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.

A total of 3,868,199 archaeal and bacterial 16S rRNA gene sequences, with an average length of 260 bp, remained after primer removal, quality-filtering, and chimera-checking. These sequences were clustered into 6,381 OTUs following the removal of OTUs containing less than ten sequences and prior to random subsampling of each sample to 24,500 sequences. These OTUs were assigned to 28 different phyla and 478 genera. Six phyla, however, accounted for 97% of the sequences: Firmicutes, Proteobacteria, Tenericutes, Actinobacteria, Bacteroidetes, and Euryarchaeota (Additional file 5: Fig. S2 ). The 20 most relatively abundant genera are shown in Fig. 1. At the genus-level in particular, there was considerable interindividual variability among cattle over the 14-d sampling period. For example, Mycoplasma and Psychrobacter each comprised greater than 12.0% of the total sequences overall, however, the range for Mycoplasma and Psychrobacter in individual cattle was between 0.003 to 86.0% and 0.55 to 90.0%, respectively. Intriguingly, a number of the most relatively abundant genera (Methanobrevibacter, Bacteroides, Bifidobacterium, Clostridium, RC9 gut group, and Ruminococcus) in the nasopharynx contain obligate anaerobic species. Despite the large number of OTUs present among all NP samples, 43.1% of the total 16S rRNA gene sequences were assigned to only 10 OTUs. There were 52 OTUs that were shared among all cattle at all sampling times (Additional file 6: Table S4 ), comprising what may be defined as the core microbiota in this context. As expected, this core microbiota consisted of many of the most relatively abundant OTUs such as those classified as Mycoplasma, Psychrobacter, Amnibacterium, and Acinetobacter.