creating venn diagram to show shared bacterial taxa among two sample sets

Hello,

I am new to using Qiime2 and looking for some guidance on creating a venn diagram that will compare bacterial taxa shared among two species of seabirds. I have 5 samples for each seabird, and the data is in a .csv file where each sample is a row and each column represents abundance of a bacterial genus in a given sample (taken from a Qiim2 taxa barplot .csv file). Here is the general format of my excel file:

index, bacterial spp 1, bacterial spp 2, ...
gannet, 0, 234, ...
gannet, 2, 0, ...
gannet, 0, 345, ...
gannet, 0, 192, ...
gannet, 0 , 234, ...
kittiwake, 87, 0, ...
kittiwake, 67, 0, ...
kittiwake, 54, 9, ...
kittiwake, 0, 0, ...
kittiwake, 8, 1, ....

I want to know the best way to create a list of shared taxa between two groups that I could then use to make a venn diagram comparing them. Also, is it logical to say that taxa is present in the group if one sample from the group has the taxa present but the other samples do not? Are there certain restrictions that are common place or that you may think I should be considering?

Thank you!

Hello!
Yes, you can perform it in qiime2 (partially).

Step 1. Filter your feature tables by group. If you have 2 groups, there should be 2 feature tables, one for each level.

Step 2. Run core-features plugin for each table. It will create lists of core features at different tresholds (for example, 100% - 5/5 samples, 80% - 4/5).

Step3. Use that lists to create Venn diagrams. For example, with this or this online tools.

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