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Background  The nasopharyngeal (NP) microbiota plays an important role in bovine health, comprising a rich and diverse microbial community. The nasopharynx is also the niche for potentially pathogenic agents which are associated with bovine respiratory disease (BRD), a serious and costly illness in feedlot cattle. We used 14 beef heifers from a closed and disease-free herd to assess the dynamics of the NP microbiota of cattle that are transported to a feedlot. Cattle were sampled prior to transport to the feedlot (day 0) and at days 2, 7, and 14.    Results  The structure of the NP microbiota changed significantly over the course of the study, with the largest shift occurring between day 0 (prior to transport) and day 2 (P < 0.001). Phylogenetic diversity and richness increased following feedlot placement (day 2; P < 0.05). The genera  Pasteurella, Bacillus , and  Proteus  were enriched at day 0,  Streptococcus  and  Acinetobacter  at day 2,  Bifidobacterium  at day 7, and  Mycoplasma  at day 14. The functional potential of the NP microbiota was assessed using PICRUSt, revealing that replication and repair, as well as translation pathways, were more relatively abundant in day 14 samples. These differences were driven mostly by  Mycoplasma . Although eight cattle were culture-positive for the BRD-associated bacterium  Pasteurella multocida  at one or more sampling times, none were culture-positive for  Mannheimia haemolytica  or  Histophilus somni .    Conclusions  This study investigated the effect that feedlot placement has on the NP microbiota of beef cattle over a 14-d period. Within two days of transport to the feedlot, the NP microbiota changed significantly, increasing in both phylogenetic diversity and richness. These results demonstrate that there is an abrupt shift in the NP microbiota of cattle after transportation to a feedlot. This may have importance for understanding why cattle are most susceptible to BRD after feedlot placement.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-0978-6) contains supplementary material, which is available to authorized users.

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