I wanna construct a phylogenetic tree of an insect microbiota to show how microbiota differ across insects (same genus but different species). How can i do this analysis?
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Vishy001 •
1 answer
I don't think a phylogenetic tree is a good model to capture relationships between microbiomes because phylogenetic trees model vertical ancestry, which is likely not the case for these microbiota. You can cluster abundance data somehow, e.g., using the Bray-Curtis metric, but this comes with a bunch of methodological problems as well see f.e..
If you only have two species with shotgun metagenomes and only a handful of samples to compare, I suggest plotting Sankey diagrams for easy visual assessment of the abundances by taxonomic group. You can use Pavian on the output generated by Kraken or MethaPhlAn. If you have more samples and targeted (16s) OTUs, plot a clustered distance matrix (heatmap) of Bray-Curtis distances computed with the vegan package in R unless a reviewer asks for more.
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