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.

Although there was considerable inter-individual variability, many of the relatively abundant genera found in the NP microbiota of the current study were also identified previously as being among the most relatively abundant in the NP of feedlot [1, 3] and dairy cattle [35] . In addition, of the 20 most relatively abundant genera, Acinetobacter, Bacillus, Corynebacterium, Mannheimia, Moraxella, Pasteurella, Proteus, Psychrobacter, and Streptococcus have all been isolated from the bovine Fig. 6 Functional predictions for the nasopharyngeal (NP) microbiota of cattle, as calculated using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). a Number of KEGG orthologies (KOs) per NP sample. b Principal coordinate analysis plot of Bray-Curtis distances for KOs in each NP sample by sampling time. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement nasopharynx using culture-based methods [1, 5, 39] . Mycoplasma, which is typically more difficult to isolate, is also frequently identified when appropriate cultureconditions are employed [40, 41] . Interestingly, Amnibacterium was the fourth most relatively abundant genus overall, although this was largely a result of 10 samples that had a relative abundance of greater than 10%. This genus, which belongs to the Microbacteriaceae family, has only been recently described [42] and included in the SILVA database, explaining its previous absence from characterizations of the NP microbiota. Species of Amnibacterium have been identified in water [42] and soil [43] perhaps indicating that the environment was the source of this genus in nasopharyngeal samples.