The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot

Holman, Devin B.; Timsit, Edouard; Amat, Samat; Abbott, D. Wade; Buret, Andre G.; Alexander, Trevor W.

The structure of the NP microbiota continued to shift during the 14-d monitoring period, however, the changes observed from day 0 to day 2, as determined using unweighted UniFrac distances (Fig. 5) , were particularly noticeable. The microbial richness and phylogenetic diversity also both significantly increased following transport to the feedlot (day 2). These early alterations in the NP microbiota may be expected given the number of changes in the external environment of the cattle during this period. For example, cattle are potentially exposed to new microbes in the feedlot pens, including those in water and feed which have different sources compared to the cow/calf farm. In addition, feedlot transport is a known stressor for cattle, influencing immune function through higher cortisol levels, altered acute-phase protein response, and modifying the concentrations of other white blood cells, which may in turn alter the microbiota [44] [45] [46] . Overall, the changes in the microbial community structure were mostly driven by the less relatively abundant taxa given the differences observed between the unweighted and weighted UniFrac distances. The NP microbiota did appear to become more homogenous over the 14-d study period as the number of OTUs shared by all animals at each sample time increased from only 76 at day 0 to an average of 313 at the days 2, 7, and 14.