Microbiome Prescription has a rich collection of annotated samples from different labs (uBiome, Ombre, Biomesight). The samples are annotated with self declared symptoms from a list of 548 different symptoms/diagnosis. 328 symptoms had statistically significant associations.

• Biomesight: 4169 samples
• Ombre: 1514 samples
• uBiome: 795 samples

There are several possibility of associations to these symptoms, including:

• Bacteria Association
• Enzyme Association
• Metabolite Association which we can decompose into
  • Production
  • Substrate (Consumers)
  • Net Metabolite (Production – Consumer)

For each of these 5 vectors, we use these three statistical methods and set out criteria to p < 0.005:

• Fisher’s exact test on prevalence of bacteria
• Mann Whitney Wilcoxon Test
• t-Test on Means

We used KEGG.JP data as a poor man method of compute metabolites.

To go directly to the page reporting data: Symptom Association

This processing took a few days hammering a PC at 90% CPU.

https://www.youtube.com/watch?v=sM4V5hesb1s

High Level Overview

Below we have counts of the associations found. It is clear that bacteria associations are weaker(fewer) than Enzymes by a factor of 4-10. With metabolites, the net metabolite appears a poorer estimator than either producers or substrates.

As would be expected, large population, we find more associations as the population increases.

Bacteria

Source	Associations
BiomeSight	33432
Thryve	28668
uBiome	9283

Enzymes

Source	Associations
BiomeSight	325170
Thryve	78485
uBiome	41707

Metabolite Production

Source	Associations
BiomeSight	226447
Thryve	49122
uBiome	26756

Metabolite Substrate

Source	Associations
BiomeSight	227053
Thryve	50164
uBiome	28162

Metabolite Net

Source	Associations
BiomeSight	123631
Thryve	25493
uBiome	14771

Data Accessibility

The findings are available on microbiome prescription

The key thing to be aware of is that the results are different using data from each lab. For background see Nightmare.

The page is simple:

• Pick the Symptoms
• Pick the number of TOP items you want from each lab.

This is then followed by 5 sortable and filterable tables.

Examples of agreement

For ME/CFS we have all three labs reporting these bacteria are significant:

• Porphyromonas genus
• Bifidobacterium genus
• Bifidobacteriaceae family
• Bifidobacteriales order
• Hungateiclostridiaceae family

For Enzymes:

• 1.1.1.65 pyridoxine 4-dehydrogenase
• 1.8.98.6 formate:CoB-CoM heterodisulfide,ferredoxin reductase
• 2.1.1.172 16S rRNA (guanine¹²⁰⁷–N²)-methyltransferase
• 2.3.2.5 glutaminyl-peptide cyclotransferase
• 2.4.1.336 monoglucosyldiacylglycerol synthase
• 2.6.1.59 dTDP-4-amino-4,6-dideoxygalactose transaminase
• 2.7.7.15 choline-phosphate cytidylyltransferase
• 2.7.8.36 undecaprenyl phosphate N,N′-diacetylbacillosamine 1-phosphate transferase
• 3.4.21.83 oligopeptidase B
• 4.1.1.31 phosphoenolpyruvate carboxylase

For Net Metabolite we have a much longer list:

