Compositions and methods are described herein that are useful for microbial culture of “uncultivable” microorganisms. The disclosure specifically ad-dresses the issues pertaining to efficient extraction of the cultivated microorganisms from growth chambers. The compositions and methods described herein are particularly useful for liquid medium but are also useful for solid media such as hydrogels or any such comparable media. In addition, the disclosure relates to, among other things, preventing cross-contamination and contamination from environmental microorganisms, especially during incubation in various natural and man-made environments and during extraction from growth chambers. Since these uncultivatable microorganisms are not initially cultured in synthetic laboratory medium, more care may be necessary to maintain sterility, and prevent the cross-contamination with environmental microorganisms.