Estimating amplification efficiency improves multiplex real-time PCR quantification of Bacillus licheniformis and Bacillus subtilis spores in animal feed

A multiplex real-time PCR assay was developed for absolute quantification in animal feed of Bacillus subtilis CH201 and Bacillus licheniformis CH200 spores, which constitute the viable component of the microbial growth promoter, BioPlus 2B®. Spores were lysed using a bead-beating protocol. DNA was extracted and purified from the lysates with the Qiagen DNeasy® Plant Kit. Two standard curves for absolute quantification were made and tested. Standard curve-1 was made from feed samples spiked with BioPlus 2B®, while standard curve-2 was made from serially diluted DNA extracted from BioPlus 2B® powder. Feed samples supplemented with BioPlus 2B® were quantified using both standard curves. The detection limit of the assay was 104 CFU g− 1 of feed. The amplification efficiency (Eff) of each PCR was determined using the LinRegPCR software and Eff differences between individual samples and standards were corrected for. When compared to plate counts, standard curve-1 slightly under-estimated the number of spores (mean = − 2.47% of plate counts). A spore density-dependent Eff was found, and Eff for standard curve-1 could not be determined. Standard curve-2 over-estimated spore numbers when not corrected for individual Eff (mean = + 5.46% of plate counts). Standard curve-2 Eff was independent (Effmean = 1.96) of spore density. The assay quantified the numbers of spores in feed samples very similar to plate counts (mean = + 0.47% of plate counts), when standard curve-2 was used and individual Eff was accounted for.