The present invention is directed to methods and kits for separating, accumulating, characterizing and/or identifying microorganisms known to be present or that may be present in a test sample. The method of the invention comprises optional lysing non-microorganism cells and/or particulates that may be present in a test sample, followed by a subsequent filtration step for isolation and/or accumulation of microorganisms. The kit of the present invention may comprise at least one filter membrane or an integrated filtration and sample transfer device for isolation and/or accumulation of microorganisms.