I'm wondering if it is significant enough to include as an objective in my study, because if the bacterial species isolated from the sample does not represent the whole population, then my study would not be able to shed much light on the mechanisms involved in the breakdown of organic matter.
You should avoid the isolation step and directly extract and analyze bacterial DNA from your sample to assess the bacterial composition. Only a very low fraction of bacteria can be isolated and these isolated bacteria are not representative of the original microbial community.
I agree to Nicolas Bernet. Evaluation of bacteria presence in your sample is possible only if you use a number of different selective media for each group of bacteria you expect to find. Usually applied for one group only.
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