beta diversity for a single specific taxa

[guianrey]

The shrimp microbiome is governed by Vibrionaceae, a family with important probiotic and disease-causing genera. After performing a comparison of the relative abundances of two conditions (healthy and diseased), both have similar relative abundance, but I don't know if the diversity of Vibrionaceae in healthy is the same as the diseased group. I could do a PCoA to analyze both diversities, but I will have the noise of the other families. My question is, Is it possible to do a PCoA considering only one particular family? How can I know if the same or different ASVs of the Vibrionaceae family are being shared between healthy and diseased shrimp?

[ChiLiubio]

Hi. What you should first do is to just extract the data of Vibrionaceae like I show somewhere in the tutorial. Please use Family instead of Phylum in the example and use f__Vibrionaceae instead of p__Proteobacteria. Then you can use d1 to do anything that you need like beta diversity analysis or venn diagram.