TABLE 2.
Summary of annotation analysis based on the hierarchy of the SEED Subsystems database showing three levels for each annotated function that have significant difference in expression between breast milk group and formula group (padj < 0.05).
| Function names (Level 1) | Function names (Level 2) | Log2 fold change* | Function names (Level 3) | Log2 fold change |
| Amino acids and derivatives | Glutamine, glutamate, aspartate and asparagine biosynthesis | NA | Glutaminase (EC 3.5.1.2) | 4.762 |
| Methionine degradation | −7.373 | Methionine gamma-lyase (EC 4.4.1.11) | −7.648 | |
| Valine degradation | −4.805 | |||
| Carbohydrates | L-fucose utilization | 6.207 | L-fucose isomerase (EC 5.3.1.25) | 7.777 |
| L-fucose mutarotase | 7.123 | |||
| L-fuculokinase (EC 2.7.1.51) | 6.274 | |||
| L-fuculose phosphate aldolase (EC 4.1.2.17) | 4.879 | |||
| D-gluconate and ketogluconates metabolism | NA | Hypothetical oxidoreductase YqhD (EC 1.1.-.-) | 4.852 | |
| Cell wall and capsule | Major outer membrane proteins | NA | Attachment invasion locus protein precursor | 5.199 |
| Capsular polysaccharides biosynthesis and assembly | NA | UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) | 4.685 | |
| Fatty acids, lipids, and isoprenoids | Carnitine metabolism in microorganisms | NA | Crotonobetainyl-CoA dehydrogenase (EC 1.3.99.-) | 7.587 |
| Protein metabolism | Glycine reductase, sarcosine reductase and betaine reductase | NA | Glycine reductase component B gamma subunit (EC 1.21.4.2) | 20.327 |
| Protein chaperones | NA | Chaperone protein HscB | 4.736 | |
| Respiration | Na+ translocating decarboxylases and related biotin-dependent enzymes | NA | Methylmalonyl-CoA:Pyruvate transcarboxylase 12S subunit (EC 2.1.3.1) | 5.247 |
| RNA metabolism | Transcription initiation, bacterial sigma factors | NA | RNA polymerase principal sigma factor HrdD | 5.355 |
| ATP-dependent RNA helicases, bacterial | NA | ATP-dependent RNA helicase YqfR | −2.919 | |
| Stress response | Periplasmic acid stress response in Enterobacteria | 9.966 | Chaperone HdeA | 8.802 |
| Acid resistance mechanisms | 6.554 | Probable glutamate/gamma-aminobutyrate antiporter | 9.128 | |
| Glutamate decarboxylase (EC 4.1.1.15) | 6.477 | |||
| Glutaredoxins | NA | Glutaredoxin 2 | 5.631 | |
| Universal stress protein family | NA | Universal stress protein D | 7.688 | |
| Sulfur metabolism | Galactosylceramide and sulfatide metabolism | NA | Alpha-galactosidase (EC 3.2.1.22) | 3.542 |
| Others | Conserved cluster in Enterobacteriaceae downstream from YqjA, a DedA family protein | NA | Inner membrane protein YqjK | 5.302 |
*A positive number in the Log2 fold change means that the breast milk group has up-regulation on that function compared to the formula group; a negative number means down-regulation in the breast milk group. The “NA” in the Log2 fold change column means that this function has no significant difference between two groups (padj > 0.05).