Can I combine fungal ITS and bacterial V4 microbiome analyses?

I have sequencing data for fungal ITS and bacterial V4 soil samples and am able to analyze these separately in QIIME2 and in R using phyloseq. I am wondering if I am able to combine the fungal and bacterial data to conduct similar analyses in R (such as creating Bray Curtis PCoA plots, PERMANOVA test of Bray Curtis data, etc.). For reference, I have 58 samples, and would like to continue to have 58 fungal&bacterial samples, opposed to 116 samples (58 fungal, 58 bacterial).
Is there any way to complete this in QIIME2 or in R?


Hello Anka!

Welcome to the forums. :qiime2:

Yes, you can merge features tables in both Qiime2 and Phyloseq. However, combining data from different regions is hard. That thread is about different regions of the 16S gene, and the problems are the same for your 16S V4 and ITS reads.

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