• C01142 (3S)-3,6-Diaminohexanoate
• C20748 (E)-4-(Trimethylammonio)but-2-enoyl-CoA
• C02612 (R)-2-Methylmalate
• C06010 (S)-2-Acetolactate
• C00424 (S)-Lactaldehyde
• C07281 [eIF5A-precursor]-lysine
• C15811 [Enzyme]-cysteine
• C15812 [Enzyme]-S-sulfanylcysteine
• C16236 [Protein]-N6-(octanoyl)-L-lysine
• C16832 [Protein]-N6-[(R)-dihydrolipoyl]-L-lysine
• C21440 [Protein]-S-sulfanyl-L-cysteine
• C01302 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
• C04751 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate
• C04677 1-(5′-Phosphoribosyl)-5-amino-4-imidazolecarboxamide
• C06364 1,2-Diacyl-3-alpha-D-glucosyl-sn-glycerol
• C00641 1,2-Diacyl-sn-glycerol
• C15606 1,2-Dihydroxy-5-(methylthio)pent-1-en-3-one
• C03657 1,4-Dihydroxy-2-naphthoate
• C11437 1-Deoxy-D-xylulose 5-phosphate
• C04006 1D-myo-Inositol 3-phosphate
• C11811 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate
• C03972 2,3,4,5-Tetrahydrodipicolinate
• C00691 2,4,6/3,5-Pentahydroxycyclohexanone
• C21607 2,6-Di-O-alpha-D-mannosyl-1-phosphatidyl-1D-myo-inositol
• C04691 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
• C20905 2-Iminobutanoate
• C20904 2-Iminopropanoate
• C21609 2-O-(6-O-Acyl-alpha-D-mannosyl)-1-phosphatidyl-1D-myo-inositol
• C05807 2-Polyprenylphenol
• C16463 3′,5′-Cyclic diGMP
• C20934 3-Deoxy-D-glycero-D-galacto-non-2-ulopyranosonate
• C04478 3-Deoxy-D-manno-octulosonate 8-phosphate
• C00587 3-Hydroxybenzoate
• C00141 3-Methyl-2-oxobutanoic acid
• C00053 3′-Phosphoadenylyl sulfate
• C00197 3-Phospho-D-glycerate
• C11435 4-(Cytidine 5′-diphospho)-2-C-methyl-D-erythritol
• C11355 4-Amino-4-deoxychorismate
• C04752 4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate
• C00568 4-Aminobenzoate
• C00334 4-Aminobutanoate
• C04327 4-Methyl-5-(2-phosphooxyethyl)thiazole
• C01180 4-Methylthio-2-oxobutanoic acid
• C22411 4-O-{Poly[(2R)-glycerophospho]-(2R)-glycerophospho}-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
• C21502 4-O-Di[(2R)-1-glycerophospho]-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
• C03393 4-Phospho-D-erythronate
• C00445 5,10-Methenyltetrahydrofolate
• C00143 5,10-Methylenetetrahydrofolate
• C03089 5-Methylthio-D-ribose
• C00119 5-Phospho-alpha-D-ribose 1-diphosphate
• C01300 6-(Hydroxymethyl)-7,8-dihydropterin
• C01019 6-Deoxy-L-galactose
• C04807 6-Hydroxymethyl-7,8-dihydropterin diphosphate
• C20176 8-Oxo-dGDP
• C22235 8-Oxo-GDP
• C22382 Aceneuramate
• C00033 Acetate
• C00227 Acetyl phosphate
• C00024 Acetyl-CoA
• C00147 Adenine
• C00212 Adenosine
• C06508 Adenosyl cobinamide
• C06506 Adenosyl cobyrinate a,c diamide
• C00008 ADP
• C00179 Agmatine
• C00069 Alcohol
• C00267 alpha-D-Glucose
• C20237 alpha-Maltose 1-phosphate
• C00014 Ammonia
• C00020 AMP
• C00002 ATP
• C05345 beta-D-Fructose 6-phosphate
• C00663 beta-D-Glucose 1-phosphate
• C00576 Betaine aldehyde
• C20568 beta-L-Arabinofuranosyl-(1->2)-beta-L-arabinofuranose
• C00120 Biotin
• C00323 Caffeoyl-CoA
• C00169 Carbamoyl phosphate
• C00090 Catechol
• C00307 CDP-choline
• C00269 CDP-diacylglycerol
• C00513 CDP-glycerol
• C00114 Choline
• C00588 Choline phosphate
• C00011 CO2
• C00010 CoA
• C06504 Cob(II)yrinate a,c diamide
• C11545 Cobalt-precorrin 8
• C05773 Cobyrinate
• C00876 Coenzyme F420
• C00063 CTP
• C03492 D-4′-Phosphopantothenate
• C00405 D-Amino acid
• C00239 dCMP
• C17010 Dehypoxanthine futalosine
• C02269 Deoxynucleoside
• C00677 Deoxynucleoside triphosphate
• C04666 D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate
• C00095 D-Fructose
• C00354 D-Fructose 1,6-bisphosphate
• C00333 D-Galacturonate
