Welcome to the forum, @mosmasha!
This sounds like it may be an issue with the taxonomy classification step, unless if you were expecting 100% Clostridia.
- how did you classify your sequences taxonomically? (method, source of the reference/classifier, etc)
- how many sequences do you have per sample? Were there any upstream processing issues that might cause a problem?
- What were you expecting to see?
- Could you share your taxa-bar-plots.qzv so that we can take a look?
There are several topics regarding taxonomy errors listed inside the following topic, these might give you some ideas of what may have gone wrong:
Thanks!