The effect of an ionophore, essential oils and a probiotic on the rumen and jejunal microbiome of South African Bonsmara cattle raised under feedlot conditions

Thesis (PhD (Animal Science))--University of Pretoria, 2022.Feed additives are commonly used to modify the rumen microbiome towards more energy efficient pathways, such as the production of propionate. The urgency for the replacement or decrease in use of antibiotic growth promoters (AGP) and the reduction of methane emissions has necessitated the investigation of alternative feed additives, such as probiotics and essential oils, and its effect on the gastrointestinal tract microbiome. Microorganisms in the gastrointestinal tract of ruminants play an essential role in the health and production of the animal. The microbes in the rumen degrade feedstuff into energy the animal can utilize while the microorganisms in the small intestine can affect the health of the animal. The overall aim of this study was to investigate the effect of an ionophore, a probiotic and essential oils on the rumen and jejunal microbiome of Bonsmara cattle raised under feedlot conditions using 16S rRNA and internal transcriber spacer (ITS) amplicon sequencing. Forty-eight Bonsmara bull calves (228 ± 22 kg) were backgrounded and fed a starter, grower, and finisher diet for 120 days. The bulls were blocked by weight and randomly divided into four groups: a basal diet (CON) and the basal diet supplemented with monensin (MON), essential oils (EO) or a probiotic (PRO). Four animals from each group were selected at the start of the trial to have rumen content collected using a stomach tube in each phase. Rumen content and jejunum digesta samples were also collected from all the animals at slaughter. Extracted DNA was sent for 16S rRNA (V3-V4) and ITS1 sequencing. Quality control of the sequencing data was performed, and alpha and beta diversity was calculated. The Kruskal-Wallis and Dunn tests were used to determine significant differences in the relative abundance of the taxa and alpha diversity between the feedlot diets, the feed additive groups, and the sampling methods. The first objective of this study was to determine the changes in the rumen microbiome composition through the growth phases in cattle raised under feedlot conditions. There was a significant difference in the microbiome composition among the feedlot diets, with the alpha diversity of the rumen bacteria and the abundance of Bacteroidetes decreasing as the concentrate component in the feed increased from backgrounding to the finisher phase. The effect of feeding monensin was compared to the effect of essential oils and probiotics on the rumen microbiome composition of cattle fed feedlot diets. There was no substantial difference in the rumen microbiome composition of CON, EO or PRO compared to MON. The high abundance of Proteobacteria in the finisher phase has been associated with an imbalance in the rumen microbiome. The abundance of Proteobacteria in finisher phase of the PRO group was lower compared to the other groups while the alpha diversity was higher. The effect of monensin and essential oils on the rumen microbiome decreased as the feedlot period progressed from the starter to the finisher phases which could be an indication of the adaptation of the microbes to the feed additives. The effect of the different feed additives on the jejunum microbiome was investigated and it was observed that all three feed additives had a significant effect on the jejunum bacterial diversity and composition. A higher diversity was observed within the PRO and CON groups with higher abundances of beneficial microbes that has been associated with healthier animals such as Roseburia, Blautia and Eubacterium, compared to MON and EO. The supplementation of probiotics has been reported to result in an increase in commensal and beneficial bacteria. The inclusion of monensin and essential oils decreased the diversity and the abundance of pathogenic and beneficial microbes. The microbial composition of rumen samples collected via different sampling techniques was studied and it was observed that samples collected via stomach tube differed significantly from those collected at slaughter. This might be due to the withdrawal of feed before the animals were slaughtered. Minimal significant differences were observed among monensin, essential oils and probiotics on the rumen microbiome of the cattle in this study, therefore essential oils and probiotics can be considered alternatives to the use of monensin. Large scale feeding studies are needed to validate the findings of this study.Animal and Wildlife SciencesPhD (Animal Science)Unrestricte