• C00257 D-Gluconic acid
• C00198 D-Glucono-1,5-lactone
• C00329 D-Glucosamine
• C00031 D-Glucose
• C00103 D-Glucose 1-phosphate
• C00258 D-Glycerate
• C00235 Dimethylallyl diphosphate
• C00013 Diphosphate
• C17556 di-trans,poly-cis-Undecaprenyl phosphate
• C00159 D-Mannose
• C00636 D-Mannose 1-phosphate
• C00039 DNA
• C00110 Dolichyl phosphate
• C03862 Dolichyl phosphate D-mannose
• C00121 D-Ribose
• C01151 D-Ribose 1,5-bisphosphate
• C03319 dTDP-L-rhamnose
• C00365 dUMP
• C00460 dUTP
• C00231 D-Xylulose 5-phosphate
• C00125 Ferricytochrome c
• C00126 Ferrocytochrome c
• C00406 Feruloyl-CoA
• C00061 FMN
• C00122 Fumarate
• C16999 Futalosine
• C02686 Galactosylceramide
• C00096 GDP-mannose
• C00353 Geranylgeranyl diphosphate
• C00051 Glutathione
• C00116 Glycerol
• C00184 Glycerone
• C00111 Glycerone phosphate
• C00037 Glycine
• C00266 Glycolaldehyde
• C00160 Glycolate
• C02412 Glycyl-tRNA(Gly)
• C00048 Glyoxylate
• C00044 GTP
• C00080 H+
• C00288 HCO3-
• C06250 Holo-[carboxylase]
• C04298 Holo-[citrate (pro-3S)-lyase]
• C00283 Hydrogen sulfide
• C06399 Hydrogenobyrinate
• C00530 Hydroquinone
• C15603 Hydroquinone
• C15809 Iminoglycine
• C00130 IMP
• C00463 Indole
• C03506 Indoleglycerol phosphate
• C00885 Isochorismate
• C00129 Isopentenyl diphosphate
• C03508 L-2-Amino-3-oxobutanoic acid
• C15556 L-3,4-Dihydroxybutan-2-one 4-phosphate
• C00041 L-Alanine
• C00886 L-Alanyl-tRNA
• C00049 L-Aspartate
• C00441 L-Aspartate 4-semialdehyde
• C20750 L-Carnitinyl-CoA
• C00327 L-Citrulline
• C02291 L-Cystathionine
• C00097 L-Cysteine
• C02700 L-Formylkynurenine
• C00025 L-Glutamate
• C01165 L-Glutamate 5-semialdehyde
• C00064 L-Glutamine
• C02047 L-Leucyl-tRNA
• C00073 L-Methionine
• C00077 L-Ornithine
• C00508 L-Ribulose
• C00065 L-Serine
• C00188 L-Threonine
• C00083 Malonyl-CoA
• C05819 Menaquinol
• C00409 Methanethiol
• C06717 Mycothiol
• C00137 myo-Inositol
• C04916 N-(5′-Phospho-D-1′-ribulosylformimino)-5-amino-1-(5”-phospho-D-ribosyl)-4-imidazolecarboxamide
• C20390 N-Acetyl-alpha-D-glucosaminyl-diphospho-trans,octacis-decaprenol
• C00140 N-Acetyl-D-glucosamine
• C00003 NAD+
• C00004 NADH
• C00006 NADP+
• C00005 NADPH
• C00436 N-Carbamoylputrescine
• C00153 Nicotinamide
• C00201 Nucleoside triphosphate
• C00979 O-Acetyl-L-serine
• C00009 Orthophosphate
• C22151 Oxidized [2Fe-2S] ferredoxin
• C01134 Pantetheine 4′-phosphate
• C00864 Pantothenate
• C00472 p-Benzoquinone
• C00416 Phosphatidate
• C03167 Phosphonoacetaldehyde
• C19692 Polysulfide
• C06408 Precorrin 8X
• C00585 Protein tyrosine
• C01167 Protein tyrosine phosphate
• C02880 Protochlorophyllide
• C00134 Putrescine
• C00250 Pyridoxal
• C00022 Pyruvate
• C15602 Quinone
• C22150 Reduced [2Fe-2S] ferredoxin
• C01080 Reduced coenzyme F420
• C00473 Retinol
• C00255 Riboflavin
• C00046 RNA
• C00021 S-Adenosyl-L-homocysteine
• C00019 S-Adenosyl-L-methionine
• C04188 S-Methyl-5-thio-D-ribose 1-phosphate
• C04582 S-Methyl-5-thio-D-ribulose 1-phosphate
• C00623 sn-Glycerol 1-phosphate
• C00315 Spermidine
• C03539 S-Ribosyl-L-homocysteine
• C00059 Sulfate
• C00704 Superoxide
• C00378 Thiamine
• C00422 Triacylglycerol
• C00066 tRNA
• C01642 tRNA(Gly)
• C01645 tRNA(Leu)
• C00015 UDP
• C19725 UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate
• C00043 UDP-N-acetyl-alpha-D-glucosamine
• C00203 UDP-N-acetyl-D-galactosamine
• C01050 UDP-N-acetylmuramate
• C05892 UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine
• C00105 UMP
• C00106 Uracil
• C01051 Uroporphyrinogen III
• C00001 Water
• C00385 Xanthine
• C00655 Xanthosine 5′-phosphate

For Metabolite Producers:

• C22302 (+)-6-Hydroxypinoresinol
• C19831 (1R,6S)-6-Amino-5-oxocyclohex-2-ene-1-carboxylate
• C05161 (2R,5S)-2,5-Diaminohexanoate
• C04236 (2S)-2-Isopropyl-3-oxosuccinate
• C20258 (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate
• C01142 (3S)-3,6-Diaminohexanoate
• C00566 (3S)-Citryl-CoA
• C01186 (3S,5S)-3,5-Diaminohexanoate
• C00712 (9Z)-Octadecenoic acid
• C20748 (E)-4-(Trimethylammonio)but-2-enoyl-CoA
• C22385 (L-Cysteinyl)adenylate
• C02489 (R)-2-Hydroxyacid
• C02612 (R)-2-Methylmalate
• C04352 (R)-4′-Phosphopantothenoyl-L-cysteine
• C00810 (R)-Acetoin
• C00937 (R)-Lactaldehyde
• C03912 (S)-1-Pyrroline-5-carboxylate
• C06010 (S)-2-Acetolactate
• C11838 (S)-4,5-Dihydroxypentane-2,3-dione
• C03656 (S)-5-Amino-3-oxohexanoic acid
• C00424 (S)-Lactaldehyde
• C21068 [5-(Aminomethyl)furan-3-yl]methyl phosphate
• C15977 [Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine
• C16254 [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
• C07282 [eIF5A-precursor]-deoxyhypusine
• C07281 [eIF5A-precursor]-lysine
• C15811 [Enzyme]-cysteine
• C15812 [Enzyme]-S-sulfanylcysteine
• C22155 [Fe-S] cluster scaffold protein
• C01281 [L-Glutamate:ammonia ligase (ADP-forming)]
• C20730 [Protein]-FMN-L-Threonine
• C16236 [Protein]-N6-(octanoyl)-L-lysine
• C16832 [Protein]-N6-[(R)-dihydrolipoyl]-L-lysine
• C01242 [Protein]-S8-aminomethyldihydrolipoyllysine
• C21440 [Protein]-S-sulfanyl-L-cysteine
• C21879 1-(5-O-Phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate
• C04751 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate
• C04823 1-(5′-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole
• C04677 1-(5′-Phosphoribosyl)-5-amino-4-imidazolecarboxamide
• C04734 1-(5′-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide
• C02490 1,2-beta-D-Glucan
• C00641 1,2-Diacyl-sn-glycerol
• C00986 1,3-Diaminopropane
• C06485 1,5-Anhydro-D-fructose
• C00234 10-Formyltetrahydrofolate
• C21835 12,18-Didecarboxysiroheme
• C04230 1-Acyl-sn-glycero-3-phosphocholine
• C11437 1-Deoxy-D-xylulose 5-phosphate
• C04006 1D-myo-Inositol 3-phosphate
• C11557 1-Phosphatidyl-1D-myo-inositol 5-phosphate
• C19771 2′-(5-Triphosphoribosyl)-3′-dephospho-CoA
• C04640 2-(Formamido)-N1-(5′-phosphoribosyl)acetamidine
• C01159 2,3-Bisphospho-D-glycerate
• C00691 2,4,6/3,5-Pentahydroxycyclohexanone
• C20424 2,4-Diacetamido-2,4,6-trideoxy-D-mannopyranose
• C21896 2,4-Diacetylphloroglucinol
• C02780 2,5-Didehydro-D-gluconate
• C21607 2,6-Di-O-alpha-D-mannosyl-1-phosphatidyl-1D-myo-inositol
• C00900 2-Acetolactate
• C17234 2-Aminobut-2-enoate
• C11453 2-C-Methyl-D-erythritol 2,4-cyclodiphosphate
• C04442 2-Dehydro-3-deoxy-6-phospho-D-gluconate
• C04691 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
• C03827 2-Dehydro-3-deoxy-L-fuconate
• C06892 2-Deoxy-5-keto-D-gluconic acid
• C00672 2-Deoxy-D-ribose 1-phosphate
• C06196 2′-Deoxyinosine 5′-phosphate
• C19970 2-Hydroxy-dAMP
• C20905 2-Iminobutanoate
• C02631 2-Isopropylmaleate
• C02222 2-Maleylacetate
• C02226 2-Methylmaleate
• C21608 2-O-(6-O-Acyl-alpha-D-mannosyl)-6-O-alpha-D-mannosyl-1-phosphatidyl-1D-myo-inositol
• C19792 2-O-(alpha-D-Glucopyranosyl)-D-glycerate
• C03586 2-Oxo-2,3-dihydrofuran-5-acetate
• C06054 2-Oxo-3-hydroxy-4-phosphobutanoate
• C00109 2-Oxobutanoate
• C00026 2-Oxoglutarate
• C11436 2-Phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol
• C00631 2-Phospho-D-glycerate
• C13309 2-Phytyl-1,4-naphthoquinone
• C05807 2-Polyprenylphenol
• C01267 3-(Imidazol-4-yl)-2-oxopropyl phosphate
• C00575 3′,5′-Cyclic AMP
• C16463 3′,5′-Cyclic diGMP
• C20772 3-[(1-Carboxyvinyl)oxy]benzoate
• C00944 3-Dehydroquinate
• C02637 3-Dehydroshikimate
• C20934 3-Deoxy-D-glycero-D-galacto-non-2-ulopyranosonate
• C21383 3-Deoxy-D-glycero-D-galacto-non-2-ulopyranosonate 9-phosphate
• C04046 3-D-Glucosyl-1,2-diacylglycerol
• C20960 3-Hydroxy-5-phosphooxypentane-2,4-dione
• C00141 3-Methyl-2-oxobutanoic acid
• C03069 3-Methylcrotonyl-CoA
• C00685 3-Oxoacyl-[acyl-carrier protein]
• C02941 3-Oxo-Delta1-steroid
• C00619 3-Oxo-Delta4-steroid
• C00053 3′-Phosphoadenylyl sulfate
• C00197 3-Phospho-D-glycerate
• C00236 3-Phospho-D-glyceroyl phosphate
• C03232 3-Phosphonooxypyruvate
• C02798 3-Phosphonopyruvate
• C22313 3-Sulfinopropanoate
• C11435 4-(Cytidine 5′-diphospho)-2-C-methyl-D-erythritol
• C16144 4,4′-Diapophytoene
• C04556 4-Amino-2-methyl-5-(phosphooxymethyl)pyrimidine
• C01279 4-Amino-5-hydroxymethyl-2-methylpyrimidine
• C04752 4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate
• C00334 4-Aminobutanoate
• C05848 4-Hydroxy-3-polyprenylbenzoate
• C00156 4-Hydroxybenzoate
• C00233 4-Methyl-2-oxopentanoate
• C04327 4-Methyl-5-(2-phosphooxyethyl)thiazole
• C22411 4-O-{Poly[(2R)-glycerophospho]-(2R)-glycerophospho}-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
• C02964 4-O-beta-D-Glucopyranosyl-D-mannose
• C19877 4-O-Phospho-alpha-Kdo-(2->6)-lipid IVA
• C03082 4-Phospho-L-aspartate
• C04294 5-(2-Hydroxyethyl)-4-methylthiazole
• C04896 5-(5-Phospho-D-ribosylaminoformimino)-1-(5-phosphoribosyl)-imidazole-4-carboxamide
• C00445 5,10-Methenyltetrahydrofolate
• C00431 5-Aminopentanoate
• C21877 5-Carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate
• C15667 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole
• C16737 5-Deoxy-D-glucuronate
• C22288 5-Deoxy-D-ribose
• C03089 5-Methylthio-D-ribose
• C01269 5-O-(1-Carboxyvinyl)-3-phosphoshikimate
• C02805 5-Oxoprolyl-peptide
• C00119 5-Phospho-alpha-D-ribose 1-diphosphate
• C03838 5′-Phosphoribosylglycinamide
• C19787 5′-S-Methyl-5′-thioinosine
• C03773 6-Acetyl-beta-D-galactoside
• C20773 6-Amino-6-deoxyfutalosine
• C02954 6-Aminopenicillanate
• C20830 6-Deoxy-6-sulfo-D-fructose
• C19859 6-Methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol
• C00345 6-Phospho-D-gluconate
• C01037 7,8-Diaminononanoate
• C15858 7,9,7′,9′-tetracis-Lycopene
• C19759 7,9,9′-tricis-Neurosporene
• C04643 7-Oxodeoxycholate
• C20176 8-Oxo-dGDP
• C19968 8-Oxo-dGMP
• C22235 8-Oxo-GDP
• C14909 9alpha-Hydroxyandrosta-1,4-diene-3,17-dione
• C00028 Acceptor
• C00033 Acetate
• C05744 Acetoacetyl-[acp]
• C00207 Acetone
• C00227 Acetyl phosphate
• C00024 Acetyl-CoA
• C00147 Adenine
• C00212 Adenosine
• C06507 Adenosyl cobyrinate hexaamide
• C01299 Adenylyl-[L-glutamate:ammonia ligase (ADP-forming)]
• C00008 ADP
• C20784 ADP-5-ethyl-4-methylthiazole-2-carboxylate
• C00498 ADP-glucose
• C00499 Allantoate
• C04145 all-trans-Nonaprenyl diphosphate
• C04146 all-trans-Octaprenyl diphosphate
• C04465 alpha,alpha’-Trehalose 6,6′-bismycolate
• C00446 alpha-D-Galactose 1-phosphate
• C00936 alpha-D-Mannose
• C02504 alpha-Isopropylmalate
• C06365 alpha-Kojibiosyldiacylglycerol
• C01888 Aminoacetone
• C03373 Aminoimidazole ribotide
• C00014 Ammonia
• C00020 AMP
• C06697 Arsenite
• C00002 ATP
• C21336 beta-1,2-Mannobiose
• C05345 beta-D-Fructose 6-phosphate
• C00221 beta-D-Glucose
• C00663 beta-D-Glucose 1-phosphate
• C01172 beta-D-Glucose 6-phosphate
• C20569 beta-L-Arabinofuranose
• C01563 Carbamate
• C00169 Carbamoyl phosphate
• C04419 Carboxybiotin-carboxyl-carrier protein
• C20969 Carboxyphosphate
• C05980 Cardiolipin
• C00307 CDP-choline
• C00269 CDP-diacylglycerol
• C00789 CDP-ribitol
• C05306 Chlorophyll a
• C00114 Choline
• C01794 Choloyl-CoA
• C00251 Chorismate
• C00417 cis-Aconitate
• C00158 Citrate
• C20419 CMP-N,N’-diacetyllegionaminate
• C00011 CO2
• C00010 CoA
• C00175 Cobalt ion
• C16242 Cobalt-precorrin 5A
• C11545 Cobalt-precorrin 8
• C05773 Cobyrinate
• C19724 Cobyrinate c-monamide
• C04832 Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
• C03263 Coproporphyrinogen III
• C00063 CTP
• C00475 Cytidine
• C22216 Cytidine 5′-{[hydroxy(2-hydroxyethyl)phosphonoyl]phosphate}
• C04122 D-1-Aminopropan-2-ol O-phosphate
• C03492 D-4′-Phosphopantothenate
• C00993 D-Alanyl-D-alanine
• C00405 D-Amino acid
• C00360 dAMP
• C00705 dCDP
• C00239 dCMP
• C03112 Deacetylcephalosporin C
• C00857 Deamino-NAD+
• C15495 Decylubiquinol
• C15853 Dehydrospermidine
• C17010 Dehypoxanthine futalosine
• C21084 Demethylphylloquinol
• C00330 Deoxyguanosine
• C00677 Deoxynucleoside triphosphate
• C00882 Dephospho-CoA
• C04666 D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate
• C00279 D-Erythrose 4-phosphate
• C00354 D-Fructose 1,6-bisphosphate
• C01094 D-Fructose 1-phosphate
• C00085 D-Fructose 6-phosphate
• C00905 D-Fructuronate
• C01113 D-Galactose 6-phosphate
• C00333 D-Galacturonate
• C00257 D-Gluconic acid
• C01236 D-Glucono-1,5-lactone 6-phosphate
• C00329 D-Glucosamine
• C00352 D-Glucosamine 6-phosphate
• C00103 D-Glucose 1-phosphate
• C00092 D-Glucose 6-phosphate
• C00217 D-Glutamate
• C00118 D-Glyceraldehyde 3-phosphate
• C00258 D-Glycerate
• C19879 D-glycero-alpha-D-manno-Heptose 1,7-bisphosphate
• C19882 D-glycero-D-manno-Heptose 7-phosphate
• C02965 D-Hexose 6-phosphate
• C06419 D-Histidine
• C05925 Dihydroneopterin phosphate
• C20300 Dimethylarsinous acid
• C00013 Diphosphate
• C04574 di-trans,poly-cis-Undecaprenyl diphosphate
• C17556 di-trans,poly-cis-Undecaprenyl phosphate
• C00159 D-Mannose
• C00636 D-Mannose 1-phosphate
• C00275 D-Mannose 6-phosphate
• C04299 D-myo-Inositol 1,2-cyclic phosphate
• C00039 DNA
• C03391 DNA 6-methylaminopurine
• C01246 Dolichyl beta-D-glucosyl phosphate
• C00621 Dolichyl diphosphate
• C00515 D-Ornithine
• C01151 D-Ribose 1,5-bisphosphate
• C00117 D-Ribose 5-phosphate
• C00199 D-Ribulose 5-phosphate
• C01097 D-Tagatose 6-phosphate
• C11930 dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose
• C06620 dTDP-3,4-dioxo-2,6-dideoxy-D-glucose
• C00688 dTDP-4-dehydro-beta-L-rhamnose
• C00842 dTDP-glucose
• C16581 D-threo-Aldono-1,5-lactone
• C00364 dTMP
• C00365 dUMP
• C00310 D-Xylulose
• C00231 D-Xylulose 5-phosphate
• C05359 e-
• C00016 FAD
• C00923 Ferricytochrome
• C00125 Ferricytochrome c
• C00126 Ferrocytochrome c
• C00406 Feruloyl-CoA
