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Additional file 2. Relative abundance of bacterial genera in the sequenced mock community standards along with their expected abundance.

Additional file 4. Differentially abundant ASVs between the yeast and control diets (ileum, caecum). A ileum, d 7 PW, B ileum, d 14 PW, C ileum, d 14 PW (family level), D caecum, d 7 PW (phylum level), E caecum, d 14 PW (phylum level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 5. Differentially abundant ASVs between the yeast and control diets (caecum). A, caecum, d 7 PW, B caecum, d 14 PW, C caecum, d 7 PW (family level), D caecum, d 14 PW (family level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 6. Differentially abundant ASVs between the yeast and control diets (colon). A colon, d 7 PW, B colon, d 14 PW, C colon, d 7 PW (family level), D colon, d 14 PW (family level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 3. Alpha bacterial diversity as measured by a) Observed species and b) Shannon diversity index. The average values between the control and yeast group are represented as mean values with standard deviation (SD) along with medians with inter-quartile ranges (IQR). Comparison pairs that correspond to p-values less than 0.05 (MWW test) are given in bold.

Additional file 8. Association of liver index with individual bacterial groups, and colonic butyrate concentration. Panel A: Principal component analysis performed on the relative abundance of Spirochaetaceae, Faecalibacterium and the liver index of pigs measured at days 7 and 14 PW (n = 32 but 2 dots are not shown). The dots are coloured by the diet (control pink; yeast dark cyan). The vectors represent the degree of correlation between the bacterial groups data and the liver index data. Panel B: Correlation plot of colonic butyrate concentration (measured in μM per gram of intestinal contents) against liver index measured in the control group pigs at days 7 and 14 PW (n = 16). The dots are coloured by the diet (control pink). Pearson’s rho is reported above the regression line. Panel C: Correlation plot of colonic butyrate concentration (μM/gram of intestinal contents) against liver index measured in the yeast group pigs at days 7 and 14 PW (n = 16). The dots are coloured by the diet (yeast dark cyan). Pearson’s rho is reported above the regression line.

Additional file 7. Association of colonic butyrate concentration with individual bacterial groups. Panel A: Correlation plot of colonic butyrate concentration (measured in μM per gram of intestinal contents) against F. prausnitzii relative abundance measured at days 7 and 14 PW (n = 32). The dots are coloured by the diet (control pink; yeast dark cyan). Pearson’s rho is reported above the regression line. Panel B: Principal component analysis performed on the relative abundance of Spirochaetaceae, Faecalibacterium, Dialister and molarities of butyrate in the colon of pigs measured at days 7 and 14 PW (n = 32 but 3 dots are not shown). The dots are coloured by the diet (control pink; yeast dark cyan). The vectors represent the degree of correlation between the bacterial groups data and the butyrate concentration data.

Additional file 1. Comparison of bacterial CFUs on the selective agar plates. The values are the group medians (IQR) of logCFUs per gram of lumen contents. The bold font indicates statistically significant level (p