Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia.

Specific nasopharyngeal bacterial communities can provide colonization resistance against respiratory pathogens in cattle. However, the role of bacterial communities of the lower airways in respiratory health remains largely unknown. Therefore, our objective was to compare nasopharyngeal and tracheal bacterial communities between healthy feedlot cattle and those with bronchopneumonia (BP). Deep nasal swabs and trans-tracheal aspiration samples were collected from steers with (n = 60) and without (n = 60) BP at 4 feedlots in Western Canada. After DNA extraction, 16S rRNA gene (V4) was amplified and sequenced. Alpha-diversity analysis revealed a lower bacterial diversity in the nasopharynx and trachea of steers with BP compared to healthy pen-mates. Bacterial communities present within the airways clustered into 4 distinct metacommunities that were associated with sampling locations and health status. Metacommunity 1, enriched with Mycoplasma bovis, Mannheimia haemolytica and Pasteurella multocida, was dominant in the nasopharynx and trachea of steers with BP. In contrast, metacommunity 3, enriched with Mycoplasma dispar, Lactococcus lactis and Lactobacillus casei, was mostly present in the trachea of healthy steers. Metacommunity 4, enriched with Corynebacterium, Jeotgalicoccus, Psychrobacter and Planomicrobium, was present in the nasopharynx only. Metacommunity 2, enriched with Histophilus somni, Moraxella and L. lactis, was present in both healthy and sick steers, but was primarily detected in one feedlot. We concluded that distinct bacterial metacommunities inhabited the nasopharynx and trachea of healthy feedlot cattle and those with BP. Because L. lactis and L. casei can inhibit M. haemolytica growth in vitro, their presence in healthy steers may have provided colonization resistance against bacterial respiratory pathogens.