• C05199 Flavodoxin semiquinone
• C06108 Fluoroacetate
• C00061 FMN
• C00798 Formyl-CoA
• C00122 Fumarate
• C16999 Futalosine
• C02686 Galactosylceramide
• C00035 GDP
• C01222 GDP-4-dehydro-6-deoxy-D-mannose
• C19881 GDP-D-glycero-alpha-D-manno-heptose
• C00096 GDP-mannose
• C00341 Geranyl diphosphate
• C21217 Geranylgeranyl bacteriochlorophyllide a
• C00353 Geranylgeranyl diphosphate
• C02282 Glutaminyl-tRNA
• C00051 Glutathione
• C00127 Glutathione disulfide
• C05730 Glutathionylspermidine
• C00116 Glycerol
• C00111 Glycerone phosphate
• C00037 Glycine
• C00160 Glycolate
• C02412 Glycyl-tRNA(Gly)
• C00144 GMP
• C00581 Guanidinoacetate
• C00242 Guanine
• C01228 Guanosine 3′,5′-bis(diphosphate)
• C04494 Guanosine 3′-diphosphate 5′-triphosphate
• C19871 Guanylyl molybdenum cofactor
• C00080 H+
• C00462 Halide
• C04649 Heparan sulfate N-acetyl-alpha-D-glucosaminide
• C06250 Holo-[carboxylase]
• C00282 Hydrogen
• C01528 Hydrogen selenide
• C00283 Hydrogen sulfide
• C06399 Hydrogenobyrinate
• C06503 Hydrogenobyrinate a,c diamide
• C15603 Hydroquinone
• C00530 Hydroquinone
• C00262 Hypoxanthine
• C00130 IMP
• C00463 Indole
• C00311 Isocitrate
• C03281 Kanamycin A 3′-phosphate
• C06026 KDO2-lipid A
• C03508 L-2-Amino-3-oxobutanoic acid
• C05231 L-3-Aminobutyryl-CoA
• C00041 L-Alanine
• C20958 L-Alanyl-L-glutamate
• C00886 L-Alanyl-tRNA
• C00062 L-Arginine
• C02163 L-Arginyl-tRNA(Arg)
• C00152 L-Asparagine
• C03402 L-Asparaginyl-tRNA(Asn)
• C00049 L-Aspartate
• C00441 L-Aspartate 4-semialdehyde
• C20750 L-Carnitinyl-CoA
• C02291 L-Cystathionine
• C00506 L-Cysteate
• C00097 L-Cysteine
• C02882 L-Cysteine-S-conjugate
• C03125 L-Cysteinyl-tRNA(Cys)
• C02045 L-Erythrulose
• C00025 L-Glutamate
• C00064 L-Glutamine
• C03287 L-Glutamyl 5-phosphate
• C02987 L-Glutamyl-tRNA(Glu)
• C00135 L-Histidine
• C02988 L-Histidyl-tRNA(His)
• C00155 L-Homocysteine
• C16238 Lipoyl-AMP
• C00666 LL-2,6-Diaminoheptanedioate
• C21386 L-Leucyl-L-arginyl-protein
• C21457 L-Leucyl-L-aspartyl-protein
• C21455 L-Leucyl-L-glutamyl-protein
• C21387 L-Leucyl-L-lysyl-protein
• C02047 L-Leucyl-tRNA
• C00047 L-Lysine
• C01931 L-Lysyl-tRNA
• C00073 L-Methionine
• C15999 L-Methionine (S)-S-oxide
• C02430 L-Methionyl-tRNA
• C01826 L-Norvaline
• C02434 Long-chain ester
• C00077 L-Ornithine
• C03511 L-Phenylalanyl-tRNA(Phe)
• C02702 L-Prolyl-tRNA(Pro)
• C00508 L-Ribulose
• C01101 L-Ribulose 5-phosphate
• C02553 L-Seryl-tRNA(Ser)
• C00188 L-Threonine
• C20641 L-Threonylcarbamoyladenylate
• C02992 L-Threonyl-tRNA(Thr)
• C02839 L-Tyrosyl-tRNA(Tyr)
• C02554 L-Valyl-tRNA(Val)
• C04536 Magnesium protoporphyrin monomethyl ester
• C01209 Malonyl-[acyl-carrier protein]
• C00083 Malonyl-CoA
• C01935 Maltodextrin
• C02995 Maltose 6′-phosphate
• C04809 Membrane-derived-oligosaccharide 6-(glycerophospho)-D-glucose
• C05819 Menaquinol
• C01732 Mesaconate
• C00680 meso-2,6-Diaminoheptanedioate
• C11440 Methionyl peptide
• C00546 Methylglyoxal
• C05924 Molybdopterin
• C06717 Mycothiol
• C00137 myo-Inositol
• C15854 N-(4-Aminobutylidene)-[eIF5A-precursor]-lysine
• C04916 N-(5′-Phospho-D-1′-ribulosylformimino)-5-amino-1-(5”-phospho-D-ribosyl)-4-imidazolecarboxamide
• C03406 N-(L-Arginino)succinate
• C20562 N-[(7,8-Dihydropterin-6-yl)methyl]-4-(beta-D-ribofuranosyl)aniline 5′-phosphate
