Hello, Can you provide some more information on what data you would like to remove bacterial reads from and what your desired outcome is? This will help in answering your question.
Look forward to hearing from you again!
Thanks for using Galaxy!
Cheers, Mo Heydarian
Did you check the quality of the reads before and after Trimmomatic cleaning/filtering ?
FastQC is an excellent option and as far as I know you can have a first check towards this kind of (supposed?) contamination by checking the section "Overrepresented sequences". Eventually you can quickly blast these sequences in order to get some clues.
Maybe this can be of some help,