Abstract
The advent of next-generation sequencing technologies has uncovered the importance of commensal microbial populations in the lower respiratory tract (LRT) for mucosal health and their role in the development of bovine respiratory disease (BRD). In this study, we aimed to characterize and compare the LRT microbiota in healthy and BRD-affected calves in Egypt. After assessing clinical respiratory scores in both groups, post-mortem lung samples from the cranial lobes of six clinically healthy calves and six calves affected by BRD were collected following slaughter. The most prevalent bacterial families in all samples were Moraxellaceae (11.06%), Enterobacteriaceae (8.23%), and Flavobacteriaceae (8.13%). The most common bacterial genera across all samples were Acinetobacter (13.1%), Gracilibacillus (7.9%), and Pseudomonas (5.0%). Notably, the overall microbial community structures differed significantly between healthy and BRD-affected calves. Alpha diversity analysis revealed significant differences in the Shannon (p = 0.0043) and Chao1 (p = 0.0001) indices between the two groups. This study highlights the substantial impact of BRD on the LRT microbiota of calves, highlighting the intricate relationship between host health and the LRT microbial ecosystem. Further investigations involving a larger sample size are necessary to establish the clinical significance of LRT microbiota in maintaining bovine respiratory health.