Crystal Digital PCR™ Enables Precise Quantification of Species Abundance in Microbial Mixtures

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.