I was wondering how to estimate the p-value for statistical comparison between the phyla of two different subjects. Is there a way to do this in QIIME 2?

For example, I require something like this " The phyla abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002, pseudo r2 = 0.09; Permutest: P = 0.093). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001) and more Actinobacteria (2.09-fold change, P = 0.002). Faecal samples contained significantly more Lentisphaerae (1.74-fold change, P = 0.050)."

Depends on what you want to use to do your analysis, but the short answer is not the way you’d like.

In QIIME, the primary implementation is ANCOM, which calculates a W statistic. Please check out this prior discussion around why the ANCOM W is not a P and ways to approach that.

An alternative is to use q2-gneiss, PhILR or Phylofactor (both in R) to get a split based on a partition in the data. But, that won’t give you exactly what you want, either.