Effects of feed additives on gut microbial diversity of Clostridium perfringens challenged broilers

The interactions between host and gut microbiota are a rapidly developing field with a plethora of implications. Recent developments in identification and quantification methods of gut microbes allow for a better understanding of said interactions. For the local broiler production industry, studying the microbiome of the gastrointestinal tract (GIT) is imperative to ensure ease of transitioning into an antibiotic-free feeding practice. Clostridium perfringens infections are a major burden for the global poultry industry and can lead to necrotic enteritis (NE). The economic losses induced by NE in the South African broiler industry are estimated to be $68.81 million per annum. In this trial, day-old Ross 308 broiler males were randomly placed in an environmentally controlled house and subjected to eight dietary treatments with 12 replicate pens each containing 23 birds. The antibiotic growth promoter (AGP), zinc bacitracin (ZB), was used as the positive control, and three additional feed additives were used either alone or in combination. The three feed additives are classified as a direct fed microbial (DFM), an essential oil mixture (EO), and finally a mixture of EOs and organic acids (OAs). To induce C. perfringens infection, birds received a coccidial vaccine (Immunocox, Ceva) of 10x the prescribed dosage at 10 days of age and were orally inoculated with a broth of C. perfringens at 14 days of age. Both ileal and caecal digesta samples were collected at 21 and 35 days of age. Bacterial 16S rRNA sequencing was performed on these samples using a customized chip containing 100 selected intestinal bacteria. Age had the most significant effect on microbial abundance in both the ileum and the caeca. The dominant bacterial phylum regardless of age was Firmicutes, followed by Bacteroidetes and Proteobacteria. The ileum samples showed that microbial diversity increased with age, whereas the caecal samples revealed a reduction in diversity in the older samples. For the 35-day samples, the DFM and EO treatments increased ileal Lactobacillus and Lachnospiraceae respectively when compared to the negative control (no additives). Increased Lactobacillus and Lachnospiraceae are beneficial for broiler health and production. No significant differences were observed between the positive control (AGP) and the other treatment groups except for the EO + AGP combination group. Further research on the microbiome of the chicken’s intestinal tract is necessary.Dissertation (MSc)--University of Pretoria, 2019.CargillAnimal and Wildlife SciencesMSc (Agric)Unrestricte