ST001192 A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
List of human metabolic pathways and metabolites (REACTOME)

Pathway name (# of metabolites detected in study)Reactome pathway
Abacavir metabolism (1) 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 (5) 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) (4) REACT_147904
Activation of Na-permeable Kainate Receptors (1) REACT_21343
Acyl chain remodeling of DAG and TAG (1) REACT_121122
Adenosine P1 receptors (1) REACT_18288
Adrenaline,noradrenaline inhibits insulin secretion (1) REACT_18339
Adrenaline signalling through Alpha-2 adrenergic receptor (1) REACT_19180
Adrenoceptors (1) REACT_16927
Aflatoxin activation and detoxification (2) REACT_228214
Agmatine biosynthesis (2) REACT_14800
alpha-linolenic acid (ALA) metabolism (1) REACT_121147
Alpha-oxidation of phytanate (2) REACT_17003
Amino acid synthesis and interconversion (transamination) (9) REACT_238
Amino acid transport across the plasma membrane (22) REACT_13796
Antigen Presentation: Folding, assembly and peptide loading of class I MHC (19) REACT_75795
Antigen processing: Ubiquitination & Proteasome degradation (19) REACT_75842
Arachidonate production from DAG (2) REACT_19308
Arachidonic acid metabolism (1) REACT_147851
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 (4) REACT_111118
Branched-chain amino acid catabolism (5) REACT_197
Carnitine synthesis (4) REACT_2125
Catecholamine biosynthesis (5) REACT_15551
Cholesterol biosynthesis (2) REACT_9405
Circadian Clock (4) REACT_24941
Citric acid cycle (TCA cycle) (3) REACT_1785
Class A/1 (Rhodopsin-like receptors) (7) 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 (2) REACT_163862
Collagen biosynthesis and modifying enzymes (3) 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
COX reactions (1) REACT_1396
Creatine metabolism (7) REACT_813
CREB phosphorylation through the activation of CaMKII (2) REACT_20642
Cross-presentation of soluble exogenous antigens (endosomes) (19) REACT_111056
CYP2E1 reactions (1) REACT_13797
Cysteine formation from homocysteine (1) REACT_115589
Cytosolic sulfonation of small molecules (3) REACT_6913
Cytosolic tRNA aminoacylation (19) REACT_15306
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE (1) REACT_169439
degradation of AXIN (1) REACT_200766
Degradation of cysteine and homocysteine (2) REACT_115654
Degradation of GABA (3) REACT_23964
Digestion of dietary lipid (7) REACT_9518
DNA methylation (1) REACT_267652
Downregulation of SMAD2/3:SMAD4 transcriptional activity (1) REACT_121111
Endogenous sterols (5) REACT_13812
Endosomal/Vacuolar pathway (19) REACT_111168
eNOS activation (3) REACT_12477
Enzymatic degradation of dopamine by COMT (1) REACT_15548
Enzymatic degradation of Dopamine by monoamine oxidase (1) REACT_15511
EPHB-mediated forward signaling (2) REACT_228085
ER-Phagosome pathway (19) REACT_111178
Fatty acids (2) REACT_13814
Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion (4) REACT_19193
Fatty acid, triacylglycerol, and ketone body metabolism (1) REACT_22279
Fatty Acyl-CoA Biosynthesis (1) REACT_1319
FMO oxidises nucleophiles (1) REACT_13653
formation of the beta-catenin:TCF transactivating complex (1) REACT_200753
Free fatty acid receptors (12) REACT_21268
GABA synthesis (1) REACT_24020
G alpha (12/13) signalling events (1) REACT_18407
G alpha (i) signalling events (11) REACT_19231
G alpha (q) signalling events (15) REACT_18283
G alpha (s) signalling events (9) REACT_19327
G alpha (z) signalling events (1) REACT_19333
Glucocorticoid biosynthesis (2) REACT_11036
Gluconeogenesis (4) REACT_1520
Glucuronidation (2) REACT_6784
Glutamate Neurotransmitter Release Cycle (2) REACT_12591
Glutathione synthesis and recycling (20) REACT_6960
Glycolysis (1) REACT_1383
Glycosphingolipid metabolism (1) REACT_116105
Glyoxylate metabolism (4) REACT_16925
HDMs demethylate histones (2) REACT_228178
Heme biosynthesis (3) 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
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis (1) REACT_494
HS-GAG degradation (1) REACT_120752
Hydrolysis of LPC (2) REACT_120977
Hydrolysis of LPE (1) REACT_120785
Hydroxycarboxylic acid-binding receptors (2) REACT_163785
Hypusine synthesis from eIF5A-lysine (1) REACT_12469
Import of palmitoyl-CoA into the mitochondrial matrix (1) REACT_11082
Inactivation, recovery and regulation of the phototransduction cascade (1) REACT_163919
Inositol transporters (1) REACT_19188
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate (1) REACT_25367
Interconversion of polyamines (4) REACT_14805
Iron uptake and transport (1) REACT_25060
Ligand-gated ion channel transport (2) 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 (4) REACT_14820
Metabolism of serotonin (2) REACT_15532
Methionine salvage pathway (2) REACT_75881
Methylation (3) REACT_6946
Mineralocorticoid biosynthesis (1) REACT_11047
Miscellaneous substrates (1) REACT_13425
Mitochondrial iron-sulfur cluster biogenesis (1) REACT_150353
Mitochondrial tRNA aminoacylation (19) 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 (3) REACT_13583
NGF-independant TRKA activation (1) REACT_11046
Nicotinamide salvaging (3) REACT_11213
