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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Postaru M, Tucaliuc A, Cascaval D, Galaction AI. Cellular Stress Impact on Yeast Activity in Biotechnological Processes-A Short Overview. Microorganisms 2023; 11:2522. [PMID: 37894181 PMCID: PMC10609598 DOI: 10.3390/microorganisms11102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
The importance of Saccharomyces cerevisiae yeast cells is known worldwide, as they are the most used microorganisms in biotechnology for bioethanol and biofuel production. Also, they are analyzed and studied for their similar internal biochemical processes to human cells, for a better understanding of cell aging and response to cell stressors. The special ability of S. cerevisiae cells to develop in both aerobic and anaerobic conditions makes this microorganism a viable model to study the transformations and the way in which cellular metabolism is directed to face the stress conditions due to environmental changes. Thus, this review will emphasize the effects of oxidative, ethanol, and osmotic stress and also the physiological and genetic response of stress mitigation in yeast cells.
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Affiliation(s)
- Madalina Postaru
- Department of Biomedical Science, Faculty of Medical Bioengineering, “Grigore T. Popa” University of Medicine and Pharmacy of Iasi, M. Kogălniceanu 9-13, 700454 Iasi, Romania;
| | - Alexandra Tucaliuc
- Department of Organic, Biochemical and Food, “Cristofor Simionescu” Faculty of Chemical, Engineering and Environmental Protection, Engineering, “Gheorghe Asachi” Technical University of Iasi, D. Mangeron 73, 700050 Iasi, Romania; (A.T.); (D.C.)
| | - Dan Cascaval
- Department of Organic, Biochemical and Food, “Cristofor Simionescu” Faculty of Chemical, Engineering and Environmental Protection, Engineering, “Gheorghe Asachi” Technical University of Iasi, D. Mangeron 73, 700050 Iasi, Romania; (A.T.); (D.C.)
| | - Anca-Irina Galaction
- Department of Biomedical Science, Faculty of Medical Bioengineering, “Grigore T. Popa” University of Medicine and Pharmacy of Iasi, M. Kogălniceanu 9-13, 700454 Iasi, Romania;
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Konstantinidis I, Crothers K, Kunisaki KM, Drummond MB, Benfield T, Zar HJ, Huang L, Morris A. HIV-associated lung disease. Nat Rev Dis Primers 2023; 9:39. [PMID: 37500684 PMCID: PMC11146142 DOI: 10.1038/s41572-023-00450-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2023] [Indexed: 07/29/2023]
Abstract
Lung disease encompasses acute, infectious processes and chronic, non-infectious processes such as chronic obstructive pulmonary disease, asthma and lung cancer. People living with HIV are at increased risk of both acute and chronic lung diseases. Although the use of effective antiretroviral therapy has diminished the burden of infectious lung disease, people living with HIV experience growing morbidity and mortality from chronic lung diseases. A key risk factor for HIV-associated lung disease is cigarette smoking, which is more prevalent in people living with HIV than in uninfected people. Other risk factors include older age, history of bacterial pneumonia, Pneumocystis pneumonia, pulmonary tuberculosis and immunosuppression. Mechanistic investigations support roles for aberrant innate and adaptive immunity, local and systemic inflammation, oxidative stress, altered lung and gut microbiota, and environmental exposures such as biomass fuel burning in the development of HIV-associated lung disease. Assessment, prevention and treatment strategies are largely extrapolated from data from HIV-uninfected people. Smoking cessation is essential. Data on the long-term consequences of HIV-associated lung disease are limited. Efforts to continue quantifying the effects of HIV infection on the lung, especially in low-income and middle-income countries, are essential to advance our knowledge and optimize respiratory care in people living with HIV.
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Affiliation(s)
- Ioannis Konstantinidis
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kristina Crothers
- Veterans Affairs Puget Sound Healthcare System and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ken M Kunisaki
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, USA
| | - M Bradley Drummond
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital, Amager and Hvidovre, Hvidovre, Denmark
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Laurence Huang
- Division of Pulmonary and Critical Care 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
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Kreniske JS, Kaner RJ, Glesby MJ. Pathogenesis and management of emphysema in people with HIV. Expert Rev Respir Med 2023; 17:873-887. [PMID: 37848398 PMCID: PMC10872640 DOI: 10.1080/17476348.2023.2272702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
INTRODUCTION Since early in the HIV epidemic, emphysema has been identified among people with HIV (PWH) and has been associated with increased mortality. Smoking cessation is key to risk reduction. Health maintenance for PWH and emphysema should ensure appropriate vaccination and lung cancer screening. Treatment should adhere to inhaler guidelines for the general population, but inhaled corticosteroid (ICS) should be used with caution. Frontiers in treatment include targeted therapeutics. Major knowledge gaps exist in the epidemiology of and optimal care for PWH and emphysema, particularly in low and middle-income countries (LMIC). AREAS COVERED Topics addressed include risk factors, pathogenesis, current treatment and prevention strategies, and frontiers in research. EXPERT OPINION There are limited data on the epidemiology of emphysema in LMIC, where more than 90% of deaths from COPD occur and where the morbidity of HIV is most heavily concentrated. The population of PWH is aging, and age-related co-morbidities such as emphysema will only increase in salience. Over the next 5 years, the authors anticipate novel trials of targeted therapy for emphysema specific to PWH, and we anticipate a growing body of evidence to inform optimal clinical care for lung health among PWH in LMIC.
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Affiliation(s)
- Jonah S. Kreniske
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, USA
| | - Robert J. Kaner
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, USA
- Department of Genetic Medicine, Weill Cornell Medical College, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Weill Cornell Medical College, USA
- Department of Population Health Sciences, Weill Cornell Medical College, USA
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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Oliveira M, Pinto M, Simões H, Gomes JP, Veríssimo C, Sabino R. Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosis. Infect Dis Now 2023; 53:104633. [PMID: 36375764 DOI: 10.1016/j.idnow.2022.11.002] [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: 09/25/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Aspergillosis diagnosis depends on the detection of Aspergillus in biological samples ─ usually using cultural and immunoenzyme techniques ─ but their sensitivity and specificity varies. We aimed to study the prevalence of Aspergillus in patients at higher risk of chronic pulmonary aspergillosis (i.e., HIV-infected patients and individuals with active or previous tuberculosis), and to determine the potential role of molecular approaches to increase detection of Aspergillus in respiratory samples. METHODS The DNA extracted from 43 respiratory samples that had been previously analyzed by immunoenzyme and/or cultural techniques was amplified by real-time multiplex PCR, and the results of these methods were compared. We also sequenced the ITS1 region and the calmodulin gene in 10 respiratory samples to perform a pilot metagenomic study to understand the ability of this methodology to detect potential pathogenic fungi in the lung mycobiome. RESULTS Real-time Aspergillus PCR test exhibited a higher positivity rate than the conventional techniques used for aspergillosis diagnosis, particularly in individuals at risk for chronic pulmonary aspergillosis. The metagenomic analysis allowed for the detection of various potentially pathogenic fungi. CONCLUSIONS Molecular techniques, including metagenomics, have great ability to detect potentially pathogenic fungi rapidly and efficiently in human biological samples.
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Affiliation(s)
- M Oliveira
- Animal Biology Department, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal; Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - M Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - H Simões
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - J P Gomes
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - C Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - R Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health, Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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7
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Miao Q, Liang T, Pei N, Liu C, Pan J, Li N, Wang Q, Chen Y, Chen Y, Ma Y, Jin W, Zhang Y, Su Y, Yao Y, Huang Y, Zhou C, Bao R, Xu X, Chen W, Hu B, Li J. Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing. Respir Res 2022; 23:345. [PMCID: PMC9748891 DOI: 10.1186/s12931-022-02230-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.
Methods
Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.
Results
The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.
Conclusions
To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.
