Fig 1.
Venn diagram featuring common and unique enriched gene-set expression patterns.
(A) Colored spheres represent different experimental diets. The white number at the core of the Venn diagram represents the number of common overlapping gene-sets and black numbers towards the periphery of each sphere represent the number of unique gene-sets. (B) Functional interaction network for the common overlapping gene-sets. The colored nodes denote the GO term significantly (FDR < 0.001) overrepresented in the enriched gene-sets. The edges represent interactions between gene-set as determined by BiNGO. Sky blue color nodes relate to immune processes and light pink color nodes relate to metabolic processes. Arrows represent directed interactions. The diameter of the nodes represents the number of genes associated with that particular GO term. SBM, soybean meal; CAS, casein; DWP, partially delactosed whey powder; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm.
Table 1.
Differential gene expression and number of enriched gene-sets in ileal mucosa of mice fed experimental diets with indicated protein sources relative to a diet with SBM.
Table 2.
Key or hub genes of the functional network downregulated in mice fed soybean meal (SBM)-based diet.
Fig 2.
The ileal microbiome composition profiles based on the relative abundance at the family level.
Bacterial families are represented with different colors (shown in key). Hierarchical clustering of the microbial family composition is indicated above the composition profile. * Represents significant difference (P < 0.05) of microbiota at family level compared to SBM-fed mice. Members of microbial family belonging to ‘others’ are listed in S3 Table. SBM, soybean meal; CAS, casein; DWP, partially delactosed whey powder; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm.
Fig 3.
Ileal microbial profiles of mice fed diets containing protein from different sources.
(A) and (B) show the microbiota distribution at the phylum level; (C) shows the Firmicutes/Bacteroidetes ratio in the various groups of mice; (D-G) show the microbiota distribution at the family level. Bacterial abundance is shown as a percentage of the total 16s RNA gene sequences per group. SBM, soybean meal; CAS, casein; DWP, partially delactosed whey powder; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm.
Fig 4.
Endogenous levels of phosphorylated mTOR in cells derived from ileal tissue of mice fed with different experimental diets.
Bars and whiskers represents means values ± SEM (n = 12, six biological replicates and two technical replicates); *P < 0.05, **P < 0.005, ***P < 0.0005 compared to SBM-fed mice fed. Here, SBM, soybean meal; CAS, casein; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm.
Fig 5.
Immunohistochemistry of PFA-fixed paraffin-embedded tissue sections with anti-mTOR antibody in ileal tissue of mice fed with different experimental diets.
(A) Brown color indicates positive reaction in the image of tissue type control (testis) and a positive ileal tissue section (CAS). No positivity was observed in the same tissue by withholding the primary antibody (i.e. anti-mTOR antibody) during the staining procedure. (B) Immunohistochemistry of PFA-fixed paraffin-embedded ileum sections with anti-mTOR antibody of mice fed with different experimental diets. Brown color in the tissue section indicates positive reaction. SBM, soybean meal; CAS, casein; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm. Scale bar: 50 μm.
Fig 6.
Concentrations of serum granulocyte-colony stimulating factor (G-CSF) of mice fed diets containing different dietary proteins.
Bars and whiskers represents means values ± SEM (n = 6), recorded at the end of experiment. *P < 0.05 compared to SBM-fed mice fed. SBM, soybean meal; CAS, casein; DWP, partially delactosed whey powder; SDPP, spray dried porcine plasma; WGM, wheat gluten meal and YMW, yellow meal worm.