• Bacterial infection
• cystic fibrosis
• opportunist lung infections
• respiratory infection

The application of molecular non-culture-based techniques designed for characterising bacterial communities, such as 16S rRNA gene profiling by terminal restriction fragment length polymorphisms (T-RFLPs) or pyrosequencing, has provided new insights into the microbiology of cystic fibrosis (CF) lung disease.1–3 Studies have revealed that rather than being dominated by a single or small numbers of microorganisms, the CF lung is populated by a much more diverse polymicrobial community, including facultative anaerobic bacterial species. Analyses of CF airway samples by strict anoxic culture and culture-independent molecular methods have demonstrated that the anaerobic species can be repeatedly isolated, suggesting that their presence is persistent rather than transient, and are present in numbers comparable with those of the typical aerobic bacterial pathogens.1–9 The anaerobes present often represent those that usually colonise the oropharynx. The relative abundance of anaerobes in samples, and differences in composition of anaerobic species between mouthwash specimens and sputum samples, suggests that they are not oral contaminants but do truly originate from the lower respiratory tract.5 9 10 That anaerobes are present in the CF lung is perhaps not surprising. There is a steep oxygen gradient within the CF airway, with regions of hypoxia within mucus plugs. During chronic infection, the major CF pathogen, Pseudomonas aeruginosa, adapts to these conditions by increasing alginate production, forming biofilms and changing to an anaerobic metabolism.11 Regions of anoxia in a warm, humid, nutrient-rich environment combined with a defective mucociliary clearance mechanism may allow obligate anaerobic bacteria to colonise or infect the CF lung. Although there is compelling evidence that obligate anaerobic species are part …