Document Type


Date of Degree Completion

Spring 2019

Degree Name

Master of Science (MS)



Committee Chair

Holly Pinkart

Second Committee Member

Mary E. Poulson

Third Committee Member

April K. Binder


As many health phenomena seem to be affected directly and indirectly by the microbiome, gut microbiome research has increased in the last decade. Issues such as allergies, cancer, obesity, and other health complications have been shown to be influenced by the microbiome. Most of gut microbiome research is done by collecting and sequencing the DNA of the microbiome of the fecal matter from model organisms or human subjects. Studies that use this method of sample collection and analysis assume that fecal matter microbiomes are similar to intestinal microbiomes, and that it can be used as a proxy. At present, no published studies exist which directly compare stool microbial composition and intestinal microbial composition. Bacterial composition was found to be different at all levels of taxonomy between stool and the different portions of the intestines tested. Uni-variate analysis shows significance between the two main phyla Firmicutes and Bacteroidetes, as well as main genera like Odoribacter, Porphyromonas and Alistipes. Relevant species Desulfovibrio desulfuricans and Odoribacter splanchicus were also found to be significantly different in relative abundance between stool and some parts of the intestines. Alpha-diversity was not significantly different between all parts of the intestine and stool. Beta-diversity was significantly different between the ileum and stool, with stool having slightly higher diversity. Looking at the bacterial composition of both environments and the relative abundances of the dominant taxa, one can see that that there are key differences between the intestines and stool. The microbial composition at all levels of taxonomy was found to be different, therefore, research that targets the gut microbiome should look closely at the specific taxa being observed. Phyla like Firmicutes and Bacteroidetes were found to have different abundance within the portions of the intestine and stool, suggesting that phyla level analysis should be performed by observing each community separately. Interestingly, diversity analysis was not found to be significant, suggesting the composition is different, but the number of different taxa is similar across the intestinal tract and stool.