Author: Holman, Devin B.; Timsit, Edouard; Amat, Samat; Abbott, D. Wade; Buret, Andre G.; Alexander, Trevor W.
Title: The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot Document date: 2017_3_22
ID: 1nni3vhm_13
Snippet: To account for uneven sequencing depth across samples, each sample was randomly subsampled to 24,500 sequences, with the loss of one sample in the day 0 group. The bacterial and archaeal diversity, evenness, and richness in each sample was calculated within QIIME using the Shannon index [22] , phylogenetic diversity (PD whole tree) [23] , and equitability. The bacterial and archaeal community structure (beta-diversity) of each group and sampling .....
Document: To account for uneven sequencing depth across samples, each sample was randomly subsampled to 24,500 sequences, with the loss of one sample in the day 0 group. The bacterial and archaeal diversity, evenness, and richness in each sample was calculated within QIIME using the Shannon index [22] , phylogenetic diversity (PD whole tree) [23] , and equitability. The bacterial and archaeal community structure (beta-diversity) of each group and sampling time was evaluated using the unweighted and weighted UniFrac distances [24] and visualized as principal coordinate analysis (PCoA) plots using Emperor [25] .
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