Food Science and Technology Department


Date of this Version

Spring 5-2015


A Thesis Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Food Science & Technology, Under the Supervision of Professor Heather E. Hallen-Adams. Lincoln, Nebraska May, 2015.

Copyright 2015 Mallory J. Suhr


Gastrointestinal microbiome studies have failed to include fungi in total community analyses. As a result, their diversity and function in the gut is poorly understood. Recent work has begun to uncover the role intestinal fungi play in diet, immune system development, interactions with other microorganisms in the gut, and pathogenesis of diseases. Advances in sequencing technologies allow for the ability to profile the fungal gut microbiome (“mycobiome”) in healthy and diseased states. This thesis explores the mycobiome in 1) healthy humans with a vegetarian diet and 2) pediatric small bowel transplant recipients that develop fungal bloodstream infections.

The gut mycobiome from healthy adult humans with a vegetarian diet was determined using two sequencing technologies and a commercially available probe-based method. The use of three culture-independent methods demonstrated that the gut mycobiome is best characterized using a combination of methods, as each method has strengths, weakness, and biases. In addition, this study provides insight into the allochthonous nature of fungal inhabitants in the gut and demonstrates that fungal diversity in the gastrointestinal tract is diet related. It is apparent that a wide variety of fungi can be identified from the human gastrointestinal tract.

Further, the intestinal mycobiome of seven pediatric small bowel transplant recipients was characterized. Transplant patients are subject to multiple risk factors and have a correspondingly high incidence of candidemia. Molecular typing methods were used to assess whether candidemia in small bowel transplant recipients was acquired endogenously (from their own gut microbiota) or exogenously. Our results suggest that small bowel transplant patients are infected both by Candida colonizing their gastrointestinal tract and from exogenous sources. Ultimately, these results underline the importance of Candida surveillance in small bowel transplant institutes.

Adviser: Heather E. Hallen-Adams