Evaluating the Metagenome of Two Sampling Locations in the Nasal Cavity of Cattle with Bovine Respiratory Disease Complex (BRDC)

Bovine respiratory disease complex (BRDC) is a multi-factor disease, and disease incidence may be associated with an animal’s commensal microbiota (metagenome). Evaluation of the animal’s resident microbiota in the nasal cavity may help us to understand the impact of the metagenome on incidence of BRDC in cattle. Our objective was to determine whether metagenome populations of the nasal cavity vary based on sampling location. Therefore, two sampling locations (upper nasal and deep nasal pharyngeal) were evaluated. Nasal swabs from calves were collected when the animal was diagnosed with BRDC after weaning in the feedlot. Samples from healthy cohorts were also collected for each time point evaluated in the feedlot to compare metagenome profiles of healthy and sick animals. For each animal one swab was inserted into the nasal cavity approximately 6 inches for sampling of the upper nasal region and a second swab was inserted approximately 8 inches for sampling of the deep nasal pharyngeal region. Samples were pooled in groups based on when the animal was diagnosed with BRDC (one week, two weeks, or three weeks after weaning), type of sample (upper nasal or deep pharyngeal), and health status (control or diagnosed with BRDC). To evaluate and compare the metagenome of each pooled sample, the variable region (V1-V3) along the 16S ribosomal RNA gene was amplified by PCR. These amplified products were sequenced using next-generation sequencing (Illumina MiSeq) and sequence reads were analyzed by WebMGA and GreenGenes to identify the bacterial taxa present. In order to assess the similarities or differences between sampling sites we needed a measure that would reflect changes in the metagenome as a whole, accounting for differences in incidence of all detected bacterial taxa simultaneously. The Jaccard distance between samples is such a measure. Jaccard distances between sampling sites for the same animal group were small relative to the distribution of inter-sampling site distances between animal groups generated by permutation (P = 0.00069). In summary, bacterial populations were similar between upper nasal and deep pharyngeal sampling locations. These results demonstrate that shorter, less invasive nasal swabs produce similar results to deep nasal pharyngeal swabs.