Well, extracting antimicrobial biomolecules from bacteria is a real challenge. The most common methodologies used are solvent extraction, preparation of free-cells supernatants from liquid cultures, among others. Some people have also used inactivated bacterial cultures by heat, and test the antimicrobial activity.
Do you know which bacterial genus are you working on? So you could know what kind of antimicrobials are produced by your strain (or at least the reported)... then, you could have an idea about their nature and start planning the extraction.
If one is extracting an antimicrobial protein of interest, it might be helpful to run an electrophoresis set up for protein separation rather than DNA sep
I recommend you to read the following article: antibacterial activity of actinomycetes isolated from different soil samples of Sheopur (A city of central India). I'm leaving the link below: