Table 2 Metabolic pathways differential abundance in each of the RF comparisons
Comparison | MetaCyc pathway ID | Average abundance (CPM) | Random Forest MDA (%) | LEfSe results | |||
|---|---|---|---|---|---|---|---|
Low SD/PS | High SD/PS | Direction | LDA Effect size | K-W test FDR value | |||
Mother - Social Disadvantage (SD) | PWY-7198: pyrimidine deoxyribonucleotides de novo biosynthesis IV | 61.9 | 100.9 | ↑ | 5.38 | 1.30 | 9.6×10−5 |
PWY-5384: sucrose degradation IV (sucrose phosphorylase) | 31.2 | 61.8 | ↑ | 3.78 | 1.19 | 5.7×10−4 | |
PWY-6549: L-glutamine biosynthesis III | 35.2 | 60.1 | ↑ | 3.65 | 1.13 | 9.6×10−5 | |
GLYCOCAT-PWY: glycogen degradation I | 38.7 | 72.7 | ↑ | 3.01 | 1.21 | 4.7×10−3 | |
UDPNAGSYN-PWY: UDP-N-acetyl-D-glucosamine biosynthesis I | 172.4 | 208.8 | ↑ | 2.91 | 1.27 | 0.018 | |
THRESYN-PWY: superpathway of L-threonine biosynthesis | 313.6 | 339.2 | ↑ | 2.67 | 1.17 | 0.046 | |
PWY-241: C4 photosynthetic carbon assimilation cycle, NADP-ME type | 45.8 | 84.0 | ↑ | 2.20 | 1.30 | 5.9×10−4 | |
PWY-6901: superpathway of glucose and xylose degradation | 106.1 | 138.2 | ↑ | 2.04 | 1.21 | 1.5×10−3 | |
PWY-5913: partial TCA cycle (obligate autotrophs) | 42.4 | 85.9 | ↑ | 1.86 | 1.35 | 4.7×10−4 | |
PWY-622: starch biosynthesis | 26.9 | 64.7 | ↑ | 1.82 | 1.28 | 5.7×10−4 | |
PWY-6731: starch degradation III | 22.3 | 42.3 | ↑ | 1.73 | 1.00 | 1.9×10−3 | |
NAGLIPASYN-PWY: lipid IVA biosynthesis (E. coli) | 80.9 | 58.2 | ↓ | 3.04 | 1.10 | 0.022 | |
Mother - Psychological Stressors (PS) | ANAGLYCOLYSIS-PWY: glycolysis III (from glucose) | 392.8 | 427.7 | ↑ | 4.52 | 1.27 | 3.2×10−3 |
GLYCOGENSYNTH-PWY: glycogen biosynthesis I (ADP-D-Glucose) | 297.0 | 382.7 | ↑ | 4.16 | 1.60 | 2.6×10−3 | |
RHAMCAT-PWY: L-rhamnose degradation I | 140.9 | 168.7 | ↑ | 3.48 | 1.22 | 8.9×10−3 | |
VALSYN-PWY: L-valine biosynthesis | 493.6 | 540.3 | ↑ | 2.74 | 1.36 | 8.9×10−3 | |
THISYNARA-PWY: superpathway of thiamine diphosphate biosyn. III | 214.5 | 242.2 | ↑ | 2.69 | 1.14 | 0.017 | |
PWY-7237: myo-, chiro- and scyllo-inositol degradation | 225.9 | 285.6 | ↑ | 2.57 | 1.49 | 7.4×10−3 | |
PWY-6731: starch degradation III | 24.0 | 42.9 | ↑ | 2.56 | 1.01 | 8.9×10−3 | |
PWY-7357: thiamine phosphate formation from pyrithiamine &oxythiamine | 283.5 | 333.4 | ↑ | 2.41 | 1.38 | 5.5×10−3 | |
NONOXIPENT-PWY: pentose phosphate pathway (non-oxidative branch) I | 252.0 | 300.2 | ↑ | 2.33 | 1.36 | 9.8×10−3 | |
PWY-622: starch biosynthesis | 34.1 | 61.1 | ↑ | 2.12 | 1.14 | 8.9×10−3 | |
