Table 1.
Summary of the significantly enriched pathways
| Pathway name | Genes | Metabolites |
| Signal transduction** | ||
| Signaling by GPCR** | 6/4 | 1/16 |
| GPCR ligand binding* | 3/3 | 1/13 |
| Class A/1 rhodopsin-like receptors* | 1/2 | 0/11 |
| GPCR downstream signaling* | 5/3 | 1/9 |
| Diseases** | ||
| Glycogen storage diseases* | 6/7 | 1/9 |
| Metabolic disorders of oxidation enzymes** | 3/6 | 1/33 |
| Gene expression** | 6/9 | 1/17 |
| Metabolism** | ||
| Biological oxidations** | 1/2 | 1/22 |
| Metabolism of amino acids, derivatives, and urea cycle** | 2/7 | 1/24 |
| Tyrosine metabolism* | 0/3 | 1/7 |
| Metabolism of vitamins and cofactors* | 2/1 | 1/8 |
| Metabolism of lipids and lipoproteins* | 7/5 | 2/16 |
| Protein digestion and absorption** | 2/2 | 1/19 |
| Fatty acid, TAG, and ketone metabolism** | 3/2 | 0/10 |
| Purine metabolism* | 3/1 | 1/8 |
| Transmembrane transport of small molecules** | ||
| SLC-mediated transport** | 5/4 | 2/38 |
| Transport of glucose/other sugars** | 3/1 | 0/22 |
| ABC transporters** | 3/1 | 1/25 |
Pathways were detected as significantly enriched (*P < 0.05; **P < 0.001) in S. trenchii-containing hosts vs. S. minutum-containing hosts when FDR <0.05 and at least three genes or metabolites were present. The numbers of down-regulated/up-regulated genes and metabolites in S. trenchii-colonized hosts are shown. A list of the genes/metabolites in each pathway is provided in Dataset S6.