU after severe blunt trauma. To do so, we used 16S ribosomal RNA gene amplicon sequencing of endotracheal aspirate samples obtained on ICU admission (n = 74) and at 48 hours after admission (n = 30). Cigarette smoke exposure (quantified using plasma cotinine), ARDS development, and other clinical parameters were correlated with lung microbiota composition. MEASUREMENTS AND MAIN RESULTS Smoking status was significantly associated with lung bacterial community composition at ICU admission (P = 0.007 by permutational multivariate ANOVA [PERMANOVA]) and at 48 hours (P = 0.03 by PERMANOVA), as well as with significant enrichment of potential pathogens, including Streptococcus, Fusobacterium, Prevotella, Haemophilus, and Treponema. ARDS development was associated with lung community composition at 48 hours (P = 0.04 by PERMANOVA) and was characterized by relative enrichment of Enterobacteriaceae and of specific taxa enriched at baseline in smokers, including Prevotella and Fusobacterium. CONCLUSIONS After severe blunt trauma, a history of smoking is related to lung microbiota composition, both at the time of ICU admission and at 48 hours. ARDS development is also correlated with respiratory microbial community structure at 48 hours and with taxa that are relatively enriched in smokers at ICU admission. The data derived from this pilot study suggest that smoking-related changes in the lung microbiota could be related to ARDS development after severe trauma.
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Affiliation(s)
| | - Susan V Lynch
- 1 Division of Gastroenterology, Department of Medicine
| | - Chaz Langelier
- 2 Division of Infectious Diseases, Department of Medicine
| | - Jason D Christie
- 3 Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Mary Nelson
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Christopher K Cheung
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Neal L Benowitz
- 6 Division of Clinical Pharmacology, Department of Medicine.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Mitchell J Cohen
- 7 Department of Surgery, Denver Health Medical Center, Denver, Colorado; and.,8 Department of Surgery, University of Colorado, Aurora, Colorado
| | - Carolyn S Calfee
- 9 Division of Pulmonary and Critical Care Medicine, Department of Medicine.,10 Department of Anesthesia.,11 Cardiovascular Research Institute, and.,12 Center for Tobacco Control Research and Education, University of California, San Francisco, San Francisco, California
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35
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Abstract
The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.
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Affiliation(s)
- Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA.
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36
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Rao M, Dodoo E, Zumla A, Maeurer M. Immunometabolism and Pulmonary Infections: Implications for Protective Immune Responses and Host-Directed Therapies. Front Microbiol 2019; 10:962. [PMID: 31134013 PMCID: PMC6514247 DOI: 10.3389/fmicb.2019.00962] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/16/2019] [Indexed: 12/12/2022] Open
Abstract
The biology and clinical efficacy of immune cells from patients with infectious diseases or cancer are associated with metabolic programming. Host immune- and stromal-cell genetic and epigenetic signatures in response to the invading pathogen shape disease pathophysiology and disease outcomes. Directly linked to the immunometabolic axis is the role of the host microbiome, which is also discussed here in the context of productive immune responses to lung infections. We also present host-directed therapies (HDT) as a clinically viable strategy to refocus dysregulated immunometabolism in patients with infectious diseases, which requires validation in early phase clinical trials as adjuncts to conventional antimicrobial therapy. These efforts are expected to be continuously supported by newly generated basic and translational research data to gain a better understanding of disease pathology while devising new molecularly defined platforms and therapeutic options to improve the treatment of patients with pulmonary infections, particularly in relation to multidrug-resistant pathogens.
