Additional file 10: Table S7. Matrix of KO counts per Sample. KO counts per MAG (Table S3) were multiplied by the abundance of each MAG per sample (Table S5) to generate a KO per sample matrix representing the functional potential of the microbiome associated with each sample to be used as input for phyloseq and DESeq2 analyses.

Additional file 10: Table S7. Matrix of KO counts per Sample. KO counts per MAG (Table S3) were multiplied by the abundance of each MAG per sample (Table S5) to generate a KO per sample matrix representing the functional potential of the microbiome associated with each sample to be used as input for phyloseq and DESeq2 analyses.

Additional file 14: Table S11. Taxonomy Table of MAGs. Complete taxonomy table adapted from Table S1 to be used as input for phyloseq and DESeq2 analyses.

Additional file 13: Table S10. Metadata Table for Metagenome Samples. Metadata table containing Sample ID, Period, Animal and Diet treatment information for each sample adapted from Table 7 to be used as input for phyloseq and DESeq2 analyses.

Additional file 11: Table S8. Overall significantly differentially abundant KOs. Significantly differentially abundant KOs associated with metabolically important pathways in the rumen when comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)

Additional file 14: Table S11. Taxonomy Table of MAGs. Complete taxonomy table adapted from Table S1 to be used as input for phyloseq and DESeq2 analyses.

Additional file 12: Table S9. Contribution of differentially abundant MAGs to metabolic pathways. Absolute counts of KOs associated with significantly differentially abundant MAGs comparing 40% and 60% MER diet treatments versus the 80% treatment. Counts for each taxonomic group in each diet treatment are aggregated into metabolically important pathways within the rumen (KO counts). Using the absolute counts, the log 2 fold change (LFC) of the counts in the 40% and 60% diet treatments has been calculated to give proportional change in contribution of each taxonomic group to each metabolic pathway when compared to the 80% diet treatment (LFC vs 80%).

Additional file 15: R Script for DESeq2 and phyloseq analyses. R script to perform MAG and KO level using the likelihood ratio test (LRT) in DESeq2. Analyses identify significantly differentially abundant MAGs and KOs when the more restrictive 40% and 60% MER diet treatments are contrasted against the 80% MER diet treatment. Statistical analysis of the ruminal community structure is performed using the Adonis2 PERMANOVA analysis. Principal coordinate analysis (PCoA) and canonical analysis of principal coordinates (CAP) ordination plots are generated using phyloseq and ggplot2.

Additional file 6: Table S3. KEGG Functional Annotations of MAGs. Counts of proteins in each MAG with a hit in the KEGG database for a KEGG ortholog (KO_Counts).

Additional file 11: Table S8. Overall significantly differentially abundant KOs. Significantly differentially abundant KOs associated with metabolically important pathways in the rumen when comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)