Research Question: New inoculum taxonomy doesn't match individual taxonomy

Hello Qiime2 community,
I generated a taxonomy of a new bacteria inoculum that i used from 4 pregnant mothers fecal samples and I also generated a taxonomy for each of the 4 pregnant mother fecal samples. However the new bacterial inoculum doesn't match the individual pregnant mothers. Does anyone know why this has occurred? May you point me to the research literature that describes this phenomenon?

Hello Antonio,

Welcome to the forums! :qiime2:

There are many ways to approach taxonomy classification; small changes can make big differences in the results. This paper discusses the decisions behind the Qiime2 taxonomy classifiers.

If you can tell us more about how you generated taxonomy, we can look for the source of these differences.