1
|
Iyer P, Ojcius DM. Unveiling the mycobiota: The fungal frontier of human health. Biomed J 2024; 47:100751. [PMID: 38838983 DOI: 10.1016/j.bj.2024.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
The microbiota and its effect on health has been extensively studied over the past decade. In many studies, the term microbiota has become synonymous with the bacterial component of the microbiota. Other microbes in the microbiota, such as viruses and fungi, have been neglected until recently. This special issue provides some background on the mycobiota and explores the role of gut fungi in human diseases such as cancer, metabolic diseases, and infection by Clostridiodes difficile, and describes the incidence of fungal infections in transplant patients. The mycobiota, once overlooked, now garners increasing attention.
Collapse
Affiliation(s)
- Parvati Iyer
- Department of Diagnostic Sciences, University of the Pacific, Arthur Dugoni School of Dentistry, San Francisco, CA, USA
| | - David M Ojcius
- Department of Biomedical Sciences, University of the Pacific, Arthur Dugoni School of Dentistry, San Francisco, CA, USA.
| |
Collapse
|
2
|
Vänni P, Turunen J, Äijälä VK, Tapiainen VV, Paalanne M, Pokka T, Paalanne N, Tejesvi MV, Ruuska TS. Gut Mycobiome in Atopic Dermatitis and in Overweight Young Children: A Prospective Cohort Study in Finland. J Fungi (Basel) 2024; 10:333. [PMID: 38786688 PMCID: PMC11122208 DOI: 10.3390/jof10050333] [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: 02/18/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Gut bacterial alterations have been previously linked to several non-communicable diseases in adults, while the association of mycobiome is not well understood in these diseases, especially in infants and children. Few studies have been conducted on the association between gut mycobiome and non-communicable diseases in children. We investigated gut mycobiome composition using 194 faecal samples collected at birth, 6 months after birth, and 18 months after birth in relation to atopic dermatitis (AD) and overweight diagnoses at the age of 18 or 36 months. The mycobiome exhibited distinct patterns, with Truncatella prevalent in the meconium samples of both overweight and non-overweight groups. Saccharomyces took precedence in overweight cases at 6 and 18 months, while Malassezia dominated non-overweight samples at 6 months. Saccharomyces emerged as a consistent high-abundance taxon across groups that had dermatitis and were overweight. We found a weak association between gut mycobiome and AD at birth and overweight at 18 months when using machine learning (ML) analyses. In ML, unidentified fungi, Alternaria, Rhodotorula, and Saccharomyces, were important for classifying AD, while Saccharomyces, Thelebolus, and Dothideomycetes were important for classifying overweight. Gut mycobiome might be associated with the development of AD and overweight in children.
Collapse
Affiliation(s)
- Petri Vänni
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
| | - Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Biocenter Oulu, University of Oulu, 8000 Oulu, Finland
| | - Ville K. Äijälä
- Department of Paediatrics and Adolescent Medicine, Oulu University Hospital, 8000 Oulu, Finland; (V.K.Ä.); (V.V.T.)
| | - Vilja V. Tapiainen
- Department of Paediatrics and Adolescent Medicine, Oulu University Hospital, 8000 Oulu, Finland; (V.K.Ä.); (V.V.T.)
| | - Marika Paalanne
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Department of Paediatrics and Adolescent Medicine, Oulu University Hospital, 8000 Oulu, Finland; (V.K.Ä.); (V.V.T.)
| | - Tytti Pokka
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Research Service Unit, Oulu University Hospital, 8000 Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Department of Paediatrics and Adolescent Medicine, Oulu University Hospital, 8000 Oulu, Finland; (V.K.Ä.); (V.V.T.)
| | - Mysore V. Tejesvi
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Ecology and Genetics, Faculty of Science, University of Oulu, 8000 Oulu, Finland
| | - Terhi S. Ruuska
- Research Unit of Clinical Medicine, University of Oulu, 8000 Oulu, Finland; (J.T.); (M.P.); (T.P.); (N.P.); (M.V.T.); (T.S.R.)
- Biocenter Oulu, University of Oulu, 8000 Oulu, Finland
- Department of Paediatrics and Adolescent Medicine, Oulu University Hospital, 8000 Oulu, Finland; (V.K.Ä.); (V.V.T.)
| |
Collapse
|
3
|
Hurraß J, Heinzow B, Walser-Reichenbach S, Aurbach U, Becker S, Bellmann R, Bergmann KC, Cornely OA, Engelhart S, Fischer G, Gabrio T, Herr CE, Joest M, Karagiannidis C, Klimek L, Köberle M, Kolk A, Lichtnecker H, Lob-Corzilius T, Mülleneisen N, Nowak D, Rabe U, Raulf M, Steinmann J, Steiß JO, Stemler J, Umpfenbach U, Valtanen K, Werchan B, Willinger B, Wiesmüller GA. AWMF mold guideline "Medical clinical diagnostics for indoor mold exposure" - Update 2023 AWMF Register No. 161/001. Allergol Select 2024; 8:90-198. [PMID: 38756207 PMCID: PMC11097193 DOI: 10.5414/alx02444e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/04/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Julia Hurraß
- Section for Hygiene in Healthcare Facilities, Division of Infection Control and Environmental Hygiene, Cologne Health Department, Cologne
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Birger Heinzow
- Formerly: State Agency for Social Services (LAsD) Schleswig-Holstein, Kiel
- Co-author
| | - Sandra Walser-Reichenbach
- Formerly: State Agency for Social Services (LAsD) Schleswig-Holstein, Kiel
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Ute Aurbach
- Laboratory Dr. Wisplinghoff
- ZfMK – Center for Environment, Hygiene and Mycology Cologne, Cologne
- Co-author
| | - Sven Becker
- Department for Otorhinolaryngology, Head and Neck Surgery, University Medical Center Tübingen, Tübingen, Germany
- Co-author
| | - Romuald Bellmann
- Department of Internal Medicine I, Medical University of Innsbruck, Innsbruck, Austria
- Co-author
| | - Karl-Christian Bergmann
- Institute of Allergology Charité, Charité – University Medicine Berlin, Berlin
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Oliver A. Cornely
