The characteristic that differentiates eukaryal microbes from bacteria is the membrane bound nucleus. Bacteria are all examples of prokaryotic cells, while eukaryal microbes are eukaryotes. One of the major difference between eukaryotic cells and prokaryotic cells is that prokaryotic cells lack membrane bound nucleus and also other membrane bound organelles, while eukaryotic cells contain membrane bound organelles including nucleus. So like other prokaryotes bacteria lack membrane bound nucleus and the membrane bound organelles.