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 within-sample or alpha-diversity metrics were compared by sampling time using the PROC MIXED procedure in SAS 9.4 [29] with sampling time as a repeated measure and individual animal as the random effect. Tukey's honestly significant difference post-hoc test was then used to compare means and adjust for multiple pairwise comparisons. Linear discriminant analysis effect size (LEfSe) was used to determine the genera that were associated with a specific sampling time. LEfSe uses the Kruskal-Wallis test to identify significantly different (P < 0.05) genera among groups of samples and estimates the effect size of each of these using linear discriminant analysis [30] . A linear discriminant analysis (LDA) score of 4.0 was used as the threshold for plotting differentially abundant taxa. The unweighted and weighted UniFrac distances were compared using ANOSIM (analysis of similarities) with 999 permutations. An ANOVA followed by the Benjamini-Hochberg false discovery rate (FDR) correction for multiple comparisons was used to compare the relative abundance of KEGG level 2 pathways by sampling time using STAMP v. 2.1.3 [31] . Bray-Curtis distances [32] were utilized to assess changes in the predicted functional profile of each sample based on KOs. All results were considered significant at P < 0.05 or FDR < 0.05.