Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease

Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.