An assessment of the surrogate host metagenome-assembled genome decontamination for non-model host organisms : Proof-of-concept

Sammanfattning: In this study, a novel method has been assessed to bridge the gap between bioinformatics and ecological conservation efforts to gain evidence to further base conservational plans on. Herein, the validity of using a provisional host metagenome-assembled metagenome to decontaminate the data from host contamination was concluded. To achieve this, 11 samples of increasing host contamination were devised by simulating reads from 100 genomes representing Platanthera bifolia and Platanthera chlorantha endophytic root microbiomes. By following the Critical Interpretation of Metagenome Interpretation benchmarking framework, the method was evaluated on assembly and binning performance. The study concluded strong negative correlations with host contamination that is derived by the lowered proportion of endophytic sequence depth at the higher host contamination levels. Furthermore, statistically significant difference between the control and the perfect GHOST-MAGNET was determined when accounting for the proportion of bins being endophytic.