Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC)

Abstract

Bovine respiratory disease complex (BRDC) is a multifactor disease, and disease incidence may be associated with an animal's commensal bacterial populations (microbiome) in the upper nasal cavity. Identifying these commensal bacterial populations in the upper nasal cavity may help us to understand the impact of the microbiome on incidence of BRDC in cattle. Various sampling techniques have previously been utilized to evaluate the microbiome of different locations of the upper nasal cavity in cattle. Therefore, our objective was to determine whether bacterial populations of the nasal cavity vary based on these sampling locations. Two common sampling techniques were evaluated, including 6-inch nasal swabs and deep nasopharyngeal swabs. Nasal swabs from calves were collected when the animal was diagnosed with BRDC after weaning in the feedlot in addition to collection of samples from asymptomatic cohorts. Samples were pooled in groups based on year the animal was in the feedlot (2015 or 2016), when the animal was diagnosed with BRDC (1 to 5 weeks after weaning), type of sample (6-inch nasal swab or deep nasopharyngeal swab), and health status (diagnosis with BRDC or control). Variable regions 1 through 3 along the 16S rRNA gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Overall, sampling site did not consistently influence diversity of the bacterial populations of the upper nasal cavity. However, the effect of disease incidence on the microbiome was depended on sampling time after weaning (P = 0.0462) for 2015, while the main effects of sampling time after weaning (P = 0.00992) and disease phenotype (P = 0.012) were significant for 2016. These data for 2016 demonstrate that in addition to bacterial profiles changing throughout weaning, calves diagnosed with BRDC have different bacterial profiles compared to their control cohorts. In addition, evaluation of the microbiome identified predominant bacteria genera in the upper nasal cavity included those previously reported to be associated with cattle diagnosed with BRDC including Mycoplasma sp., Psychrobacter sp., and Mannheimia sp. In summary, these results demonstrate that shorter, less invasive 6-inch nasal swabs produce similar results to deep nasopharyngeal swabs.

Figure 1.

The mean distance between sampling sites within pool. Mean distance between sampling sites (deep nasopharyngeal swab and 6-inch nasal swab) was determined for 2015 (a) and 2016 (b) samples. The mean distance between sampling site within pool was 0.325 for 2015 and 0.286 for 2016, as identified by the red dashed line (a and b). Mean distance in taxa composition (microbiome) between sampling sites was lower than expected by chance; P = 0.018 for 2015 and P = 2 × 10^–6 for 2016.

Figure 2.

Taxonomy classification for 2015. Percentage of 16S rRNA gene sequence reads classified to genus level for 2015 nasal swabs. Top eight bacterial genera in abundance are reported and remaining genera of low abundance are grouped and identified as other. Sequence reads that could not be classified to the genus level and are identified as unclassified.

Figure 3.

Taxonomy classification for 2016. Percentage of 16S rRNA gene sequence reads classified to genus level for 2016 nasal swabs. Top eight bacterial genera in abundance are reported and remaining genera of low abundance are grouped and identified as other. Sequence reads that could not be classified to the genus level and are identified as unclassified.