Hi Li,

           After running the isolated DNA on agarose gel electrophoreis you can separate it based on size and then elute the desired DNA using gel elution method.

Based on the need, you can seperate the Proakaryote DNA from Eukaryote contamination, 

As Girish said, you can seperate it.

since Human genomic DNA is higher in size, it will be in upper phase of the 0.5% gel and you can see ur microbial DNA goes below easily.

You may use exonuclease to degrade eukaryotic DNA. so add exonuclease to the mixture and run it on the gel to eparate.