Nasal pathobiont abundance does not differ between dairy cattle with or without clinical symptoms of bovine respiratory disease

Abstract

Background: Bovine respiratory disease (BRD) remains a significant health and economic problem to the dairy cattle industry. Multiple risk factors contribute to BRD susceptibility including the bacterial pathobionts Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Studies have characterized and quantified the abundance of these bacteria in the nasal cavity of cattle to infer and help disease diagnosis; nonetheless, there is still discrepancy in the results observed of when these microbes are commensal or pathogenic. Additionally, some of these studies are limited to a specific farm. The goal of this study is to compare the nasal microbiome community (diversity and composition) and the abundance of the four bacterial pathogens (by qPCR) in the nasal cavity to identify differences between dairy calves that are apparently healthy and those identified to have BRD. Nasal swabs were collected from approximately 50 apparently healthy and 50 BRD-affected calves sampled from five different dairy farms in the US (CA, IN, NY (two farms), and TX).

Results: Calves diagnosed with BRD in NY, and TX had lower nasal microbiome diversity compared to the apparently healthy calves. Differences in the nasal microbiome composition were observed between the different farms predicted by Bray-Curtis and weighted UniFrac dissimilarities. Commensal and pathobiont genera Acinetobacter, Moraxella, Psychrobacter, Histophilus, Mannheimia, Mycoplasma, and Pasteurella were prevalent in the bovine nasal microbiome regardless of farm or disease status. The BRD-pathobiont H. somni was the most prevalent pathobiont among all the samples and M. bovis the least prevalent. Only in CA was the abundance of a pathobiont different according to disease status, where M. haemolytica was significantly more abundant in the BRD-affected animals than apparently healthy animals.

Conclusions: This study offers insight into the nasal microbiome community composition in both animals diagnosed with BRD and healthy animals, and shows that the farm effect plays a more significant role in determining the microbiome community than disease status in young dairy calves.

Keywords: 16S rRNA gene; BRD-pathobionts; Bovine respiratory disease; Dairy calves; qPCR.

Fig. 1

Dairy cattle nasal microbiome taxa with an average relative abundance > 2% per sample at the phylum (a), family (b) and genus (c) taxonomic levels in BRD-affected and apparently healthy animals. If only one group (apparently healthy or BRD) surpassed the 2% threshold (red dashed line), then both groups were reported

Fig. 2

Genera from dairy cattle nasal swabs with an average relative abundance > 2% (red dashed line) in at least one health group (BRD-affected and apparently healthy cattle) from at least one of the four states. If only one group (apparently healthy or BRD) surpassed the 2% threshold (red dashed line), then both groups were reported

Fig. 3

Differentially abundant taxa in between all the BRD-affected and apparently healthy animals (a) in the samples collected from IN (b), and in the samples collected from NY (c)

Fig. 4

Alpha diversity metrics between apparently healthy and BRD-affected calves (a), separated by farm (b) and between all the farms (c). Red triangles represent the group mean

Fig. 5

Beta diversity between apparently healthy separated by farm predicted by Bray-Curtis Dissimilarity (a) and Weighted UniFrac (b)

Fig. 6

Prevalence of the BRD-pathobionts between apparently healthy and BRD-affected dairy calves sampled from CA, IN, NY, and TX farms. Prevalence values represent only the calves that tested positive (present) for each bacterium

Fig. 7

BRD-pathobiont abundance (log₁₀) between disease status and divided by farm. Gold and blue triangles represent the group mean