The purpose of the tests was to compare the identity of species and strains present in the products to what was stated on their respective labels. An Illumnia® MiSeq® sequencer was utilized to produce whole genome sequence files of the mixture of bacteria contained in the probiotic. Sequencing produced DNA fragments associated with each strain contained in the sample and was the basis for analyses to determine the amount and type of active ingredients contained in the probiotics.
For the side-by-side testing, the FDA used conventional k-mer approach developed in house. CosmosID® used its GENIUS® product, NmerCE.Overall, both the FDA's k-mer and CosmosID®'s NmerCE approaches were able to determine the active ingredients in each probiotic, as well as whether contaminants were present. The advantage of CosmosID®'s Genius® product over the FDA's k-mer counting was both the speed at which the CosmosID's® NmerCE was able to complete the analysis, and the ability to provide enhanced specificity in separating different species groups into specific strains. The results were summarized in an abstract submitted by the FDA at the 133rd General Meeting of the American Society for Microbiology (ASM), which stated "In total, we developed a package of molecular approaches that stratifies genetic depth and regulatory need for appropriate strain identification for voluntary submissions but have widely useful applications from GMP surveillance for unexpected pathogens."
Results will be presented May 19 at the ASM Denver meeting.According to CosmosID®'s CTO and lead scientist, Dr. Thomas A. Cebula, and Dr. Nur A. Hasan, director, CosmosID® Genomics R&D, "Utilization of our algorithms helps remove the computational bottleneck associated with metagenomic analyses, thus facilitating rapid detection, identification, and quantification of microbes in complex samples. As probiotic bacteria are becoming increasingly important in the context of human health, CosmosID GENIUS ® product will be extremely valuable for the industry in speed of use, quality control, quality assessment, and safety evaluations.""CosmosID®'s Genius® product will enable manufacturers of probiotics to quickly and accurately validate the labeling of their products for GMP surveillance for unexpected pathogens, or aid in developing and testing new probiotic products," stated CosmosID®'s chief executive officer, Doug Brenner.
"Widespread use of strain-specific analysis of probiotics and their effects on microbial populations will level the playing field in the probiotics industry to assist in documenting efficacy and support labeling claims of companies that conduct rigorous testing against those that choose not to do so."