Extended Data Fig. 9: Metagenomic analysis of the virome in an independent cohort of n = 166 bronchiectasis patients recruited from Singapore, Malaysia, Scotland, and Italy.

To gain further insight into the respiratory virome we conducted an analysis of n = 166 metagenomes from sputum. a, A schematic overview of the analysis pipeline used to construct virome profiles. Virome profiles were derived by first generating a metagenomic assembly using all available metagenomic sequences trimmed and free of contaminating human DNA followed by detection of viral contigs using Virfinder with subsequent refinement using CONCOCT yielding 702 contigs present in at least 1% relative abundance in 5% of patients. Taxonomic assignment was performed using Demovir and BLAST. b, Relative abundance of viral families identified across samples from Singapore (SG) Kuala Lumpur (KL) Scotland (DD) and Italy (IT). c, Relative abundance of viral families identified in wSNF clusters SC1 and SC2. d, LEfSe discriminant taxa analysis comparing viral families observed in SC1 and SC2. e, BLAST analysis of identified viral contigs in SC1 and SC2. f, Analysis of antibiotic resistance gene family distribution in SC1 versus SC2 (RPKM - Reads Per Kilobase of transcript, per Million mapped reads).