Identifying Bovine Respiratory Disease (BRD) through the Nasal Microbiome

Bovine respiratory disease (BRD) is an ongoing health and economic issue in the dairy and beef cattle industry. Also, there are multiple risk factors that make an animal susceptible to BRD and it's diagnosis and treatment is a challenge for producers. Four bacterial species, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis have been associated with BRD mortalities. Hence, this study aims to characterize the cattle nasal microbiome as a potential additional diagnostic method to identify animals suspected to have a lung infection. Quantitative PCR and 16S rRNA gene sequencing were used to determine the bacterial load of these four bacterial pathogens in the nasal microbiome of apparently healthy (N=75) and (N=58) affected by BRD Holstein steers. We then sought to identify a value or equation that could be used to discriminate between BRD and healthy animals using a Linear Discriminant Model (LDA). Additionally, co-occurrence between commensal bacterial and BRD-pathogens were also identified. Cattle diagnosed with BRD presented lower richness, evenness and phylogenetic diversity than healthy pen-mates. Bacterial species and genera Truperella pyrogenes and Bibersteina were increased in the BRD group, and the species Mycoplasma bovirhinis and Clostridium sensu stricto increased in the healthy group. Prevalence of H. somni (98%) and P. multocida (97%) were the highest regardless of disease diagnosis in all the samples. Prevalence of M. haemolytica (81 vs. 61%) and M. bovis (74 vs. 50.7%) were higher in the BRD group. The bacterial density of M. haemolytica and M. bovis was also higher in the BRD group, whereas Histophilus somni was lower in the BRD group. Five different models were tested using LDA, and one model produced a sensitivity and specificity of 60% and 81% agreement with diagnosis based on animal symptoms. Co-occurrence analysis demonstrated that the nasal microbiome members are more likely to interact with each other than associations between BRD-pathogens and nasal microbiome members. This study offers insight into the BRD-pathogens prevalence and difference in nasal microbiome between healthy and BRD animals and provides a potential platform for future studies and potential pen-side diagnostic testing.