PWY-7115: C4 photosynthetic carbon assimilation cycle, NAD-ME type | 43.4 | 63.2 | ↑ | 2.02 | 1.01 | 0.022 | |
DTDPRHAMSYN-PWY: dTDP-β-L-rhamnose biosynthesis | 539.2 | 574.2 | ↑ | 2.01 | 1.26 | 0.026 | |
COMPLETE-ARO-PWY: superpathway of aromatic amino acid biosynthesis | 435.5 | 470.6 | ↑ | 1.93 | 1.22 | 8.9×10−3 | |
GLUTORN-PWY: L-ornithine biosynthesis I | 307.3 | 359.2 | ↑ | 1.91 | 1.38 | 8.9×10−3 | |
Child - Psychological Stressors (PS) | PWY-7210: pyrimidine deoxyribonucleotides biosynthesis from CTP | 29.2 | 78.8 | ↑ | 5.08 | 1.42 | 6.8×10−4 |
PWY−5505: L-glutamate and L-glutamine biosynthesis | 9.3 | 38.7 | ↑ | 5.01 | 1.20 | 9.5×10−6 | |
PWY-6897: thiamine diphosphate salvage II | 167.3 | 223.2 | ↑ | 4.01 | 1.43 | 3.8×10−4 | |
GOLPDLCAT-PWY: superpath. of glycerol degradation to 1,3-propanediol | 35.1 | 58.2 | ↑ | 3.48 | 1.00 | 1.7×10−3 | |
PWY0-1296: purine ribonucleosides degradation | 205.7 | 255.8 | ↑ | 3.46 | 1.39 | 0.032 | |
PWY-6549: L-glutamine biosynthesis III | 33.9 | 58.5 | ↑ | 3.16 | 1.12 | 3.8×10−4 | |
PWY-6470: peptidoglycan biosynthesis V (β-lactam resistance) | 26.6 | 74.8 | ↑ | 3.03 | 1.34 | 3.8×10−4 | |
PWY-6124: inosine-5’-phosphate biosynthesis II | 275.7 | 341.1 | ↑ | 2.73 | 1.54 | 6.8×10−4 | |
PWY-6700: queuosine biosynthesis I (de novo) | 207.5 | 292.3 | ↑ | 2.72 | 1.61 | 8.1×10−4 | |
TEICHOICACID-PWY: poly(glycerol phosphate) wall teichoic acid biosyn. | 21.8 | 48.9 | ↑ | 2.59 | 1.15 | 5.1×10−4 | |
PWY-1042: glycolysis IV | 396.4 | 483.2 | ↑ | 2.54 | 1.60 | 1.7×10−3 | |
PWY0−1479: tRNA processing | 187.7 | 132.5 | ↓ | 3.74 | 1.46 | 1.8×10−3 | |
Child - Social Disadvantage (SD) | TRPSYN-PWY: L-tryptophan biosynthesis | 266.0 | 321.2 | ↑ | 3.39 | 1.43 | 0.015 |
PWY-6549: L-glutamine biosynthesis III | 29.2 | 56.9 | ↑ | 3.25 | 1.15 | 6.5×10−4 | |
PWY-241: C4 photosynthetic carbon assimilation cycle, NADP-ME type | 83.4 | 119.1 | ↑ | 2.48 | 1.26 | 0.015 | |
ANAEROFRUCAT-PWY: homolactic fermentation | 281.5 | 331.0 | ↑ | 2.43 | 1.39 | 0.015 | |
PWY−5505: L-glutamate and L-glutamine biosynthesis | 13.5 | 37.6 | ↑ | 2.37 | 1.13 | 7.4×10−4 | |
PANTOSYN-PWY: superpathway of coenzyme A biosynthesis I (bacteria) | 230.8 | 281.5 | ↑ | 2.34 | 1.43 | 0.024 | |
PWY−4981: L-proline biosynthesis II (from arginine) | 68.9 | 115.6 | ↑ | 2.10 | 1.42 | 0.015 | |
PWY-6731: starch degradation III | 59.1 | 86.1 | ↑ | 1.99 | 1.16 | 0.034 | |
FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation | 76.4 | 53.8 | ↓ | 2.36 | 1.08 | 0.024 | |