- Institute for Translational Research, CECAD Cluster of Excellence, University of Cologne, Cologne, Germany and Department I for Internal Medicine, Cologne University Hospital, Cologne
- Co-author
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Guido Fischer
- Baden-Württemberg State Health Office in the Stuttgart Regional Council, Stuttgart
- Co-author
| | - Thomas Gabrio
- Formerly: Baden-Württemberg State Health Office in the Stuttgart Regional Council, Stuttgart
- Co-author
| | - Caroline E.W. Herr
- Bavarian Health and Food Safety Authority, Munich
- Environmental Health and Prevention, Institute and Polyclinic for Occupational, Social and Environmental Medicine, University of Munich Hospital Ludwig-Maximilians-University, Munich
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Marcus Joest
- Allergological-Immunological Laboratory, Helios Lung and Allergy Center Bonn, Bonn
- Co-author
| | - Christian Karagiannidis
- Faculty of Health, Professorship for Extracorporeal Lung Replacement Procedures, University of Witten/Herdecke, Witten/Herdecke
- Lung Clinic Cologne Merheim, Clinics of the City of Cologne, Cologne
- Co-author
| | - Ludger Klimek
- Center for Rhinology and Allergology, Wiesbaden
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Martin Köberle
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of Munich, Munich
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Annette Kolk
- Institute for Occupational Safety and Health (IFA) of the German Social Accident Insurance (DGUV), Unit Biological Agents, Sankt Augustin
- Co-author
| | - Herbert Lichtnecker
- Medical Institute for Environmental and Occupational Medicine MIU GmbH Erkrath, Erkrath
- Co-author
| | - Thomas Lob-Corzilius
- Scientific working group of environmental medicine of the German Society of Pediatric Allergology (GPAU)
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Norbert Mülleneisen
- Asthma and Allergy Center Leverkusen, Leverkusen
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Dennis Nowak
- Institute and Polyclinic for Occupational, Social and Environmental Medicine, member of the German Center for Lung Research, Hospital of the University of Munich, Munich
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Uta Rabe
- Center for Allergology and Asthma, Johanniter Hospital Treuenbrietzen, Treuenbrietzen
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Monika Raulf
- Institute for Prevention and Occupational Medicine of the German Statutory Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Jörg Steinmann
- Center for Pediatrics and Adolescent Medicine, University Hospital Giessen and Marburg GmbH, Giessen
- Co-author
| | - Jens-Oliver Steiß
- Specialized Practice in Allergology and Pediatric Pulmonology in Fulda, Fulda
- Institute for Clinical Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Private Medical University Nuremberg Clinic, Nuremberg
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Jannik Stemler
- Institute for Translational Research, CECAD Cluster of Excellence, University of Cologne, Cologne, Germany and Department I for Internal Medicine, Cologne University Hospital, Cologne
- Co-author
| | - Ulli Umpfenbach
- Doctor for Pediatrics and Adolescent Medicine, Pediatric Pulmonology, Environmental Medicine, Classical Homeopathy, Asthma Trainer, Neurodermatitis Trainer, Viersen
- Co-author
| | - Kerttu Valtanen
- FG II 1.4 Microbiological Risks, German Environment Agency, Berlin
- Co-author
| | - Barbora Werchan
- German Pollen Information Service Foundation (PID), Berlin, Germany
- Co-author
| | - Birgit Willinger
- Department of Laboratory Medicine, Division of Clinical Microbiology – Medical University of Vienna, Vienna, Austria, and
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| | - Gerhard A. Wiesmüller
- Laboratory Dr. Wisplinghoff
- ZfMK – Center for Environment, Hygiene and Mycology Cologne, Cologne
- Institute for Occupational, Social and Environmental Medicine, Uniclinic RWTH Aachen, Aachen, Germany
- Co-author
- Member of a scientific medical society, a society or a medical association with voting rights
| |
Collapse
|
4
|
Rodriguez KA, Gurung M, Talatala R, Rearick JR, Ruebel ML, Stephens KE, Yeruva L. The Role of Early Life Gut Mycobiome on Child Health. Adv Nutr 2024; 15:100185. [PMID: 38311313 PMCID: PMC10907404 DOI: 10.1016/j.advnut.2024.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
The human gut microbiota is composed of bacteria (microbiota or microbiome), fungi (mycobiome), viruses, and archaea, but most of the research is primarily focused on the bacterial component of this ecosystem. Besides bacteria, fungi have been shown to play a role in host health and physiologic functions. However, studies on mycobiota composition during infancy, the factors that might shape infant gut mycobiota, and implications to child health and development are limited. In this review, we discuss the factors likely shaping gut mycobiota, interkingdom interactions, and associations with child health outcomes and highlight the gaps in our current knowledge of this ecosystem.
Collapse
Affiliation(s)
- Kayleigh Amber Rodriguez
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States
| | - Manoj Gurung
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Rachelanne Talatala
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States
| | - Jolene R Rearick
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Meghan L Ruebel
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Kimberly E Stephens
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States.
| | - Laxmi Yeruva
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States.
| |
Collapse
|
5
|
Ali MJ. Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5. Br J Ophthalmol 2024; 108:317-322. [PMID: 36270766 DOI: 10.1136/bjo-2022-322433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO). METHODS A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database. RESULTS The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples. CONCLUSION The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.
