The microbial landscape of the lower airways in infants with CF
We profiled BALF-associated bacterial and fungal communities using amplicon-sequencing strategies. To monitor DNA contamination by laboratory reagents and clinical instrumentation, we processed and sequenced negative extraction controls and bronchoscope washes alongside the BALF specimens (see Methods section for a comprehensive description). We observed a good correspondence between microorganisms detected by culture and molecular methods (Table SMean concentrations of microbial DNA were similar between instrument and negative extraction controls, and lower than BALF specimens (Fig. SWe obtained ITS2 library amplification from 37/121 (31%) of the BALF DNA extracts. The fungal profiles were dominated by taxa from the Phyla To evaluate whether early bacterial communities are related to different clinical outcomes, we performed a community-based clustering using Dirichlet Multinomial Mixtures [Early microbial assemblies associate with contrasting inflammatory outcomes. 