Publication Date


Document Type


First Advisor

Duvall, Melvin R.

Second Advisor

Yin, Yanbin

Degree Name

Ph.D. (Doctor of Philosophy)

Legacy Department

Department of Biological Sciences


Carbohydrates are immensely important biomolecule found in all organisms on earth, serving roles in structure, energy storage, protection and/or cell signaling. Carbohydrates are composed of an immense diversity of linkages, monosaccharide moieties and substitutions making them likely the most diverse biomolecule on earth, as well as the most abundant, being synthesized by plants and algae. Carbohydrates are synthesized and degraded by all organisms on earth through the expression of carbohydrate active enzymes, or ‘CAZymes’. In bacteria, CAZymes have been characterized to cluster in with transporters, regulators and/or other genes in so-called ‘polysaccharide utilization loci’, or PULs, to degrade carbohydrate substrates from plant and algal tissues. PULs are increasingly being shown to be important mechanisms of polysaccharide degradation by microbes in mammalian guts (i.e. gut microbiome) and can subsequently influence host health outcomes. The goals of this dissertation are to i) perform a literature review on experimentally characterized PULs in bacteria that act on different carbohydrate substrates, as well as review the current state of bioinformatic tools for CAZyme and PUL research, ii) develop a new bioinformatic tool for PUL research, dbCAN-PUL, that seeks to improve upon existing resources as well as drive research forward for PUL discovery in understudied taxa, and iii) investigate CAZymes and other genes that may drive pathogenesis in a newly sequenced strain of Clostridium perfringens.


234 pages




Northern Illinois University

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