|MadSci Network: Microbiology|
Different bacteria (and for that matter, other different micro-organisms i.e. those that are microscopic in size, such a fungi, algae, etc..) are different colors due to the presence of different colored substances in the cells. For instance, algae contain chlorophyll (in the chloroplast, where the algae turns light energy into chemical energy) and thus are green.Other "bugs" contain pigments such as carotenoids, and are thus red or brown. Other colors, ranging from purple to pink occur in bacteria which use variants of the chlorophyll that gives plants and algae their green color. The bacterial versions absorb light of different wavelengths and thus are viewed as the various colors.
As far as I know, color per se doesn't mean anything in terms of being dangerous to man or animals. Just like M & M' s; color is just color.
Hope that answers your question.
Try the links in the MadSci Library for more information on Microbiology.