Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients

Cystic fibrosis (CF) is an autorecessive disease affecting one in 3,500 Caucasian live births in the USA [1]. CF results from a mutation in the gene that encodes the CF transmembrane conductance regulator (CFTR) protein [2,3]. A defect in the CFTR protein leads to a malfunctioning cyclic AMP-activated chloride channel in secretory epithelia [4]. This defect in the lung leads to the inability to secrete chloride and to the excess re-absorption of sodium [4]. Thus, there is decreased fluid secretion and the mucus becomes immobilised and adheres to the epithelial cells. Overproduction of mucus in the airway results in congestion of the respiratory tract and increases susceptibility to bronchopulmonary infection. CF patients often suffer from infections with Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa and Burkholderia cenocepacia [5]. These chronic infections by highly adapted lung microbes cause inflammation and, eventually, lung damage; therefore, lung disease is the major cause of morbidity and mortality among these patients [6,7].It has also been estimated that less than 1 per cent of eubacteria in the environment can be cultured [8,9]. Thus, these identification methods will fail to detect all pathogens that might be causing the lung infection. Fortunately, with the advent of molecular techniques, culturing for identification purposes can be circumvented [10]. Recent molecular studies using terminal restriction fragment length analysis and sequencing have shown that the lung community is complex. Achromobacter (Alcaligenes) xylosoxidans, Rhodotorula mucilaginosa, Abiotrophia spp, Bacteroides gracilis, Eubacterium brachy, Mycobacterium mucilaginosus, Mycoplasma salivarium, Porphyromonas salivae, Ralstonia spp, Staphylococcus hominis, Streptococcus anginosus, Treponema vincentii, Veillonella spp, Burkholderia gladioli, Stenotrophomonas maltophilia and Pandoraea atypical have all been demonstrated to be members of this polymicrobial infection