Collapse
Affiliation(s)
- Mohammad Javed Ali
- Govindram Seksaria Institute of Dacryology, LV Prasad Eye Institute, Hyderabad, India
| |
Collapse
|
6
|
Han G, Vaishnava S. Microbial underdogs: exploring the significance of low-abundance commensals in host-microbe interactions. Exp Mol Med 2023; 55:2498-2507. [PMID: 38036729 PMCID: PMC10767002 DOI: 10.1038/s12276-023-01120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 12/02/2023] Open
Abstract
Our understanding of host-microbe interactions has broadened through numerous studies over the past decades. However, most investigations primarily focus on the dominant members within ecosystems while neglecting low-abundance microorganisms. Moreover, laboratory animals usually do not have microorganisms beyond bacteria. The phenotypes observed in laboratory animals, including the immune system, have displayed notable discrepancies when compared to real-world observations due to the diverse microbial community in natural environments. Interestingly, recent studies have unveiled the beneficial roles played by low-abundance microorganisms. Despite their rarity, these keystone taxa play a pivotal role in shaping the microbial composition and fulfilling specific functions in the host. Consequently, understanding low-abundance microorganisms has become imperative to unravel true commensalism. In this review, we provide a comprehensive overview of important findings on how low-abundance commensal microorganisms, including low-abundance bacteria, fungi, archaea, and protozoa, interact with the host and contribute to host phenotypes, with emphasis on the immune system. Indeed, low-abundance microorganisms play vital roles in the development of the host's immune system, influence disease status, and play a key role in shaping microbial communities in specific niches. Understanding the roles of low-abundance microbes is important and will lead to a better understanding of the true host-microbe relationships.
Collapse
Affiliation(s)
- Geongoo Han
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Shipra Vaishnava
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| |
Collapse
|
7
|
Prisnee TL, Rahman R, Fouhse JM, Van Kessel AG, Brook RK, Willing BP. Tracking the fecal mycobiome through the lifespan of production pigs and a comparison to the feral pig. Appl Environ Microbiol 2023; 89:e0097723. [PMID: 37902410 PMCID: PMC10686082 DOI: 10.1128/aem.00977-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE This work provides evidence that early-life fungal community composition, or host genetics, influences long-term mycobiome composition. In addition, this work provides the first comparison of the feral pig mycobiome to the mycobiome of intensively raised pigs.
Collapse
Affiliation(s)
- Tausha L. Prisnee
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Rajibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Janelle M. Fouhse
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew G. Van Kessel
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ryan K. Brook
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Benjamin P. Willing
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
8
|
Li H, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Wenzel SE, Zein J, Bleecker ER, Meyers DA, Chen Y, Li X. Investigations of a combination of atopic status and age of asthma onset identify asthma subphenotypes. J Asthma 2023; 60:1843-1852. [PMID: 36940238 PMCID: PMC10528448 DOI: 10.1080/02770903.2023.2193634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/27/2023] [Accepted: 03/16/2023] [Indexed: 03/21/2023]
Abstract
OBJECTIVE Subphenotypes of asthma may be determined by age onset and atopic status. We sought to characterize early or late onset atopic asthma with fungal or non-fungal sensitization (AAFS or AANFS) and non-atopic asthma (NAA) in children and adults in the Severe Asthma Research Program (SARP). SARP is an ongoing project involving well-phenotyped patients with mild to severe asthma. METHODS Phenotypic comparisons were performed using Kruskal-Wallis or chi-square test. Genetic association analyses were performed using logistic or linear regression. RESULTS Airway hyper-responsiveness, total serum IgE levels, and T2 biomarkers showed an increasing trend from NAA to AANFS and then to AAFS. Children and adults with early onset asthma had greater % of AAFS than adults with late onset asthma (46% and 40% vs. 32%; P < 0.00001). In children, AAFS and AANFS had lower % predicted FEV1 (86% and 91% vs. 97%) and greater % of patients with severe asthma than NAA (61% and 59% vs. 43%). In adults with early or late onset asthma, NAA had greater % of patients with severe asthma than AANFS and AAFS (61% vs. 40% and 37% or 56% vs. 44% and 49%). The G allele of rs2872507 in GSDMB had higher frequency in AAFS than AANFS and NAA (0.63 vs. 0.55 and 0.55), and associated with earlier age onset and asthma severity. CONCLUSIONS Early or late onset AAFS, AANFS, and NAA have shared and distinct phenotypic characteristics in children and adults. AAFS is a complex disorder involving genetic susceptibility and environmental factors.
Collapse
Affiliation(s)
- Huashi Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - John V. Fahy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Benjamin Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana, USA
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David T Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, USA
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eugene R. Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | | |
Collapse
|
9
|
Debourgogne A, Monpierre L, Sy KA, Valsecchi I, Decousser JW, Botterel F. Interactions between Bacteria and Aspergillus fumigatus in Airways: From the Mycobiome to Molecular Interactions. J Fungi (Basel) 2023; 9:900. [PMID: 37755008 PMCID: PMC10533028 DOI: 10.3390/jof9090900] [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: 07/31/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Interactions between different kingdoms of microorganisms in humans are common but not well described. A recent analysis of the mycobiome has described the presence of different fungi and their positive and/or negative interactions with bacteria and other fungi. In chronic respiratory diseases, these different microorganisms form mixed biofilms to live inside. The interactions between Gram-negative bacteria and filamentous fungi in these biofilms have attracted more attention recently. In this review, we analyse the microbiota of the respiratory tract of healthy individuals and patients with chronic respiratory disease. Additionally, we describe the regulatory mechanisms that rule the mixed biofilms of Aspergillus fumigatus and Gram-negative bacteria and the effects of this biofilm on clinical presentations.
Collapse
Affiliation(s)
- Anne Debourgogne
- UR 7300, Stress Immunité Pathogène, Université de Lorraine, 54000 Vandoeuvre les Nancy, France;
| | - Lorra Monpierre
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Khadeeja Adam Sy
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Institut National de la Santé et de la Recherche Médicale (Inserm) U955, 94010 Créteil, France
| | - Isabel Valsecchi
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Jean-Winoc Decousser
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Department of Infection Control, University Hospital Henri Mondor, Assistance Publique—Hôpitaux de Paris, 94000 Créteil, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| |
Collapse
|
10
|
Lupu A, Jechel E, Mihai CM, Mitrofan EC, Fotea S, Starcea IM, Ioniuc I, Mocanu A, Ghica DC, Popp A, Munteanu D, Sasaran MO, Salaru DL, Lupu VV. The Footprint of Microbiome in Pediatric Asthma-A Complex Puzzle for a Balanced Development. Nutrients 2023; 15:3278. [PMID: 37513696 PMCID: PMC10384859 DOI: 10.3390/nu15143278] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023] Open
Abstract
Considered to be of greater complexity than the human genome itself, the microbiome, the structure of the body made up of trillions of bacteria, viruses, and fungi, has proven to play a crucial role in the context of the development of pathological processes in the body, starting from various infections, autoimmune diseases, atopies, and culminating in its involvement in the development of some forms of cancer, a diagnosis that is considered the most disabling for the patient from a psychological point of view. Therefore, being a cornerstone in the understanding and optimal treatment of a multitude of ailments, the body's microbiome has become an intensively studied subject in the scientific literature of the last decade. This review aims to bring the microbiome-asthma correlation up to date by classifying asthmatic patterns, emphasizing the development patterns of the microbiome starting from the perinatal period and the impact of pulmonary dysbiosis on asthmatic symptoms in children. Likewise, the effects of intestinal dysbiosis reflected at the level of homeostasis of the internal environment through the intestine-lung/vital organs axis, the circumstances in which it occurs, but also the main methods of studying bacterial variability used for diagnostic purposes and in research should not be omitted. In conclusion, we draw current and future therapeutic lines worthy of consideration both in obtaining and maintaining remission, as well as in delaying the development of primary acute episodes and preventing future relapses.
