Uncovering the Viral Microbiome in COPD Lungs through Metagenomics
Sophie Harrison 1*, Martha Clokie 1, Andrew Millard 1
- University of Leicester
- Leicester Centre for Phage Research
Chronic Obstructive Pulmonary Disease (COPD) encompasses progressive lung conditions, including emphysema and chronic bronchitis. COPD is currently the third major cause of mortality in the United States and in the United Kingdom. Within COPD patient sputum, there are higher-than-average loads of bacterial counts; these are dominated by Haemophilus influenzae, Streptococcus pneumoniae, Pseudomonas aeruginosa and Moraxella catarrhalis. To date, even with the bacterial community known, very little has been studied or uncovered about the viral airway microbiome. To understand and observe any viral presence within these lungs, what is the best method of DNA quantification? From a sputum sample the removal of eukaryotic and bacterial particles is an easy process, leaving behind any viral fragments which can be extracted. Yet this obscures the presence of any temperate bacteriophages, and possibly any actively bound phage potentially in the community. If the whole sputum sample is extracted for DNA, the correct measurements must be obtained to analyze all present viral data. In this study, we aim to uncover and identify any putative viral contigs (vOTUs) found in previously extracted DNA from whole sputum samples. From 59 sputum samples, 16,671 vOTUs were found. These vOTUs were compared to known vOTUs to find: the complete viral genomes, viral family groups, lytic or temperate life cycles predictions, and the host prediction range. With this new data, a baseline of identification and COPD viral biome understanding can be implemented in future studies.