creating a phylogenetic tree for iTOL

Dear @thermokarst @BecksHawaii

A quick question (beginner one)

I have an OTU table (~100 rows, 9 columns) of bacterial taxa with relative abundance in two types of soils. Header like this:

Phylum Class Order Family Genus Species OTU Treatment1 Treatment2
Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter Acinetobacter OTU388 60.15 39.85
Actinobacteria Actinobacteria Micrococcales Micrococcaceae Pseudarthrobacter Pseudarthrobacter OTU872 55.48 44.52

I want to transform it into a “photogenic tree file” and then further annotate the tree in iTOL. I have searched and found many articles, they used MEGA, FastTree or R to prepare the tree file and used iTOL for annotation. Now I did go through the iTOL tutorial and seems pretty understandable at first look, but I do not know the how to prepare that specific tree file from an OTU table using these software. If any of you could guide me with this situation, I shall be really grateful.

*I have never used MEGA or FastTree but R.
*The photogenic Tree I want to construct is something like in this paper:

“Rhizosphere microbiome functional diversity and
pathogen invasion resistance build up during plant

If you need any information, please let me know