The task was not described enough to offer the best solution. Please, say about targeted bacteria and sample type. Isolation of bacteria from clinical sample, plant, soil, water have specific features. It is easier when your targeted bacteria of known species with available PCR/IFA tests. If you isolate new bacteria, you must get pure culture and sequence 16S rRNA (as large part as possible) as very first step. Other tests depend on taxonomic position of the microbe.
Additionally to Alex's answer, the specific media could be designed to known species or strains not for the unknown species which needs to be isolated and characterized. We in our lab isolate novel species of anaerobic bacteria and you can imagine how difficult it is. If it is so easy to just isolate any unknown bacteria just by using any particular media, microbial taxonomy would look much more different than what it is today.
@Faisal - can you please explain to us all, why you recommend GC/MS for the isolation and identification of bacterial species, and how would you use it?
I am saying about the fatty acid profiling. I think you can modify and standardize the method on your own way. this is one of the simple and better method we practiced for some environmental bacteria.
Sure we can do that, but that poses the same problem as metagenomics. You have information about any novel bug, then what? How would we isolate it? What media, what optimum temperature, what salts? I don't see any option other yet to the traditional method of culturing and growing/trying in different media.