I would appreciate suggestions for other modes of antibiotic visualization, preferably electrophoresis or gel based.
The classical way of analysing for antibiotics is to run TLC with the culture supernatant (initially just plain silica gel with a number of different solvents), then after developing and drying the plates transfer the antibiotic to large enough agar-plates ("stamping") and do an antibiogram to identify where the active molecules have run to. After that, they can be scratched out and analysed further (e.g. by GC-MS or else).
yes, If your antibiotic compound is polypeptide in nature then you can use SDS-PAGE or native page for the confirmation of antibiotic. but the for the determination of structure of antibiotics IR, NMR and GC-MS is needed.
antibiotics produced by bacteria are usually small molecules (< 1kD) so TLC should be better option to separate such small molecules. Native PAGE is good to separate polypeptides larger than 10 kD.
As said by other, unless your antibiotic is a polypeptide you'll not be able to see it.
Even though it is a polypeptide it is likely to be small (under 15kDa) so if you think that you have this type of antibiotic make sure to optimize your separation for small molecules (high % of acrylamide for example).
if it is not a polypeptide the best is to use metabolomics methods to identify your peak and then to characterize the molecule..
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