Abstract
Accurate bacterial quantification is critical in many biological fields, from clinical diagnostics to environmental microbiology. Here, we establish a robust workflow for absolute quantification of bacterial species within mixed communities using Crystal Digital PCR(TM). Using a synthetic consortium of Clostridium acetobutylicum and Nitratidesulfovibrio vulgaris, we optimized primer design for species-specific detection and demonstrated that Crystal Digital PCR(TM) enables reliable quantification of low-abundance species, down to a 1:10,000 ratio. We further show that the presence of one species does not interfere with the quantification of another. Finally, we demonstrate that Crystal Digital PCR(TM) can also be used to determine plasmid-to-chromosome copy number ratios in bacteria carrying megaplasmids.