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Affiliation(s)
- Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Ernest Dodoo
- Department of Oncology and Haematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London, NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal.,Department of Oncology and Haematology, Krankenhaus Nordwest, Frankfurt, Germany
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Martinsen EMH, Eagan TML, Leiten EO, Nordeide E, Bakke PS, Lehmann S, Nielsen R. Motivation and response rates in bronchoscopy studies. Multidiscip Respir Med 2019; 14:14. [PMID: 31069076 PMCID: PMC6495518 DOI: 10.1186/s40248-019-0178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background Bronchoscopy is frequently used to sample the lower airways in lung microbiome studies. Despite being a safe procedure, it is associated with discomfort that may result in reservations regarding participation in research bronchoscopy studies. Information on participation in research bronchoscopy studies is limited. We report response rates, reasons for non-response, motivation for participation, and predictors of participation in a large-scale single-centre bronchoscopy study (“MicroCOPD”). Methods Two hundred forty-nine participants underwent at least one bronchoscopy in addition to being examined by a physician, having lung function tested, and being offered a CT scan of the heart and lungs (subjects > 40 years). Each participant was asked an open question regarding motivation. Non-response reasons were gathered, and response rates were calculated. Results The study had a response rate just above 50%, and men had a significantly higher response rate than women (56.5% vs. 44.8%, p = 0.01). Procedural fear was the most common non-response reason. Most participants participated due to perceived personal benefit, but a large proportion did also participate to help others and contribute to science. Men were less likely to give exclusive altruistic motives, whereas subjects with asthma were more likely to report exclusive personal benefit as main motive. Conclusion Response rates of about 50% in bronchoscopy studies make large bronchoscopy studies feasible, but the fact that participants are motivated by their own health status places a large responsibility on the investigators regarding the accuracy of the provided study information. Electronic supplementary material The online version of this article (10.1186/s40248-019-0178-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Einar M H Martinsen
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
| | - Tomas M L Eagan
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway.,2Department of Thoracic Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Elise O Leiten
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
| | - Eli Nordeide
- 2Department of Thoracic Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Per S Bakke
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
| | - Sverre Lehmann
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway.,2Department of Thoracic Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Rune Nielsen
- 1Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway.,2Department of Thoracic Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
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38
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Shenoy MK, Fadrosh DW, Lin DL, Worodria W, Byanyima P, Musisi E, Kaswabuli S, Zawedde J, Sanyu I, Chang E, Fong S, McCauley K, Davis JL, Huang L, Lynch SV. Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction. MICROBIOME 2019; 7:37. [PMID: 30857553 PMCID: PMC6413461 DOI: 10.1186/s40168-019-0651-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/22/2019] [Indexed: 05/23/2023]
Abstract
Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local inflammatory response, gut microbiota has been shown to correlate with the degree of peripheral immune activation (IL6 and IP10 expression) in HIV-infected patients. We thus hypothesized that both airway and gut microbiota are perturbed in HIV-infected pneumonia patients, that the gut microbiota is related to peripheral CD4+ cell counts, and that its associated products differentially program immune cell populations necessary for controlling microbial infection in CD4-high and CD4-low patients. To assess these relationships, paired bronchoalveolar lavage and stool microbiota (bacterial and fungal) from a large cohort of Ugandan, HIV-infected patients with pneumonia were examined, and in vitro tests of the effect of gut microbiome products on macrophage effector phenotypes performed. While lower airway microbiota stratified into three compositionally distinct microbiota as previously described, these were not related to peripheral CD4 cell count. In contrast, variation in gut microbiota composition significantly related to CD4 cell count, lung microbiota composition, and patient mortality. Compared with patients with high CD4+ cell counts, those with low counts possessed more compositionally similar airway and gut microbiota, evidence of microbial translocation, and their associated gut microbiome products reduced macrophage activation and IL-10 expression and increased IL-1β expression in vitro. These findings suggest that the gut microbiome is related to CD4 status and plays a key role in modulating macrophage function, critical to microbial control in HIV-infected patients with pneumonia.
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Affiliation(s)
- Meera K Shenoy
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Biomedical Sciences Graduate Program, UCSF, San Francisco, CA, USA
- Current address: Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas W Fadrosh
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Din L Lin
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - William Worodria
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Patrick Byanyima
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Emmanuel Musisi
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Sylvia Kaswabuli
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Josephine Zawedde
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Emily Chang
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
| | - Serena Fong
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
| | - Kathryn McCauley
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - J Lucian Davis
- Department of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Laurence Huang
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA.
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA.
