Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Life Sciences

Major Professor

Robert L. Hettich

Committee Members

Jeffrey M. Becker, Mircea Podar, Chongle Pan, Loren J. Hauser


Microbes inhabit all parts of human body that are exposed to the environment and their interactions with human host mutually benefit each other and play significant roles in human health and diseases. The human gastrointestinal tract harbors the largest population of the microbiota and has gained broad research attention and efforts over the past decade. Colonization of the gut by microbes begins at birth and this early-life bacterial establishment can impact infants’ health and even the human health and lifestyle across an entire life span. Recent studies on community structure and composition of infant gut microbiota have revealed the species shifts and variations during early bacterial colonization of the infant gut. However, little is known about functional activities of the community and how these functions change in response to different life events. Therefore, comprehensive proteomic characterization of the infant gut microbiome is needed to elucidate biological activities in this complex ecosystem. In this dissertation, we first developed a metaproteomics pipeline integrating both experimental and informatics components with careful considerations to simultaneously access microbial and human host proteins contained in infant fecal samples. The developed approach was applied in a longitudinal study of a healthy premature infant gut, revealing the overall metabolic cooperation between the human host and the gut microbiota and the temporal functional shifts in both microbiome and corresponding host response during the colonization process. To further investigate the commonalities and differences of gut microbiome between individuals, time-series metaproteomic studies were performed in three more premature infants, uncovering common core proteins/metabolic pathways established during early life microbiome establishment, as well as unique pathways that were specific to particular infants or present in certain colonization time period. In a broad perspective, the approaches and results presented in v this dissertation have provided insights into functions and activities of human gut ecosystem, and developed techniques and outlined general considerations that can be extended to proteome characterization of all complex ecosystems.

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