Rumen microbial diversity of Bonsmara cattle using amplicon sequencing during a 120-day growth trial

Improved understanding of the microbial populations during intensive feeding of feedlot cattle holds potential for optimizing production efficiency. Ionophores are used to increase the production and efficiency of ruminants and are commonly used in South African feedlots. Bonsmara bull calves (n=24) were subject to a four-phase feedlot diet in a growth trial commencing with backgrounding, followed by starter, grower and finisher diets. Animals were randomly divided into two groups: control and a group provided the in-feed ionophore monensin. Four animals from each group were randomly selected for rumen content collection using an oesophageal tube during the phases in the trial. Samples were analysed using 16S rRNA and internal transcribed spacers amplicon sequencing. Totals of 42 008 and 35 442 amplicon sequence variants were identified from 16S rRNA and internal transcribed spacers amplicon sequencing. The rumen microbiome composition and alpha diversity differed significantly between the phases, whereas no significant difference was observed between the control and monensin groups. Backgrounding had the highest bacterial richness, whereas the grower phase had the highest fungal richness. Bacteroidetes, Firmicutes and Proteobacteria were the most abundant phyla, with Bacteroidetes being most abundant in the backgrounding and starter phases, whereas Proteobacteria was the most abundant in the grower and finisher phases. Ascomycota, Basidiomycota and Neocallistigomycota were the most abundant fungal phyla. Improved knowledge of the shift in microbiome population during the growth period could assist in adapting feeding strategies to improve the efficiency of beef production.