201
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Glendinning L, Wright S, Pollock J, Tennant P, Collie D, McLachlan G. Variability of the Sheep Lung Microbiota. Appl Environ Microbiol 2016; 82:3225-3238. [PMID: 26994083 PMCID: PMC4959240 DOI: 10.1128/aem.00540-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/15/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Sequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n = 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota. IMPORTANCE Until recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the "lung microbiota." In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Steven Wright
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jolinda Pollock
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
- Monogastric Science Research Centre, Scotland's Rural College (SRUC), Edinburgh, Midlothian, United Kingdom
| | - Peter Tennant
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - David Collie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Gerry McLachlan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
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202
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Smits HH, van der Vlugt LE, von Mutius E, Hiemstra PS. Childhood allergies and asthma: New insights on environmental exposures and local immunity at the lung barrier. Curr Opin Immunol 2016; 42:41-47. [PMID: 27254380 DOI: 10.1016/j.coi.2016.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 12/11/2022]
Abstract
While certain bacteria and respiratory viruses promote local inflammation and disease onset, a more diverse colonization of the different species in the (gut) microbiome may be linked to more regulatory responses and protection against asthma and allergies. These processes are also influenced in part by food intake, both targeting the composition of the gut microbiome and influencing the immune system via metabolites. Early life environmental microbial exposure also contributes to protection against asthma and allergy and is linked with an early activation of the innate immune system and the development of regulatory immune responses. Although greater mechanistic insight is needed, it is tempting to speculate that part of the environmental effect can be explained by modulation of the microbiome composition at mucosal surfaces, epithelial barrier function and/or local immunity. A review of the latest studies is provided.
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Affiliation(s)
- Hermelijn H Smits
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Luciën Epm van der Vlugt
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands; Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Erika von Mutius
- Dr von Hauner Children's Hospital, Ludwig Maximilians University of Munich, Munich, Germany; Comprehensive Pneumology Centre Munich (CPC-M), Member of the German Center for Lung Research, Germany
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
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203
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Nguyen AT, Oglesby-Sherrouse AG. Interactions between Pseudomonas aeruginosa and Staphylococcus aureus during co-cultivations and polymicrobial infections. Appl Microbiol Biotechnol 2016; 100:6141-6148. [PMID: 27236810 DOI: 10.1007/s00253-016-7596-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa and Staphylococcus aureus are versatile bacterial pathogens and common etiological agents in polymicrobial infections. Microbial communities containing both of these pathogens are shaped by interactions ranging from parasitic to mutualistic, with the net impact of these interactions in many cases resulting in enhanced virulence. Polymicrobial communities of these organisms are further defined by multiple aspects of the host environment, with important implications for disease progression and therapeutic outcomes. This mini-review highlights the impact of these interactions on the host and individual pathogens, the molecular mechanisms that underlie these interactions, and host-specific factors that drive interactions between these two important pathogens.
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Affiliation(s)
- Angela T Nguyen
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Amanda G Oglesby-Sherrouse
- School of Pharmacy, Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA. .,School of Medicine, Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.
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204
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de Steenhuijsen Piters WAA, Sanders EAM, Bogaert D. The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0294. [PMID: 26150660 DOI: 10.1098/rstb.2014.0294] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form-together with harmless commensal bacteria, viruses and fungi-intricate ecological networks, collectively known as the 'microbiome'. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands
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205
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Lim MY, Yoon HS, Rho M, Sung J, Song YM, Lee K, Ko G. Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans. Sci Rep 2016; 6:23745. [PMID: 27030383 PMCID: PMC4814871 DOI: 10.1038/srep23745] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/14/2016] [Indexed: 01/30/2023] Open
Abstract
Recent studies showing clear differences in the airway microbiota between healthy and diseased individuals shed light on the importance of the airway microbiota in health. Here, we report the associations of host genetics and lifestyles such as smoking, alcohol consumption, and physical activity with the composition of the sputum microbiota using 16S rRNA gene sequence data generated from 257 sputum samples of Korean twin-family cohort. By estimating the heritability of each microbial taxon, we found that several taxa, including Providencia and Bacteroides, were significantly influenced by host genetic factors. Smoking had the strongest effect on the overall microbial community structure among the tested lifestyle factors. The abundances of Veillonella and Megasphaera were higher in current-smokers, and increased with the pack-year value and the Fagerstrom Test of Nicotine Dependence (FTND) score. In contrast, Haemophilus decreased with the pack-year of smoking and the FTND score. Co-occurrence network analysis showed that the taxa were clustered according to the direction of associations with smoking, and that the taxa influenced by host genetics were found together. These results demonstrate that the relationships among sputum microbial taxa are closely associated with not only smoking but also host genetics.
