If I have not mistaken your question you may group bacteria using 16SrRNA techniques. it is most widely used techniques for group baterial with homologous sequence.
Question is not clear. Are you talking about bacteria, if so go for few simple test like Gram staining, spore or capsule staining etc. then try to grow them on some differential and selective media, in this way you will be able to group them. Then you can try 16SrRNA sequencing as suggested by Jitendra.
sir ur question is not clear .You can group the microorganisms based on its morphological ,biochemical and physiological conditions .16s rRna sequencing method is also used to group and identify the microorganism it is a reliable molecular method to identify and group the microorganisms .
In the following paper and websites you will find alternative methods for SDS-PAGE.
(1) Wessels HJ, et al (2009). LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics, 9(17):4221-4228. (Attached)
(2) An Automated Alternative to SDS-PAGE for Protein Analysis, The website in the following link: