ST001683 A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism.
List of human metabolic pathways and metabolites (REACTOME)

Pathway name (# of metabolites detected in study)Reactome pathway
5-Phosphoribose 1-diphosphate biosynthesis (1) REACT_850
Abacavir metabolism (2) REACT_121388
ABH2 mediated Reversal of Alkylation Damage (2) REACT_526
ABH3 mediated Reversal of Alkylation Damage (2) REACT_1662
Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate (1) REACT_160183
Abnormal metabolism in phenylketonuria (6) REACT_121117
Acetylcholine Neurotransmitter Release Cycle (2) REACT_15309
Acetylcholine regulates insulin secretion (1) REACT_18405
Activation of AMPA receptors (1) REACT_18338
Activation of Ca-permeable Kainate Receptor (1) REACT_21346
Activation of gene expression by SREBF (SREBP) (2) REACT_147904
Activation of G protein gated Potassium channels (1) REACT_75831
Activation of Na-permeable Kainate Receptors (1) REACT_21343
Activation of the phototransduction cascade (1) REACT_163932
Adenosine P1 receptors (1) REACT_18288
Adenylate cyclase activating pathway (1) REACT_15312
Aflatoxin activation and detoxification (2) REACT_228214
Agmatine biosynthesis (3) REACT_14800
Alpha-oxidation of phytanate (2) REACT_17003
Amino acid synthesis and interconversion (transamination) (9) REACT_238
Amino acid transport across the plasma membrane (23) REACT_13796
Androgen biosynthesis (1) REACT_11059
Antigen Presentation: Folding, assembly and peptide loading of class I MHC (18) REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation (18) REACT_75842
Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 (1) REACT_13721
Astrocytic Glutamate-Glutamine Uptake And Metabolism (2) REACT_13639
Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB (2) REACT_416
Biotin transport and metabolism (1) REACT_11153
BMAL1:CLOCK,NPAS2 activates circadian gene expression (2) REACT_111118
Branched-chain amino acid catabolism (3) REACT_197
Ca2+ pathway (1) REACT_172761
Cam-PDE 1 activation (1) REACT_15408
Carnitine synthesis (5) REACT_2125
Catecholamine biosynthesis (3) REACT_15551
cGMP effects (1) REACT_23767
Chondroitin sulfate biosynthesis (1) REACT_120989
Circadian Clock (2) REACT_24941
Citric acid cycle (TCA cycle) (5) REACT_1785
Class A/1 (Rhodopsin-like receptors) (6) REACT_14828
Class C/3 (Metabotropic glutamate/pheromone receptors) (7) REACT_18319
Class II GLUTs (1) REACT_19281
Cleavage of the damaged purine (2) REACT_1729
Cleavage of the damaged pyrimidine (3) REACT_2156
Cobalamin (Cbl, vitamin B12) transport and metabolism (3) REACT_163862
Coenzyme A biosynthesis (2) REACT_11218
Collagen biosynthesis and modifying enzymes (2) REACT_121139
Condensation of Prophase Chromosomes (3) REACT_172744
Conjugation of benzoate with glycine (2) REACT_6933
Conjugation of phenylacetate with glutamine (2) REACT_6800
Conjugation of salicylate with glycine (2) REACT_6812
Creatine metabolism (8) REACT_813
CREB phosphorylation through the activation of Adenylate Cyclase (1) REACT_20625
CREB phosphorylation through the activation of CaMKII (2) REACT_20642
Cross-presentation of soluble exogenous antigens (endosomes) (18) REACT_111056
CYP2E1 reactions (1) REACT_13797
Cysteine formation from homocysteine (3) REACT_115589
Cytosolic iron-sulfur cluster assembly (1) REACT_160176
Cytosolic sulfonation of small molecules (4) REACT_6913
Cytosolic tRNA aminoacylation (18) REACT_15306
DARPP-32 events (1) REACT_15334
Defective MTR causes methylmalonic aciduria and homocystinuria type cblG (1) REACT_169149
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE (1) REACT_169439
degradation of AXIN (1) REACT_200766
Degradation of cysteine and homocysteine (5) REACT_115654
Degradation of GABA (4) REACT_23964
Dermatan sulfate biosynthesis (1) REACT_120800
Digestion of dietary lipid (4) REACT_9518
DNA methylation (1) REACT_267652
Dopamine clearance from the synaptic cleft (1) REACT_15514
Dopamine Neurotransmitter Release Cycle (1) REACT_15293
Dopamine receptors (1) REACT_16968
Downregulation of SMAD2/3:SMAD4 transcriptional activity (1) REACT_121111
Endogenous sterols (6) REACT_13812
Endosomal/Vacuolar pathway (18) REACT_111168
eNOS activation (4) REACT_12477
Enzymatic degradation of dopamine by COMT (2) REACT_15548
Enzymatic degradation of Dopamine by monoamine oxidase (1) REACT_15511
EPHB-mediated forward signaling (2) REACT_228085
ER-Phagosome pathway (18) REACT_111178