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Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis. mSphere 2019; 4:4/1/e00679-18. [PMID: 30728283 PMCID: PMC6365615 DOI: 10.1128/msphere.00679-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is a major human health problem that significantly reduces quality of life. While various microbes have been implicated, there is no clear understanding of the role they play in CRS pathogenesis. Another equally important observation made for CRS patients is that the epithelial barrier in the sinonasal cavity is defective. Finding a robust approach to subtype CRS patients would be the first step toward unravelling the pathogenesis of this heterogeneous condition. Previous work has explored stratification based on the clinical presentation of the disease (with or without polyps), inflammatory markers, pathology, or microbial composition. Comparisons between the different stratification approaches used in these studies have not been possible due to the different cohorts, analytical methods, or sample sites used. In this study, two approaches for subtyping CRS patients were compared, and the underlying drivers of the heterogeneity in CRS were also explored. Chronic rhinosinusitis (CRS) is a heterogeneous condition characterized by persistent sinus inflammation and microbial dysbiosis. This study aimed to identify clinically relevant subgroups of CRS patients based on distinct microbial signatures, with a comparison to the commonly used phenotypic subgrouping approach. The underlying drivers of these distinct microbial clusters were also investigated, together with associations with epithelial barrier integrity. Sinus biopsy specimens were collected from CRS patients (n = 23) and disease controls (n = 8). The expression of 42 tight junction genes was evaluated using quantitative PCR together with microbiota analysis and immunohistochemistry for measuring mucosal integrity and inflammation. CRS patients clustered into two distinct microbial subgroups using probabilistic modelling Dirichlet (DC) multinomial mixtures. DC1 exhibited significantly reduced bacterial diversity and increased dispersion and was dominated by Pseudomonas, Haemophilus, and Achromobacter. DC2 had significantly elevated B cells and incidences of nasal polyps and higher numbers of Anaerococcus, Megasphaera, Prevotella, Atopobium, and Propionibacterium. In addition, each DC exhibited distinct tight junction gene and protein expression profiles compared with those of controls. Stratifying CRS patients based on clinical phenotypic subtypes (absence or presence of nasal polyps [CRSsNP or CRSwNP, respectively] or with cystic fibrosis [CRSwCF]) accounted for a larger proportion of the variation in the microbial data set than with DC groupings. However, no significant differences between CRSsNP and CRSwNP cohorts were observed for inflammatory markers, beta-dispersion, and alpha-diversity measures. In conclusion, both approaches used for stratifying CRS patients had benefits and pitfalls, but DC clustering provided greater resolution when studying tight junction impairment. Future studies in CRS should give careful consideration to the patient subtyping approach used. IMPORTANCE Chronic rhinosinusitis (CRS) is a major human health problem that significantly reduces quality of life. While various microbes have been implicated, there is no clear understanding of the role they play in CRS pathogenesis. Another equally important observation made for CRS patients is that the epithelial barrier in the sinonasal cavity is defective. Finding a robust approach to subtype CRS patients would be the first step toward unravelling the pathogenesis of this heterogeneous condition. Previous work has explored stratification based on the clinical presentation of the disease (with or without polyps), inflammatory markers, pathology, or microbial composition. Comparisons between the different stratification approaches used in these studies have not been possible due to the different cohorts, analytical methods, or sample sites used. In this study, two approaches for subtyping CRS patients were compared, and the underlying drivers of the heterogeneity in CRS were also explored.
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Pulvirenti G, Parisi GF, Giallongo A, Papale M, Manti S, Savasta S, Licari A, Marseglia GL, Leonardi S. Lower Airway Microbiota. Front Pediatr 2019; 7:393. [PMID: 31612122 PMCID: PMC6776601 DOI: 10.3389/fped.2019.00393] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/12/2019] [Indexed: 12/14/2022] Open
Abstract
During the last several years, the interest in the role of microbiota in human health has grown significantly. For many years, the lung was considered a sterile environment, and only recently, with the use of more sophisticated techniques, has it been demonstrated that colonization by a complex population of microorganisms in lower airways also occurs in healthy subjects; a predominance of some species of Proteobacteria, Firmicutes, and Bacteroidetes phyla and with a peculiar composition in some disease conditions, such as asthma, have been noted. Lung microbiota derives mainly from the higher airways microbiota. Although we have some information about the role of gut microbiota in modulation of immune system, less it is known about the connection between lung microbiota and local and systemic immunity. There is a correlation between altered microbiota composition and some diseases or chronic states; however, despite this correlation, it has not been clearly demonstrated whether the lung microbiota dysbiosis could be a consequence or a cause of these diseases. We are far from a scientific approach to the therapeutic use of probiotics in airway diseases, but we are only at the starting point of a knowledge process in this fascinating field that could reveal important surprises, and randomized prospective studies in future could reveal more about the clinical possibilities for controlling lung microbiota. This review was aimed at updating the current knowledge in the field of airway microbiota.
