This protocol describes how to isolate bacteria in order to label its biomass using 13C-glucose and 15N-ammonia. The first steps aim to isolate candidate bacteria that are able of growing on the chosen substrates for isotopic labeling.The protocol was applied to the isolation of bacetria from freshwater algal cultures, although it can be applied to natural samples.The M9 media used in the protocol is based on the media from Marley, Lu and Bracken (2001).References:Marley, J., Lu, M., & Bracken, C. (2001). A method for efficient isotopic labeling of recombinant proteins. Journal of Biomolecular Nmr, 20(1), 71–75.