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Affiliation(s)
- Mi Young Lim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hyo Shin Yoon
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Mina Rho
- Division of Computer Science and Engineering, College of Engineering, Hanyang University, Seoul, Republic of Korea
| | - Joohon Sung
- Department of Epidemiology, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Center for Human and Environmental Microbiome, Seoul National University, Seoul, Republic of Korea
- N-Bio, Seoul National University, Seoul, Republic of Korea
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206
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Hiergeist A, Reischl U, Gessner A. Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. Int J Med Microbiol 2016; 306:334-342. [PMID: 27052158 DOI: 10.1016/j.ijmm.2016.03.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 02/06/2023] Open
Abstract
The composition of human as well as animal microbiota has increasingly gained in interest since metabolites and structural components of endogenous microorganisms fundamentally influence all aspects of host physiology. Since many of the bacteria are still unculturable, molecular techniques such as high-throughput sequencing have dramatically increased our knowledge of microbial communities. The majority of microbiome studies published thus far are based on bacterial 16S ribosomal RNA (rRNA) gene sequencing, so that they can, at least in principle, be compared to determine the role of the microbiome composition for host metabolism and physiology, developmental processes, as well as different diseases. However, differences in DNA preparation and purification, 16S rDNA PCR amplification, sequencing procedures and platforms, as well as bioinformatic analysis and quality control measures may strongly affect the microbiome composition results obtained in different laboratories. To systematically evaluate the comparability of results and identify the most influential methodological factors affecting these differences, identical human stool sample replicates spiked with quantified marker bacteria, and their subsequent DNA sequences were analyzed by nine different centers in an external quality assessment (EQA). While high intra-center reproducibility was observed in repetitive tests, significant inter-center differences of reported microbiota composition were obtained. All steps of the complex analysis workflow significantly influenced microbiome profiles, but the magnitude of variation caused by PCR primers for 16S rDNA amplification was clearly the largest. In order to advance microbiome research to a more standardized and routine medical diagnostic procedure, it is essential to establish uniform standard operating procedures throughout laboratories and to initiate regular proficiency testing.
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Affiliation(s)
- Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Udo Reischl
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
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207
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Kawano H, Kayama H, Nakama T, Hashimoto T, Umemoto E, Takeda K. IL-10-producing lung interstitial macrophages prevent neutrophilic asthma. Int Immunol 2016; 28:489-501. [PMID: 26976823 DOI: 10.1093/intimm/dxw012] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/09/2016] [Indexed: 12/15/2022] Open
Abstract
Inflammatory responses contribute to host defense against harmful organisms and allergens, whereas a failure of immune tolerance can cause chronic inflammation including asthma. The lung has several innate myeloid cell subsets. Among these subsets, there are two types of macrophages: alveolar macrophages (AMs) and interstitial macrophages (IMs). However, compared with AMs, the role of IMs in lung homeostasis remains poorly understood. In this study, we characterized AMs and IMs in healthy and inflammatory conditions. Pulmonary IMs constitutively produce the anti-inflammatory cytokine IL-10 through activation of the TLR4/MyD88 pathway in a microbiota-independent manner. In addition to IMs, Foxp3+ Treg cells show persistent IL-10 expression in the lung, with IL-10-producing IMs more prevalent than Foxp3+ Treg cells. IMs, but not Foxp3+ Treg cells, increased IL-10 production in house dust mite (HDM)-challenged mice, a model of human asthma. HDM-challenged Il10 -/- mice exhibited severe lung pathology characterized by neutrophilia compared with that of wild-type mice. In addition, transplantation of wild-type IMs reduced neutrophilic inflammation, goblet cell mucus production and decreased expression of lung IL-13 and Th17-related neutrophil-activating cytokines such as IL-17, GM-CSF, and TNF-α. Together these results demonstrate that IL-10-producing IMs negatively regulate Th2- and Th17-mediated inflammatory responses, helping prevent neutrophilic asthma.