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Shajiei A, Liu L, Seinen J, Dieperink W, Hammerschmidt S, Maarten van Dijl J, Harmsen HJ. Specific associations between fungi and bacteria in broncho-alveolar aspirates from mechanically ventilated intensive care unit patients. Virulence 2022; 13:2022-2031. [PMID: 36384379 PMCID: PMC9673952 DOI: 10.1080/21505594.2022.2146568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the "mycobiome" of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate ("sputum") samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.
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Affiliation(s)
- Arezoo Shajiei
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands,Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lei Liu
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolien Seinen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands,Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Willem Dieperink
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J.M. Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands,CONTACT Hermie J.M. Harmsen
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9
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Li S, Yang X, Moog C, Wu H, Su B, Zhang T. Neglected mycobiome in HIV infection: Alterations, common fungal diseases and antifungal immunity. Front Immunol 2022; 13:1015775. [PMID: 36439143 PMCID: PMC9684632 DOI: 10.3389/fimmu.2022.1015775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/26/2022] [Indexed: 09/16/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection might have effects on both the human bacteriome and mycobiome. Although many studies have focused on alteration of the bacteriome in HIV infection, only a handful of studies have also characterized the composition of the mycobiome in HIV-infected individuals. Studies have shown that compromised immunity in HIV infection might contribute to the development of opportunistic fungal infections. Despite effective antiretroviral therapy (ART), opportunistic fungal infections continue to be a major cause of HIV-related mortality. Human immune responses are known to play a critical role in controlling fungal infections. However, the effect of HIV infection on innate and adaptive antifungal immunity remains unclear. Here, we review recent advances in understanding of the fungal microbiota composition and common fungal diseases in the setting of HIV. Moreover, we discuss innate and adaptive antifungal immunity in HIV infection.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaodong Yang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
- Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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10
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Alsayed AR, Al-Dulaimi A, Alkhatib M, Al Maqbali M, Al-Najjar MAA, Al-Rshaidat MMD. A comprehensive clinical guide for Pneumocystis jirovecii pneumonia: a missing therapeutic target in HIV-uninfected patients. Expert Rev Respir Med 2022; 16:1167-1190. [PMID: 36440485 DOI: 10.1080/17476348.2022.2152332] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Pneumocystis jirovecii is an opportunistic, human-specific fungus that causes Pneumocystis pneumonia (PCP). PCP symptoms are nonspecific. A patient with P. jirovecii and another lung infection faces a diagnostic challenge. It may be difficult to determine which of these agents is responsible for the clinical symptoms, preventing effective treatment. Diagnostic and treatment efforts have been made more difficult by the rising frequency with which coronavirus 2019 (COVID-19) and PCP co-occur. AREAS COVERED Herein, we provide a comprehensive review of clinical and pharmacological recommendations along with a literature review of PCP in immunocompromised patients focusing on HIV-uninfected patients. EXPERT OPINION PCP may be masked by identifying co-existing pathogens that are not necessarily responsible for the observed infection. Patients with severe form COVID-19 should be examined for underlying immunodeficiency, and co-infections must be considered as co-infection with P. jirovecii may worsen COVID-19's severity and fatality. PCP should be investigated in patients with PCP risk factors who come with pneumonia and suggestive radiographic symptoms but have not previously received PCP prophylaxis. PCP prophylaxis should be explored in individuals with various conditions that impair the immune system, depending on their PCP risk.
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Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Abdullah Al-Dulaimi
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome "Tor Vergata", Roma, Italy
| | - Mohammed Al Maqbali
- Department of Nursing Midwifery and Health, Northumbria University, Newcastle-Upon-Tyne, UK
| | - Mohammad A A Al-Najjar
- Department of Pharmaceutical Sciences and Pharmaceutics, Applied Science Private University, Amman, Kingdom of Jordan
| | - Mamoon M D Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman, Jordan
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11
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Yi X, Gao J, Wang Z. The human lung microbiome-A hidden link between microbes and human health and diseases. IMETA 2022; 1:e33. [PMID: 38868714 PMCID: PMC10989958 DOI: 10.1002/imt2.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome. The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
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12
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Lima R, Ribeiro FC, Colombo AL, de Almeida JN. The emerging threat antifungal-resistant Candida tropicalis in humans, animals, and environment. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:957021. [PMID: 37746212 PMCID: PMC10512401 DOI: 10.3389/ffunb.2022.957021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/28/2022] [Indexed: 09/26/2023]
Abstract
Antifungal resistance in humans, animals, and the environment is an emerging problem. Among the different fungal species that can develop resistance, Candida tropicalis is ubiquitous and causes infections in animals and humans. In Asia and some Latin American countries, C. tropicalis is among the most common species related to candidemia, and mortality rates are usually above 40%. Fluconazole resistance is especially reported in Asian countries and clonal spread in humans and the environment has been investigated in some studies. In Brazil, high rates of azole resistance have been found in animals and the environment. Multidrug resistance is still rare, but recent reports of clinical multidrug-resistant isolates are worrisome. The molecular apparatus of antifungal resistance has been majorly investigated in clinical C. tropicalis isolates, revealing that this species can develop resistance through the conjunction of different adaptative mechanisms. In this review article, we summarize the main findings regarding antifungal resistance and Candida tropicalis through an "One Health" approach.
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Affiliation(s)
- Ricardo Lima
- Special Mycology Laboratory, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Felipe C. Ribeiro
- Special Mycology Laboratory, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Arnaldo L. Colombo
- Special Mycology Laboratory, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Joăo N. de Almeida
- Special Mycology Laboratory, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
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13
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Gorgone M, Singhvi D, Nouraie SM, Finkelman M, Zhang Y, Pu J, Chandra D, Zhang Y, Kitsios GD, Morris A, Sciurba FC, Bon J. Circulating 1,3-Beta-D-Glucan is Associated with Lung Function, Respiratory Symptoms, and Mediators of Matrix Degradation in Chronic Obstructive Pulmonary Disease. CHRONIC OBSTRUCTIVE PULMONARY DISEASES (MIAMI, FLA.) 2022; 9:325-335. [PMID: 35550241 PMCID: PMC9448008 DOI: 10.15326/jcopdf.2022.0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Introduction Factors beyond cigarette smoke likely contribute to chronic obstructive pulmonary disease (COPD) pathogenesis. Prior studies demonstrate fungal colonization of the respiratory tract and increased epithelial barrier permeability in COPD. We sought to determine whether 1,3-beta-d-glucan (BDG), a polysaccharide component of the fungal cell wall, is detectable in the plasma of individuals with COPD and associates with clinical outcomes and matrix degradation proteins. Methods BDG was measured in the plasma of current and former smokers with COPD. High BDG was defined as a value greater than the 95th percentile of BDG in smokers without airflow obstruction. Pulmonary function, emphysema, and symptoms were compared between COPD participants with high versus low BDG. The relationship between plasma BDG, matrix metalloproteinases (MMP) 1, 7, and 9, and tissue inhibitor of matrix metalloproteinases (TIMP) 1, 2, and 4 was assessed adjusting for age, sex, and smoking status. Results COPD participants with high BDG plasma levels (19.8%) had lower forced expiratory volume in 1 second to forced vital capacity ratios (median 31.9 versus 39.3, p=0.025), higher St George's Respiratory Questionnaire symptom scores (median 63.6 versus 57.4, p=0.016), and greater prevalence of sputum production (69.4% versus 52.0%) and exacerbations (69.4% versus 48%) compared to COPD participants with low BDG. BDG levels directly correlated with MMP1 (r=0.27, p<0.001) and TIMP1 (r=0.16, p=0.022) in unadjusted and adjusted analyses. Conclusions Elevated plasma BDG levels correlate with worse lung function, greater respiratory morbidity, and circulating markers of matrix degradation in COPD. These findings suggest that targeting dysbiosis or enhancing epithelial barrier integrity may have disease-modifying effects in COPD.
