The latter three taxa include established pathogens in acute exacerbations [24]. Here they are also implicated in increasing the frequency

of exacerbation events. In contrast, the significance of taxa such as Rhodobacteraceae that are not routinely identified by standard culture is unknown. It is possible that they may be pathogenic, enhance the pathogenicity of clinically significant taxa or contribute to airway inflammation and decline in lung function [25, 26]. In this study, there are inherent limitations; the patient cohort was consecutively recruited from an NCFBr out-patients clinic, hence, the administration of varying RG7204 order antibiotic regimens to individuals within the cohort may be a confounding factor. We identified 25 patients that had not received antibiotics for one month prior to sample collection. Ordination analyses (Figure 1) showed

that these individuals did not have significantly different bacterial communities to those who were receiving antibiotic therapy. Our data suggests that antibiotics do not significantly perturb bacterial communities in the lower airway, however, transient impacts on abundance and diversity have been observed in longitudinal studies looking at microbial communities in sputum from CF patients [15, 20]. The clinical benefit of antibiotic therapy Doxorubicin datasheet in chronic lung infection may, therefore, be due to the reduction in bacterial load present [27]. A longitudinal study is required to confirm if a similar transient response is observed in NCFBr microbial communities. Other limitations

are that in this cross sectional study we cannot gauge the level of temporal change within the lung microbiome, which if significant, may confound analyses showing differences in communities between individual patients. However, examining DGGE analyses of longitudinal samples from 35 individuals within this cohort (unpublished data) and other data using pyrosequencing approaches [10] shows that bacterial communities within an individual are relatively stable through time. A third issue, is that pyrosequencing relies on relatively short amplicons that lack sufficient resolution to confidently assign taxa to species, certainly not to strain-level. In many cases Amoxicillin there is no independent culture data to support the metagenomic analyses and clinically significant strain differences are undetectable [24]. Finally, although exacerbations at time of sampling were clinically defined, and those in the preceding 12 months were determined where possible from patient records, some of the exacerbations episodes were self-reported by patients and as a result may not reflect the clinical definition used at time of sampling. Conclusions In summary, we have demonstrated that the microbial community of the lower airway in NCFBr is dominated by three bacterial taxa Pasteurellaceae, Streptococcaceae and Pseudomonadaceae.