Thesis (Ph.D.) - University of Queensland, 2005. / 2 papers by the author and others, folded in pocket inside back cover. Includes bibliography.

Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 56-62). Also available on the World Wide Web.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 101-109). Also available on the World Wide Web.

Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 42-47). Also available on the World Wide Web.

Thesis (Ph. D.)--University of Idaho, 2006. / Abstract. "July 2006." Includes bibliographical references. Also available online in PDF format.

Human gastrointestinal tract is complex and highly dynamic environment, harboring trillions of microbes that collectively play a pivotal role in host metabolism, immune function, and the maintenance of general health. However, studying the gut microbes and their interplay with host requires measurements at multiple dimensions is challenging since we currently lack the tools to directly measure these microorganisms at many different levels, which hinders our ability to unravel the ecology of gut microbes and their mechanistic underpinnings in human health and disease. Here, I present a set of novel techniques to study gut microbe and host-microbe interactions at unprecedented resolution, providing tremendous innovative insights to comprehensively understand the gut microbes and their environment. First, I leverage a high-throughput automation system to build a machine learning guided culturomics platform, enabling rapid isolation and culturing of personalized gut strains. Second, to better characterize the functions of these non-model microorganisms, I describe a ribonuclease-based ribosomal RNA depletion approach for microbe, paving the way for high-throughput bacterial transcriptome profiling. Next, shifting from gut microbes to the interaction with the host, I develop a technique of fecal exfoliome sequencing to robustly profile host gastrointestinal transcriptome in a non-invasive way, providing a powerful approach to study the temporal behaviors of gut cells in health and disease. Finally, to study massive genetic variants in microbiome arena, I describe a template-mediated synthesis approach for rapid and efficient generation of genetic variants sequences and demonstrate its utility in a few cases. Taken together, these techniques provide in-depth novel measurements into the ecology and physiology of human gut microbes, collectively making up an exciting set of tools for future studies.

No description available.

published_or_final_version / abstract / Botany / Master / Master of Philosophy

published_or_final_version / abstract / Biological Sciences / Doctoral / Doctor of Philosophy

Li, Lei. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 85-91). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.