Date of Graduation


Document Type


Degree Name

Master of Science in Animal Science (MS)

Degree Level



Animal Science


Jiangchao Zhao

Committee Member

Kenneth P. Coffey

Second Committee Member

Xiaolun Sun


antibiotic replacement, chicken, Clostridium perfringens, microbiota, necrotic enteritis, tributyrin


Poultry is a staple protein source for most of the planet. Until recently, antibiotic growth promoters (AGPs) were used to prevent illnesses in commercial chicken production. Currently, this is not possible due to regulations and consumer concern, but without such a preventative, diseases like necrotic enteritis (NE) have reemerged, posing a threat to bird health, and ultimately, our food source. Necrotic enteritis is a severe gastrointestinal disease caused by the gram-positive pathogen, Clostridium perfringens. Clinical features of this disease are diarrhea, intestinal lesions, and death, with a high transmission rate. In a subclinical form, growth performance is diminished and is the primary cause of economic loss to producers. Butyrate substances have been introduced to replace AGPs. Studies show these substances appear to relieve intestinal damage that is caused by NE. The relationship between gut health and gut microbiota community structure is well established in human studies. It is expected that animals are affected by their gut microbiota composition similarly. It is unclear whether the butyrate treatment influences the chicken GI microbiota composition or if such a change would help explain the mechanisms that improve intestinal lesions in birds affected by NE. By using 16S rRNA High-Throughput Next Generation (HTNG) amplicon gene sequencing, we compared the microbial composition of the cecum and ileum of birds from three different groups: T1, nonmedicated, unchallenged with C. perfringens (negative control group), T2, nonmedicated, challenged with C. perfringens (positive control group), and T6, treated with butyrin (Butyrin SR130, Perstorp) in the feed at 0.5kg/metric ton from day 0 to day 14 and at 0.25 kg/metric ton from day 14 to 20 (variable dose) and challenged with C. perfringens (Hofacre, et al., 2020). The objective of this study was 1) to assess the efficacy using gut microbial communities as a novel measure of NE in broiler chickens, and 2) to assess the efficacy of a butyrate treatment for NE in chickens. The results indicated no significant effect on beta diversity of microbial community structure among the three treatment groups. The disease challenge in groups T2 and T6 was observable and significant, yet the microbial composition and abundance of C. perfringens were visually indistinguishable among the three groups of birds. Random Forest analysis identified some enriched features in the T1 and T6 groups that were rarely present in the T2 group of the ileum and cecum. This thesis explores the potential explanations for the lack of microbial diversity between unchallenged birds, and birds intentionally inoculated with a known pathogen, as well as a further look into the enriched features identified by Random Forest. These features may play a small role in the recovery of NE through tributyrin treatment that additional research could explain.