Nicotinate metabolism (2) REACT_11088
Nitric oxide stimulates guanylate cyclase (2) REACT_23862
NoRC negatively regulates rRNA expression (1) REACT_200856
Norepinephrine Neurotransmitter Release Cycle (1) REACT_15418
Organic anion transport (3) REACT_22310
Organic anion transporters (5) REACT_19372
Organic cation transport (7) REACT_22357
Orphan transporters (13) 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 (4) REACT_505
Passive transport by Aquaporins (1) REACT_23826
Phagosomal maturation (early endosomal stage) (2) REACT_121256
Phenylalanine and tyrosine catabolism (6) REACT_1786
phospho-PLA2 pathway (1) REACT_15466
Plasmalogen biosynthesis (1) REACT_1407
Platelet degranulation (1) REACT_318
PPARA activates gene expression (7) REACT_116145
PRC2 methylates histones and DNA (1) REACT_200808
Presynaptic function of Kainate receptors (1) REACT_21254
Proline catabolism (2) REACT_1002
Prostanoid ligand receptors (1) REACT_18425
Proton-coupled monocarboxylate transport (2) REACT_20515
Proton-coupled neutral amino acid transporters (3) REACT_19348
Proton/oligonucleotide cotransporters (19) REACT_19328
Purine catabolism (7) REACT_2086
Purine ribonucleoside monophosphate biosynthesis (4) REACT_1776
Purine salvage (6) REACT_1923
Pyrimidine biosynthesis (4) REACT_21376
Pyrimidine catabolism (11) REACT_1023
Pyrimidine salvage reactions (7) REACT_655
Pyruvate metabolism (2) REACT_2071
Ras activation uopn Ca2+ infux through NMDA receptor (2) REACT_20546
Recycling of bile acids and salts (10) REACT_11042
Regulation by TREX1 (1) REACT_163652
Regulation of HSF1-mediated heat shock response (1) REACT_200780
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) (4) REACT_19241
Regulation of pyruvate dehydrogenase (PDH) complex (1) REACT_12528
Retinoid cycle disease events (1) REACT_160130
Retinoid metabolism and transport (3) REACT_24968
Reuptake of GABA (2) REACT_23910
REV-ERBA represses gene expression (4) REACT_118789
RMTs methylate histone arginines (1) REACT_228108
Role of phospholipids in phagocytosis (2) REACT_160158
RORA activates circadian gene expression (4) REACT_118659
Senescence-Associated Secretory Phenotype (SASP) (1) REACT_169168
Serine biosynthesis (3) REACT_115789
Serotonin and melatonin biosynthesis (4) 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
snRNP Assembly (1) REACT_11066
Sodium-coupled sulphate, di- and tri-carboxylate transporters (1) REACT_20646
Sphingolipid de novo biosynthesis (4) REACT_115810
Stimuli-sensing channels (1) REACT_160189
Sulfur amino acid metabolism (7) REACT_115639
Synthesis and interconversion of nucleotide di- and triphosphates (3) REACT_21330
Synthesis of 12-eicosatetraenoic acid derivatives (1) REACT_150201
Synthesis of 15-eicosatetraenoic acid derivatives (1) 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 (3) REACT_11054
Synthesis of bile acids and bile salts via 27-hydroxycholesterol (3) REACT_11048
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol (10) REACT_11041
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) (1) REACT_150417
Synthesis of Hepoxilins (HX) and Trioxilins (TrX) (1) REACT_150292
Synthesis of IP2, IP, and Ins in the cytosol (1) REACT_150352
Synthesis of Leukotrienes (LT) and Eoxins (EX) (3) REACT_150420
Synthesis of PA (2) REACT_120906
Synthesis of PC (3) REACT_121238
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 (2) REACT_22394
Synthesis of very long-chain fatty acyl-CoAs (2) REACT_380
Synthesis, secretion, and deacylation of Ghrelin (2) REACT_19189
Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) (12) REACT_24019
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) (5) REACT_23824
TET1,2,3 and TDG demethylate DNA (3) REACT_200682
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation (2) REACT_111176
The canonical retinoid cycle in rods (twilight vision) (3) REACT_160156
The retinoid cycle in cones (daylight vision) (1) REACT_160083
Thyroxine biosynthesis (2) REACT_15292
Transcriptional activation of mitochondrial biogenesis (4) REACT_200608
Transcriptional regulation of white adipocyte differentiation (4) REACT_27161
Transport of fatty acids (7) REACT_23892
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds (2) REACT_19305
Transport of glycerol from adipocytes to the liver by Aquaporins (1) REACT_23809
Transport of inorganic cations/anions and amino acids/oligopeptides (3) REACT_19397
Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane (14) REACT_1206
Transport of organic anions (6) REACT_23988
Triglyceride Biosynthesis (2) REACT_1190
Tryptophan catabolism (8) REACT_916
Ubiquinol biosynthesis (1) REACT_160111
Unblocking of NMDA receptor, glutamate binding and activation (2) REACT_20594
Urea cycle (5) REACT_847
Utilization of Ketone Bodies (1) REACT_59
VEGFR2 mediated cell proliferation (1) REACT_228024
VEGFR2 mediated vascular permeability (2) REACT_228016
Vitamin B1 (thiamin) metabolism (1) REACT_11117
Vitamin B2 (riboflavin) metabolism (1) REACT_11070
Vitamin C (ascorbate) metabolism (1) REACT_11202
Vitamins B6 activation to pyridoxal phosphate (2) REACT_25012
YAP1- and WWTR1 (TAZ)-stimulated gene expression (4) REACT_118713
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