This depends on the type of analysis you are using. If the 'colony forming units' are normally distributed (Bell Shaped) you can use a parametric statistical test such as the t-test or the analysis of variance.
If you have two traits to compare , and have 30 and up observations, you can use t - test, otherwise if you have only two means you can use chi square. If you have more variables, you better go to experimental designs such as factorial arrangement or a split plot, and so on. Good luck.