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Affiliation(s)
- Matthew Gorgone
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- *Authors contributed equally
| | - Deepti Singhvi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- *Authors contributed equally
| | - Seyed Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Malcolm Finkelman
- Associates of Cape Cod Incorporated, East Falmouth, Massachusetts, United States
| | - Yonglong Zhang
- Associates of Cape Cod Incorporated, East Falmouth, Massachusetts, United States
| | - Jiantao Pu
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Divay Chandra
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Frank C. Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Jessica Bon
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
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14
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Gosalbes MJ, Jimenéz-Hernandéz N, Moreno E, Artacho A, Pons X, Ruíz-Pérez S, Navia B, Estrada V, Manzano M, Talavera-Rodriguez A, Madrid N, Vallejo A, Luna L, Pérez-Molina JA, Moreno S, Serrano-Villar S. Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV. Gut Microbes 2022; 14:2089002. [PMID: 35748016 PMCID: PMC9235884 DOI: 10.1080/19490976.2022.2089002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We assessed the inter-kingdom mycobiome-bacteriome interactions, the impact of diet, and the association with the innate and adaptive immunity in PWH on antiretroviral therapy. We included 24 PWH individuals and 12 healthy controls. We sequenced the Internal Transcribed Spacer 2 amplicons, determined amplicon sequence variants, measured biomarkers of the innate and adaptive immunity in blood and relations with diet. Compared to healthy controls, PWH subjects exhibited a distinct and richer mycobiome and an enrichment for Debaryomyces hansenii, Candida albicans, and Candida parapsilosis. In PWH, Candida and Pichia species were strongly correlated with several bacterial genera, including Faecalibacterium genus. Regarding the links between the mycobiome and systemic immunology, we found a positive correlation between Candida species and the levels of proinflammatory cytokines (sTNF-R2 and IL-17), interleukin 22 (a cytokine implicated in the regulation of mucosal immunity), and CD8+ T cell counts. This suggests an important role of the yeasts in systemic innate and adaptive immune responses. Finally, we identified inter-kingdom interactions implicated in fiber degradation, short-chain fatty acid production, and lipid metabolism, and an effect of vegetable and fiber intake on the mycobiome. Therefore, despite the great differences in abundance and diversity between the bacterial and fungal communities of the gut, we defined the changes associated with HIV, determined several different inter-kingdom associations, and found links between the mycobiome, nutrient metabolism, and systemic immunity.
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Affiliation(s)
- María José Gosalbes
- CIBER de Epidemiología y Salud Pública, Madrid, Spain,Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain,CONTACT María José Gosalbes Genomics and Health Area, FISABIO-Salud Pública46020Valencia, Spain
| | - Nuria Jimenéz-Hernandéz
- CIBER de Epidemiología y Salud Pública, Madrid, Spain,Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Elena Moreno
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Alejandro Artacho
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Xavier Pons
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Sonia Ruíz-Pérez
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain
| | - Beatriz Navia
- Department of Nutrition and Food Science, Universidad Complutense de Madrid, Madrid, Spain
| | - Vicente Estrada
- CIBER de Enfermedades Infecciosas, Madrid, Spain,HIV Unit, Hospital Clínico San Carlos, Madrid, Spain
| | - Mónica Manzano
- Department of Nutrition and Food Science, Universidad Complutense de Madrid, Madrid, Spain
| | - Alba Talavera-Rodriguez
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Nadia Madrid
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Alejandro Vallejo
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Laura Luna
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - José A. Pérez-Molina
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain,CIBER de Enfermedades Infecciosas, Madrid, Spain,Sergio Serrano-Villar Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
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15
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Russo C, Colaianni V, Ielo G, Valle MS, Spicuzza L, Malaguarnera L. Impact of Lung Microbiota on COPD. Biomedicines 2022; 10:biomedicines10061337. [PMID: 35740358 PMCID: PMC9219765 DOI: 10.3390/biomedicines10061337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
There is a fine balance in maintaining healthy microbiota composition, and its alterations due to genetic, lifestyle, and environmental factors can lead to the onset of respiratory dysfunctions such as chronic obstructive pulmonary disease (COPD). The relationship between lung microbiota and COPD is currently under study. Little is known about the role of the microbiota in patients with stable or exacerbated COPD. Inflammation in COPD disorders appears to be characterised by dysbiosis, reduced lung activity, and an imbalance between the innate and adaptive immune systems. Lung microbiota intervention could ameliorate these disorders. The microbiota’s anti-inflammatory action could be decisive in the onset of pathologies. In this review, we highlight the feedback loop between microbiota dysfunction, immune response, inflammation, and lung damage in relation to COPD status in order to encourage the development of innovative therapeutic goals for the prevention and management of this disease.
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Affiliation(s)
- Cristina Russo
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Valeria Colaianni
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Giuseppe Ielo
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Maria Stella Valle
- Laboratory of Neuro-Biomechanics, Section of Physiology, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, 95123 Catania, Italy
- Correspondence: (M.S.V.); (L.M.)
| | - Lucia Spicuzza
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Lucia Malaguarnera
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
- Correspondence: (M.S.V.); (L.M.)
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16
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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17
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Singh S, Natalini JG, Segal LN. Lung microbial-host interface through the lens of multi-omics. Mucosal Immunol 2022; 15:837-845. [PMID: 35794200 PMCID: PMC9391302 DOI: 10.1038/s41385-022-00541-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, our understanding of the microbial world within us has been revolutionized by the use of culture-independent techniques. The use of multi-omic approaches can now not only comprehensively characterize the microbial environment but also evaluate its functional aspects and its relationship with the host immune response. Advances in bioinformatics have enabled high throughput and in-depth analyses of transcripts, proteins and metabolites and enormously expanded our understanding of the role of the human microbiome in different conditions. Such investigations of the lower airways have specific challenges but as the field develops, new approaches will be facilitated. In this review, we focus on how integrative multi-omics can advance our understanding of the microbial environment and its effects on the host immune tone in the lungs.