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Affiliation(s)
- Giulio Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giuseppe Fabio Parisi
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alessandro Giallongo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Papale
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Sara Manti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Unit of Pediatric Emergency, Department of Human Pathology of the Adult and Developmental Age "Gaetano Barresi", University of Messina, Messina, Italy
| | - Salvatore Savasta
- Department of Pediatrics, Foundation IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Amelia Licari
- Department of Pediatrics, Foundation IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Pediatrics, Foundation IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Salvatore Leonardi
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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Libertucci J, Young VB. The role of the microbiota in infectious diseases. Nat Microbiol 2018; 4:35-45. [PMID: 30546094 DOI: 10.1038/s41564-018-0278-4] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
Abstract
The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.
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Affiliation(s)
- Josie Libertucci
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Sharpton SR, Yong GJM, Terrault NA, Lynch SV. Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease. Hepatol Commun 2018; 3:29-43. [PMID: 30619992 PMCID: PMC6312661 DOI: 10.1002/hep4.1284] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
The gut microbiome, the multispecies community of microbes that exists in the gastrointestinal tract, encodes several orders of magnitude more functional genes than the human genome. It also plays a pivotal role in human health, in part due to metabolism of environmental, dietary, and host‐derived substrates, which produce bioactive metabolites. Perturbations to the composition and associated metabolic output of the gut microbiome have been associated with a number of chronic liver diseases, including nonalcoholic fatty liver disease (NAFLD). Here, we review the rapidly evolving suite of next‐generation techniques used for studying gut microbiome composition, functional gene content, and bioactive products and discuss relationships with the pathogenesis of NAFLD.
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Affiliation(s)
- Suzanne R Sharpton
- Department of Medicine, Division of Gastroenterology University of California San Francisco San Francisco CA
| | - Germaine J M Yong
- Department of Medicine, Division of Gastroenterology University of California San Francisco San Francisco CA
| | - Norah A Terrault
- Department of Medicine, Division of Gastroenterology University of California San Francisco San Francisco CA
| | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology University of California San Francisco San Francisco CA
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Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status. mSystems 2018; 3:mSystems00199-18. [PMID: 30417108 PMCID: PMC6208642 DOI: 10.1128/msystems.00199-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 12/16/2022] Open
Abstract
Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases. Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease. Community structure analyses revealed three distinct microbial compositions, which were significantly correlated with bacterial biomass, human Th17 immune response, and COPD exacerbation frequency. Specifically, samples with transcriptionally active Streptococcus, Rothia, or Pseudomonas had bacterial loads 16 times higher than samples enriched for Escherichia and Ralstonia. These high-bacterial-load samples also tended to undergo a stronger Th17 immune response. Furthermore, an increased proportion of lymphocytes was found in samples with active Pseudomonas. In addition, COPD patients with active Streptococcus or Rothia infections tended to have lower rates of exacerbations than patients with active Pseudomonas and patients with lower bacterial biomass. Our results support the idea of a stratified structure of the active lung microbiome and a significant host-microbe interaction. We speculate that diverse lung microbiomes exist in the population and that their presence and activities could either influence or reflect different aspects of lung health. IMPORTANCE Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.
