ST000570 Metabolome analysis of the cecal contents of GF mice and GF mice colonized with dominant gut microbes present in the ceca of neonatal and adult mice
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 (7) 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 (2) REACT_160183
Abnormal metabolism in phenylketonuria (7) REACT_121117
Acetylation (2) REACT_6732
Acetylcholine Neurotransmitter Release Cycle (3) 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 G protein gated Potassium channels (1) REACT_75831
Activation of Na-permeable Kainate Receptors (1) REACT_21343
Activation of PPARGC1A (PGC-1alpha) by phosphorylation (1) REACT_200686
Adenosine P1 receptors (1) REACT_18288
Aflatoxin activation and detoxification (4) REACT_228214
Agmatine biosynthesis (3) REACT_14800
alpha-linolenic acid (ALA) metabolism (4) REACT_121147
Alpha-oxidation of phytanate (4) REACT_17003
Amine ligand-binding receptors (1) REACT_16983
Amino acid synthesis and interconversion (transamination) (12) REACT_238
Amino acid transport across the plasma membrane (26) REACT_13796
AMPK inhibits chREBP transcriptional activation activity (1) REACT_1988
Androgen biosynthesis (2) REACT_11059
Antigen Presentation: Folding, assembly and peptide loading of class I MHC (20) REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation (21) 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
A tetrasaccharide linker sequence is required for GAG synthesis (2) REACT_121408
Attenuation phase (1) REACT_200624
Beta oxidation of butanoyl-CoA to acetyl-CoA (1) REACT_419
Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA (2) REACT_1708
Beta oxidation of hexanoyl-CoA to butanoyl-CoA (2) REACT_1887
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA (2) REACT_735
Beta oxidation of myristoyl-CoA to lauroyl-CoA (2) REACT_2108
Beta oxidation of octanoyl-CoA to hexanoyl-CoA (2) REACT_1697
Beta oxidation of palmitoyl-CoA to myristoyl-CoA (2) REACT_2025
Beta-oxidation of pristanoyl-CoA (2) REACT_17017
Beta-oxidation of very long chain fatty acids (2) REACT_17062
Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB (3) REACT_416
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein (2) REACT_22433
Biotin transport and metabolism (2) REACT_11153
Branched-chain amino acid catabolism (9) REACT_197
Cam-PDE 1 activation (1) REACT_15408
Carnitine synthesis (6) REACT_2125
Catecholamine biosynthesis (5) REACT_15551
Cell redox homeostasis (2) REACT_121394
Cholesterol biosynthesis (3) REACT_9405
Chondroitin sulfate biosynthesis (2) REACT_120989
Citric acid cycle (TCA cycle) (8) REACT_1785
Class A/1 (Rhodopsin-like receptors) (5) REACT_14828
Class C/3 (Metabotropic glutamate/pheromone receptors) (5) REACT_18319
Class II GLUTs (1) REACT_19281
Cleavage of the damaged purine (1) REACT_1729
Cleavage of the damaged pyrimidine (2) REACT_2156
Cobalamin (Cbl, vitamin B12) transport and metabolism (5) REACT_163862
Coenzyme A biosynthesis (2) REACT_11218
Collagen biosynthesis and modifying enzymes (3) REACT_121139
Condensation of Prophase Chromosomes (4) REACT_172744
Conjugation of benzoate with glycine (3) REACT_6933
Conjugation of phenylacetate with glutamine (2) REACT_6800
Conjugation of salicylate with glycine (3) REACT_6812
Creatine metabolism (8) REACT_813
CREB phosphorylation through the activation of CaMKII (2) REACT_20642
Cross-presentation of particulate exogenous antigens (phagosomes) (1) REACT_111174
Cross-presentation of soluble exogenous antigens (endosomes) (20) 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 (2) REACT_6913
Cytosolic tRNA aminoacylation (21) REACT_15306
DARPP-32 events (1) REACT_15334
Deadenylation of mRNA (1) REACT_20514
