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.

To compare the culture results with those of the 16S rRNA gene sequencing, the representative sequence for each OTU that was assigned to the genus Pasteurella or Mannheimia by the UCLUST consensus taxonomy assigner, was further characterized using BLASTn (blast.ncbi.nlm.nih.gov; Additional file 4: Table S3 ) across all time points. H. somni was excluded as it was not detected by culturing or sequencing. Pasteurella spp. OTUs comprised 3.2% of total sequences and overall, 28 out of 29 of these OTUs were identified as P. multocida based on the top BLASTn results. There were 28 OTUs that were classified as Mannheimia spp., with a total relative abundance of 1.5%. However, the majority of these OTUs (19/28) were identified via BLASTn as M. varigena, rather than M. haemolytica (8/28), which may explain the absence of detection via culturing. Although we did not attempt to culture Mycoplasma, due to its potential role in BRD and high prevalence in the 16S rRNA gene sequencing results (13.1% relative abundance), we used BLASTn to identify the five most relatively abundant Mycoplasma OTUs. These five OTUs contained more than 99% of Mycoplasma sequences and among these sequences, Mycoplasma bovirhinis and Mycoplasma dispar comprised equal proportions (6.2% each). Candidatus Mycoplasma haemobos, with a relative abundance of 0.91% was the only other Mycoplasma species among the top five OTUs analyzed.