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Affiliation(s)
- Hideo Kawano
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine and Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Department of Dermatology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Hisako Kayama
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine and Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
| | - Takekuni Nakama
- Department of Dermatology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Takashi Hashimoto
- Kurume University Institute of Cutaneous Cell Biology, Kurume, Fukuoka 830-0011, Japan
| | - Eiji Umemoto
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine and Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine and Laboratory of Mucosal Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
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208
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Protective and pro-inflammatory roles of intestinal bacteria. ACTA ACUST UNITED AC 2016; 23:67-80. [PMID: 26947707 DOI: 10.1016/j.pathophys.2016.02.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 02/06/2023]
Abstract
The intestinal mucosal surface in all vertebrates is exposed to enormous numbers of microorganisms that include bacteria, archaea, fungi and viruses. Coexistence of the host with the gut microbiota represents an active and mutually beneficial relationship that helps to shape the mucosal and systemic immune systems of both mammals and teleosts (ray-finned fish). Due to the potential for enteric microorganisms to invade intestinal tissue and induce local and/or systemic inflammation, the mucosal immune system has developed a number of protective mechanisms that allow the host to mount an appropriate immune response to invading bacteria, while limiting bystander tissue injury associated with these immune responses. Failure to properly regulate mucosal immunity is thought to be responsible for the development of chronic intestinal inflammation. The objective of this review is to present our current understanding of the role that intestinal bacteria play in vertebrate health and disease. While our primary focus will be humans and mice, we also present the new and exciting comparative studies being performed in zebrafish to model host-microbe interactions.
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209
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Xu Z, Takizawa F, Parra D, Gómez D, von Gersdorff Jørgensen L, LaPatra SE, Sunyer JO. Mucosal immunoglobulins at respiratory surfaces mark an ancient association that predates the emergence of tetrapods. Nat Commun 2016; 7:10728. [PMID: 26869478 PMCID: PMC4754351 DOI: 10.1038/ncomms10728] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/14/2016] [Indexed: 12/24/2022] Open
Abstract
Gas-exchange structures are critical for acquiring oxygen, but they also represent portals for pathogen entry. Local mucosal immunoglobulin responses against pathogens in specialized respiratory organs have only been described in tetrapods. Since fish gills are considered a mucosal surface, we hypothesized that a dedicated mucosal immunoglobulin response would be generated within its mucosa on microbial exposure. Supporting this hypothesis, here we demonstrate that following pathogen exposure, IgT+ B cells proliferate and generate pathogen-specific IgT within the gills of fish, thus providing the first example of locally induced immunoglobulin in the mucosa of a cold-blooded species. Moreover, we demonstrate that gill microbiota is predominantly coated with IgT, thus providing previously unappreciated evidence that the microbiota present at a respiratory surface of a vertebrate is recognized by a mucosal immunoglobulin. Our findings indicate that respiratory surfaces and mucosal immunoglobulins are part of an ancient association that predates the emergence of tetrapods. In teleost fish the gills perform—in addition to respiration—functions such as immune defence. Here the authors show that IgT, a teleost specific Ig previously shown to be involved in gut and skin mucosal immunity, is locally induced in the gill, where it plays a key role in immunity in rainbow trout.
