Development of a nucleic acid based assay to monitor and quantify viable yeast cells

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Cattle industry is one of the major Canadian agriculture sectors, which provides the animal proteins (milk andmeat) to humans. Recently, the direct fed microbes have been considered as one of the powerful approaches tohave long term effect to improve the animal productivity and health through enhancing microbial fermentation.Biomate, manufactured by AB Mauri North America (LaSalle, QC) is one of the commercial available liveyeast products (Saccharomyces cerevisiae variety) that can improve fiber digestion and prevent the ruminalmetabolic dysfunction, resulting cattle with greater productivity and better health. On farm, the Biomate isusually mixed with the feed and provided to the animals through the day to achieve the maximum effect of theproduct. Therefore, it is essential to maintain the high level of the viable cells in feed. Currently, the evaluationof the activity of this product in feed uses the culture dependent methods. To evaluate the viable cells of yeastin feed, the cultivation of the yeast is usually performed at AB Mauri's lab, which takes 3-4 days that is timeconsuming and labor costly. Also, this method has a large error margin due to the manual nature of countingcolonies. In addition, the cultivability of yeast sometime is affected by the high content of minerals or othercomponents in feed, which results in an underestimation of viable yeast in the sample. Although the PCRmethod can be used to monitor the population of targeted organisms, it can't differentiate the proportion ofnon-viable and viable cells, which could lead to over-estimation of the viable cells in the sample. In this study,we propose to identify and target "marker genes" for viable yeast cells using microbial genomics and molecularbiological based approaches. We will identify the DNA markers by aligning ~120 existing yeast genomes andthen develop a single or multiplex PCR assay. The assay will then be validated using the mixed feed samplesfrom AB Mauri, together with the comparison of the cultured based methods. The rapid and effectiveDNA/RNA based method will provide a reliable assay to quantify and to monitor the alive yeast cells in feedfor AB Mauri lab.