Part 4: Compare metaT & metaG at mOTU level

Because the mOTUs2 method uses the same housekeeping genes to estimate the abundance of taxa in a metagenomics sample, it can also be used to profile a metatranscriptome.

You can find the output of mOTUs2 at metagenomic and metatranscriptomic level in /work/projects/embomicrobial2020/data/metaT/taxonomy/$mySample. Try, if you can visualize this in the same way as the KO data in the previous part.

Here is an example with scatter plots at multiple taxonomic ranks:

_images/Taxonomy_mOTU_plot.png

In this tree-visualization, which is part of IMP3’s report, you can also see the names and phylogeny of the taxa. The nodes are coloured according to the relative abundance.

_images/Taxonomy_mg_mOTU_tree.png

If you compare this to metatranscriptomic output below, you see some subtle differences:

_images/Taxonomy_mt_mOTU_tree.png

Comment

With a few lines of code, you can concatenate data from several samples to do statistical analyses on the mOTU-profiles. Since this taxonomic profile data does not meet all the assumptions of the DESeq2 test, it’s better to analyse them with statistical packages developed for microbiome data, e.g. ANCOM-II or corncob.