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Affiliation(s)
- Zhen Xu
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA.,Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Fumio Takizawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
| | - David Parra
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Daniela Gómez
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
| | - Louise von Gersdorff Jørgensen
- Laboratory of Aquatic Pathobiology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiskberg DK-1870, Denmark
| | - Scott E LaPatra
- Research Division, Clear Springs Foods Inc., P O Box 712, Buhl, Idaho 83316, USA
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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210
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Hiemstra PS, Amatngalim GD, van der Does AM, Taube C. Antimicrobial Peptides and Innate Lung Defenses: Role in Infectious and Noninfectious Lung Diseases and Therapeutic Applications. Chest 2016; 149:545-551. [PMID: 26502035 DOI: 10.1378/chest.15-1353] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/31/2015] [Accepted: 09/21/2015] [Indexed: 11/01/2022] Open
Abstract
Respiratory infections are a major clinical problem, and treatment is increasingly complicated by the emergence of microbial antibiotic resistance. Development of new antibiotics is notoriously costly and slow; therefore, alternative strategies are needed. Antimicrobial peptides, central effector molecules of the immune system, are being considered as alternatives to conventional antibiotics. These peptides display a range of activities, including not only direct antimicrobial activity, but also immunomodulation and wound repair. In the lung, airway epithelial cells and neutrophils in particular contribute to their synthesis. The relevance of antimicrobial peptides for host defense against infection has been demonstrated in animal models and is supported by observations in patient studies, showing altered expression and/or unfavorable circumstances for their action in a variety of lung diseases. Importantly, antimicrobial peptides are active against microorganisms that are resistant against conventional antibiotics, including multidrug-resistant bacteria. Several strategies have been proposed to use these peptides in the treatment of infections, including direct administration of antimicrobial peptides, enhancement of their local production, and creation of more favorable circumstances for their action. In this review, recent developments in antimicrobial peptides research in the lung and clinical applications for novel therapies of lung diseases are discussed.
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Affiliation(s)
- Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Gimano D Amatngalim
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anne M van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christian Taube
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
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211
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Affiliation(s)
- Linh Nguyen
- Centre d'immunologie et d'infectiologie de Lille (BDEEP), Inserm U1019, CNRS UMR 8204, Institut Pasteur de Lille, université de Lille Nord de France, 1, rue du Professeur Calmette, 59019 Lille Cedex, France
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212
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Andréjak C, Delhaes L. [The lung microbiome in 2015: a window on chronic lung diseases]. Med Sci (Paris) 2015; 31:971-8. [PMID: 26576604 DOI: 10.1051/medsci/20153111011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recent development of high-throughput sequencing methods has shown that the human respiratory tract (including lower airways) is not sterile as formerly thought, but composed of a previously unappreciated complex microbial community referred as the lung microbiome and composed of bacteria, viruses and fungi. However, many questions remain unresolved, especially in terms of lung microbiome role, its interactions with host but also with environmental pathogens. Although data are still limited, links have already been demonstrated between lung microbiome and chronic respiratory diseases (such as asthma, chronic obstructive pulmonary disease or cystic fibrosis). This lung microbiome appears to play an important role both in disease genesis and evolution, and consequently offers an emerging research field.
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Affiliation(s)
- Claire Andréjak
- Service de pneumologie et réanimation respiratoire, CHU d'Amiens, EA 4294, université de Picardie Jules Verne, 80000 Amiens, France
| | - Laurence Delhaes
- Centre d'immunologie et d'infectiologie de Lille (BDEEP), Inserm U1019, CNRS UMR 8204, Institut Pasteur de Lille, université de Lille Nord de France, 1, rue du Professeur Calmette, 59019 Lille Cedex, France - Laboratoire de parasitologie-mycologie, CHRU de Lille, faculté de médecine, université Lille2, Lille, France - Adresse actuelle : Service de parasitologie- Mycologie, CHU de Bordeaux, université de Bordeaux, France
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213
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Patarčić I, Gelemanović A, Kirin M, Kolčić I, Theodoratou E, Baillie KJ, de Jong MD, Rudan I, Campbell H, Polašek O. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis. Sci Rep 2015; 5:16119. [PMID: 26524966 PMCID: PMC4630784 DOI: 10.1038/srep16119] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022] Open
Abstract
Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.
