Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Poultry Science (PhD)

Degree Level



Poultry Science


Young Min Kwon

Committee Member

Billy M. Hargis

Second Committee Member

Jiangchao Zhao

Third Committee Member

Guillermo Tellez-Isaias


16S rRNA gene sequencing, Clostridium septicum, Microbiota, Poultry, Probiotics, Salmonella Enteritidis


The microbiotas play vital roles in health and diseases of both humans and animals. 16S rRNA genes sequence analysis is one of the most popular and commonly used methods in the analysis of microbiotas associated with hosts. In this dissertation, the microbiotas of chickens (broilers, breeders, and layers) and turkeys were evaluated by 16S rRNA gene sequencing. Characterization of the culturable subpopulations of Lactobacillus in the chicken gut can serve as a valuable resource for probiotic development. In Chapter 2, Lactobacillus subpopulations recovered on MRS from chicken gut were defined comprehensively for the first time using 16S rRNA gene profiling, where they varied with different regions (cecum vs. ileum) and locations (lumen vs. mucosa) with in the same region. In Chapter 3, we investigated the effect of cell densities as determined by varying levels of sample dilution on the culture-enriched microbiota profiles using MRS agar medium as a model system. The dilution levels of original samples was found to alter the resulting culture-enriched microbiota profiles via unknown density-dependent mechanisms. In chapter 4, Bacillus isolates (B. subtilis and B. amyloliquefaciens) were used to evaluate their therapeutic and prophylactic effects against Salmonella Enteritidis, and found their potentialities to reduce S. Enteritidis colonization and improve the intestinal health in broiler chickens possibly through altering the composition and functions of gut microbiota. In chapter 5, we investigated the cecal microbiota and egg production in two strains of Hy-Line (Brown and W-36) housed in conventional cages (CC) and enriched colony cages (EC), and noticed differences in egg production and cecal microbiota between strains and housing types. In chapter 6, we performed a comprehensive survey of the litter microbiotas using booty swab samples in the 5 commercial turkey farms of the Northwest Arkansas. The litter microbiotas were found to differ between farms, and flocks which were further affected by the ages of turkeys. In Chapter 7, we developed and evaluated the nested TaqMan probe based qPCR assay for the quantitative detection of Clostridium septicum that targets the alpha toxin gene (csa).