Collapse
Affiliation(s)
- Ancuta Lupu
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Jechel
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | | | - Silvia Fotea
- Clinical Medical Department, Faculty of Medicine and Pharmacy, "Dunarea de Jos" University of Galati, 800008 Galati, Romania
| | - Iuliana Magdalena Starcea
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ileana Ioniuc
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adriana Mocanu
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dragos Catalin Ghica
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Alina Popp
- Faculty of General Medicine, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Dragos Munteanu
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Maria Oana Sasaran
- Faculty of General Medicine, "George Emil Palade" University of Medicine, Pharmacy, Science and Technology, 540142 Targu Mures, Romania
| | - Delia Lidia Salaru
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Vasile Valeriu Lupu
- Faculty of General Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| |
Collapse
|
11
|
Kozik AJ, Begley LA, Lugogo N, Baptist A, Erb-Downward J, Opron K, Huang YJ. Airway microbiota and immune mediator relationships differ in obesity and asthma. J Allergy Clin Immunol 2023; 151:931-942. [PMID: 36572355 PMCID: PMC10566565 DOI: 10.1016/j.jaci.2022.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Asthma and obesity are both complex conditions characterized by chronic inflammation, and obesity-related severe asthma has been associated with differences in the microbiome. However, whether the airway microbiome and microbiota-immune response relationships differ between obese persons with or without nonsevere asthma is unestablished. OBJECTIVE We compared the airway microbiome and microbiota-immune mediator relationships between obese and nonobese subjects, with and without mild-moderate asthma. METHODS We performed cross-sectional analyses of the airway (induced sputum) microbiome and cytokine profiles from blood and sputum using 16S ribosomal RNA gene and internal transcribed spacer region sequencing to profile bacteria and fungi, and multiplex immunoassays. Analysis tools included QIIME 2, linear discriminant analysis effect size (aka LEfSe), Piphillin, and Sparse inverse covariance estimation for ecological association inference (aka SPIEC-EASI). RESULTS Obesity, irrespective of asthma status, was associated with significant differences in sputum bacterial community structure and composition (unweighted UniFrac permutational analysis of variance, P = .02), including a higher relative abundance of Prevotella, Gemella, and Streptococcus species. Among subjects with asthma, additional differences in sputum bacterial composition and fungal richness were identified between obese and nonobese individuals. Correlation network analyses demonstrated differences between obese and nonobese asthma in relationships between cytokine mediators, and these together with specific airway bacteria involving blood PAI-1, sputum IL-1β, GM-CSF, IL-8, TNF-α, and several Prevotella species. CONCLUSION Obesity itself is associated with an altered sputum microbiome, which further differs in those with mild-moderate asthma. The distinct differences in airway microbiota and immune marker relationships in obese asthma suggest potential involvement of airway microbes that may affect mechanisms or outcomes of obese asthma.
Collapse
Affiliation(s)
- Ariangela J Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich.
| | - Lesa A Begley
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Njira Lugogo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Alan Baptist
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Ann Arbor, Mich
| | - John Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Kristopher Opron
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Ann Arbor, Mich; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Mich.
| |
Collapse
|
12
|
Carroll OR, Pillar AL, Brown AC, Feng M, Chen H, Donovan C. Advances in respiratory physiology in mouse models of experimental asthma. Front Physiol 2023; 14:1099719. [PMID: 37008013 PMCID: PMC10060990 DOI: 10.3389/fphys.2023.1099719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/07/2023] [Indexed: 03/18/2023] Open
Abstract
Recent advances in mouse models of experimental asthma coupled with vast improvements in systems that assess respiratory physiology have considerably increased the accuracy and human relevance of the outputs from these studies. In fact, these models have become important pre-clinical testing platforms with proven value and their capacity to be rapidly adapted to interrogate emerging clinical concepts, including the recent discovery of different asthma phenotypes and endotypes, has accelerated the discovery of disease-causing mechanisms and increased our understanding of asthma pathogenesis and the associated effects on lung physiology. In this review, we discuss key distinctions in respiratory physiology between asthma and severe asthma, including the magnitude of airway hyperresponsiveness and recently discovered disease drivers that underpin this phenomenon such as structural changes, airway remodeling, airway smooth muscle hypertrophy, altered airway smooth muscle calcium signaling, and inflammation. We also explore state-of-the-art mouse lung function measurement techniques that accurately recapitulate the human scenario as well as recent advances in precision cut lung slices and cell culture systems. Furthermore, we consider how these techniques have been applied to recently developed mouse models of asthma, severe asthma, and asthma-chronic obstructive pulmonary disease overlap, to examine the effects of clinically relevant exposures (including ovalbumin, house dust mite antigen in the absence or presence of cigarette smoke, cockroach allergen, pollen, and respiratory microbes) and to increase our understanding of lung physiology in these diseases and identify new therapeutic targets. Lastly, we focus on recent studies that examine the effects of diet on asthma outcomes, including high fat diet and asthma, low iron diet during pregnancy and predisposition to asthma development in offspring, and environmental exposures on asthma outcomes. We conclude our review with a discussion of new clinical concepts in asthma and severe asthma that warrant investigation and how we could utilize mouse models and advanced lung physiology measurement systems to identify factors and mechanisms with potential for therapeutic targeting.
