Hi @nvtravan,
In the taxonomic assignment, those underscores are not present (they only appear when you visualize these data, e.g., as a barplot or collapse a feature table on taxonomy).
See this post
So in your case you want something like this:
qiime feature-table filter-features \
--i-table table.qza \
--m-metadata-file taxonomy.qza \
--p-where "Taxon='k__Bacteria' \
--o-filtered-table filtered-table.qza
I hope that helps! Let me know if you’re still having trouble.