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Affiliation(s)
- Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jake G. Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY,NYU Langone Lung Transplant Institute, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
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18
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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19
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Campbell CD, Barnett C, Sulaiman I. A clinicians’ review of the respiratory microbiome. Breathe (Sheff) 2022; 18:210161. [PMID: 36338247 PMCID: PMC9584600 DOI: 10.1183/20734735.0161-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
The respiratory microbiome and its impact in health and disease is now well characterised. With the development of next-generation sequencing and the use of other techniques such as metabolomics, the functional impact of microorganisms in different host environments can be elucidated. It is now clear that the respiratory microbiome plays an important role in respiratory disease. In some diseases, such as bronchiectasis, examination of the microbiome can even be used to identify patients at higher risk of poor outcomes. Furthermore, the microbiome can aid in phenotyping. Finally, development of multi-omic analysis has revealed interactions between the host and microbiome in some conditions. This review, although not exhaustive, aims to outline how the microbiome is investigated, the healthy respiratory microbiome and its role in respiratory disease. The respiratory microbiome encompasses bacterial, fungal and viral communities. In health, it is a dynamic structure and dysbiotic in disease. Dysbiosis can be related to disease severity and may be utilised to predict patients at clinical risk.https://bit.ly/3pNSgnA
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20
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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21
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Tiew PY, Mac Aogáin M, Chotirmall SH. The current understanding and future directions for sputum microbiome profiling in chronic obstructive pulmonary disease. Curr Opin Pulm Med 2022; 28:121-133. [PMID: 34839338 DOI: 10.1097/mcp.0000000000000850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Next-generation sequencing (NGS) has deepened our understanding of the respiratory microbiome in health and disease. The number of microbiome studies employing sputum as an airway surrogate has continued to increase over the past decade to include multiple large multicentre and longitudinal studies of the microbiome in chronic obstructive pulmonary disease (COPD). In this review, we summarize the recent advances to our understanding of the bacteriome, virome and mycobiome in COPD. RECENT FINDINGS Diverse microbiome profiles are reported in COPD. The neutrophilic Haemophilus-predominant bacteriome remains a prominent COPD phenotype, relatively stable over time and during exacerbations. Studies of the virome remain limited but reveal a potential involvement of viruses and bacteriophages particularly during COPD exacerbations and advancing disease severity. Mycobiome signatures, even in stable COPD are associated with poorer clinical outcomes including mortality. SUMMARY The sputum microbiome in COPD is being increasingly recognized for its clinical relevance, even in the stable state. Future studies integrating microbial kingdoms holistically (i.e. bacterial, viral and fungal) will provide deeper insight into its functionality including the relevance of microbial interactions and effect of treatment on microbiome-associated clinical outcomes.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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22
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Pattaroni C, Macowan M, Chatzis R, Daunt C, Custovic A, Shields MD, Power UF, Grigg J, Roberts G, Ghazal P, Schwarze J, Gore M, Turner S, Bush A, Saglani S, Lloyd CM, Marsland BJ. Early life inter-kingdom interactions shape the immunological environment of the airways. MICROBIOME 2022; 10:34. [PMID: 35189979 PMCID: PMC8862481 DOI: 10.1186/s40168-021-01201-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns. RESULTS We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns. CONCLUSION These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health. TRIAL REGISTRATION NHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016. https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/ Video abstract.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Matthew Macowan
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Roxanne Chatzis
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Carmel Daunt
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Adnan Custovic
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael D. Shields
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Jonathan Grigg
- Centre for Child Health, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham Roberts
- Human Development in Health School, University of Southampton Faculty of Medicine, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Peter Ghazal
- School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Jürgen Schwarze
- Centre for Inflammation Research, Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Mindy Gore
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
- NHS Grampian, Aberdeen, UK
| | - Andrew Bush
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Sejal Saglani
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Clare M. Lloyd
- National Heart & Lung Institute, Imperial College London, London, UK
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23
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Tipton L, Zahn GL, Darcy JL, Amend AS, Hynson NA. Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography. MICROBIAL ECOLOGY 2022; 83:48-57. [PMID: 33742230 DOI: 10.1007/s00248-021-01730-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.
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Affiliation(s)
- Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | | | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony S Amend
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA.
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24
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Chang S, Guo H, Li J, Ji Y, Jiang H, Ruan L, Du M. Comparative Analysis of Salivary Mycobiome Diversity in Human Immunodeficiency Virus-Infected Patients. Front Cell Infect Microbiol 2021; 11:781246. [PMID: 34926323 PMCID: PMC8671614 DOI: 10.3389/fcimb.2021.781246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Reports on alterations in the oral mycobiome of HIV-infected patients are still limited. This study was designed to compare the salivary mycobiome between 30 human immunodeficiency virus (HIV) infections and 30 healthy controls and explore the effect of antiretroviral therapy (ART) administration on the oral mycobiome of HIV infections. Results showed that the diversity and richness of salivary mycobiome in HIV-infected individuals were higher than those of controls (P < 0.05). After ART, the diversity and richness of salivary mycobiome in HIV-infected patients were reduced significantly (P < 0.05). Candida, Mortierella, Malassezia, Simplicillium, and Penicillium were significantly enriched in the HIV group and dramatically decreased after ART. While the relative abundance of Verticillium, Issatchenkia, and Alternaria significantly increased in patients with HIV after ART. Correlation analysis revealed that Mortierella, Malassezia, Simplicillium, and Chaetomium were positively correlated with viral load (VL), whereas Thyrostroma and Archaeorhizomyces were negatively related to VL and positively related to CD4+ T-cell counts. All results showed that HIV infection and ART administration affected the composition of salivary mycobiome communities. Furthermore, differences of salivary mycobiome in HIV infections after ART were complex and might mirror the immune state of the body.
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Affiliation(s)
- Shenghua Chang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Haiying Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jin Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaoting Ji
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Han Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lianguo Ruan
- Department of Infectious Diseases Treatment, Wuhan Medical Treatment Center, Wuhan, China
| | - Minquan Du
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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25
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Cardoso J, Ferreira AJ, Guimarães M, Oliveira AS, Simão P, Sucena M. Treatable Traits in COPD - A Proposed Approach. Int J Chron Obstruct Pulmon Dis 2021; 16:3167-3182. [PMID: 34824530 PMCID: PMC8609199 DOI: 10.2147/copd.s330817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
The well-recognized individual heterogeneity within COPD patients has led to a growing interest in greater personalization in the approach of these patients. Thus, the treatable traits strategy has been proposed as a further step towards precision medicine in the management of chronic airway disease, both in stable phase and acute exacerbations. The aim of this paper is to perform a critical review on the treatable traits strategy and propose a guide to approach COPD patients in the light of this new concept. An innovative stepwise approach is proposed - a multidisciplinary model based on two distinct phases, with the potential to be implemented in both primary care and hospital settings. The first phase is the initial and focused assessment of a selected subset of treatable traits, which should be addressed in all COPD patients in both settings (primary care and hospital). As some patients may present with advanced disease at diagnosis or may progress despite this initial treatment requiring a more specialized assessment, they should progress to a second phase, in which a broader approach is recommended. Beyond stable COPD, we explore how the treatable traits strategy may be applied to reduce the risk of future exacerbations and improve the management of COPD exacerbations. Since many treatable traits have already been related to exacerbation risk, the strategy proposed here represents an opportunity to be proactive. Although it still lacks prospective validation, we believe this is the way forward for the future of the COPD approach.
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Affiliation(s)
- João Cardoso
- Pulmonology Department, Centro Hospitalar Universitário de Lisboa Central, Lisboa, Portugal.,NOVA Medical School, Nova University Lisbon, Lisboa, Portugal
| | - António Jorge Ferreira
- Pulmonology Department, Centro Hospitalar Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Guimarães
- Pulmonology Department, Centro Hospitalar Vila Nova de Gaia/Espinho EPE, Vila Nova de Gaia, Portugal
| | - Ana Sofia Oliveira
- Pulmonology Department, Centro Hospitalar Universitário de Lisboa Norte EPE, Lisboa, Portugal
| | - Paula Simão
- Pulmonology Department, Unidade Local de Saúde de Matosinhos EPE, Matosinhos, Portugal
| | - Maria Sucena
- Pulmonology Department, Centro Hospitalar Universitário do Porto EPE, Porto, Portugal.,Lung Function and Ventilation Unit, Centro Hospitalar Universitário do Porto EPE, Porto, Portugal
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26
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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27
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Mishra K, Bukavina L, Ghannoum M. Symbiosis and Dysbiosis of the Human Mycobiome. Front Microbiol 2021; 12:636131. [PMID: 34630340 PMCID: PMC8493257 DOI: 10.3389/fmicb.2021.636131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.
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Affiliation(s)
- Kirtishri Mishra
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Laura Bukavina
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mahmoud Ghannoum
- Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Center for Medical Mycology, and Integrated Microbiome Core, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Dermatology, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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28
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McGinniss JE, Whiteside SA, Simon-Soro A, Diamond JM, Christie JD, Bushman FD, Collman RG. The lung microbiome in lung transplantation. J Heart Lung Transplant 2021; 40:733-744. [PMID: 34120840 PMCID: PMC8335643 DOI: 10.1016/j.healun.2021.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Culture-independent study of the lower respiratory tract after lung transplantation has enabled an understanding of the microbiome - that is, the collection of bacteria, fungi, and viruses, and their respective gene complement - in this niche. The lung has unique features as a microbial environment, with balanced entry from the upper respiratory tract, clearance, and local replication. There are many pressures impacting the microbiome after transplantation, including donor allograft factors, recipient host factors such as underlying disease and ongoing exposure to the microbe-rich upper respiratory tract, and transplantation-related immunosuppression, antimicrobials, and postsurgical changes. To date, we understand that the lung microbiome after transplant is dysbiotic; that is, it has higher biomass and altered composition compared to a healthy lung. Emerging data suggest that specific microbiome features may be linked to host responses, both immune and non-immune, and clinical outcomes such as chronic lung allograft dysfunction (CLAD), but many questions remain. The goal of this review is to put into context our burgeoning understanding of the lung microbiome in the postlung transplant patient, the interactions between microbiome and host, the role the microbiome may play in post-transplant complications, and critical outstanding research questions.