Collapse
Affiliation(s)
- Olivia R. Carroll
- Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Amber L. Pillar
- Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Alexandra C. Brown
- Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Min Feng
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Hui Chen
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Chantal Donovan
- Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
- *Correspondence: Chantal Donovan,
| |
Collapse
|
13
|
Losol P, Sokolowska M, Chang YS. Interactions between microbiome and underlying mechanisms in asthma. Respir Med 2023; 208:107118. [PMID: 36641058 DOI: 10.1016/j.rmed.2023.107118] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Microbiome primes host innate immunity in utero and play fundamental roles in the development, training, and function of the immune system throughout the life. Interplay between the microbiome and immune system maintains mucosal homeostasis, while alterations of microbial community dysregulate immune responses, leading to distinct phenotypic features of immune-mediated diseases including asthma. Microbial imbalance within the mucosal environments, including upper and lower airways, skin, and gut, has consistently been observed in asthma patients and linked to increased asthma exacerbations and severity. Microbiome research has increased to uncover hidden microbial members, function, and immunoregulatory effects of bacterial metabolites within the mucosa. This review provides an overview of environmental and genetic factors that modulate the composition and function of the microbiome, and the impacts of microbiome metabolites and skin microbiota on immune regulation in asthma.
Collapse
Affiliation(s)
- Purevsuren Losol
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea; Medical Research Center, Seoul National University, Seoul, South Korea; Department of Molecular Biology and Genetics, School of Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Herman-Burchard Strasse 9, CH7265, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea; Medical Research Center, Seoul National University, Seoul, South Korea.
| |
Collapse
|
14
|
Understanding the Functional Role of the Microbiome and Metabolome in Asthma. Curr Allergy Asthma Rep 2023; 23:67-76. [PMID: 36525159 DOI: 10.1007/s11882-022-01056-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 12/23/2022]
Abstract
PURPOSE OF REVIEW Asthma is a heterogenous respiratory disease characterized by airway inflammation and obstruction. However, the causes of asthma are unknown. Several studies have reported microbial and metabolomic dysbiosis in asthmatic patients; but, little is known about the functional role of the microbiota or the host-microbe metabolome in asthma pathophysiology. Current multi-omic studies are linking both the metabolome and microbiome in different organ systems to help identify the interactions involved in asthma, with the goal of better identifying endotypes/phenotypes, causal links, and potential targets of treatment. This review thus endeavors to explore the benefits of and current advances in studying microbiome-metabolome interactions in asthma. RECENT FINDINGS This is a narrative review of the current state of research surrounding the interaction between the microbiome and metabolome and their role in asthma. Associations with asthma onset, severity, and phenotype have been identified in both the microbiome and the metabolome, most frequently in the gut. More recently, studies have begun to investigate the role of the respiratory microbiome in airway disease and its association with the systemic metabolome, which has provided further insights into its role in asthma phenotypes. This review also identifies gaps in the field in understanding the direct link between respiratory microbiome and metabolome, hypothesizes the benefits for conducting such studies in the future for asthma treatment and prevention, and identifies current analytical limitations that need to be addressed to advance the field. This is a comprehensive review of the current state of research on the interaction between the microbiome and metabolome and their role in asthma.
Collapse
|
15
|
Lo YL, Lin HC, Lo CY, Huang HY, Lin TY, Lin CH, Hsieh MH, Fang YF, Lin SM, Huang YT, Liao TW, Wang CH, Lin CY. Clinical manifestations and outcomes of fungus-associated asthma: A multi-institution database study in Taiwan. Microbiol Res 2023; 266:127234. [DOI: 10.1016/j.micres.2022.127234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/20/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
|
16
|
Marathe SJ, Snider MA, Flores-Torres AS, Dubin PJ, Samarasinghe AE. Human matters in asthma: Considering the microbiome in pulmonary health. Front Pharmacol 2022; 13:1020133. [PMID: 36532717 PMCID: PMC9755222 DOI: 10.3389/fphar.2022.1020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/15/2022] [Indexed: 07/25/2023] Open
Abstract
Microbial communities form an important symbiotic ecosystem within humans and have direct effects on health and well-being. Numerous exogenous factors including airborne triggers, diet, and drugs impact these established, but fragile communities across the human lifespan. Crosstalk between the mucosal microbiota and the immune system as well as the gut-lung axis have direct correlations to immune bias that may promote chronic diseases like asthma. Asthma initiation and pathogenesis are multifaceted and complex with input from genetic, epigenetic, and environmental components. In this review, we summarize and discuss the role of the airway microbiome in asthma, and how the environment, diet and therapeutics impact this low biomass community of microorganisms. We also focus this review on the pediatric and Black populations as high-risk groups requiring special attention, emphasizing that the whole patient must be considered during treatment. Although new culture-independent techniques have been developed and are more accessible to researchers, the exact contribution the airway microbiome makes in asthma pathogenesis is not well understood. Understanding how the airway microbiome, as a living entity in the respiratory tract, participates in lung immunity during the development and progression of asthma may lead to critical new treatments for asthma, including population-targeted interventions, or even more effective administration of currently available therapeutics.
