The present invention provides a method for isolating a microbe whereby a sample of microbe cells is encapsulated in agarose gel particulates, wherein some of the particulates contain a single cell, and the other particulates contain more than one cell; incubating the particulates in nutritional and environmental conditions that enable the microbe contained in the sample solution that can grow on a plate of a plate culture method to grow in the agarose gel particulate; and isolating the particulates having single cells from the group of the particulates having more than one cell.