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Affiliation(s)
- John E McGinniss
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Samantha A Whiteside
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aurea Simon-Soro
- Department of Orthodontics and Divisions of Community Oral Health and Pediatric Dentistry, School of Dental Medicine at the University of Pennsylvania
| | - Joshua M Diamond
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fredrick D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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29
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Martinsen EMH, Eagan TML, Leiten EO, Haaland I, Husebø GR, Knudsen KS, Drengenes C, Sanseverino W, Paytuví-Gallart A, Nielsen R. The pulmonary mycobiome-A study of subjects with and without chronic obstructive pulmonary disease. PLoS One 2021; 16:e0248967. [PMID: 33826639 PMCID: PMC8026037 DOI: 10.1371/journal.pone.0248967] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/08/2021] [Indexed: 12/12/2022] Open
Abstract
Background The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD). Methods Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids. Results The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids. Conclusion Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.
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Affiliation(s)
| | - Tomas M. L. Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Elise O. Leiten
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingvild Haaland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gunnar R. Husebø
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Kristel S. Knudsen
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christine Drengenes
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | | | | | - Rune Nielsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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30
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Rayens E, Noble B, Vicencio A, Goldman DL, Bunyavanich S, Norris KA. Relationship of Pneumocystis antibody responses to paediatric asthma severity. BMJ Open Respir Res 2021; 8:8/1/e000842. [PMID: 33762359 PMCID: PMC7993353 DOI: 10.1136/bmjresp-2020-000842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although asthma is the most commonly diagnosed respiratory disease, its pathogenesis is complex, involving both genetic and environmental factors. A role for the respiratory microbiome in modifying asthma severity has been recently recognised. Airway colonisation by Pneumocystis jirovecii has previously been associated with multiple chronic lung diseases, including chronic obstructive pulmonary disease (COPD) and severe asthma (SA). Decreased incidence of Pneumocystis pneumonia in HIV-infected individuals and reduced severity of COPD is associated with naturally occurring antibody responses to the Pneumocystis antigen, Kexin (KEX1). METHODS 104 paediatric patients were screened for KEX1 IgG reciprocal end point titre (RET), including 51 with SA, 20 with mild/moderate asthma, 20 non-asthma and 13 with cystic fibrosis (CF) in a cross-sectional study. RESULTS Patients with SA had significantly reduced Pneumocystis KEX1 titres compared with patients with mild/moderate asthma (p=0.018) and CF (p=0.003). A binary KEX1 RET indicator was determined at a threshold of KEX1 RET=1000. Patients with SA had 4.40 (95% CI 1.28 to 13.25, p=0.014) and 17.92 (95% CI 4.15 to 66.62, p<0.001) times the odds of falling below that threshold compared with mild/moderate asthma and patients with CF, respectively. Moreover, KEX1 IgG RET did not correlate with tetanus toxoid IgG (r=0.21, p=0.82) or total IgE (r=0.03, p=0.76), indicating findings are specific to antibody responses to KEX1. CONCLUSIONS Paediatric patients with SA may be at higher risk for chronic Pneumocystis infections and asthma symptom exacerbation due to reduced levels of protective antibodies. Plasma KEX1 IgG titre may be a useful parameter in determining the clinical course of treatment for paediatric patients with asthma.
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Affiliation(s)
- Emily Rayens
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Brenda Noble
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Alfin Vicencio
- Pediatrics, Division of Pediatric Pulmonology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David L Goldman
- Departments of Pediatrics, Microbiology & Immunology, Children's Hospital at Montefiore, Bronx, New York, USA
| | - Supinda Bunyavanich
- Pediatrics, Division of Pediatric Pulmonology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karen A Norris
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
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31
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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32
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Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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33
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Tiew PY, Dicker AJ, Keir HR, Poh ME, Pang SL, Mac Aogáin M, Chua BQY, Tan JL, Xu H, Koh MS, Tee A, Abisheganaden JA, Chew FT, Miller BE, Tal-Singer R, Chalmers JD, Chotirmall SH. A high-risk airway mycobiome is associated with frequent exacerbation and mortality in COPD. Eur Respir J 2021; 57:2002050. [PMID: 32972986 DOI: 10.1183/13993003.02050-2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The chronic obstructive pulmonary disease (COPD) bacteriome associates with disease severity, exacerbations and mortality. While COPD patients are susceptible to fungal sensitisation, the role of the fungal mycobiome remains uncertain. METHODS We report the largest multicentre evaluation of the COPD airway mycobiome to date, including participants from Asia (Singapore and Malaysia) and the UK (Scotland) when stable (n=337) and during exacerbations (n=66) as well as nondiseased (healthy) controls (n=47). Longitudinal mycobiome analysis was performed during and following COPD exacerbations (n=34), and examined in terms of exacerbation frequency, 2-year mortality and occurrence of serum specific IgE (sIgE) against selected fungi. RESULTS A distinct mycobiome profile is observed in COPD compared with controls as evidenced by increased α-diversity (Shannon index; p<0.001). Significant airway mycobiome differences, including greater interfungal interaction (by co-occurrence), characterise very frequent COPD exacerbators (three or more exacerbations per year) (permutational multivariate ANOVA; adjusted p<0.001). Longitudinal analyses during exacerbations and following treatment with antibiotics and corticosteroids did not reveal any significant change in airway mycobiome profile. Unsupervised clustering resulted in two clinically distinct COPD groups: one with increased symptoms (COPD Assessment Test score) and Saccharomyces dominance, and another with very frequent exacerbations and higher mortality characterised by Aspergillus, Curvularia and Penicillium with a concomitant increase in serum sIgE levels against the same fungi. During acute exacerbations of COPD, lower fungal diversity associates with higher 2-year mortality. CONCLUSION The airway mycobiome in COPD is characterised by specific fungal genera associated with exacerbations and increased mortality.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Alison J Dicker
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Holly R Keir
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Mau Ern Poh
- Dept of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sze Lei Pang
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| | - Branden Qi Yu Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| | - Jiunn Liang Tan
- Dept of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Huiying Xu
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Mariko Siyue Koh
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Augustine Tee
- Dept of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | | | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore
| | | | | | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
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Ran Z, Liu J, Wang F, Xin C, Xiong B, Song Z. Pulmonary Micro-Ecological Changes and Potential Microbial Markers in Lung Cancer Patients. Front Oncol 2021; 10:576855. [PMID: 33537234 PMCID: PMC7848173 DOI: 10.3389/fonc.2020.576855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
The relationship between the microbiome and disease has been investigated for many years. As a highly malignant tumor, biomarkers for lung cancer are diverse. However, precision of these biomarkers has not yet been achieved. It has been confirmed that lung microecology changes in lung cancer patients compared with healthy individuals. Furthermore, the abundance of some bacterial species shows obvious changes, suggesting their potential use as a microbial marker for the detection of lung cancer. In addition, recent studies have confirmed that inflammation, immune response, virulence factors, and metabolism may be potential mechanisms linking the microbiome with carcinogenesis. In this review, microbiome studies of lung cancer, potential mechanisms, potential microbial markers, and the influence of the microbiome on the diagnosis and treatment of lung cancer are summarized, providing theoretical strategies for the diagnosis and treatment of lung cancer.
