Yeast cells tend to be larger than bacteria so you could filter by size. Else plate them and pick individual colonies. You could also select against yeasts using some fungicides.

Hi there,

Centrifugation is very effective as yeast is very dense compared to bacteria. For instance you can pellet S. cerevisiae just by spinning your sample for 1 minute at 1000g while you need at least 10 minutes at 6000g to pellet E. coli...

Hi Viruni,

This depends on what you are planning to do afterwards.

If you want to separate these to grow and maintain cultures I'd split your samples and then use a strong antibiotic in one (get rid of bacteria so you would have all the fungi) and strong mycocide on the other one (to get rid of bacteria). This is economical, but would not guarantee to eliminate all the fungi/bacteria etc. So you might have to do some tests to figure out accurate doses etc.

If this is for some sequencing/identification purpose, your bacterial or fungal specific primers should take care of the problem.