Defective B3GAT3 causes JDSSDHD (1) REACT_267659
Defective CHSY1 causes TPBS (1) REACT_267682
Defective EXT1 causes exostoses 1, TRPS2 and CHDS (1) REACT_267674
Defective EXT2 causes exostoses 2 (1) REACT_267654
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE (1) REACT_169439
degradation of AXIN (2) REACT_200766
Degradation of cysteine and homocysteine (5) REACT_115654
Degradation of GABA (5) REACT_23964
Detoxification of Reactive Oxygen Species (1) REACT_172715
Digestion of dietary lipid (2) REACT_9518
DNA methylation (2) 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 (2) REACT_121111
Eicosanoids (1) REACT_13645
Electron transport from NADPH to Ferredoxin (1) REACT_150128
Endogenous sterols (1) REACT_13812
Endosomal/Vacuolar pathway (20) REACT_111168
eNOS activation (3) REACT_12477
Enzymatic degradation of dopamine by COMT (3) REACT_15548
Enzymatic degradation of Dopamine by monoamine oxidase (2) REACT_15511
EPHB-mediated forward signaling (2) REACT_228085
ER-Phagosome pathway (20) REACT_111178
Establishment of Sister Chromatid Cohesion (1) REACT_150266
Estrogen biosynthesis (1) REACT_11037
Ethanol oxidation (3) REACT_34
Factors involved in megakaryocyte development and platelet production (1) REACT_24970
Fatty acids (1) REACT_13814
Fatty acid, triacylglycerol, and ketone body metabolism (1) REACT_22279
Fatty Acyl-CoA Biosynthesis (4) REACT_1319
FCERI mediated NF-kB activation (1) REACT_163994
FMO oxidises nucleophiles (2) REACT_13653
Formation of the active cofactor, UDP-glucuronate (2) REACT_6737
formation of the beta-catenin:TCF transactivating complex (3) REACT_200753
Free fatty acid receptors (2) 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
Galactose catabolism (1) REACT_532
G alpha (i) signalling events (12) REACT_19231
G alpha (q) signalling events (10) REACT_18283
G alpha (s) signalling events (7) REACT_19327
Glucocorticoid biosynthesis (2) REACT_11036
Gluconeogenesis (10) REACT_1520
Glucuronidation (2) REACT_6784
Glutamate Neurotransmitter Release Cycle (2) REACT_12591
Glutathione synthesis and recycling (21) REACT_6960
Glycogen breakdown (glycogenolysis) (1) REACT_1008
Glycogen synthesis (2) REACT_169208
Glycolysis (6) REACT_1383
Glycosphingolipid metabolism (2) REACT_116105
Glyoxylate metabolism (5) REACT_16925
HATs acetylate histones (1) REACT_172610
HDMs demethylate histones (2) REACT_228178
Heme biosynthesis (2) REACT_9465
Heme degradation (3) 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 (5) REACT_1249
HS-GAG biosynthesis (3) REACT_121248
HS-GAG degradation (2) REACT_120752
Hydrolysis of LPC (2) REACT_120977
Hydrolysis of LPE (1) REACT_120785
Hydroxycarboxylic acid-binding receptors (3) REACT_163785
Hypusine synthesis from eIF5A-lysine (3) REACT_12469
Import of palmitoyl-CoA into the mitochondrial matrix (1) REACT_11082
Inactivation, recovery and regulation of the phototransduction cascade (1) 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 (6) REACT_14805
Iron uptake and transport (2) REACT_25060
ISG15 antiviral mechanism (1) REACT_115831
Keratan sulfate biosynthesis (3) REACT_121120
Ligand-gated ion channel transport (3) REACT_25387
Linoleic acid (LA) metabolism (3) REACT_121100
Lysine catabolism (6) REACT_1298
Meiotic recombination (2) REACT_27271
Metabolism of folate and pterines (4) REACT_11167
Metabolism of nucleotides (3) REACT_1698
Metabolism of polyamines (6) REACT_14820
Metabolism of serotonin (3) REACT_15532
Methionine salvage pathway (3) REACT_75881
Methylation (6) REACT_6946
Mineralocorticoid biosynthesis (2) REACT_11047
Miscellaneous substrates (1) REACT_13425
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) (1) REACT_228019