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Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur Respir J 2018; 52:13993003.00810-2018. [PMID: 30093571 DOI: 10.1183/13993003.00810-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+ cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+ samples, 27% of the lower airway samples were enriched with Mycobacterium A mycobacteriome approach identified Mycobacterium in a greater percentage of samples, including some nonpathogenic strains. In NTM+ lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Patrick Malecha
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin Scaglione
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jing Wang
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Ashwin Basavaraj
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samuel Chung
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Katrina Bantis
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Joseph Carpenito
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nan Shen
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamie Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gaetene Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Donington
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Charissa Naidoo
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Grant Theron
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Gail Schattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Suzette Garofano
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - David Kamelhar
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Doreen Addrizzo-Harris
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Dept of Medicine, New York University School of Medicine, New York, NY, USA
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Cillóniz C, García-Vidal C, Moreno A, Miro JM, Torres A. Community-acquired bacterial pneumonia in adult HIV-infected patients. Expert Rev Anti Infect Ther 2018; 16:579-588. [PMID: 29976111 DOI: 10.1080/14787210.2018.1495560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Despite active antiretroviral therapy (ART), community-acquired pneumonia (CAP) remains a major cause of morbidity and mortality among human immunodeficiency virus (HIV)-infected patients and incurs high health costs. Areas covered: This article reviews the most recent publications on bacterial CAP in the HIV-infected population, focusing on epidemiology, prognostic factors, microbial etiology, therapy, and prevention. The data discussed here were mainly obtained from a non-systematic review using Medline, and references from relevant articles. Expert commentary: HIV-infected patients are more susceptible to bacterial CAP. Although ART improves their immune response and has reduced CAP incidence, these patients continue to present increased risk of pneumonia in part because they show altered immunity and because immune activation persists. The risk of CAP in HIV-infected patients and the probability of polymicrobial or atypical infections are inversely associated with the CD4 cell count. Mortality in HIV-infected patients with CAP ranges from 6% to 15% but in well-controlled HIV-infected patients on ART the mortality is low and similar to that seen in HIV-negative individuals. Vaccination and smoking cessation are the two most important preventive strategies for bacterial CAP in well-controlled HIV-infected patients on ART.
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Affiliation(s)
- Catia Cillóniz
- a Department of Pulmonary Medicine Institut Clinic del Tórax, Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) , University of Barcelona (UB) - SGR 911- Ciber de Enfermedades Respiratorias (Ciberes) , Barcelona , Spain
| | - Carolina García-Vidal
- b Infectious Diseases Service, Hospital Clinic-IDIBAPS , University of Barcelona , Barcelona , Spain
| | - Asunción Moreno
- b Infectious Diseases Service, Hospital Clinic-IDIBAPS , University of Barcelona , Barcelona , Spain
| | - José M Miro
- b Infectious Diseases Service, Hospital Clinic-IDIBAPS , University of Barcelona , Barcelona , Spain
| | - Antoni Torres
- a Department of Pulmonary Medicine Institut Clinic del Tórax, Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) , University of Barcelona (UB) - SGR 911- Ciber de Enfermedades Respiratorias (Ciberes) , Barcelona , Spain
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Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent findings on the lung microbiome in HIV-infected patients and associated pulmonary diseases, and the relationship of airway microbial communities to metabolic and immune signatures within this patient population. RECENT FINDINGS The lung microbiome in HIV infection is a relatively new and rapidly developing field; early studies in the field produced inconclusive evidence as to whether HIV-infection changes the lower airway microbiome. More recent microbiome investigations have addressed these inconsistencies by incorporating systems biology approaches and laboratory models. Several investigations have now identified enrichment of Prevotella, Veillonella, and Streptococcus in the lower airways as consistent correlates of advanced HIV-infection and HIV-associated pulmonary diseases. These bacteria are associated with specific metabolic and immune profiles within the lung and circulation, providing the first indication that the lung microbiome may play a functional role in the pathogenesis of HIV-infection and HIV-associated pulmonary disease. SUMMARY This review summarizes knowledge to date on the lung microbiome in HIV infection, as well as challenges and accomplishments in the field within the last 2 years. Although the lung microbiome in HIV infection is still an emerging field, recent studies have formed a framework for future functional analysis of microbes in HIV pathogenesis.
