The Effects of Breed and Residual Feed Intake Divergence on the Abundance and Active Population of Rumen Microbiota in Beef Cattle

SIMPLE SUMMARY: This study assessed the effects of breed and feed efficiency on rumen microbiota in a total of 96 beef steers, with three breeds and divergent residual feed intakes. The abundance and activity of the total bacteria, archaea, protozoa, and fungi in the rumens were estimated by measuring the copy numbers of their respective marker genes at both DNA (abundance) and RNA (activity) levels. Our results evidence the effect of breed on four microbial groups. Past studies have been mainly focused on bacteria and archaea, yet ours is the first study to reveal the effect of breed (host genetics) on rumen eukaryotes, suggesting that host genetics can regulate the rumen microbiota as a whole, highlighting the potential of manipulating and obtaining desirable and efficient rumen microbiota using breeding and genetic selection. ABSTRACT: To assess the effects of residual feed intake (RFI) and breed on rumen microbiota, the abundance (DNA) and active population (RNA) of the total bacteria, archaea, protozoa, and fungi in the rumen of 96 beef steers from three different breeds (Angus (AN), Charolais (CH), and Kinsella Composite (KC)), and divergent RFIs (High vs Low), were estimated by measuring their respective maker gene copies using qRT-PCR. All experimental animals were kept under the same feedlot condition and fed with the same high-energy finishing diet. Rumen content samples were collected at slaughter and used for the extraction of genetic material (DNA and RNA) and further analysis. There was a significant difference (p < 0.01) between the marker gene copies detected for abundance and active populations for all four microbial groups. AN steers had a higher abundance of bacteria (p < 0.05) and a lower abundance of eukaryotes (protozoa and fungi, p < 0.05) compared to KC steers, while the abundance of protozoa (p < 0.05) in the AN cattle and fungi (p < 0.05) in the KC cattle were lower and higher, respectively, than those in the CH steers. Meanwhile, the active populations of bacteria, archaea, and protozoa in the KC steers were significantly lower than those in the AN and CH animals (p < 0.01). This work demonstrates that cattle breed can affect rumen microbiota at both the abundance and activity level. The revealed highly active protozoal populations indicate their important role in rumen microbial fermentation under a feedlot diet, which warrants further study.