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) (1) REACT_228145
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids (2) REACT_160
Mitochondrial iron-sulfur cluster biogenesis (2) REACT_150353
Mitochondrial tRNA aminoacylation (21) REACT_15302
Molybdenum cofactor biosynthesis (5) REACT_25073
MPS IIIC - Sanfilippo syndrome C (1) REACT_147860
mRNA Capping (2) REACT_1470
mRNA decay by 3' to 5' exoribonuclease (3) REACT_20619
mRNA decay by 5' to 3' exoribonuclease (3) REACT_20518
Mtb iron assimilation by chelation (1) REACT_121118
Muscarinic acetylcholine receptors (1) REACT_16943
Na+/Cl- dependent neurotransmitter transporters (26) REACT_20506
NADPH regeneration (2) REACT_16904
Neurotransmitter Clearance In The Synaptic Cleft (2) REACT_13583
NGF-independant TRKA activation (1) REACT_11046
N-glycan trimming and elongation in the cis-Golgi (1) REACT_25210
Nicotinamide salvaging (3) REACT_11213
Nicotinate metabolism (5) REACT_11088
Nitric oxide stimulates guanylate cyclase (3) REACT_23862
NoRC negatively regulates rRNA expression (2) REACT_200856
Norepinephrine Neurotransmitter Release Cycle (1) REACT_15418
O-linked glycosylation of mucins (1) REACT_115606
Organic anion transport (3) REACT_22310
Organic anion transporters (6) REACT_19372
Organic cation transport (9) REACT_22357
Orphan transporters (5) REACT_267716
Oxidative Stress Induced Senescence (4) 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
P2Y receptors (1) REACT_18289
PAOs oxidise polyamines to amines (5) REACT_505
PDE3B signalling (1) REACT_1451
Pentose phosphate pathway (hexose monophosphate shunt) (2) REACT_1859
Peroxisomal lipid metabolism (1) REACT_16957
Phagosomal maturation (early endosomal stage) (3) REACT_121256
Phenylalanine and tyrosine catabolism (7) REACT_1786
Phosphate bond hydrolysis by NUDT proteins (2) REACT_150237
Plasmalogen biosynthesis (1) REACT_1407
Platelet degranulation (1) REACT_318
PRC2 methylates histones and DNA (2) REACT_200808
Pregnenolone biosynthesis (1) REACT_11038
Pre-NOTCH Processing in Golgi (2) REACT_118798
Pre-NOTCH Processing in the Endoplasmic Reticulum (1) REACT_118722
Presynaptic function of Kainate receptors (1) REACT_21254
Proline catabolism (3) REACT_1002
Proton-coupled monocarboxylate transport (2) REACT_20515
Proton-coupled neutral amino acid transporters (3) REACT_19348
Proton/oligonucleotide cotransporters (20) REACT_19328
Purine catabolism (11) REACT_2086
Purine ribonucleoside monophosphate biosynthesis (8) REACT_1776
Purine salvage (11) REACT_1923
Pyrimidine biosynthesis (6) REACT_21376
Pyrimidine catabolism (14) REACT_1023
Pyrimidine salvage reactions (9) REACT_655
Pyruvate metabolism (4) REACT_2071
Ras activation uopn Ca2+ infux through NMDA receptor (2) REACT_20546
Recycling of bile acids and salts (5) REACT_11042
Regulation by TREX1 (1) REACT_163652
Regulation of AMPK activity via LKB1 (1) REACT_21285
Regulation of HSF1-mediated heat shock response (2) REACT_200780
Regulation of pyruvate dehydrogenase (PDH) complex (2) REACT_12528
Regulation of Rheb GTPase activity by AMPK (1) REACT_21393
Regulation of thyroid hormone activity (1) REACT_15297
Removal of the Flap Intermediate (3) REACT_70
Removal of the Flap Intermediate from the C-strand (3) REACT_7999
Resolution of Sister Chromatid Cohesion (1) REACT_150425
Respiratory electron transport (2) REACT_22393
Retinoid cycle disease events (1) REACT_160130
Retinoid metabolism and transport (1) REACT_24968
Reuptake of GABA (4) REACT_23910
RMTs methylate histone arginines (2) REACT_228108
RNA Polymerase I Transcription Initiation (1) REACT_953
Role of phospholipids in phagocytosis (1) REACT_160158
Scavenging by Class A Receptors (1) REACT_163699
