**Dilip Nazareth**

**1**

mellitus [4–6].

**Chapter 1**

**Abstract**

Cystic Fibrosis

briefly discussed in this chapter.

mycobacteria, *Aspergillus*

both health and disease.

**1. Introduction**

The Pulmonary Microbiome in

The chronic colonisation of the lower airways by bacterial pathogens is the leading cause of morbidity and mortality in patients with cystic fibrosis (CF). The use of novel culture-independent techniques such as next-generation sequencing (NGS) to analyse the lungs has allowed us to further understand the diversity, the complexity, the effects of acute exacerbations and the use of antibiotics on the bacterial communities. The understanding of the CF microbiome to airway disease remains a fascinating area of research; it presents new opportunities for disease management in CF and has the potential to explore the effects of cystic fibrosis transmembrane conductance regulator (CFTR) modulators. It also allows further appreciation regarding the roles played by anaerobic organisms within the CF airways. It is also of interest that a number of studies have demonstrated that the fluctuations of microbiome are not necessarily associated with the patient's clinical status. Despite the available evidence, there remain many challenges that must be overcome if microbiome profiling is going to influence future clinical practice. The effects of fungus and the emergence of nontuberculous mycobacteria in CF are also

**Keywords:** cystic fibrosis, microbiome, CFTR modulators, nontuberculous

Traditional culture techniques rely on growing bacteria on media in laboratory conditions often optimised for growth of specific organisms so that they can then subsequently be identified. In the last 20 years, novel techniques utilising nextgeneration sequencing (NGS) to identify bacteria have become available, enabling detection and description of bacterial communities without the need for conventional culture. These technologies have allowed a greater understanding of bacterial communities throughout the human body and have revealed functional roles in

A healthy human gut, for example, is home to a highly diverse community of bacteria, termed as microbiome, which has symbiotic functions including metabolism of otherwise indigestible compounds and defence against opportunistic pathogens [1, 2]. Furthermore, bacteria in the gut influence the stimulation and development of the innate mucosal immune system [3]. In addition to the roles in health, there has been significant interest in the relationship between microbiomes and diseases such as obesity, inflammatory bowel disease and diabetes

*Freddy J. Frost, Dilip Nazareth and Dennis Wat*

Consultant Chest Physician, Adult Cystic Fibrosis Unit, Liverpool Heart and Chest Hospital, Liverpool, UK

Honorary Senior Lecturer, Institute of Infection and Global Health, University of Liverpool, UK
