The Microbiome in Cystic Fibrosis

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Abstract

Observations from studies during the last decade have changed the conventional view of cystic fibrosis (CF) microbiology, which has traditionally focused on a limited suite of opportunistic bacterial pathogens. It is now appreciated that CF airways typically harbor complex microbial communities, and that changes in the structure and activity of these communities have a bearing on patient clinical condition and lung disease progression. Recent studies of gut microbiota also suggest that disordered bacterial ecology of the CF gastrointestinal tract is associated with pulmonary outcomes. These new insights may alter future clinical management of CF.

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Most cited references 37

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The role of the bacterial microbiome in lung disease.

Robert P. Dickson, Gary Huffnagle, John Erb-Downward (2013)

Novel culture-independent techniques have recently demonstrated that the lower respiratory tract, historically considered sterile in health, contains diverse communities of microbes: the lung microbiome. Increasing evidence supports the concept that a distinct microbiota of the lower respiratory tract is present both in health and in various respiratory diseases, although the biological and clinical significance of these findings remains undetermined. In this article, the authors review and synthesize published reports of the lung microbiota of healthy and diseased subjects, discuss trends of microbial diversity and constitution across disease states, and look to the extrapulmonary microbiome for hypotheses and future directions for study.

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Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis.

Robert P. Dickson, John Erb-Downward, Gary Huffnagle (2014)

Pneumonia is a major cause of morbidity and mortality for which no new methods of treatment have entered clinical practice since the discovery of antibiotics. Innovations in the techniques of culture-independent microbial identification have shown that the lungs, previously deemed sterile in the absence of infection, contain diverse and dynamic communities of microbes. In this Personal View, we argue that these observations have shown the inadequacy of traditional conceptual models of lung microbiology and the pathogenesis of pneumonia, hampering progress in research and practice. We propose three new conceptual models to replace the traditional models of lung microbiology: an adapted island model of lung biogeography, the effect of environmental gradients on lung microbiota, and pneumonia as an emergent phenomenon propelled by unexplored positive feedback loops. We argue that the ecosystem of lung microbiota has all of the features of a complex adaptive system: diverse entities interacting with each other within a common space, showing interdependent actions and possessing the capacity to adapt to changes in conditions. Complex adaptive systems are fundamentally different in behaviour from the simple, linear systems typified by the traditional model of pneumonia pathogenesis, and need distinct analytical approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

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The lung mycobiome: an emerging field of the human respiratory microbiome

Linh D. N. Nguyen, Eric Viscogliosi, Laurence Delhaes (2015)

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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Author and article information

Contributors

Yvonne J. Huang

Journal

Journal ID (nlm-ta): Clin Chest Med

Journal ID (iso-abbrev): Clin. Chest Med

Title: Clinics in Chest Medicine

Publisher: Elsevier Inc.

ISSN (Print): 0272-5231

ISSN (Electronic): 1557-8216

Publication date PMC-release: 23 December 2015

Publication date (Print): March 2016

Publication date (Electronic): 23 December 2015

Volume: 37

Issue: 1

Pages: 59-67

Affiliations

[a ]Division of Pulmonary/Critical Care Medicine, University of Michigan Medical School, 6301 MSRB III/SPC 5642, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA

[b ]Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, 8323 MSRB III/SPC 5646, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA

Author notes

[∗ ]Corresponding author. 6301 MSRB III/SPC 5642, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5642. yvjhuang@ 123456umich.edu

Article

Publisher ID: S0272-5231(15)00137-9

DOI: 10.1016/j.ccm.2015.10.003

PMC ID: 5154676

PubMed ID: 26857768

SO-VID: af7daac9-25e7-4079-909e-1efa307cdfac

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Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

The Microbiome in Cystic Fibrosis

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Inflamed lung in vitro co-culture models

Most cited references 37

The role of the bacterial microbiome in lung disease.

Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis.

The lung mycobiome: an emerging field of the human respiratory microbiome

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