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Sun X, Song L, Feng S, Li L, Yu H, Wang Q, Wang X, Hou Z, Li X, Li Y, Zhang Q, Li K, Cui C, Wu J, Qin Z, Wu Q, Chen H. Fatty Acid Metabolism is Associated With Disease Severity After H7N9 Infection. EBioMedicine 2018; 33:218-229. [PMID: 29941340 PMCID: PMC6085509 DOI: 10.1016/j.ebiom.2018.06.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human infections with the H7N9 virus could lead to lung damage and even multiple organ failure, which is closely associated with a high mortality rate. However, the metabolic basis of such systemic alterations remains unknown. METHODS This study included hospitalized patients (n = 4) with laboratory-confirmed H7N9 infection, healthy controls (n = 9), and two disease control groups comprising patients with pneumonia (n = 9) and patients with pneumonia who received steroid treatment (n = 10). One H7N9-infected patient underwent lung biopsy for histopathological analysis and expression analysis of genes associated with lung homeostasis. H7N9-induced systemic alterations were investigated using metabolomic analysis of sera collected from the four patients by using ultra-performance liquid chromatography-mass spectrometry. Chest digital radiography and laboratory tests were also conducted. FINDINGS Two of the four patients did not survive the clinical treatments with antiviral medication, steroids, and oxygen therapy. Biopsy revealed disrupted expression of genes associated with lung epithelial integrity. Histopathological analysis demonstrated severe lung inflammation after H7N9 infection. Metabolomic analysis indicated that fatty acid metabolism may be inhibited during H7N9 infection. Serum levels of palmitic acid, erucic acid, and phytal may negatively correlate with the extent of lung inflammation after H7N9 infection. The changes in fatty acid levels may not be due to steroid treatment or pneumonia. INTERPRETATION Altered structural and secretory properties of the lung epithelium may be associated with the severity of H7N9-infection-induced lung disease. Moreover, fatty acid metabolism level may predict a fatal outcome after H7N9 virus infection.
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Affiliation(s)
- Xin Sun
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Lijia Song
- Department of Respiratory Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Shuang Feng
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Li Li
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Hongzhi Yu
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Qiaoxing Wang
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Xing Wang
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Zhili Hou
- Department of Tuberculosis, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Xue Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Yu Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Qiuyang Zhang
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Kuan Li
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China
| | - Chao Cui
- Department of Thoracic Surgery, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Junping Wu
- Department of Respiratory Medicine, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Zhonghua Qin
- Department of Clinical Laboratory, Tianjin Haihe Hospital, Tianjin 300350, China
| | - Qi Wu
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China; Department of Respiratory Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China; Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China.
| | - Huaiyong Chen
- Department of Basic Medicine, Haihe Clinical College of Tianjin Medical University, Tianjin 300070, China; Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin 300350, China.
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Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV, Boushey HA. Bacterial biogeography of adult airways in atopic asthma. MICROBIOME 2018; 6:104. [PMID: 29885665 PMCID: PMC5994066 DOI: 10.1186/s40168-018-0487-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/25/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will require large longitudinal studies, for which bronchoscopy is poorly suited. Studies of samples obtained by sputum induction and nasopharyngeal brushing or lavage have also reported asthma-associated microbiota characteristics. It remains unknown, however, whether the microbiota detected in these less-invasive sample types reflect the composition of bronchial microbiota in asthma. RESULTS Bacterial microbiota in paired protected bronchial brushings (BB; n = 45), induced sputum (IS; n = 45), oral wash (OW; n = 45), and nasal brushings (NB; n = 27) from adults with mild atopic asthma (AA), atopy without asthma (ANA), and healthy controls (HC) were profiled using 16S rRNA gene sequencing. Though microbiota composition varied with sample type (p < 0.001), compositional similarity was greatest for BB-IS, particularly in AAs and ANAs. The abundance of genera detected in BB correlated with those detected in IS and OW (r median [IQR] 0.869 [0.748-0.942] and 0.822 [0.687-0.909] respectively), but not with those in NB (r = 0.004 [- 0.003-0.011]). The number of taxa shared between IS-BB and NB-BB was greater in AAs than in HCs (p < 0.05) and included taxa previously associated with asthma. Of the genera abundant in NB, only Moraxella correlated positively with abundance in BB; specific members of this genus were shared between the two compartments only in AAs. Relative abundance of Moraxella in NB of AAs correlated negatively with that of Corynebacterium but positively with markers of eosinophilic inflammation in the blood and BAL fluid. The genus, Corynebacterium, trended to dominate all NB samples of HCs but only half of AAs (p = 0.07), in whom abundance of this genus was negatively associated with markers of eosinophilic inflammation. CONCLUSIONS Induced sputum is superior to nasal brush or oral wash for assessing bronchial microbiota composition in asthmatic adults. Although compositionally similar to the bronchial microbiota, the microbiota in induced sputum are distinct, reflecting enrichment of oral bacteria. Specific bacterial genera are shared between the nasal and the bronchial mucosa which are associated with markers of systemic and bronchial inflammation.
