Metagenomic profile analysis of Mt. Erebus, Antarctica ...

• Main Author: Herbold, Craig
• Format: Article in Journal/Newspaper
• Language: English
• Published: Zenodo 2024
• Subjects: metagenome; microbial ecology; Ecosystems; Microbiology; FOS Biological sciences; Tramway Ridge; Antarc*; Antarctica
• Online Access: https://dx.doi.org/10.5281/zenodo.10928974; https://zenodo.org/doi/10.5281/zenodo.10928974

This is a R markdown script and all necessary data to reproduce an analysis of publicly available and unrestricted metagenomes from the Integrated Microbial Genomes System (IMG-DOE). This analysis was used to place pfam-based functional profiles of microbial communities from Tramway Ridge, Mt. Erebus, Antarctica in context of other metagenomic datasets. Jaccard Presence-absence patterns were chosen to calculate dissimilarity because for many datasets, abundance information is not available. This also meant that the dataset needed to be filtered for both total length and total number of pfams detected to avoid a saturation effect, where the number of pfams detected approaches unity in extremely deeply sequenced or sufficiently large metagenomes. Finally, samples with a large median dissimilarity to all samples were removed. This dataset was classified by environment and examined for bulk distance (boxplots / Tukey's test) and relational distance between individual samples (PcoA and tSNE). ...