Fig. 4

Rumen microbiota, differences by weaning strategy. (A) Box plots of Shannon’s Index at the genus level, stratified by weaning strategy across collection days. Boxes represent the 25th to 75th percentile; horizontal line represents the median; and whiskers indicate 1.5× the interquartile range (IQR), P values from Type-III ANOVA, weaning groups with different superscript letters were significantly different. (B) Non-metric multidimensional scaling (NMDS) ordination plots based on Bray–Curtis distances at the genus level colored by weaning strategy. P value and R² values from PERMANOVA testing. (C) Differential abundance of microbial genera between fence-line and truck weaned calves at different collection days, expressed as log2 fold change (LogFC). Statistically significant logFC (adjusted P < 0.05) are depicted in red and non-significant in grey. Circle diameter is proportional to the average abundance of each phylum across all samples