File Name : figures1.tif

Caption : figure s1 heatmap of the impact of experimental treatments on bacterial phyla observed in faecal samples on various sampling days (3, 9 and 15). ctr: no additives in the diet; syn: prebiotic + probiotic additives in the diet; opn: osteopontin in the diet; con: synbiotic + osteopontin in the diet. n = 8. * indicates p < 0.1; ** indicates p < 0.05.

File Name : figures2.tif

Caption : figure s2 heatmap of the impact of experimental treatments on bacterial families observed in faecal samples on various sampling days (3, 9 and 15). ctr: no additives in the diet; syn: prebiotic + probiotic additives in the diet; opn: osteopontin in the diet; con: synbiotic + osteopontin in the diet. n = 8. * indicates p < 0.1; ** indicates p < 0.05.

File Name : figures3.tif

Caption : figure s3 heatmap of the impact of experimental treatments on bacterial genera observed in faecal samples on various sampling days (3, 9 and 15). ctr: no additives in the diet; syn: prebiotic + probiotic additives in the diet; opn: osteopontin in the diet; con: synbiotic + osteopontin in the diet. n = 8. * indicates p < 0.1; ** indicates p < 0.05.

File Name : figures4.tif

Caption : figure s4 heatmap of correlations between colonic short-chain fatty acids (scfa) concentration and bacterial families detected on faecal samples from day 15. bcfa, branched-chain fatty acids. *indicates p < 0.05 and statistical difference present.

File Name : figures5.tif

Caption : figure s5 heatmap of correlations between colonic short-chain fatty acids (scfa) concentration and bacterial genera detected on faecal samples from day 15. bcfa, branched-chain fatty acids. *indicates p < 0.05 and statistical difference present.

File Name : figures6.tif

Caption : figure s6 heatmap of correlations between jejunal gene expression and asvs detected on faecal samples from day 15. *indicates p < 0.05 and statistical difference present.

File Name : figures7.tif

Caption : figure s7 heatmap of correlations between jejunal gene expression and bacterial genera detected on faecal samples from day 15. *indicates p < 0.05 and statistical difference present.

File Name : figures8.tif

Caption : figure s8 heatmap of correlations between histology (jejunal, ileal and colonic) and asvs detected on faecal samples from day 15. j=jejunal, i=ileal, c=colonic. vh=villus height; cd=crypt depth; vh.cd=ratio villus height:crypt depth. *indicates p < 0.05 and statistical difference present.

File Name : figures9.tif

Caption : figure s9 heatmap of correlations between histology (jejunal and ileal) and bacterial families detected on faecal samples from day 15. j=jejunum, i=ileum. vh=villus height; cd=crypt depth; vh.cd=ratio villus height:crypt depth. *indicates p < 0.05 and statistical difference present.