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Affiliation(s)
- Inga Patarčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Andrea Gelemanović
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Mirna Kirin
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Midlothian, UK.,Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, Split, Croatia.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
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214
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Barfod KK, Vrankx K, Mirsepasi-Lauridsen HC, Hansen JS, Hougaard KS, Larsen ST, Ouwenhand AC, Krogfelt KA. The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment. Open Microbiol J 2015; 9:167-79. [PMID: 26668669 PMCID: PMC4676059 DOI: 10.2174/1874285801509010167] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022] Open
Abstract
Most microbiome research related to airway diseases has focused on the gut microbiome. This is despite advances
in culture independent microbial identification techniques revealing that even healthy lungs possess a unique dynamic
microbiome. This conceptual change raises the question; if lung diseases could be causally linked to local dysbiosis
of the local lung microbiota. Here, we manipulate the murine lung and gut microbiome, in order to show that the lung microbiota
can be changed experimentally. We have used four different approaches: lung inflammation by exposure to carbon
nano-tube particles, oral probiotics and oral or intranasal exposure to the antibiotic vancomycin. Bacterial DNA was
extracted from broncho-alveolar and nasal lavage fluids, caecum samples and compared by DGGE. Our results show that:
the lung microbiota is sex dependent and not just a reflection of the gut microbiota, and that induced inflammation can
change lung microbiota. This change is not transferred to offspring. Oral probiotics in adult mice do not change lung microbiome
detectible by DGGE. Nasal vancomycin can change the lung microbiome preferentially, while oral exposure
does not. These observations should be considered in future studies of the causal relationship between lung microbiota
and lung diseases.
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Affiliation(s)
| | - Katleen Vrankx
- Applied Maths, Keistraat 120, 9830 Sint-Martens-Latem, Belgium
| | | | - Jitka Stilund Hansen
- National Research Centre for the Working Environment, Lersø parkallé 105, 2100 Denmark
| | - Karin Sørig Hougaard
- National Research Centre for the Working Environment, Lersø parkallé 105, 2100 Denmark
| | - Søren Thor Larsen
- National Research Centre for the Working Environment, Lersø parkallé 105, 2100 Denmark
| | - Arthur C Ouwenhand
- Active Nutrition, Dupont Nutrition & Health, Sokeritehtaantie 20, 02460 Kantvik Finland
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215
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Babickova J, Gardlik R. Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease. World J Gastroenterol 2015; 21:11321-11330. [PMID: 26525290 PMCID: PMC4616208 DOI: 10.3748/wjg.v21.i40.11321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/26/2015] [Accepted: 09/14/2015] [Indexed: 02/06/2023] Open
Abstract
The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided.
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216
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Kwon O, Lee S, Kim JH, Kim H, Lee SW. Altered Gut Microbiota Composition in Rag1-deficient Mice Contributes to Modulating Homeostasis of Hematopoietic Stem and Progenitor Cells. Immune Netw 2015; 15:252-9. [PMID: 26557809 PMCID: PMC4637346 DOI: 10.4110/in.2015.15.5.252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 01/11/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) can produce all kind of blood lineage cells, and gut microbiota that consists of various species of microbe affects development and maturation of the host immune system including gut lymphoid cells and tissues. However, the effect of altered gut microbiota composition on homeostasis of HSPCs remains unclear. Here we show that compositional change of gut microbiota affects homeostasis of HSPCs using Rag1-/- mice which represent lymphopenic condition. The number and proportions of HSPCs in Rag1-/- mice are lower compared to those of wild types. However, the number and proportions of HSPCs in Rag1-/- mice are restored as the level of wild types through alteration of gut microbiota diversity via transferring feces from wild types. Gut microbiota composition of Rag1-/- mice treated with feces from wild types shows larger proportions of family Prevotellaceae and Helicobacterceae whereas lower proportions of family Lachnospiraceae compared to unmanipulated Rag1-/- mice. In conclusion, gut microbiota composition of lymphopenic Rag1-/- mice is different to that of wild type, which may lead to altered homeostasis of HSPCs.
