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Phenotypic Methods of Classifying and Identifying Microorganisms. Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities Phenotypic Methods of Classifying and Identifying Microorganisms Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Microorganisms can be classified on the basis of cell structure, cellular metabolism, or on differences in cell components such as DNA, fatty acids, pigments, antigens, and quinones.