How to create an OTU table out of phyla abundance?

General Discussion
1

Dear community,

I have a very special problem. I’ve got data only about the abundance of specific phyla in a patient cohort. That means that I know how many of each Phyla a patient has, like:

Patient 1: 10 of phyla 1, 21 of phyla 2, 300 of phyla 3, … etc.

Patient 2: 15 of pyhla 1, 26 of phyla 2, 365 of phyla 3, … etc.

…

However I want to go on with microbiome analysis but therefore I need OTUs. However, OTUs are used to classify bacteria at the genus level, but now I have the data on phyla level and I have no 16S sequencing data. How can I create an OTU only by having the phyla abundance? Is is possible?

Do I really need OTUs? Can I analyse alpha-/beta-diversity without OTUs?

I would be really glad about any help!

Kind regards,
Hashirama

2

Hi @Hashirama,

Welcome to the :qiime2: forum!

Unfortunately, you cannot use a phylum-level table to go back to a more refined feature. It's sort of like trying to pull your baked cake :cake: apart to just get the flour out.

You can, in theory, run non-phylogenetic metrics on collapsed data - look at the q2-diversity plugin for some options. The better question should you, and for a specific patient cohort, my answer would be no. You are probably better off trying to get th rawest data you can from the original source.

Best,
Justine

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