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Affiliation(s)
- Ohseop Kwon
- Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Seungwon Lee
- Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ji-Hae Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Hyekang Kim
- Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Seung-Woo Lee
- Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea. ; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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217
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Cillóniz C, Civljak R, Nicolini A, Torres A. Polymicrobial community-acquired pneumonia: An emerging entity. Respirology 2015; 21:65-75. [PMID: 26494527 DOI: 10.1111/resp.12663] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/21/2015] [Accepted: 07/28/2015] [Indexed: 12/13/2022]
Abstract
Polymicrobial aetiology in community-acquired pneumonia (CAP) is more common than previously recognized. This growing new entity can influence inflammation, host immunity and disease outcomes in CAP patients. However, the true incidence is complicated to determine and probably underestimated due mainly to many cases going undetected, particularly in the outpatient setting, as the diagnostic yield is restricted by the sensitivity of currently available microbiologic tests and the ability to get certain types of clinical specimens. The observed rate of polymicrobial cases may also lead to new antibiotic therapy considerations. In this review, we discuss the pathogenesis, microbial interactions in pneumonia, epidemiology, biomarkers and antibiotic therapy for polymicrobial CAP.
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Affiliation(s)
- Catia Cillóniz
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona (UB)-SGR 911-, Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Rok Civljak
- University of Zagreb School of Medicine, 'Dr. Fran Mihaljevic' University Hospital for Infectious Diseases, Zagreb, Croatia
| | | | - Antoni Torres
- Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona-August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona (UB)-SGR 911-, Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
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218
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Bikov A, Boots A, Bjerg A, Jacinto T, Olland A, Skoczyński S. 13th ERS Lung Science Conference. The most important take home messages: News from the Underground. Breathe (Sheff) 2015; 11:149-52. [PMID: 26306116 PMCID: PMC4487375 DOI: 10.1183/20734735.04015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The 13th ERS Lung Science Conference (LSC) was organised to bring academics together from all over the world to present and discuss the latest developments regarding lung infection and immunity. The conference took place in breathtaking Estoril, Portugal; however, it wasn't the beautiful surroundings that were our main motivation to attend, but instead the scientific merit of the conference and the chance to create new scientific collaborations. The scientific programme [1] was packed with the most up-to-date content in the field of lung infection and immunity and included some of the top researchers within this exciting area. Moreover, the convenient size of the LSC offered the opportunity to renew and intensify friendships and collaborations. In particular, for researchers at the start of their career, this is a great feature and we therefore warmly recommend the LSC to ERS Juniors Members!
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Affiliation(s)
- Andras Bikov
- Dept of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Agnes Boots
- Dept of Pharmacology and Toxicology, Maastricht University, Maastricht, the Netherlands
| | - Anders Bjerg
- Krefting Research Center, Dept of Internal Medicine and Clinical Nutrition, University of Gothenburg, Göteborg, Sweden
| | | | - Anne Olland
- Lung Transplantation Group, Thoracic Surgery Dept, University Hospital Strasbourg, France
| | - Szymon Skoczyński
- Lung Transplantation Group, Thoracic Surgery Dept, University Hospital Strasbourg, France
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219
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de Steenhuijsen Piters WAA, Sanders EAM, Bogaert D. The role of the local microbial ecosystem in respiratory health and disease. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140294. [PMID: 26150660 PMCID: PMC4528492 DOI: 10.1098/rstb.2014.0294;] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form-together with harmless commensal bacteria, viruses and fungi-intricate ecological networks, collectively known as the 'microbiome'. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.
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Affiliation(s)
- Wouter A. A. de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands,Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, The Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht, The Netherlands,e-mail:
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220
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Abstract
The respiratory disease field is changing because of recent advances in our understanding of the airway microbiome. Central to this is dysbiosis, an imbalance of microbial communities that can lead to and flag inflammation in the airways. The increasing momentum of research in this area holds promise for novel treatment strategies.
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Affiliation(s)
- Olawale Salami
- Department of Biology and Medicine, Service de Pneumologie, CHUV-UNIL, Lausanne, Switzerland
| | - Benjamin J Marsland
- Department of Biology and Medicine, Service de Pneumologie, CHUV-UNIL, Lausanne, Switzerland
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221
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Abstract
Microbes are ubiquitous on the human body and comprise approximately 90% of the cells and 99% of the genes of the human supraorganism. High-throughput sequencing technology has permitted the development of culture-independent means to identify the microbiota that are unique to the various microenvironments of the body and probably contribute some function. Although the respiratory tract interfaces with the environment, the lungs were always thought to be a sterile environment - until recently, when these techniques were applied to healthy and disease states. Further, there appears to be a complex interplay between the development of the gastrointestinal and respiratory microbiota and the regulation of immune function. The contribution of this dynamic metabolic mass to respiratory disease in the newborn is unknown. This article will review emerging data from recent human and murine studies that suggest there is a microbial influence on the development of respiratory disease, but it will also highlight many of the gaps that remain in understanding the function of the respiratory microbiome.