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Affiliation(s)
- Zhuonan Ran
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jiexing Liu
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Bin Xiong
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China
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35
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Dirajlal-Fargo S, El-Kamari V, Weiner L, Shan L, Sattar A, Kulkarni M, Funderburg N, Nazzinda R, Karungi C, Kityo C, Musiime V, McComsey GA. Altered Intestinal Permeability and Fungal Translocation in Ugandan Children With Human Immunodeficiency Virus. Clin Infect Dis 2021; 70:2413-2422. [PMID: 31260509 DOI: 10.1093/cid/ciz561] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Children with perinatally acquired human immunodeficiency virus (HIV; PHIVs) face a lifelong cumulative exposure to HIV and antiretroviral therapy (ART). The relationship between gut integrity, microbial translocation, and inflammation in PHIV is poorly understood. METHODS This is a cross-sectional study in 57 PHIVs, 59 HIV-exposed but uninfected children, and 56 HIV-unexposed and -uninfected children aged 2-10 years old in Uganda. PHIVs were on stable ART with HIV-1 RNA <400 copies/mL. We measured markers of systemic inflammation, monocyte activation, and gut integrity. Kruskal-Wallis tests were used to compare markers by group and the Spearman correlation was used to assess correlations between biomarkers. RESULTS The mean age of all participants was 7 years and 55% were girls. Among PHIVs, the mean CD4 % was 34%, 93% had a viral load ≤20 copies/mL, and 79% were on a nonnucleoside reverse transcriptase inhibitor regimen. Soluble cluster of differentiation 14 (sCD14), beta-D-glucan (BDG), and zonulin were higher in the PHIV group (P ≤ .01). Intestinal fatty acid binding protein (I-FABP) and lipopolysaccharide binding protein (LBP) did not differ between groups (P > .05). Among PHIVs who were breastfed, levels of sCD163 and interleukin 6 (IL6) were higher than levels in PHIV who were not breastfed (P < .05). Additionally, in PHIVs with a history of breastfeeding, sCD14, BDG, LBP, zonulin, and I-FABP correlated with several markers of systemic inflammation, including high-sensitivity C-reactive protein, IL6, d-dimer, and systemic tumor necrosis factor receptors I and II (P ≤ .05). CONCLUSIONS Despite viral suppression, PHIVs have evidence of altered gut permeability and fungal translocation. Intestinal damage and the resultant bacterial and fungal translocations in PHIVs may play a role in the persistent inflammation that leads to many end-organ diseases in adults.Despite viral suppression, children with perinatally acquired human immunodeficiency virus (HIV) in Uganda have evidence of alterations in intestinal permeability and fungal translocation, compared to HIV-exposed but uninfected and HIV-unexposed children, which may play a role in HIV-associated chronic inflammation.
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Affiliation(s)
- Sahera Dirajlal-Fargo
- University Hospitals Cleveland Medical Center, Columbus.,Rainbow Babies and Children's Hospital, Columbus.,Case Western Reserve University, Columbus
| | | | | | | | | | - Manjusha Kulkarni
- Ohio State University School of Health and Rehabilitation Sciences, Columbus
| | - Nicholas Funderburg
- Ohio State University School of Health and Rehabilitation Sciences, Columbus
| | | | | | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | - Victor Musiime
- Joint Clinical Research Centre, Kampala, Uganda.,Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Grace A McComsey
- University Hospitals Cleveland Medical Center, Columbus.,Rainbow Babies and Children's Hospital, Columbus.,Case Western Reserve University, Columbus
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36
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Quinones Tavarez Z, Li D, Croft DP, Gill SR, Ossip DJ, Rahman I. The Interplay Between Respiratory Microbiota and Innate Immunity in Flavor E-Cigarette Vaping Induced Lung Dysfunction. Front Microbiol 2020; 11:589501. [PMID: 33391205 PMCID: PMC7772214 DOI: 10.3389/fmicb.2020.589501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Global usage of electronic nicotine delivery systems (ENDS) has been increasing in the last decade. ENDS are non-combustible tobacco products that heat and aerosolize a liquid containing humectants, with added flavorings and often nicotine. Though ENDS are promoted as a less harmful alternative to smoking, current evidence links their use to a wide range of deleterious health effects including acute and chronic lung damage. ENDS can elicit an inflammatory response and impair the innate immune response in the lungs. Exposure to ENDS flavorings results in abnormal activation of the lung epithelial cells and β-defensins, dysfunction of the macrophage phagocytic activity, increased levels of mucin (MUC5AC) and abnormal activation of the neutrophilic response (NETosis). ENDS menthol flavorings disrupt innate immunity and might be associated with allergies and asthma through activation of transient receptor potential ankyrin 1 (TRAP1). Recent studies have expanded our understanding of the relationship between the homeostasis of lung innate immunity and the immunomodulatory effect of the host-microbiota interaction. Alterations of the normal respiratory microbiota have been associated with chronic obstructive pulmonary disease (COPD), asthma, atopy and cystic fibrosis complications which are strongly associated with smoking and potentially with ENDS use. Little is known about the short-and long-term effects of ENDS on the respiratory microbiota, their impact on the innate immune response and their link to pulmonary health and disease. Here we review the interaction between the innate immune system and the respiratory microbiota in the pathogenesis of ENDS-induced pulmonary dysfunction and identify future areas of research.
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Affiliation(s)
- Zahira Quinones Tavarez
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Daniel P Croft
- Department of Medicine, Pulmonary Diseases and Critical Care, University of Rochester, Rochester, NY, United States
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Deborah J Ossip
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
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Abstract
The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.
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Affiliation(s)
- Patricia I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY
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38
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The Domestic Environment and the Lung Mycobiome. Microorganisms 2020; 8:microorganisms8111717. [PMID: 33147738 PMCID: PMC7693370 DOI: 10.3390/microorganisms8111717] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8.0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status.
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39
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Liu J, Ran Z, Wang F, Xin C, Xiong B, Song Z. Role of pulmonary microorganisms in the development of chronic obstructive pulmonary disease. Crit Rev Microbiol 2020; 47:1-12. [PMID: 33040638 DOI: 10.1080/1040841x.2020.1830748] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic obstructive respiratory disease characterized by irreversible airway limitation and persistent respiratory symptoms. The main clinical symptoms of COPD are dyspnoea, chronic cough, and sputum. COPD is often accompanied by other respiratory diseases, which can cause worsening of the disease. COPD patients with dyspnoea and aggravation of cough and sputum symptoms represent acute exacerbations of COPD (AECOPD). There is mounting evidence suggesting that dysbiosis of pulmonary microbiota participates in the disease. However, investigations of dysbiosis of pulmonary microbiota and the disease are still in initial phases. To screen, diagnose, and treat this respiratory disease, integrating data from different studies can improve our understanding of the occurrence and development of COPD and AECOPD. In this review, COPD epidemiology and the primary triggering mechanism are explored. Emerging knowledge regarding the association of inflammation, caused by pulmonary microbiome imbalance, and changes in lung microbiome flora species involved in the development of the disease are also highlighted. These data will further our understanding of the pathogenesis of COPD and AECOPD and may yield novel strategies for the use of pulmonary microbiota as a potential therapeutic intervention.
