Profiling the bacterial communities in feedlot cattle affected with bovine foot rot and bovine digital dermatitis lesions using 16S rRNA gene sequencing and quantitative real-time PCR

The primary infectious foot diseases in cattle are bovine foot rot (BFR) and bovine digital dermatitis (BDD), typically associated with Fusobacterium necrophorum and Treponema spp., respectively. However, both infections have now been identified considered as polybacterial with additional bacteria involved such as Porphyromonas levii, Bacteroides pyogenes, and F. mortiferum. Using 16S rRNA gene (V3-V4 region) sequencing and quantitative real-time PCR, we detected and quantified these bacteria and bacterial communities present in foot lesion biopsies of feedlot cattle with visually confirmed cases of BFR (32), M2 (active; 17), and M4 (chronic; 12) stages of BDD in contrast to inconclusive (14) clinical cases and healthy (25) cattle. Skin biopsy samples were taken from lesions and healthy feet. DNA was extracted using QIAGEN DNeasy kit and eluted using molecular-grade water. Sequencing was performed on the Illumina MiSeq platform at the Center for Health Genomics and Informatics (CHGI), Calgary.