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Affiliation(s)
- Barbara B. Warner
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO USA
| | - Aaron Hamvas
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO USA
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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222
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Bagdonas E, Raudoniute J, Bruzauskaite I, Aldonyte R. Novel aspects of pathogenesis and regeneration mechanisms in COPD. Int J Chron Obstruct Pulmon Dis 2015; 10:995-1013. [PMID: 26082624 PMCID: PMC4459624 DOI: 10.2147/copd.s82518] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), a major cause of death and morbidity worldwide, is characterized by expiratory airflow limitation that is not fully reversible, deregulated chronic inflammation, and emphysematous destruction of the lungs. Despite the fact that COPD is a steadily growing global healthcare problem, the conventional therapies remain palliative, and regenerative approaches for disease management are not available yet. We aim to provide an overview of key reviews, experimental, and clinical studies addressing lung emphysema development and repair mechanisms published in the past decade. Novel aspects discussed herein include integral revision of the literature focused on lung microflora changes in COPD, autoimmune component of the disease, and environmental risk factors other than cigarette smoke. The time span of studies on COPD, including emphysema, chronic bronchitis, and asthmatic bronchitis, covers almost 200 years, and several crucial mechanisms of COPD pathogenesis are described and studied. However, we still lack the holistic understanding of COPD development and the exact picture of the time-course and interplay of the events during stable, exacerbated, corticosteroid-treated COPD states, and transitions in-between. Several generally recognized mechanisms will be discussed shortly herein, ie, unregulated inflammation, proteolysis/antiproteolysis imbalance, and destroyed repair mechanisms, while novel topics such as deviated microbiota, air pollutants-related damage, and autoimmune process within the lung tissue will be discussed more extensively. Considerable influx of new data from the clinic, in vivo and in vitro studies stimulate to search for novel concise explanation and holistic understanding of COPD nowadays.
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Affiliation(s)
- Edvardas Bagdonas
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
| | - Jovile Raudoniute
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
| | - Ieva Bruzauskaite
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
| | - Ruta Aldonyte
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
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223
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Boer MC, Joosten SA, Ottenhoff THM. Regulatory T-Cells at the Interface between Human Host and Pathogens in Infectious Diseases and Vaccination. Front Immunol 2015; 6:217. [PMID: 26029205 PMCID: PMC4426762 DOI: 10.3389/fimmu.2015.00217] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 12/20/2022] Open
Abstract
Regulatory T-cells (Tregs) act at the interface of host and pathogen interactions in human infectious diseases. Tregs are induced by a wide range of pathogens, but distinct effects of Tregs have been demonstrated for different pathogens and in different stages of infection. Moreover, Tregs that are induced by a specific pathogen may non-specifically suppress immunity against other microbes and parasites. Thus, Treg effects need to be assessed not only in homologous but also in heterologous infections and vaccinations. Though Tregs protect the human host against excessive inflammation, they probably also increase the risk of pathogen persistence and chronic disease, and the possibility of disease reactivation later in life. Mycobacterium leprae and Mycobacterium tuberculosis, causing leprosy and tuberculosis, respectively, are among the most ancient microbes known to mankind, and are master manipulators of the immune system toward tolerance and pathogen persistence. The majority of mycobacterial infections occur in settings co-endemic for viral, parasitic, and (other) bacterial coinfections. In this paper, we discuss recent insights in the activation and activity of Tregs in human infectious diseases, with emphasis on early, late, and non-specific effects in disease, coinfections, and vaccination. We highlight mycobacterial infections as important models of modulation of host responses and vaccine-induced immunity by Tregs.
