Depending on the situation, this phenotype might have arisen through mutation or recombination. For example, a mutation that confers both phage resistance and poor growth will be selected for when phage are present and selected against when phage are absent from the growth conditions. A selection always provides strains of the demanded phenotype, but not necessarily of the desired genotype . You will therefore typically need to further analyze the generated strains to verify their genetic makeup. Such factors need to be taken into account in the actual timing and conditions employed in a particular screen.
Some hunts work differently at different stages of cell growth .
A chemical that might have a profound effect on spore germination might have a very different effect if vegetative cells are used in the analysis. In general, the permeability and growth requirements of microorganisms change rather dramatically depending on the stage of the growth cycle. Such considerations are particularly important for those prokaryotes that go through a more dramatic form of differentiation like sporulation. If in reality one sees a frequency of occurrence that is very different, this is a strong suggestion that either one's perception of the underlying genetic and biochemical reality is incorrect or something curious happened in the selection itself . In general, selections and screens nearly always work, in that they give you isolates of the demanded, and expected, phenotypes.