Change solvent of bacterial solution
I'm assuming that you have a solution of bacteria in your buffer directly after growing them for some time, and without performing a lysis step yet. The 2% SDS step looks like it is for lysis of your cells.

In that case, centrifuging the bacteria and resuspending them in lysis buffer is a very common step in many protocols. Separating whole bacteria from medium or buffer by centrifugation is pretty easy and should just work. But if at any of your previous steps you already lysed your bacteria, this won't work because the cells aren't intact anymore.