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Affiliation(s)
- Mardi C Boer
- Department of Infectious Diseases, Leiden University Medical Center , Leiden , Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center , Leiden , Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center , Leiden , Netherlands
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224
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DeRiemer K, Thompson G. Lung Microbiomes: New Frontiers? Am J Respir Crit Care Med 2015; 191:870-1. [DOI: 10.1164/rccm.201502-0226ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Kathryn DeRiemer
- School of MedicineUniversity of California, DavisDavis, California
| | - George Thompson
- School of MedicineUniversity of California, DavisDavis, California
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225
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Schröder PC, Li J, Wong GWK, Schaub B. The rural-urban enigma of allergy: what can we learn from studies around the world? Pediatr Allergy Immunol 2015; 26:95-102. [PMID: 25620193 DOI: 10.1111/pai.12341] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 12/27/2022]
Abstract
Childhood asthma and related allergic conditions have become the most common chronic disorders in the Western world. Many studies from around the world have demonstrated an increasing trend of asthma prevalence over the last few decades (Lancet, 368, 2004, 733). A few recent reports also suggested that childhood asthma prevalence may be showing a plateau or even a decline in few developed countries. Given the rapid changes in the prevalence over a short period of time, environmental factors are the more likely candidates explaining such trend. One of the most consistent epidemiological findings was that subjects living in the rural areas had lower prevalence of allergies when compared to those from urban areas (Clin Exp Allergy 30, 2000, 187; Pediatr Pulmonol 44, 2009, 793). Clear understanding of the mechanisms of how the environmental determinants in the rural environment may affect the early immune system resulting in lower risk of allergies and asthma will facilitate the development of future primary preventive strategies. In this study, we review recent data from around the world and explore the epidemiology and mechanistic studies that may explain the rural-urban difference of allergies.
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Affiliation(s)
- Paul C Schröder
- LMU Munich, University Children's Hospital, Munich, Germany; Member of the German Center for Lung Research (DZL), Munich, Germany
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226
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Nguyen LDN, Viscogliosi E, Delhaes L. The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol 2015; 6:89. [PMID: 25762987 PMCID: PMC4327734 DOI: 10.3389/fmicb.2015.00089] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/23/2015] [Indexed: 01/29/2023] Open
Abstract
The lung microbiome, which is believed to be stable or at least transient in healthy people, is now considered as a poly-microorganism component contributing to disease pathogenesis. Most research studies on the respiratory microbiome have focused on bacteria and their impact on lung health, but there is evidence that other non-bacterial organisms, comprising the viruses (virome) and fungi (mycobiome), are also likely to play an important role in healthy people as well as in patients. In the last few years, the lung mycobiome (previously named the fungal microbiota or microbiome) has drawn closer attention. There is growing evidence that the lung mycobiome has a significant impact on clinical outcome of chronic respiratory diseases (CRD) such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis. Thanks to advances in culture independent methods, especially next generation sequencing, a number of fungi not detected by culture methods have been molecularly identified in human lungs. It has been shown that the structure and diversity of the lung mycobiome vary in different populations (healthy and different diseased individuals) which could play a role in CRD. Moreover, the link between lung mycobiome and different biomes of other body sites, especially the gut, has also been unraveled. By interacting with the bacteriome and/or virome, the respiratory mycobiome appears to be a cofactor in inflammation and in the host immune response, and therefore may contribute to the decline of the lung function and the disease progression. In this review, we report the recent limited explorations of the human respiratory mycobiome, and discuss the mycobiome’s connections with other local microbial communities, as well as the relationships with the different biomes of other body sites. These studies suggest several outlooks for this understudied emerging field, which will certainly call for a renewal of our understanding of pulmonary diseases.
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Affiliation(s)
- Linh D N Nguyen
- Biology and Diversity of Emerging Eukaryotic Pathogens, Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, Lille Pasteur Institute, University of Lille Nord de France , Lille, France
| | - Eric Viscogliosi
- Biology and Diversity of Emerging Eukaryotic Pathogens, Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, Lille Pasteur Institute, University of Lille Nord de France , Lille, France
| | - Laurence Delhaes
- Biology and Diversity of Emerging Eukaryotic Pathogens, Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, Lille Pasteur Institute, University of Lille Nord de France , Lille, France ; Parasitology-Mycology Department, Hospital University Center, Faculty of Medicine , Lille, France
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