Abstract
Backgrounding (BKG) segment in beef production systems is characterized by utilization of different forages which affect growth performance and carcass characteristics. However, it is unclear how BKG systems impact rumen microbiome. We investigated rumen microbiome dynamics of beef calves under different BKG systems. At weaning, Angus and Angus x Simmental beef calves (n = 38) were stratified by age, weight, and sex in a completely randomized design into 1 of 3 BKG treatments for 55 d: 1) perennial pasture (PP; quackgrass, orchardgrass; smooth bromegrass, red clover, and alfalfa); 2) summer annual cover crop (CC; cereal oats, purple top turnips, hunter forage brassica, and graza forage radish); and 3) dry lot (DL; haylage, corn, and DDGS). After BKG, all calves were assigned to a high energy ration in a feedlot. Rumen sample was collected via esophageal tubing at weaning, BKG and feedlot. A total of 190 rumen fluid samples were used to sequence the hypervariable V4 region of the 16S rRNA bacterial gene on an Illumina MiSeq platform. The results showed that BKG systems largely influenced rumen bacterial communities. Specifically, microbiome composition and diversity were not different at weaning, diverged significantly during BKG (Shannon index, Bray Curtis distance metrics; P < 0.001) and homogenized during feedlot. During the BKG segment, the bacterial genera Agrobacterium, Coprococcus, and Ruminococcus were dominant in CC whereas Fibrobacteraceae and Mycoplasmataceae was most dominant in DL. Moreover, rumen microbiome patterns of CC and DL calves showed increased plasticity in early stages of development but not during feedlot with PP showing fewer changes over time. These results indicate that BKG systems significantly modulate the rumen microbiome of beef cattle and, underscore the importance of early developmental stages as potential targets for feeding interventions that can impact the animal microbiome to enhance animal performance.