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (2) REACT_19193
Fatty Acyl-CoA Biosynthesis (3) REACT_1319
FMO oxidises nucleophiles (1) REACT_13653
formation of the beta-catenin:TCF transactivating complex (1) REACT_200753
Free fatty acid receptors (3) REACT_21268
GABA A receptor activation (1) REACT_24987
GABA A (rho) receptor activation (1) REACT_25168
GABA B receptor activation (1) REACT_25031
GABA synthesis (2) REACT_24020
GABA synthesis, release, reuptake and degradation (1) REACT_23947
G alpha (i) signalling events (14) REACT_19231
G alpha (q) signalling events (9) REACT_18283
G alpha (s) signalling events (7) REACT_19327
G alpha (z) signalling events (1) REACT_19333
Glucagon-like Peptide-1 (GLP1) regulates insulin secretion (1) REACT_18274
Glucocorticoid biosynthesis (3) REACT_11036
Gluconeogenesis (8) REACT_1520
Glucuronidation (1) REACT_6784
Glutamate Neurotransmitter Release Cycle (2) REACT_12591
Glutathione synthesis and recycling (19) REACT_6960
Glycolysis (5) REACT_1383
Glyoxylate metabolism (4) REACT_16925
HCN channels (1) REACT_75862
HDMs demethylate histones (2) REACT_228178
Hedgehog 'off' state (1) REACT_267634
Heme biosynthesis (1) REACT_9465
Heme degradation (1) REACT_22297
Highly calcium permeable nicotinic acetylcholine receptors (1) REACT_22352
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors (1) REACT_22303
Highly sodium permeable acetylcholine nicotinic receptors (1) REACT_22223
Histamine receptors (1) REACT_16903
Histidine catabolism (4) REACT_1249
HS-GAG biosynthesis (1) REACT_121248
HS-GAG degradation (1) REACT_120752
Hydrolysis of LPC (1) REACT_120977
Hydroxycarboxylic acid-binding receptors (2) REACT_163785
Hypusine synthesis from eIF5A-lysine (2) REACT_12469
Import of palmitoyl-CoA into the mitochondrial matrix (1) REACT_11082
Inactivation, recovery and regulation of the phototransduction cascade (2) REACT_163919
Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits (1) REACT_25004
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate (1) REACT_25367
Interconversion of polyamines (3) REACT_14805
Iron uptake and transport (1) REACT_25060
Keratan sulfate biosynthesis (1) REACT_121120
Ligand-gated ion channel transport (3) REACT_25387
Linoleic acid (LA) metabolism (1) REACT_121100
Lysine catabolism (3) REACT_1298
Meiotic recombination (1) REACT_27271
Metabolism of folate and pterines (3) REACT_11167
Metabolism of polyamines (5) REACT_14820
Metabolism of serotonin (2) REACT_15532
Methionine salvage pathway (3) REACT_75881
Methylation (5) REACT_6946
Mineralocorticoid biosynthesis (2) REACT_11047
Miscellaneous substrates (3) REACT_13425
Mitochondrial iron-sulfur cluster biogenesis (2) REACT_150353
Mitochondrial tRNA aminoacylation (18) REACT_15302
Molybdenum cofactor biosynthesis (3) REACT_25073
mRNA Capping (1) REACT_1470
Muscarinic acetylcholine receptors (1) REACT_16943
Na+/Cl- dependent neurotransmitter transporters (23) REACT_20506
NADPH regeneration (1) REACT_16904
Neurotransmitter Clearance In The Synaptic Cleft (2) REACT_13583
NGF-independant TRKA activation (1) REACT_11046
Nicotinamide salvaging (2) REACT_11213
Nicotinate metabolism (2) REACT_11088
Nitric oxide stimulates guanylate cyclase (3) REACT_23862
NoRC negatively regulates rRNA expression (1) REACT_200856
Norepinephrine Neurotransmitter Release Cycle (1) REACT_15418
NOSIP mediated eNOS trafficking (1) REACT_12510
NOSTRIN mediated eNOS trafficking (1) REACT_12541
Organic anion transport (3) REACT_22310
Organic anion transporters (4) REACT_19372
Organic cation transport (9) REACT_22357
Orphan transporters (9) REACT_267716
Oxidative Stress Induced Senescence (3) REACT_169436
Oxygen-dependent asparagine hydroxylation of Hypoxia-inducible Factor Alpha (2) REACT_121226
Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha (2) REACT_120916
PAOs oxidise polyamines to amines (3) REACT_505
PDE3B signalling (1) REACT_1451
Phagosomal maturation (early endosomal stage) (2) REACT_121256
Phenylalanine and tyrosine catabolism (8) REACT_1786
PKA activation (1) REACT_15530
PKA activation in glucagon signalling (1) REACT_1946
Plasmalogen biosynthesis (1) REACT_1407
Platelet degranulation (1) REACT_318
PPARA activates gene expression (3) REACT_116145
PRC2 methylates histones and DNA (1) REACT_200808
Presynaptic function of Kainate receptors (1) REACT_21254
Proline catabolism (2) REACT_1002
Proton-coupled monocarboxylate transport (2) REACT_20515
Proton-coupled neutral amino acid transporters (3) REACT_19348
