Dear Sheryl,

I would recommend a chelex DNA extraction for your cultures, it's quick and cheap so it's worth trying.

I use QIAGEN kits.  They work well such as Leishmania protozoa.

QIAGEN kits would work more efficiently 

I use Qiagen myself but I thought MoBio was approximately the same so I recommended to try something else :)

I have used many of these kits before and had great luck with bacteria and archaea. The MoBio kit at least is not working on my flagellates.

Hello, is bacteria DNA is an issue in your study, you may also try to separate your protist and bacteria populations? You may filter the protists (gently, to avoid cell damages). Best,