Table 1.
Differentially enriched microbial pathways in each group predicted from fecal 16S RNA gene sequencing
| Group |
Number of pathways & top four enriched pathways in each group |
Total |
|||
|---|---|---|---|---|---|
| Genotype | WT | ShpKO | |||
| Separate CD | 18 | Transporters | 43 | Ribosome | 61 |
| Bacterial motility proteins | DNA repair and recombination proteins | ||||
| Flagella assembly | Phosphotransferase system | ||||
| Two-component system | Mismatch repair | ||||
| Separate WD | 12 | Transporters | 22 | Citrate cycle—tricarboxylic acid cycle | 34 |
| Bacterial motility proteins | Carbon fixation pathways in prokaryotes | ||||
| Betalain biosynthesis | Oxidative phosphorylation | ||||
| Flagella assembly | Ala, Asp, and glutamate metabolism | ||||
| Cohoused CD | 6 | Bacterial motility proteins | 11 | Carbon fixation in photosynthetic organisms | 17 |
| Flagella assembly | Nucleotide metabolism | ||||
| Bacterial chemotaxis | Bacterial secretion system | ||||
| Starch and sucrose metabolism | Cell mobility and secretion | ||||
| Cohoused WD | 12 | Pyrimidine metabolism | 0 | 12 | |
| Peptidases | |||||
| Purine metabolism | |||||
| Ribosome | |||||
| Diet | CD | WD | |||
|---|---|---|---|---|---|
| Separate WT | 5 | Peptidases | 16 | Other ion-coupled transporters | 21 |
| Streptomycin biosynthesis | Cysteine and methionine metabolism | ||||
| Other glycan degradation | Replication recombination repair proteins | ||||
| Drug metabolism other enzymes | Restriction enzyme | ||||
| Separate ShpKO | 3 | Phosphotransferase system | 12 | Other ion-coupled transporters | 15 |
| Aminoacyl tRNA biosynthesis | Pyruvate metabolism | ||||
| Staphylococcus aureus infection | Carbon fixation in photosynthetic organisms | ||||
| Inorganic ion transport and metabolism | |||||
| Cohoused WT | 4 | Methane metabolism | 5 | General function prediction only | 9 |
| Lysine biosynthesis | Other ion-coupled transporters | ||||
| C5 branched dibasic acid metabolism | Amino sugar and nucleotide sugar metabolism | ||||
| DDT degradation | Inorganic ion transport and metabolism | ||||
| Cohoused ShpKO | 35 | Ribosome | 11 | Two-component system | 46 |
| DNA repair and recombination proteins | Others | ||||
| Amino acid–related enzymes | Function unknown | ||||
| Pyrimidine metabolism | Secretion system |
| Housing | Separate | Cohoused | |||
|---|---|---|---|---|---|
| WT CD | 7 | Protein folding and associated process | 10 | Phe, Tyr, and tryptophan biosynthesis | 17 |
| Function unknown | Cysteine and methionine metabolism | ||||
| Other glycan degradation | Methane metabolism | ||||
| Amino sugar and nucleotide sugar metabolism | Nitrogen metabolism | ||||
| ShpKO CD | 0 | 5 | Val, Leu, and isoleucine biosynthesis | 5 | |
| Cell motility and secretion | |||||
| Phenylalanine metabolism | |||||
| Geraniol degradation | |||||
| WT WD | 1 | Methane metabolism | 2 | Photosynthesis proteins | 3 |
| Starch and sucrose metabolism | |||||
| ShpKO WD | 34 | Ribosome | 11 | Two-component system | 45 |
| Energy metabolism | Function unknown | ||||
| Ala, Asp, and glutamate metabolism | Secretion system | ||||
| DNA replication proteins | Others |
PICRUSt and LEfSe analyses were performed to predict enriched microbial pathways in each experimental group from fecal 16S RNA sequencing results described in Fig. 3.