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Affiliation(s)
- Juliana Durack
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Yvonne J Huang
- Department of Internal Medicine, Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Snehal Nariya
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura S Christian
- Department Microbiology/Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Department Microbiology/Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Avraham Beigelman
- Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Mario Castro
- Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St Louis, MO, USA
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Anne-Marie Dyer
- Department of Public Health Sciences, Penn State University, Hershey, PA, USA
| | - Elliot Israel
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Monica Kraft
- University of Arizona, Health Sciences, Tucson, AZ, USA
| | - Richard J Martin
- Department of Medicine, National Jewish Hospital, Denver, CO, USA
| | - David T Mauger
- Department of Public Health Sciences, Penn State University, Hershey, PA, USA
| | | | - Tonya S King
- Department of Public Health Sciences, Penn State University, Hershey, PA, USA
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Loren C Denlinger
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Fernando Holguin
- The University of Pittsburgh Asthma Institute at UPMC/UPSOM, Pittsburgh, PA, USA
| | - Stephen C Lazarus
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Njira Lugogo
- Duke Asthma, Allergy & Airway Center, Duke University School of Medicine, Durham, NC, USA
| | | | - Lewis J Smith
- Department of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Homer A Boushey
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA.
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Lee K, Pletcher SD, Lynch SV, Goldberg AN, Cope EK. Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation. Front Cell Infect Microbiol 2018; 8:168. [PMID: 29876323 PMCID: PMC5974464 DOI: 10.3389/fcimb.2018.00168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
Recent studies leveraging next-generation sequencing and functional approaches to understand the human microbiota have demonstrated the presence of diverse, niche-specific microbial communities at nearly every mucosal surface. These microbes contribute to the development and function of physiologic and immunological features that are key to host health status. Not surprisingly, several chronic inflammatory diseases have been attributed to dysbiosis of microbiota composition or function, including chronic rhinosinusitis (CRS). CRS is a heterogeneous disease characterized by inflammation of the sinonasal cavity and mucosal microbiota dysbiosis. Inflammatory phenotypes and bacterial community compositions vary considerably across individuals with CRS, complicating current studies that seek to address causality of a dysbiotic microbiome as a driver or initiator of persistent sinonasal inflammation. Murine models have provided some experimental evidence that alterations in local microbial communities and microbially-produced metabolites influence health status. In this perspective, we will discuss the clinical implications of distinct microbial compositions and community-level functions in CRS and how mucosal microbiota relate to the diverse inflammatory endotypes that are frequently observed. We will also describe specific microbial interactions that can deterministically shape the pattern of co-colonizers and the resulting metabolic products that drive or exacerbate host inflammation. These findings are discussed in the context of CRS-associated inflammation and in other chronic inflammatory diseases that share features observed in CRS. An improved understanding of CRS patient stratification offers the opportunity to personalize therapeutic regimens and to design novel treatments aimed at manipulation of the disease-associated microbiota to restore sinus health.
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Affiliation(s)
- Keehoon Lee
- Department of Biological Sciences, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven D Pletcher
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Susan V Lynch
- Division of Medicine, Department of Gastroenterology, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew N Goldberg
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Emily K Cope
- Department of Biological Sciences, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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50
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Abstract
A growing body of literature has demonstrated relationships between the composition of the airway microbiota (mixed-species communities of microbes that exist in the respiratory tract) and critical features of immune response and pulmonary function. These studies provide evidence that airway inflammatory status and capacity for repair are coassociated with specific taxonomic features of the airway microbiome. Although directionality has yet to be established, the fact that microbes are known drivers of inflammation and tissue damage suggests that in the context of chronic inflammatory airway disease, the composition and, more importantly, the function, of the pulmonary microbiome represent critical factors in defining airway disease outcomes.
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