Proton/oligonucleotide cotransporters (18) REACT_19328
Purine catabolism (8) REACT_2086
Purine ribonucleoside monophosphate biosynthesis (5) REACT_1776
Purine salvage (7) REACT_1923
Pyrimidine biosynthesis (7) REACT_21376
Pyrimidine catabolism (14) REACT_1023
Pyrimidine salvage reactions (8) REACT_655
Pyruvate metabolism (2) REACT_2071
Rap1 signalling (1) REACT_23898
Ras activation uopn Ca2+ infux through NMDA receptor (2) REACT_20546
Recycling of bile acids and salts (7) REACT_11042
Regulation by TREX1 (2) REACT_163652
Regulation of HSF1-mediated heat shock response (1) REACT_200780
Regulation of insulin secretion (1) REACT_18325
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) (2) REACT_19241
Regulation of pyruvate dehydrogenase (PDH) complex (2) REACT_12528
Regulation of thyroid hormone activity (1) REACT_15297
Respiratory electron transport (1) REACT_22393
Retinoid cycle disease events (1) REACT_160130
Retinoid metabolism and transport (2) REACT_24968
Reuptake of GABA (3) REACT_23910
REV-ERBA represses gene expression (2) REACT_118789
RMTs methylate histone arginines (1) REACT_228108
Role of phospholipids in phagocytosis (1) REACT_160158
RORA activates circadian gene expression (2) REACT_118659
Senescence-Associated Secretory Phenotype (SASP) (1) REACT_169168
Serine biosynthesis (5) REACT_115789
Serotonin and melatonin biosynthesis (6) REACT_15439
Serotonin clearance from the synaptic cleft (1) REACT_15391
Serotonin Neurotransmitter Release Cycle (1) REACT_15425
Serotonin receptors (1) REACT_17064
Sialic acid metabolism (1) REACT_200874
SIRT1 negatively regulates rRNA Expression (2) REACT_200827
Sodium-coupled sulphate, di- and tri-carboxylate transporters (2) REACT_20646
Sperm Motility And Taxes (1) REACT_163875
Sphingolipid de novo biosynthesis (3) REACT_115810
Stimuli-sensing channels (1) REACT_160189
Sulfide oxidation to sulfate (1) REACT_116010
Sulfur amino acid metabolism (9) REACT_115639
Synthesis and interconversion of nucleotide di- and triphosphates (5) REACT_21330
Synthesis of bile acids and bile salts (2) REACT_11054
Synthesis of bile acids and bile salts via 27-hydroxycholesterol (1) REACT_11048
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol (7) REACT_11041
Synthesis of Leukotrienes (LT) and Eoxins (EX) (2) REACT_150420
Synthesis of PA (1) REACT_120906
Synthesis of PC (3) REACT_121238
Synthesis of PE (1) REACT_120919
Synthesis of PG (1) REACT_121280
Synthesis of Prostaglandins (PG) and Thromboxanes (TX) (1) REACT_150149
Synthesis of PS (2) REACT_120823
Synthesis of UDP-N-acetyl-glucosamine (3) REACT_22394
Synthesis of very long-chain fatty acyl-CoAs (1) REACT_380
Synthesis, secretion, and deacylation of Ghrelin (2) REACT_19189
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) (4) REACT_24019
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) (2) REACT_23824
TET1,2,3 and TDG demethylate DNA (2) REACT_200682
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation (2) REACT_111176
The canonical retinoid cycle in rods (twilight vision) (2) REACT_160156
The retinoid cycle in cones (daylight vision) (1) REACT_160083
Thyroxine biosynthesis (4) REACT_15292
Transcriptional activation of mitochondrial biogenesis (2) REACT_200608
Transcriptional regulation of white adipocyte differentiation (2) REACT_27161
Transport of fatty acids (4) REACT_23892
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds (2) REACT_19305
Transport of inorganic cations/anions and amino acids/oligopeptides (4) REACT_19397
Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (13) REACT_1206
Transport of organic anions (4) REACT_23988
Tryptophan catabolism (9) REACT_916
Ubiquinol biosynthesis (2) REACT_160111
Unblocking of NMDA receptor, glutamate binding and activation (2) REACT_20594
Uptake and function of anthrax toxins (1) REACT_228255
Urea cycle (6) REACT_847
Utilization of Ketone Bodies (1) REACT_59
Vasopressin regulates renal water homeostasis via Aquaporins (1) REACT_24023
VEGFR2 mediated vascular permeability (3) REACT_228016
Vitamin B1 (thiamin) metabolism (1) REACT_11117
Vitamin B2 (riboflavin) metabolism (1) REACT_11070
Vitamin B5 (pantothenate) metabolism (1) REACT_11172
Vitamin D (calciferol) metabolism (1) REACT_13523
Vitamins (2) REACT_13450
Vitamins B6 activation to pyridoxal phosphate (5) REACT_25012
YAP1- and WWTR1 (TAZ)-stimulated gene expression (2) REACT_118713
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