how reliable are my taxonomic classifications if I did not identify species?

[Nicholas_Bokulich]

@Nisha

I have 16S rRNA PE data for V1-V3 region

Same issue. Species can be unreliable due to lack of species-level resolution in this region.

@Nisha

What should I do at this stage?

See my post above, but assuming you have family and genus level classifications, I'd say just move on. You could try out q2-clawback to help guide species-level classifications:

Using q2-clawback to assemble taxonomic weights

Note: This guide assumes you have installed QIIME 2 using one of the procedures in the install documents. This tutorial extends the q2-feature-classifier tutorial to show how you can improve taxonomic classification accuracy by assembling ecologically informed taxonomic weights for your samples using q2-clawback. This approach is described in this article: https://doi.org/10.1038/s41467-019-12669-6 We will retrain the naive Bayes classifier from the q2-feature-classifier to classify the ski…