Collapse
Affiliation(s)
- Sandesh J. Marathe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Mark A. Snider
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Emergency Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Armando S. Flores-Torres
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| | - Patricia J. Dubin
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Division of Pulmonology, Allergy-Immunology, and Sleep, Memphis, TN, United States
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN, United States
| |
Collapse
|
17
|
Costa PDS, Prado A, Bagon NP, Negri M, Svidzinski TIE. Mixed Fungal Biofilms: From Mycobiota to Devices, a New Challenge on Clinical Practice. Microorganisms 2022; 10:microorganisms10091721. [PMID: 36144323 PMCID: PMC9506030 DOI: 10.3390/microorganisms10091721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that allow the evaluation of fungal morphology and the identification of the etiologic agent of mycosis. Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that enable the examination of the fungi for further identification of the etiological agent of the mycosis. The isolation of fungi from pure cultures is typically recommended, as when more than one species is identified, the second agent is considered a contaminant. Fungi mostly survive in highly organized communities that provoke changes in phenotypic profile, increase resistance to antifungals and environmental stresses, and facilitate evasion from the immune system. Mixed fungal biofilms (MFB) harbor more than one fungal species, wherein exchange can occur that potentialize the effects of these virulence factors. However, little is known about MFB and their role in infectious processes, particularly in terms of how each species may synergistically contribute to the pathogenesis. Here, we review fungi present in MFB that are commensals of the human body, forming the mycobiota, and how their participation in MFB affects the maintenance of homeostasis. In addition, we discuss how MFB are formed on both biotic and abiotic surfaces, thus being a significant reservoir of microorganisms that have already been associated in infectious processes of high morbidity and mortality.
Collapse
|
18
|
Li X, Liu D, Yao J. Aerosolization of fungal spores in indoor environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153003. [PMID: 35031366 DOI: 10.1016/j.scitotenv.2022.153003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Fungi in indoor environments can cause adverse health effects through inhalation and epidermal exposure. The risk of fungal exposure originates from the aerosolization of fungal spores. However, spore aerosolization is still not well understood. This paper provides a review of indoor fungal contamination, especially the aerosolization of fungal spores. We attempted to summarize what is known today and to identify what more information is needed to predict the aerosolization of fungal spores. This paper first reviews fungal contamination in indoor environments and HVAC systems. The detachment of fungal spores from colonies and the spore aerosolization principle are then summarized. Based on the above discussion, prediction methods for spore aerosolization are discussed. This review further clarifies the current situation and future efforts required to accurately predict spore aerosolization. This information is useful for forecasting and controlling the aerosolization of fungal spores.
Collapse
Affiliation(s)
- Xian Li
- School of Civil Engineering and Architecture, Linyi University, Linyi 276000, China.
| | - Dan Liu
- School of Civil Engineering and Architecture, Linyi University, Linyi 276000, China
| | - Jian Yao
- School of Civil Engineering and Architecture, Linyi University, Linyi 276000, China
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Flores-Torres AS, Samarasinghe AE. Impact of Therapeutics on Unified Immunity During Allergic Asthma and Respiratory Infections. FRONTIERS IN ALLERGY 2022; 3:852067. [PMID: 35386652 PMCID: PMC8974821 DOI: 10.3389/falgy.2022.852067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/21/2022] [Indexed: 11/04/2022] Open
Abstract
Asthma is a common chronic respiratory disease that affects millions of people worldwide. Patients with allergic asthma, the most prevalent asthma endotype, are widely considered to possess a defective immune response against some respiratory infectious agents, including viruses, bacteria and fungi. Furthermore, respiratory pathogens are associated with asthma development and exacerbations. However, growing data suggest that the immune milieu in allergic asthma may be beneficial during certain respiratory infections. Immunomodulatory asthma treatments, although beneficial, should then be carefully prescribed to avoid misuse and overuse as they can also alter the host microbiome. In this review, we summarize and discuss recent evidence of the correlations between allergic asthma and the most significant respiratory infectious agents that have a role in asthma pathogenesis. We also discuss the implications of current asthma therapeutics beyond symptom prevention.
Collapse
Affiliation(s)
- Armando S. Flores-Torres
- Division of Pulmonology, Allergy-Immunology, and Sleep, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States
| | - Amali E. Samarasinghe
- Division of Pulmonology, Allergy-Immunology, and Sleep, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN, United States,*Correspondence: Amali E. Samarasinghe
| |
Collapse
|
21
|
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.
Collapse
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
| | | |
Collapse
|
22
|
Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
Collapse
Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
| |
Collapse
|
23
|
Liu J, Yin J. Immunotherapy With Recombinant Alt a 1 Suppresses Allergic Asthma and Influences T Follicular Cells and Regulatory B Cells in Mice. Front Immunol 2021; 12:747730. [PMID: 34804031 PMCID: PMC8602824 DOI: 10.3389/fimmu.2021.747730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
Background Alternaria is a major source of asthma-inducing allergens. Allergen-specific immunotherapy improves the progression of allergic asthma. The current treatment is based on crude Alternaria extracts. Alt a 1 is the predominant allergen in Alternaria. However, the treatment efficacy of recombinant Alt a 1 (rAlt a 1) in an asthmatic animal model and its influence on Tfh and Breg cells are unknown. Objective To explore the therapeutic treatment effects of rAlt a 1 on the progress of an asthmatic mouse model and its effect on Tfh and Breg cells. Methods We synthesized and purified rAlt a 1. Alternaria-sensitized and challenged mice received subcutaneous immunotherapy (SCIT) with four different rAlt a 1 dosages (5, 50, 100, and 150 µg) or PBS only. Finally, lung and airway inflammation, mouse mast cell protease 1 (MMCP-1), serum immunoglobulin responses, Tfh and Breg cell levels, and the correlation between asthmatic features (inflammation grades and IL-4 and IL-10 levels) and these two cell types were measured after Alternaria rechallenge. Results High purity and allergenic potency of rAlt a 1 protein were obtained. Following treatment with four different rAlt a 1 dosages, both lung and airway inflammation ameliorated, including lung pathology, serum MMCP-1 levels, inflammatory cell numbers, and cytokine levels in bronchoalveolar lavage fluid (BALF). Additionally, rAlt a 1-SCIT increased the expression of Alternaria-sIgG1, rAlt a 1-sIgG1, rAlt a 1-sIgG2a, and rAlt a 1-sIgG2b in serum. Moreover, the number and percentage of CXCR5+PD-1+Tfh cells were increased in the PC control, while they decreased in the rAlt a 1-SCIT groups. Meanwhile, the absolute numbers and proportions of Breg cells were evaluated after administration of rAlt a 1. A positive correlation was observed between CXCR5+PD-1+Tfh cells and inflammation grades (r = 0.50, p = 0.01), as well as a slightly strong positive relationship with IL-4 (r = 0.55, p = 0.005) and IL-10 (r = 0.58, p = 0.003) levels; Breg cells showed an opposite correlation with the grades of inflammation (r = -0.68, p = 0.0003), along with a negative correlation to IL-4 (r = -0.61, p = 0.001) and IL-10 (r = -0.53, p = 0.008) levels. Conclusions We verified that treatment with rAlt a 1 can alleviate asthma progression and further have a regulatory effect on Tfh and Breg cells in an Alternaria-induced asthmatic mouse model.
