Genome sequencing of bacteria after catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and multiple displacement amplification (MDA)

We evaluated the compatibility of a widely used phylogenetic staining protocol with whole genome amplification and genome sequencing. Cultures of the freshwater Betaproteobacterium Limnohabitans sp. strain RIM47 were subjected to ethanol fixation, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), flow cytometric sorting and multiple displacement amplification (MDA). Sequencing libraries were generated from up to 14 replicate MDA products and analyzed in the context of controls produced from unstained cells.