Date of Award

Spring 1-1-2014

Document Type


Degree Name

Doctor of Philosophy (PhD)

First Advisor

Kenneth S. Krauter

Second Advisor

Rob D. Knight

Third Advisor

Diana R. Nemergut

Fourth Advisor

Norman R. Pace

Fifth Advisor

Mark Winey


Recent advances in DNA sequencing technology have led to a revolution in our capacity to detect and quantify microbial organisms. A universally conserved marker gene, such as the ribosomal small subunit, is often sequenced during microbial surveys. Many of these microbes are as of yet uncultured. However, it is still possible via sequencing to correlate particular microbes, cultivated or not, with environmental conditions (e.g. limited oxygen content) or with host physiology (e.g. inflammatory bowel disease). Despite this culture-free approach, bias can still arise from the choice of PCR primers used. Secondly, sequencing projects can yield tens of millions of sequences, which presents complications for microbial ecologists: how can microbial sequence data be analyzed in a reproducible manner, and how can software to handle such analyses be made accessible to individuals without extensive computational background?