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Hey, you can use Alkaline extraction method. This is mainly used for DNA isolation and involves harvesting the targeted bacteria from a culture media and exposing it to alkaline solution. The next step here is to mix the alkaline extract with sodium dodecyl sulphate to remove the proteins. The benefit of using this method is that you can remove the DNA along with the proteins.

I would suggest you to go with Solid phase extraction method. This technique works by letting the nucleic acids to bind to solid supports. The beads are first washed with alcohol to eliminate the contaminants and then with a liquid to allow the solubility of the nucleic acids which frees the DNA from the support in a process known as elution.

Go with Cesium Chloride Gradient Centrifugation. This Is based on process of the buoyant and specific density. CsCl is a dense salt and if the solutions of this salt are subjected to centrifugation at high speeds, then the CsCl sets up a concentration gradient. If the centrifugation process ends gently then the denser solution settles at the bottom of the tube. When DNA is in the presence of a molecule it will bind to the molecule and becomes fluorescent. The molecule adjusts the density of DNA to move towards the center of the tube upon centrifugation and the contaminants will move to other positions and will separate from the DNA.