Statistical analysis output.

Statistical analysis output is split across the following sheets. “all_padj_Hommel”: list of p values obtained from running Kruskal-Wallis test, adjusted using the Hommel correction for phylogenetic diversity values: unrooted pd, BWPD, and five principal components. Grouping of samples is based on: cross-breed, line, date of birth, date of birth within distinct cross-breeds, maternal sow and nurse sow. Sample size and sample collection date is reported. “all_pvalues”: reports the p values of “all_padj_Hommel” sheet, prior to Hommel p value adjustment. “alpha_delta_cohorts”: deltas between time points are obtained per cohort and these deltas are compared using ANOVA, adjusting p values using the TukeyHSD method. “alpha_means”: the means and standard deviations of alpha diversity (unrooted pd and BWPD) obtained per time point and cohort. “alpha_time”: results of comparison between time points of alpha diversity (unrooted pd and BWPD) using the t-test and Bonferroni p value correction. “batch_post_process”: results of comparison of alpha diversity values by DNA extraction plate (1–10) after batch effect removal, run using ANOVA and TukeyHSD p value adjustment method. batch_pre_process: results of comparison of alpha diversity values by DNA extraction plate (1–10) before batch effect removal, run using ANOVA and TukeyHSD p value adjustment method. “deltas_percent_change”: comparison of alpha diversity values (unrooted pd and BWPD) between time points within distinct cohorts and within all cohorts. Sample size (n), deltas (percentage) are shown. “guppy_padj”: p values from “guppy_pvalues” are adjusted using the Bonferroni method and results are reported. “guppy_pvalues”: output of single guppy runs is analyzed by comparing beta diversity values by cohort at each time point using the pairwise t test; results of the tests are here shown. “PD_100K_vs_1M_stats”: alpha and beta diversity values obtained with PhyloSift using either 100,000 reads or 1,000,000 reads downsampling size. “weight_cohort_stats”: piglets were weighted at each time point. Deltas are obtained per piglet and means were compared between cohorts using ANOVA and TukeyHSD p value correction, results are reported. “weight_taxa”: Spearman’s rank correlation was assessed between pig weight and abundance of lineages obtained from 16S rRNA containing reads. Significance values are adjusted using the distinct methods listed. (XLSX)