Klinisk institutt 2

Midtveisevaluering - Christine Drengenes



Microbiota as the missing link in the development of COPD? A 16S rRNA gene based analysis of the microbiome in subjects with and without COPD.

The aim of the PhD project is to address some of the methodological issues that remain unresolved in the field of lung microbiome research. The most urgent issue concerns the low bacterial load in the samples acquired from the lungs. As even the smallest contamination is enough to distort the microbiota profile of a lower airway sample there is a rising concern that the lung microbiota signatures being reported upon predominantly reflect bacterial DNA contamination.

For the PhD project we are concerned about two sources of contamination which we will address separately in two publications – that from the upper airways introduced during bronchoscopic sampling of the lungs (paper one) and that introduced from reagents and kits during laboratory processing steps (paper two). The difference between the two sources is that the latter can be monitored to some degree through processing and sequencing of negative control samples. In paper 2 we explore the latest in silico strategies available for dealing with laboratory contamination in microbiome sequencing data. In paper 3 we address the lack of standards in the field with regards to sequencing methodology and bioinformatics analyses. All data was collected as a part of the Bergen COPD Microbiome study (MicroCOPD), a study of the airways microbiota in subjects with and without obstructive lung disease.