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.

The predicted functional analysis of the NP microbiome was performed using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) v. 1.0.0. PICRUSt uses the phylogenetic composition of a sample based on 16S rRNA gene sequencing to infer the functional content of the microbiota [26] . For this analysis, sequences were clustered into OTUs in QIIME using the closed reference OTU picking algorithm and the Greengenes 13_5 database [27] and all samples were randomly subsampled to 17,700 sequences. The OTU table was then normalized using the known 16S rRNA gene copy numbers for each representative sequence. The metagenome of each sample was inferred using the KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology database [28] and functional predictions were made for each sample. The KEGG orthologies (KOs) were categorized into KEGG level 2 pathways with the removal of the non-microbial pathways: organismal systems and human disease. The nearest sequenced taxon index (NSTI) was used to provide a measure of the availability of sequenced reference genomes for each OTU in a sample. It calculates the average branch length for each sample between an OTU and the nearest sequenced reference genome based on the Greengenes reference phylogeny, accounting for OTU abundance [26] .