Effect of Monensin Withdrawal on the Rumen Prokaryote Microbiome in Bos Indicus and Bos Taurus Steers Consuming Bermudagrass Hay

Abstract Monensin, a carboxylic polyether ionophore, is commonly added to ruminant diets as a strategy for improving animal production by altering ruminal fermentation. However, research concerning the effect of monensin withdrawal is limited. Therefore, the effect of monensin withdrawal and the subspecies of cattle on the rumen prokaryote microbiome was evaluated using ruminally cannulated steers (5 Bos indicus, BI and 5 Bos taurus, BT; 398 kg BW) consuming bermudagrass hay (13.7% CP). Subspecies were concurrently subjected to a two period, two treatment crossover design. Each 70-d period consisted of a 42 d adaptation phase with treatments including 0 (CON) or 200 (MON) mg·animal-1 monensin (Rumensin 90; Elanco Animal Health, Greenfield, IN) fed in 0.91 kg dried distillers grains with solubles daily. Withdrawal of monensin was then evaluated for a 28-d phase following adaptation. Rumen fluid was collected via suction strainer from the dorsal and ventral sacs of the rumen at feeding on d 1, 7, 14, 21, and 28 of the withdrawal phase and frozen until further analysis. Upon completion of the trial, samples were thawed and analyzed for microbial populations using massively parallel sequencing. The V4 region of the 16S rRNA gene was sequenced to analyze and compare rumen prokaryotic microbes within treatment groups and subspecies. Sequences were processed using QIIME 2 (q2) version 2021.2 and imported into R v4.1 for statistical analysis and graphical displays. Bray Curtis-based principle coordinate analysis (PCoA) provided visualization of microbial community clustering by monensin treatment and subspecies, facilitating identification of microbial community shifts resulting from treatments or subspecies. No monensin×subspecies×day interaction (P = 0.96) was observed. However, an effect of monensin (P = 0.01), subspecies (P ≤ 0.01), and day (P = 0.017) on the microbiome was present. The changes in microbial density that were observed with monensin withdrawal help to provide insight into the mode of action of monensin and its impact on potential methane mitigation in cattle.