There are many unique biological pathways in T. thermophilus that are not well described in KEGG database, for instance. Each organism may adopted variations in the common pathways. Following list is the knowledge of pathways gathered from T. thermophilus community. The effort of gathering is still on going.

1. Carbohydrate metabolism

1-1. Glycolysis
1-2. TCA cycle
1-3. Oxidative phosphorylation
1-4. Polysaccharide metabolism
1-5. Organic acid metabolism (glyoxylate, propanoate, butanoate, etc)
1-6. Other monosaccharides metabolism (galactose, mannose, fructose, etc.)

2. Cell surface system biosynthesis

2-1. Phospholipid synthetic pathway
2-2. Glycolipid synthetic pathway
2-3. Terpenoid synthetic pathway
2-4. Fatty acid degradation
2-5. Sec system
2-6. Peptideglycan biosynthesis
2-7. Pili assembly
2-8. Phage adsorption
2-9. Biofilm formation

3. Genetic information process

3-1. DNA reprication
3-2. Homologous recombination
3-3. Mismatch repair
3-4. Transcription
3-5. tRNA maturation
3-6. tRNA aminoacylation
3-7. Translation factor
3-8. RNA degradation

4. Amino acid metabolism

4-1. Alanine, aspartate and glutamate metabolism
4-2. Glycine, serine and threonine metabolism
4-3. Cysteine and methionine metabolism
4-4. Valine, leucine and isoleucine biosynthesis/degradation
4-5. Lysine biosynthesis/degradation
4-6. Arginine and proline metabolism
4-7. Histidine metabolism
4-8. Phenylalanine, tyrosine and tryptophan biosynthesis
4-9. Metabolism of other amino acids
4-10. Polyamine synthesis
4-11. Protein transport
4-12. Protein degradation

5. Nucleotide metabolism

5-1. Purine biosynthesis
5-2. Pyrimidine biosynthesis

6. Metabolism of cofactor and vitamin

6-1. Thiamine metabolism
6-2. Riboflavin metabolism
6-3. Vitamin B6 metabolism
6-4. Nicotinate and nicotinamide metabolism
6-5. Pantothenate and CoA biosynthesis
6-6. Biotin metabolism
6-7. Lipoic acid metabolism
6-8. Folate-dependent one-carbon metabolism
6-9. Porphyrin and chlorophyll metabolism
6-10. Ubiquinone and other terpenoid-quinones biosynthesis

7. Cell cycle

7-1. Cell division