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.

We used a disease-free and closed herd in the present study which allowed us to investigate the dynamics of the NP microbiota of beef cattle following transport and arrival at a feedlot without potential confounding factors such as antimicrobial use and vaccination. Overall, it is evident that the bovine NP microbiota undergoes a number of significant and relatively rapid changes in terms of structure and membership following arrival at the feedlot. Introduction to the feedlot environment increased both the richness and phylogenetic diversity of the NP microbiota within the first 48 h of arrival. Functional analysis using PICRUSt also predicted that pathways associated with metabolism and DNA replication and repair were differentially abundant between days 0 and 14. Although feedlot placement did not increase BRD-associated bacterial pathogens, with the exception of Mycoplasma, the relative instability of the NP microbiota immediately following feedlot placement may help explain why cattle are most susceptible to BRD during this period. Other factors such as age, vaccination status, antimicrobial use history, and mingling also need to be investigated to better define parameters throughout the beef continuum that can alter the NP microbiota, and in particular, opportunistic pathogens.