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Affiliation(s)
- Jiexing Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhuonan Ran
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Bin Xiong
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, PR China
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40
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Diaz PI, Dongari-Bagtzoglou A. Critically Appraising the Significance of the Oral Mycobiome. J Dent Res 2020; 100:133-140. [PMID: 32924741 DOI: 10.1177/0022034520956975] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent efforts to understand the oral microbiome have focused on its fungal component. Since fungi occupy a low proportion of the oral microbiome biomass, mycobiome studies rely on sequencing of internal transcribed spacer (ITS) amplicons. ITS-based studies usually detect hundreds of fungi in oral samples. Here, we review the oral mycobiome, critically appraising the significance of such large fungal diversity. When harsh lysis methods are used to extract DNA, 2 oral mycobiome community types (mycotypes) are evident, each dominated by only 1 genus, either Candida or Malassezia. The rest of the diversity in ITS surveys represents low-abundance fungi possibly acquired from the environment and ingested food. So far, Candida is the only genus demonstrated to reach a significant biomass in the oral cavity and clearly shown to be associated with a distinct oral ecology. Candida thrives in the presence of lower oral pH and is enriched in caries, with mechanistic studies in animal models suggesting it participates in the disease process by synergistically interacting with acidogenic bacteria. Candida serves as the main etiological agent of oral mucosal candidiasis, in which a Candida-bacteriome partnership plays a key role. The function of other potential oral colonizers, such as lipid-dependent Malassezia, is still unclear, with further studies needed to establish whether Malassezia are metabolically active oral commensals. Low-abundance oral mycobiome members acquired from the environment may be viable in the oral cavity, and although they may not play a significant role in microbiome communities, they could serve as opportunistic pathogens in immunocompromised hosts. We suggest that further work is needed to ascertain the significance of oral mycobiome members beyond Candida. ITS-based surveys should be complemented with other methods to determine the in situ biomass and metabolic state of fungi thought to play a role in the oral environment.
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Affiliation(s)
- P I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA.,UB Microbiome Center, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - A Dongari-Bagtzoglou
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
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Rick EM, Woolnough KF, Seear PJ, Fairs A, Satchwell J, Richardson M, Monteiro WR, Craner M, Bourne M, Wardlaw AJ, Pashley CH. The airway fungal microbiome in asthma. Clin Exp Allergy 2020; 50:1325-1341. [PMID: 32808353 DOI: 10.1111/cea.13722] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. OBJECTIVES To use high-throughput sequencing to describe the airway mycobiota in asthmatics with and without fungal sensitization and healthy controls; to compare samples representing different airway compartments; to determine whether the mycobiota was influenced by the fungal composition of outdoor air; and to compare findings with clinically relevant outcomes. METHODS We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety-seven subjects were recruited and provided sputum (83 asthmatics; 14 healthy subjects), with 29 also undergoing a bronchoscopy. A subset of airway samples were compared with matched outdoor air and mouthwash samples. RESULTS Two hundred and six taxa at the species level were identified in sputum, most at low relative abundance. Aspergillus fumigatus, Candida albicans and Mycosphaerella tassiana had the highest relative abundances and were the most prevalent species across all subjects. The airway mycobiota consisted of a complex community with high diversity between individuals. Notable shifts in the balance of fungi detected in the lung were associated with asthma status, asthma duration and biomarkers of inflammation. Aspergillus tubingensis, a member of the Aspergillus niger species complex, was most prevalent from bronchoscopic protected brush samples and significantly associated with a low sputum neutrophilia. Cryptococcus pseudolongus, from the Cryptococcus humicola species complex, was more abundant from bronchoscopy samples than sputum, and differentially more abundant in asthma than health. CONCLUSIONS AND CLINICAL RELEVANCE The airway mycobiota was dominated by a relatively small number of species, but was distinct from the oropharyngeal mycobiota and air samples. Members of the A. niger and C. humicola species complexes may play unexpected roles in the pathogenesis of asthma.
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Affiliation(s)
- Eva-Maria Rick
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Kerry F Woolnough
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Paul J Seear
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Abbie Fairs
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Jack Satchwell
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Matthew Richardson
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - William R Monteiro
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Craner
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Bourne
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Andrew J Wardlaw
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK.,Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Catherine H Pashley
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
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Santoro A, Tomino C, Prinzi G, Cardaci V, Fini M, Macera L, Russo P, Maggi F. Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens. Curr Med Chem 2020; 27:2931-2948. [PMID: 31838985 DOI: 10.2174/0929867327666191213110551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/11/2019] [Accepted: 11/25/2019] [Indexed: 12/28/2022]
Abstract
The "microbiome" is the operative term to refer to a collection of all taxa constituting microbial communities, such as bacteria, archaea, fungi and protists (originally microbiota). The microbiome consists of the indigenous microbial communities and of the host environment that they inhabit. Actually, it has been shown that there is a close relationship between the microbiome and human health and disease condition. Although, initially, the lung was considered sterile, actually, the existence of a healthy lung microbiome is usually accepted. Lung microbiome changes are reported in Chronic Obstructive Pulmonary Disease (COPD) and in its exacerbation. Viral and bacterial infections of the respiratory system are a major cause of COPD exacerbations (AECOPD) leading to increased local and systemic inflammation. Detection rates of virus in AECOPD are variable between 25-62% according to the detection method. The study of human airway and lung disease virome is quite recent and still very limited. The purpose of this review is to summarize recent findings on the lung microbiome composition with a special emphasis on virome in COPD and in AECOPD. Some drugs of natural origins active against resistant bacteria and virus are described.
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Affiliation(s)
- Alessia Santoro
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Carlo Tomino
- Scientific Direction, IRCSS San Raffaele Pisana,Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Giulia Prinzi
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Vittorio Cardaci
- Unit of Pulmonary Rehabilitation, IRCCS San Raffaele Pisana, Via della Pisana, 235, I-00163 Rome, Italy
| | - Massimo Fini
- Scientific Direction, IRCSS San Raffaele Pisana,Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Via Savi, 10, I-56126 Pisa, Italy
| | - Patrizia Russo
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Via Savi, 10, I-56126 Pisa, Italy.,Virology Division, Pisa University Hospital, Via Paradisa, 2, I-56127 Pisa, Italy
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Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. Clin Infect Dis 2020; 68:1847-1855. [PMID: 30239621 PMCID: PMC6784263 DOI: 10.1093/cid/ciy802] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Madeline Y Mayday
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Kensho Iwanaga
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Ngoc P Ly
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Meghan E McGarry
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Gwynne D Church
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Lauren E Faricy
- Division of Pulmonology, Department of Pediatrics, University of Vermont School of Medicine, Burlington
| | - Courtney M Rowan
- Division of Critical Care, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis
| | - Janet R Hume
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis
| | - Marie E Steiner
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis.,Hematology/Oncology, Department of Pediatrics, Masonic Children's Hospital, University of Minnesota School of Medicine, Minneapolis
| | - Emily D Crawford
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Charles Langelier
- Division of Infectious Diseases, Department of Internal Medicine, University of California-San Francisco School of Medicine
| | - Katrina Kalantar
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Eric D Chow
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco School of Medicine
| | - Kristen Shimano
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Alexis Melton
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Gregory A Yanik
- Division of Oncology, Department of Pediatrics, Motts Children's Hospital, University of Michigan School of Medicine, Ann Arbor
| | - Anil Sapru
- Division of Critical Care, University of California, San Francisco School of Medicine.,Division of Critical Care, Department of Pediatrics, Mattel Children's Hospital, University of California-Los Angeles, Geffen School of Medicine
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
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Evaluation of Droplet Digital Polymerase Chain Reaction (ddPCR) for the Absolute Quantification of Aspergillus species in the Human Airway. Int J Mol Sci 2020; 21:ijms21093043. [PMID: 32357408 PMCID: PMC7247686 DOI: 10.3390/ijms21093043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Prior studies illustrate the presence and clinical importance of detecting Aspergillus species in the airways of patients with chronic respiratory disease. Despite this, a low fungal biomass and the presence of PCR inhibitors limits the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of Aspergillus in specimens from the human airway. Droplet digital PCR (ddPCR) however, presents an alternative methodology allowing higher sensitivity and accuracy of such quantification but remains to be evaluated in head-to-head fashion using specimens from the human airway. Here, we implement a standard duplex TaqMan PCR protocol, and assess if ddPCR is superior in quantifying airway Aspergillus when compared to standard qPCR. METHODS The molecular approaches of qPCR and ddPCR were applied to DNA fungal extracts in n = 20 sputum specimens obtained from non-diseased (n = 4), chronic obstructive pulmonary disease (COPD; n = 8) and non-cystic fibrosis bronchiectasis (n = 8) patients where Aspergillus status was known. DNA was extracted and qPCR and ddPCR performed on all specimens with appropriate controls and head-to-head comparisons performed. RESULTS Standard qPCR and ddPCR were both able to detect, even at low abundance, Aspergillus species (Aspergillus fumigatus - A. fumigatus and Aspergillus terreus - A. terreus) from specimens known to contain the respective fungi. Importantly, however, ddPCR was superior for the detection of A. terreus particularly when present at very low abundance and demonstrates greater resistance to PCR inhibition compared to qPCR. CONCLUSION ddPCR has greater sensitivity for A. terreus detection from respiratory specimens, and is more resistant to PCR inhibition, important attributes considering the importance of A. terreus species in chronic respiratory disease states such as bronchiectasis.
