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Purine analysis is widely used to estimate microbial crude protein (MCP) flow, and the method assumes that all purines contained in feed are degraded in the rumen and that purines detected are of microbial origin. The objectives of our experiment were (1) to determine if DNA from yeast (Saccharomyces cerevisiae) contained in dried distillers grains and solubles (DDGS) escapes degradation in the rumen and (2) to estimate the proportion of yeast DNA compared with total bacterial DNA in omasal samples. Two ruminally fistulated Holstein dairy cows averaging 649 kg (SD = 42.0) and 126 d in milk (SD = 28.9) were fed in a crossover design during 2 periods of 21 d each. Treatments were (1) control, a total mixed ration (TMR) not containing DDGS and (2) a DDGS-based diet, a TMR in which DDGS were included at 30% of diet dry matter (DM). On d 20 and 21 at 0400 and 1600 h, omasal digesta samples were collected via a ruminal cannula, and DNA was extracted from each sample in duplicate. The DNA samples were subjected to a realtime PCR assay to detect the presence of DNA from yeast. Forward and reverse primers and a probe were designed to target a DNA segment contained on the second chromosome of Saccharomyces cerevisiae. Realtime PCR amplification curves indicated the presence of yeast DNA in samples from both treatments. Specifically, the estimate of relative abundance of yeast DNA from digesta samples collected from animals consuming the diet containing DDGS was 9.46 ± 0.67/g of DM and was significantly higher than that from animals consuming no DDGS, which was observed to be 0.091 ± 0.67/g of DM. Omasal samples were also analyzed for total bacterial DNA. Primers and a probe were designed from DNA encoding part of the 16S rRNA. When the DDGS-based diet was fed, the relative abundance of total bacterial DNA tended to increase from 610 to 626 ± 3.82/g of DM. Results suggest that yeast DNA is detected in the omasum and this is increased when cows consume DDGS but it does not represent a significant proportion of total microbial DNA in the omasal digesta samples.