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Additional file 11: Supplemental Figure 11. Taxonomic contributions to gene expression profiles for proteins involved in cell wall biogenesis for jejunum samples collected at day 40. Each node in the network indicates groups of orthologs corresponding to a specific E. coli gene (as indicated) involved in cell wall biogenesis. Links between nodes indicate a functional interaction as previously defined [53]. Size of the node indicates the relative expression of genes associated with each set of orthologs, with sector colours indicating the taxonomic contribution to gene expression (see key for color code). Red arrows indicate sets of orthologs that are significantly up-regulated in comparisons involving the presence/absence of AGPs.

Additional file 8: Supplemental Figure 8. Taxonomic contributions to expressed enzymes in Purine metabolic pathway across different AGP treatments and diets with Day40 ceca samples. Shown here are the De novo biosynthesis and salvage pathways for purine, integrated with data generated from ceca collected at day 40. Each pie chart represents the taxonomic distributions of an enzyme (see key for color code). The size of pie charts indicates the average expression value (with log2 transform) of genes encoding that enzyme. Pie charts with red arrows refer to enzymes that are significantly up-regulated relative to the paired (+/- AGPs) sample. The abbreviations used here can be found in Supplemental Table 11.

Additional file 4: Supplemental Figure 4. Principal component analysis based on annotated metabolic enzymes expression in ceca samples. Each node represents an individual ceca sample, with colours and shapes indicating specific treatment types (see inset key).

Additional file 7: Supplemental Figure 7. Taxonomic contributions to expressed enzymes in Purine metabolic pathway across different AGP treatments and diets with Day24 ceca samples. Shown here are the De novo biosynthesis and salvage pathways for purine, integrated with data generated from ceca collected at day 24. Each pie chart represents the taxonomic distributions of an enzyme (see key for color code). The size of pie charts indicates the average expression value (with log2 transform) of genes encoding that enzyme. Pie charts with red arrows refer to enzymes that are significantly up-regulated relative to the paired (+/- AGPs) sample. The abbreviations used here can be found in Supplemental Table 11.

Additional file 5: Supplemental Figure 5. Expression heatmap of metabolic pathways enriched in significantly differentially expressed enzymes. There are 35 KEGG metabolic pathways enriched in significantly differentially expressed enzymes associated with samples from either ceca or jejunum. Changes of the average expression value (log2) of each gene associated with an enzyme in that pathway are indicated by red-green or blue-yellow gradients for ceca and jejunum samples, respectively.

Additional file 9: Supplemental Figure 9. AGPs disrupt age related changes in metabolite profiles from chicken serum. PCA of metabolomic profiles generated from either AGP+ or AGP- samples. Samples are coloured and grouped based on age of bird from which the sample was taken.

Additional file 2: Supplemental Figure 2. Heatmap showing normalized abundance of taxa for taxa exhibiting significant differential abundance in at least one of the comparisons shown on the right. Each column in the heatmap represents a single sample, grouped by treatment. Each row indicates an individual taxon. Columns on the right indicate significant differences in abundance across each of eight pair-wise comparisons. Taxa are ordered on the basis of magnitude of fold change across the various pairwise comparisons.

Additional file 3: Supplemental Figure 3. Pie-chart heatmap of metabolic pathways enriched with significantly differentially expressed enzymes through comparisons between diets. There are 35 KEGG metabolic pathways enriched with significantly differentially expressed enzymes which were annotated from either ceca or jejunum samples based on comparisons between diets. Each node in the heatmap is a pie chart showing proportion of enzymes that were significantly up-regulated (orange), significantly down-regulated (blue), and not significantly different (white) with the wheat diet. In addition, the size of each node indicates the number of expressed enzymes in each KEGG pathway.

Additional file 3: Table S3. Proportion of samples containing the top 5 phyla and top 10 genera.

Additional file 16: Figure S4. Statistically significant association between the KEGG pathway, “Biosynthesis of secondary metabolites”, and pre-pregnancy BMI (obese sub-category). BMI_cat = Pre-pregnancy BMI.

Additional file 5: Figure S1A-E. Visual representation of the association between maternal characteristics and milk microbiota beta-diversity (weighted UniFrac metric). Principal coordinate analysis (PCoA, weighted UniFrac) plots comparing microbiota composition based on (A) maternal glucose tolerance, (B) mode of delivery, (C) pre-pregnancy BMI, (D) 3-month post-partum BMI, and (E) ethnicity. PCoA using the weighted UniFrac distance metric showed that microbiota profiles did not separate based on maternal clinical data. No statistically significant findings were observed between beta-diversity and glucose tolerance, mode of delivery, BMI, or ethnicity. Abbreviations: GDM, gestational diabetes mellitus, IGT, impaired glucose tolerance; CS, C-section.

Additional file 8: Table S6. Associations between maternal characteristics and the top 5 phyla and top 10 genera: Results where pairwise comparisons were statistically significant but group effects were not. Separate Poisson regression models were run for pre-pregnancy BMI and 3-month post-partum BMI, while adjusting for maternal glucose tolerance status, mode of delivery, DNA extraction batch, and PCR sequencing batch. Statistically significant pairwise findings shown only (p

Additional file 6: Figure S2A-E. Visual representation of the association between maternal characteristics and milk microbiota beta-diversity (Bray-Curtis metric). Principal coordinate analysis (PCoA, Bray-Curtis dissimilarity) plots comparing microbiota composition based on (A) maternal glucose tolerance, (B) mode of delivery, (C) pre-pregnancy BMI, (D) 3-month post-partum BMI, and (E) ethnicity. PCoA using the Bray-Curtis dissimilarity showed that microbiota profiles separated based on pre-pregnancy BMI (R2 = 0.037, p = 0.031), even after adjustment for maternal glucose tolerance status, mode of delivery, DNA extraction batch, and PCR sequencing batch. No statistically significant findings were observed between beta-diversity and glucose tolerance, mode of delivery, 3-month post-partum BMI or ethnicity. Abbreviations: GDM, gestational diabetes mellitus, IGT, impaired glucose tolerance; CS, C-section.

Additional file 7: Table S5. Examining the association between maternal characteristics and the milk microbiota beta-diversity. Statistically significant p-values (p