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Abstract
PURPOSE OF REVIEW In the antiretroviral therapy era, people living with HIV (PLWH) are surviving to older ages. Chronic illnesses such as chronic obstructive pulmonary disease (COPD) occur more frequently. COPD is often described as a single entity, yet multiple manifestations may be considered phenotypes. HIV is an independent risk factor for certain COPD phenotypes, and mechanisms underlying pathogenesis of these phenotypes may differ and impact response to therapy. RECENT FINDINGS Impaired diffusing capacity, airflow obstruction, and radiographic emphysema occur in PLWH and are associated with increased mortality. Age, sex, tobacco, and HIV-specific factors likely modulate the severity of disease. An altered lung microbiome and residual HIV in the lung may also influence phenotypes. COPD is prevalent in PLWH with multiple phenotypes contributing to the burden of disease. HIV-specific factors and the respiratory microbiome influence disease pathogenesis. As tobacco use remains a significant risk factor for COPD, smoking cessation must be emphasized for all PLWH.
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Affiliation(s)
- Deepti Singhvi
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Jessica Bon
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Dronamraju V, Singh N, Poon J, Shah S, Gorga J, Ojeda-Martinez H, McFarlane S. Assessment of Bronchiectasis in HIV Patients among an Urban Population. Case Rep Pulmonol 2020; 2020:8903809. [PMID: 32181043 PMCID: PMC7063221 DOI: 10.1155/2020/8903809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 12/28/2019] [Indexed: 11/17/2022] Open
Abstract
Bronchiectasis is characterized by permanent destruction of the airways that presents with productive cough, as well as bronchial wall thickening and luminal dilatation on computed tomographic (CT) scan of the chest; it is associated with high mortality. Accumulating data suggests higher rates of bronchiectasis among the HIV-positive population. This case series involves 14 patients with bronchiectasis and HIV followed at two major urban institutions from 1999 to 2018. Demographics, clinical presentation, microbiology, radiographic imaging, and outcomes were collected and compiled. Mean age was 42 years (range 12-77 years). 36% had a CD4 count greater than 500 cells/mm3, 28% had a CD4 count between 200 and 500 cells/mm3, and 36% had AIDS. 43% were treated for Pneumocystis jiroveci pneumonia (PJP) and 50% for Mycobacterium avium complex (MAC) infection. 21% had COPD, 7% had asthma, and 7% had a history of pulmonary aspergillosis. Two patients were followed up by pulmonary services after diagnosis of bronchiectasis on CT. The timeline of the follow-up in these cases was within months and after three years respectively. It is posited that the prevalence of bronchiectasis in HIV patients may be underestimated. Improving recognition and management of bronchiectasis could help diminish rehospitalization rates.
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Affiliation(s)
- Veena Dronamraju
- Department of Internal Medicine, SUNY Downstate Medical Center, USA
| | - Navneet Singh
- Department of Internal Medicine, SUNY Downstate Medical Center, USA
| | - Justin Poon
- Department of Internal Medicine, SUNY Downstate Medical Center, USA
| | - Sachi Shah
- Department of Infectious Disease, Montefiore Medical Center, USA
| | - Joseph Gorga
- Division of Pulmonary and Critical Care Medicine, New York Health and Hospitals Corporation, Kings County Hospital Center, USA
| | | | - Samy McFarlane
- Department of Internal Medicine, SUNY Downstate Medical Center, USA
- Department of Endocrinology, SUNY Downstate Medical Center, USA
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Ditz B, Christenson S, Rossen J, Brightling C, Kerstjens HAM, van den Berge M, Faiz A. Sputum microbiome profiling in COPD: beyond singular pathogen detection. Thorax 2020; 75:338-344. [PMID: 31996401 PMCID: PMC7231454 DOI: 10.1136/thoraxjnl-2019-214168] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/19/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023]
Abstract
Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question ‘who is there?’ Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions ‘what can they do?’ and ‘what are they doing?’ This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.
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Affiliation(s)
- Benedikt Ditz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands .,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, the United States
| | - John Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center, University of Groningen, Groningen, the Netherlands
| | - Chris Brightling
- Institute of Lung Health, University of Leicester, Leicester, UK
| | - Huib A M Kerstjens
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, New South Wales, Australia
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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Azzam SZ, Cayme GJ, Martinez LR. Polymicrobial interactions involving fungi and their importance for the environment and in human disease. Microb Pathog 2019; 140:103942. [PMID: 31881258 DOI: 10.1016/j.micpath.2019.103942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Understanding polymicrobial interactions involving fungi in the environment and the human mycobiome is necessary to address environmental and medically related problems such as drought or antimicrobial resistance. The diversity of these interactions highlights the complexity of fungi, considering how some interactions can be antagonistic, while others synergistic. Over the years, an increase in studies on the mycobiome have revealed similarities between the human and environmental hosts. More recently, studies have focused on microbial commensal relationships and identifying causative agents of human disease. The overlap of some of these interactions is impossible to ignore, indicating that there are areas for medical exploitation that need to be further investigated. This review provides the latest advances in polymicrobial interactions involving fungi and discusses the importance of the fungal lifestyle in the environment and in human disease.
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Affiliation(s)
- Seham Z Azzam
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Ginelle J Cayme
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Luis R Martinez
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
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Raghavan V, Aquadro CF, Alani E. Baker's Yeast Clinical Isolates Provide a Model for How Pathogenic Yeasts Adapt to Stress. Trends Genet 2019; 35:804-817. [PMID: 31526615 PMCID: PMC6825890 DOI: 10.1016/j.tig.2019.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/07/2019] [Accepted: 08/19/2019] [Indexed: 12/26/2022]
Abstract
Global outbreaks of drug-resistant fungi such as Candida auris are thought to be due at least in part to excessive use of antifungal drugs. Baker's yeast Saccharomyces cerevisiae has gained importance as an emerging opportunistic fungal pathogen that can cause infections in immunocompromised patients. Analyses of over 1000 S. cerevisiae isolates are providing rich resources to better understand how fungi can grow in human environments. A large percentage of clinical S. cerevisiae isolates are heterozygous across many nucleotide sites, and a significant proportion are of mixed ancestry and/or are aneuploid or polyploid. Such features potentially facilitate adaptation to new environments. These observations provide strong impetus for expanding genomic and molecular studies on clinical and wild isolates to understand the prevalence of genetic diversity and instability-generating mechanisms, and how they are selected for and maintained. Such work can also lead to the identification of new targets for antifungal drugs.
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Affiliation(s)
- Vandana Raghavan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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