Graduate Studies, UNL

 

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

First Advisor

Yanbin Yin

Degree Name

Doctor of Philosophy (Ph.D.)

Committee Members

Devin Rose, Etsuko Moriyama, Juan Cui, Robert Hutkins

Department

Food Science & Technology

Date of this Version

2025

Document Type

Dissertation

Citation

A dissertation presented to the faculty of the Graduate College of the University of Nebraska in partial fulfillment of requirements for the degree Doctor of Philosophy (Ph.D.)

Major: Food Science and Technology

Under the supervision of Professor

Lincoln, Nebraska, December 2025

Comments

Copyright 2025, the author. Used by permission

Abstract

Microbiomes in humans, animals, plants, and other environments are necessary components of the biosphere for global nutrient cycling and maintaining ecosystem balance. In particular, the gut microbiome plays an essential role in modulating human health through glycan utilization. Carbohydrate-active enzymes (CAZymes), CAZyme gene clusters (CGCs), and polysaccharide utilization loci (PULs) are key genomic features that determine microbial capacities for carbohydrate metabolism. Meanwhile, the arms race between phages and prokaryotes has led to the evolution of various anti-prokaryotic immune systems (APIS) in phages to counteract prokaryotic immune systems (PIS).

As bioinformatics methods used to analyze microbiome information advance rapidly, there is a growing need for integrative resources to support large-scale functional analyses of microbiomes in specific research domains, such as glycan utilization in the human gut microbiome and APIS proteins in phages/viromes. To address these needs, we developed two comprehensive databases.

The first database, dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), consists of human gut microbial CGCs from global populations. It provides glycan substrate inference based on CGC families, identifies differentially abundant CGCs and genes through diet-associated metagenomic read mapping, and improves functional annotations with predicted protein structures. The second database, dbAPIS (https://bcb.unl.edu/dbAPIS), servs as the first curated database for experimentally verified APIS genes and their associated protein families in human viromes. In addition to curated entries, it provides pre-computed data on the genomic context, predicted structures, and homology information of APIS proteins. The web server also allows users to submit their own phage genomes for the annotation of potential APIS homologs.

Together, dbCAN-HGM and dbAPIS represent foundational resources for advancing microbiome research in glycan utilization and phage-host immune interactions. They promote exploration of microbial functional genomics, bring insights into human nutrition and health, and provide perspectives on future biotechnological and therapeutic developments.

Advisor Yanbin Yin

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