Senescence-Associated Secretory Phenotype (SASP) (2) REACT_169168
Separation of Sister Chromatids (1) REACT_150471
Serine biosynthesis (6) REACT_115789
Serotonin and melatonin biosynthesis (5) 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 (3) REACT_200874
SIRT1 negatively regulates rRNA Expression (4) REACT_200827
snRNP Assembly (1) REACT_11066
Sodium-coupled sulphate, di- and tri-carboxylate transporters (2) REACT_20646
Sphingolipid de novo biosynthesis (3) REACT_115810
Sterols are 12-hydroxylated by CYP8B1 (1) REACT_13438
Stimuli-sensing channels (2) REACT_160189
Sulfide oxidation to sulfate (1) REACT_116010
Sulfur amino acid metabolism (10) REACT_115639
SUMO is conjugated to E1 (UBA2:SAE1) (1) REACT_163812
Synthesis and interconversion of nucleotide di- and triphosphates (8) REACT_21330
Synthesis of 15-eicosatetraenoic acid derivatives (2) REACT_150422
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) (1) REACT_150134
Synthesis of 5-eicosatetraenoic acids (1) REACT_150209
Synthesis of bile acids and bile salts (1) REACT_11054
Synthesis of bile acids and bile salts via 24-hydroxycholesterol (3) REACT_11053
Synthesis of bile acids and bile salts via 27-hydroxycholesterol (2) REACT_11048
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol (7) REACT_11041
Synthesis of CL (1) REACT_120920
Synthesis of Dolichyl-phosphate (1) REACT_22230
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) (1) REACT_150417
Synthesis of glycosylphosphatidylinositol (GPI) (1) REACT_952
Synthesis of IP2, IP, and Ins in the cytosol (2) REACT_150352
Synthesis of Ketone Bodies (2) REACT_1464
Synthesis of Leukotrienes (LT) and Eoxins (EX) (3) REACT_150420
Synthesis of Lipoxins (LX) (2) REACT_150320
Synthesis of PA (3) REACT_120906
Synthesis of PC (6) REACT_121238
Synthesis of PE (1) REACT_120919
Synthesis of PG (3) REACT_121280
Synthesis of PI (1) REACT_121000
Synthesis of Prostaglandins (PG) and Thromboxanes (TX) (3) REACT_150149
Synthesis of PS (2) REACT_120823
Synthesis of UDP-N-acetyl-glucosamine (4) REACT_22394
Synthesis of very long-chain fatty acyl-CoAs (2) REACT_380
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) (1) REACT_24019
Termination of O-glycan biosynthesis (1) REACT_115835
TET1,2,3 and TDG demethylate DNA (2) REACT_200682
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation (2) REACT_111176
The activation of arylsulfatases (1) REACT_121036
The canonical retinoid cycle in rods (twilight vision) (2) REACT_160156
The retinoid cycle in cones (daylight vision) (1) REACT_160083
Thyroxine biosynthesis (3) REACT_15292
Tolerance by Mtb to nitric oxide produced by macrophages (1) REACT_120983
Translocation of GLUT4 to the plasma membrane (1) REACT_147867
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 (14) REACT_1206
Transport of nucleotide sugars (3) REACT_22151
Transport of organic anions (2) REACT_23988
Transport of vitamins, nucleosides, and related molecules (1) REACT_22285
Triglyceride Biosynthesis (2) REACT_1190
Tryptophan catabolism (9) REACT_916
Ubiquinol biosynthesis (4) REACT_160111
Unblocking of NMDA receptor, glutamate binding and activation (2) REACT_20594
Urea cycle (9) REACT_847
Utilization of Ketone Bodies (3) REACT_59
VEGFA-VEGFR2 Pathway (1) REACT_228166
VEGFR2 mediated vascular permeability (3) REACT_228016
Vitamin B1 (thiamin) metabolism (2) REACT_11117
Vitamin B2 (riboflavin) metabolism (2) REACT_11070
Vitamin C (ascorbate) metabolism (1) REACT_11202
Vitamin D (calciferol) metabolism (1) REACT_13523
Vitamins (1) REACT_13450
Vitamins B6 activation to pyridoxal phosphate (4) REACT_25012
Xenobiotics (1) REACT_13543
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