Intranasal Modified-Live Virus Respiratory Vaccination and Bovine Respiratory Disease Influence the Respiratory Microbiome of Cattle

Modified-live virus (MLV) respiratory vaccines are commonly administered to beef cattle upon feedlot arrival to prevent bovine respiratory disease (BRD). Yet, the impact of these vaccines on respiratory microbial communities is unknown. The objective of this study was to evaluate the impact of an intranasal, trivalent (IBRV, BRSV, PI3V) MLV respiratory vaccine with parenteral, bivalent BVDV and a parenteral, pentavalent (BVDV type I and II, IBRV, BRSV, PI3V) MLV respiratory vaccine on the respiratory microbiome of newly received feedlot cattle. High-risk beef bull and steer calves (n =525) arrived in 5 truckload blocks and were stratified by body weight (213 ± 18.4 kg), sex, and presence of a pre-existing identification ear-tag. Pens were spatially arranged in sets of 3 and randomly assigned to vaccine treatment with an empty pen between treatment groups to minimize virus transmission among groups. The treatments included: 1) no viral respiratory vaccination (CON), 2) cattle intranasally administered a trivalent, MLV respiratory vaccine with parenteral BVDV type I and II vaccine (INT), and 3) cattle administered a pentavalent, MLV respiratory vaccine (INJ). Nasopharyngeal swabs were collected on d 0 and 28 and from cattle that were treated for BRD. For subset selection, 3 animals were chosen from each pen that were never treated for BRD and had the greatest ADG within pen to decrease the chance of selecting a false negative. Also, 3 steers classified as a BRD case were selected from each pen with number of BRD treatments administered equivalent across pens and treatments. Finally, nasal swabs from d 0 and 28 from the selected subset and from cattle classified as chronically ill and those dying from bronchopneumonia were analyzed for microbiome. The target sample size was approximately 600 samples with 50 animals per treatment in each category: healthy, morbid, chronic, and mortality. Chronic and mortality categories did not reach the 50-sample goal, and the allotment for those samples was added to healthy and morbid categories. These criteria resulted in a total of 600 nasal swab samples being selected for DNA extraction and subsequent 16S rRNA gene sequencing to characterize the microbiome of the upper respiratory tract. Nasal swabs from d 28 in healthy cattle were used to evaluate the impact of vaccination on URT microbial communities. Pairwise Wilcoxon rank-sum with Benjamini-Hochberg correction was used in the R software package to determine differences in relative abundance of specific bacteria. Tenericutes were less abundant in INT calves (n =114; P < 0.05) and this difference was specifically attributed to decreased Mycoplasma in INT calves (P = 0.04). Members of Mannheimia and Pasteurella had lower relative abundance in INT (P < 0.05). The microbial community in healthy animals on d 28 had increased Proteobacteria and decreased Tenericutes compared to animals that were treated for or died from BRD (P < 0.05). Cattle that died had a greater relative abundance of Mycoplasma in their respiratory microbiome on d 0 (P < 0.02). Overall, richness was similar on d 0 and 28, but diversity was increased for all animals on d 28 (P > 0.05). These data indicate a distinct shift in URT community composition over the first 28 d in the feedlot regardless of health status. Furthermore, BRD caused alteration of the URT microbial community and administration INT influenced microbial community structure.