BackgroundBacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. While the bacterial composition of the bovine upper respiratory tract (URT) has not been studied in detail, the nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP.However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which URT niches may contribute the most to the composition of the lung microbiota.
MethodsSeventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced.Community composition, alpha-diversity, and beta-diversity were compared among sampling locations.
ResultsMicrobiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1,137 observed sequence variants (SVs).An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma . Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar .Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella , Fusobacterium , and Streptococcus , respectively.