**11. Conclusion**

The pulmonary microbiome of people with CF diverging significantly from that of the healthy individuals has been the focus of much research in the last 5 years often producing more questions than answers. As the disease progresses, community structure becomes progressively less diverse, most likely as a consequence of long-term aggressive antibiotic therapy. The impact of acute antibiotic therapy, antifungal treatments and CFTR modulators are less well defined, and prospective clinical trials with sputum biobanking are needed to answer these questions.

## **Author details**

Freddy J. Frost, Dilip Nazareth and Dennis Wat\* Liverpool Heart and Chest Hospital, Liverpool, UK

\*Address all correspondence to: dennis.wat@lhch.nhs.uk

© 2020 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**15**

*The Pulmonary Microbiome in Cystic Fibrosis DOI: http://dx.doi.org/10.5772/intechopen.91765*

[1] Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews. Immunology. Human Molecular Genetics. 2013;**22**(R1):R88-R94

2015;**11**(7):e1004923

2016;**193**(5):504-515

2016;**4**(8):627-635

2017;**2017**:5047403

[11] Dickson RP, Huffnagle GB. The lung microbiome: New principles for respiratory bacteriology in health and disease. PLoS Pathogens.

[12] Prevaes SM et al. Concordance between upper and lower airway microbiota in infants with cystic fibrosis. The European Respiratory Journal. 2017;**49**(3):1602235

[13] Prevaes SM et al. Development of the nasopharyngeal microbiota in infants with cystic fibrosis. American Journal of Respiratory and Critical Care Medicine.

[14] Mika M et al. The nasal microbiota in infants with cystic fibrosis in the first year of life: A prospective cohort study. The Lancet Respiratory Medicine.

[15] Boutin S et al. Comparison of oropharyngeal microbiota from children with asthma and cystic fibrosis. Mediators of Inflammation.

[16] Boutin S et al. Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLoS

One. 2015;**10**(1):e0116029

2018;**14**(1):e1006798

2015;**5**:10241

[17] Muhlebach MS et al. Initial

acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children. PLoS Pathogens.

[18] Coburn B et al. Lung microbiota across age and disease stage in cystic fibrosis. Scientific Reports.

[2] Larsbrink J et al. A discrete genetic locus confers xyloglucan metabolism in select human gut bacteroidetes. Nature.

[3] Cebra JJ. Influences of microbiota on intestinal immune system development. The American Journal of Clinical Nutrition. 1999;**69**(5):1046S-1051S

[5] Brunkwall L, Orho-Melander M. The gut microbiome as a target for prevention and treatment of hyperglycaemia in type 2 diabetes: From current human evidence to future possibilities. Diabetologia.

[6] Lane ER, Zisman TL, Suskind DL. The microbiota in inflammatory bowel disease: Current and therapeutic insights. Journal of Inflammation

[7] Cox MJ et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One.

[8] Dickson RP et al. The microbiome and the respiratory tract. Annual Review of Physiology. 2016;**78**:481-504

[9] Hilty M et al. Disordered microbial communities in asthmatic airways. PLoS

Moffatt MF. Sequencing the human microbiome in health and disease.

**References**

2009;**9**(5):313-323

2014;**506**(7489):498-502

[4] Ley RE et al. Microbial ecology: Human gut microbes associated with obesity. Nature. 2006;**444**(7122):1022-1023

2017;**60**(6):943-951

Research. 2017;**10**:63-73

2010;**5**(6):e11044

One. 2010;**5**(1):e8578

[10] Cox MJ, Cookson WO,

*The Pulmonary Microbiome in Cystic Fibrosis DOI: http://dx.doi.org/10.5772/intechopen.91765*