Collapse
Affiliation(s)
- Juan Liu
- Department of Allergy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Allergy, Peking Union Medical College Hospital, Beijing Key Laboratory of Precision Medicine For Diagnosis and Treatment on Allergic Diseases, Beijing, China.,Department of Allergy, Peking Union Medical College Hospital, National Clinical Research Center for Dermatologic and Immunologic Disease, Beijing, China
| | - Jia Yin
- Department of Allergy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Allergy, Peking Union Medical College Hospital, Beijing Key Laboratory of Precision Medicine For Diagnosis and Treatment on Allergic Diseases, Beijing, China.,Department of Allergy, Peking Union Medical College Hospital, National Clinical Research Center for Dermatologic and Immunologic Disease, Beijing, China
| |
Collapse
|
24
|
Shoemaker R, Kim J. Urobiome: An outlook on the metagenome of urological diseases. Investig Clin Urol 2021; 62:611-622. [PMID: 34729961 PMCID: PMC8566783 DOI: 10.4111/icu.20210312] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/09/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
The urinary tract likely plays a role in the development of various urinary diseases due to the recently recognized notion that urine is not sterile. In this mini review, we summarize the current literature regarding the urinary microbiome and mycobiome and its relationship to various urinary diseases. It has been recently discovered that the healthy urinary tract contains a host of microorganisms, creating a urinary microbiome. The relative abundance and type of bacteria varies, but generally, deviations in the standard microbiome are observed in individuals with urologic diseases, such as bladder cancer, benign prostatic hyperplasia, urgency urinary incontinence, overactive bladder syndrome, interstitial cystitis, bladder pain syndrome, and urinary tract infections. However, whether this change is causative, or correlative has yet to be determined. In summary, the urinary tract hosts a complex microbiome. Changes in this microbiome may be indicative of urologic diseases and can be tracked to predict, prevent, and treat them in individuals. However, current analytical and sampling collection methods may present limitations to the development in the understanding of the urinary microbiome and its relationship with various urinary diseases. Further research on the differences between healthy and diseased microbiomes, the long-term effects of antibiotic treatments on the urobiome, and the effect of the urinary mycobiome on general health will be important in developing a comprehensive understanding of the urinary microbiome and its relationship to the human body.
Collapse
Affiliation(s)
- Rachel Shoemaker
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, University of California, Los Angeles, CA, USA.,Department of Urology, Gachon University College of Medicine, Incheon, Korea.
| |
Collapse
|
25
|
Ackland J, Watson A, Wilkinson TMA, Staples KJ. Interrupting the Conversation: Implications for Crosstalk Between Viral and Bacterial Infections in the Asthmatic Airway. FRONTIERS IN ALLERGY 2021; 2:738987. [PMID: 35386999 PMCID: PMC8974750 DOI: 10.3389/falgy.2021.738987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Asthma is a heterogeneous, chronic respiratory disease affecting 300 million people and is thought to be driven by different inflammatory endotypes influenced by a myriad of genetic and environmental factors. The complexity of asthma has rendered it challenging to develop preventative and disease modifying therapies and it remains an unmet clinical need. Whilst many factors have been implicated in asthma pathogenesis and exacerbations, evidence indicates a prominent role for respiratory viruses. However, advances in culture-independent detection methods and extensive microbial profiling of the lung, have also demonstrated a role for respiratory bacteria in asthma. In particular, airway colonization by the Proteobacteria species Nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) is associated with increased risk of developing recurrent wheeze and asthma in early life, poor clinical outcomes in established adult asthma and the development of more severe inflammatory phenotypes. Furthermore, emerging evidence indicates that bacterial-viral interactions may influence exacerbation risk and disease severity, highlighting the need to consider the impact chronic airway colonization by respiratory bacteria has on influencing host responses to viral infection. In this review, we first outline the currently understood role of viral and bacterial infections in precipitating asthma exacerbations and discuss the underappreciated potential impact of bacteria-virus crosstalk in modulating host responses. We discuss the mechanisms by which early life infection may predispose to asthma development. Finally, we consider how infection and persistent airway colonization may drive different asthma phenotypes, with a view to identifying pathophysiological mechanisms that may prove tractable to new treatment modalities.
Collapse
Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tom M. A. Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Karl J. Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
- *Correspondence: Karl J. Staples
| |
Collapse
|
26
|
Marczylo EL, Macchiarulo S, Gant TW. Metabarcoding of Soil Fungi from Different Urban Greenspaces Around Bournemouth in the UK. ECOHEALTH 2021; 18:315-330. [PMID: 34089413 PMCID: PMC8626400 DOI: 10.1007/s10393-021-01523-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/22/2020] [Accepted: 01/31/2021] [Indexed: 05/20/2023]
Abstract
Soil microbes are important for public health. Increasing urbanisation is adversely affecting soil microbiota, which may be contributing to the global rise of immune-related diseases. Fungi are key components of urban environments that can be negatively impacted by altered land-use, land-management and climate change, and are implicated in the development and exacerbation of non-communicable diseases such as allergy, asthma and chronic inflammatory conditions. Fungal metagenomics is building knowledge on fungi within different environments (the environmental mycobiome), fungi on and within the human body (the human mycobiome), and their association with disease. Here, we demonstrate the added value of a multi-region metabarcoding approach to analyse soil mycobiomes from five urban greenspaces (lawns, parklands, bareground, young forest and old forest). While results were comparable across the three regions (ITS1, ITS2 and LSU), each identified additional fungal taxa that were unique to the region. Combining the results therefore provided a more comprehensive analysis across all fungal taxonomic ranks, identifying statistically significant differences in the fungal composition of the five soil types. Assignment of fungal taxa into ecological guilds revealed those differences of biological relevance to public health. The greatest differences were between the soil mycobiome of lawns and forests. Of most concern was the significant increase in the known human allergens Alternaria, Bipolaris, Cladosporium and Fusarium within urban lawn and parkland vs forest soils. By improving our understanding of local variations in fungal taxa across urban greenspaces, we have the potential to boost the health of local residents through improved urban planning.
Collapse
Affiliation(s)
- Emma L Marczylo
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Campus, Chilton, Oxfordshire, OX11 0RQ, UK.
| | - Sameirah Macchiarulo
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Campus, Chilton, Oxfordshire, OX11 0RQ, UK
| | - Timothy W Gant
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Campus, Chilton, Oxfordshire, OX11 0RQ, UK
| |
Collapse
|
27
|
Deckers J, Marsland BJ, von Mutius E. Protection against allergies: Microbes, immunity, and the farming effect. Eur J Immunol 2021; 51:2387-2398. [PMID: 34415577 DOI: 10.1002/eji.202048938] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/08/2021] [Accepted: 08/17/2021] [Indexed: 12/19/2022]
Abstract
The prevalence of asthma and other allergic diseases has rapidly increased in "Westernized" countries over recent decades. This rapid increase suggests the involvement of environmental factors, behavioral changes or lifestyle, rather than genetic drift. It has become increasingly clear that the microbiome plays a key role in educating the host immune system and, thus, regulation of disease susceptibility. This review will focus on recent advances uncovering immunological and microbial mechanisms that protect against allergies, in particular, within the context of a farming environment. A whole body of epidemiological data disclosed the nature of the protective exposures in a farm. Current evidence points toward an important role of the host microbiome in setting an immunological equilibrium that determines progression toward, or protection against allergic diseases. Conclusive mechanistic insights on how microbial exposures prevent from developing allergic diseases in humans are still lacking but findings from experimental models reveal plausible immunological mechanisms. Gathering further knowledge on these mechanisms and confirming their relevance in humans is of great importance to develop preventive strategies for children at risk of developing allergies.
Collapse
Affiliation(s)
- Julie Deckers
- Laboratory of Immunoregulation and Mucosal Immunology, VIB Center for Inflammation Research, Ghent (Zwijnaarde), Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Erika von Mutius
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Lung Research, München, Germany.,Dr. von Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| |
Collapse
|
28
|
Alamri A. Diversity of Microbial Signatures in Asthmatic Airways. Int J Gen Med 2021; 14:1367-1378. [PMID: 33889017 PMCID: PMC8057789 DOI: 10.2147/ijgm.s304339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a chronic inflammatory disease affecting the respiratory system. The global incidence of asthma is rising. Clinical and experimental models of asthma clearly indicate that the disease is multifactorial in nature with a wide array of factors contributing to progression and exacerbation, including interactions between immunological markers and the microbial community populating the respiratory tract. In particular, strict hygiene compliance during the early years of life and early exposure to antibiotics are linked to alterations in the biological environment within the airways and to changes in immunological markers, leading to allergies, such as asthma. With the gap in current research knowledge on the various non-bacterial microbial communities in the asthmatic airways, this review summarizes current methods used to assess microbial diversity as well as evidence for the link between microbial alterations and asthma, including changes in the bacterial microbiome, often characterized by the outgrowth of certain bacterial phyla such as proteobacteria and Firmicutes, in addition to disrupted mycobiome, virome, and parasitome. The current review emphasizes the dynamic, context-dependent changes in the microbiome in asthma and the importance of broad-scope analyses, covering a wide range of taxa. In conclusion, the interaction between the resident microbiota and the immune system is essential and significant in modulating the inflammatory responses; however, further investigations are needed to improve our understanding of the risk factors that disrupt the diversity of the microbiome in the different body systems.
Collapse
Affiliation(s)
- Aisha Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| |
Collapse
|
29
|
Ling Z, Zhu M, Liu X, Shao L, Cheng Y, Yan X, Jiang R, Wu S. Fecal Fungal Dysbiosis in Chinese Patients With Alzheimer's Disease. Front Cell Dev Biol 2021; 8:631460. [PMID: 33585471 PMCID: PMC7876328 DOI: 10.3389/fcell.2020.631460] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023] Open
Abstract
Gut bacterial dysbiosis plays a vital role in the development of Alzheimer’s disease (AD). However, our understanding of alterations to the gut fungal microbiota and their correlations with host immunity in AD is still limited. Samples were obtained from 88 Chinese patients with AD, and 65 age- and gender-matched, cognitively normal controls. Using these samples, we investigated the fungal microbiota targeting internal transcribed spacer 2 (ITS2) rRNA genes using MiSeq sequencing, and analyzed their associations with the host immune response. Our data demonstrated unaltered fungal diversity but altered taxonomic composition of the fecal fungal microbiota in the AD patients. The analysis of the fungal microbiota was performed using 6,585,557 high-quality reads (2,932,482 reads from the controls and 3,653,075 from the AD patients), with an average of 43,042 reads per sample. We found that several key differential fungi such as Candida tropicalis and Schizophyllum commune were enriched in the AD patients, while Rhodotorula mucilaginosa decreased significantly. Interestingly, C. tropicalis and S. commune were positively correlated with IP-10 and TNF-α levels. In contrast, C. tropicalis was negatively correlated with IL-8 and IFN-γ levels, and R. mucilaginosa was negatively correlated with TNF-α level. PiCRUSt analysis revealed that lipoic acid metabolism, starch and sucrose metabolism were significantly decreased in the AD fungal microbiota. This study is the first to demonstrate fecal fungal dysbiosis in stable AD patients at a deeper level, and to identify the key differential fungi involved in regulating host systemic immunity. The analysis of the fungal microbiota in AD performed here may provide novel insights into the etiopathogenesis of AD and pave the way for improved diagnosis and treatment of AD.
Collapse
Affiliation(s)
- Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Manlian Zhu
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Xia Liu
- Department of Intensive Care Unit, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Shao
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China.,Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yiwen Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiumei Yan
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Ruilai Jiang
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Shaochang Wu
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| |
Collapse
|