• C21009 N4-Aminopropylspermidine
• C21010 N4-Bis(aminopropyl)spermidine
• C22033 N5-(Cytidine 5′-diphosphoramidyl)-L-glutamine
• C03794 N6-(1,2-Dicarboxyethyl)-AMP
• C20751 N6-L-Threonylcarbamoyladenine in tRNA
• C04501 N-Acetyl-alpha-D-glucosamine 1-phosphate
• C20390 N-Acetyl-alpha-D-glucosaminyl-diphospho-trans,octacis-decaprenol
• C00140 N-Acetyl-D-glucosamine
• C00357 N-Acetyl-D-glucosamine 6-phosphate
• C01289 N-Acetyl-D-glucosaminyldiphosphoundecaprenol
• C02297 N-Acetyldiamine
• C00645 N-Acetyl-D-mannosamine
• C05539 N-Acetyl-L-2-amino-6-oxopimelate
• C00624 N-Acetyl-L-glutamate
• C04133 N-Acetyl-L-glutamate 5-phosphate
• C01250 N-Acetyl-L-glutamate 5-semialdehyde
• C21027 N-Acetylmuramic acid alpha-1-phosphate
• C00625 N-Acyl-D-mannosamine
• C00003 NAD+
• C00004 NADH
• C00006 NADP+
• C00005 NADPH
• C00438 N-Carbamoyl-L-aspartate
• C00454 NDP
• C19609 Nickel(2+)
• C00153 Nicotinamide
• C00455 Nicotinamide D-ribonucleotide
• C00253 Nicotinate
• C00533 Nitric oxide
• C02565 N-Methylhydantoin
• C21113 NMNH
• C03523 N-Substituted amino acid
• C04462 N-Succinyl-2-L-amino-6-oxoheptanedioate
• C03419 Nucleoside 3′-phosphate
• C01117 Nucleoside 5′-phosphate
• C01077 O-Acetyl-L-homoserine
• C00979 O-Acetyl-L-serine
• C04260 O-D-Alanyl-poly(ribitol phosphate)
• C01102 O-Phospho-L-homoserine
• C00295 Orotate
• C00009 Orthophosphate
• C01118 O-Succinyl-L-homoserine
• C00313 Oxalyl-CoA
• C00139 Oxidized ferredoxin
• C02869 Oxidized flavodoxin
• C00007 Oxygen
• C01134 Pantetheine 4′-phosphate
• C00864 Pantothenate
• C00472 p-Benzoquinone
• C06564 Penicillin N
• C15653 Peptide-L-methionine (R)-S-oxide
• C03895 Peptide-L-methionine (S)-S-oxide
• C03633 Peptidylproline (omega=0)
• C15584 Phenol
• C00582 Phenylacetyl-CoA
• C00166 Phenylpyruvate
• C00416 Phosphatidate
• C00344 Phosphatidylglycerol
• C04308 Phosphatidyl-N-dimethylethanolamine
• C01241 Phosphatidyl-N-methylethanolamine
• C00074 Phosphoenolpyruvate
• C03167 Phosphonoacetaldehyde
• C00562 Phosphoprotein
• C02741 Phosphoribosyl-AMP
• C03313 Phylloquinol
• C16695 Plastoquinol-9
• C00404 Polyphosphate
• C19692 Polysulfide
• C06407 Precorrin 4
• C06416 Precorrin 5
• C06408 Precorrin 8X
• C00254 Prephenate
• C21177 Prokaryotic ubiquitin-like protein
• C00615 Protein histidine
• C02188 Protein lysine
• C04261 Protein N(pi)-phospho-L-histidine
• C16237 Protein N6-(lipoyl)lysine
• C20743 Protein N6-acetyl-L-lysine
• C00585 Protein tyrosine
• C02880 Protochlorophyllide
• C20082 Pseudaminic acid
• C01168 Pseudouridine 5′-phosphate
• C21178 Pupylated protein
• C15587 Purine
• C21851 Pyridinium-3,5-biscarboxylic acid mononucleotide
• C21767 Pyridinium-3,5-bisthiocarboxylate mononucleotide
• C21878 Pyridinium-3-carboxy-5-thiocarboxylic acid mononucleotide
• C00250 Pyridoxal
• C00627 Pyridoxine phosphate
• C00022 Pyruvate
• C22150 Reduced [2Fe-2S] ferredoxin
• C01080 Reduced coenzyme F420
• C02745 Reduced flavodoxin
• C22336 Reduced hydrogenase
• C00376 Retinal
• C00046 RNA
• C04425 S-Adenosyl-4-methylthio-2-oxobutanoate
• C00021 S-Adenosyl-L-homocysteine
• C00019 S-Adenosyl-L-methionine
• C00805 Salicylate
• C05382 Sedoheptulose 7-phosphate
• C06718 S-Formylmycothiol
• C03431 S-Inosyl-L-homocysteine
• C05778 Sirohydrochlorin
• C22360 S-methyl-1-thio-D-ribulose 5-phosphate
• C22359 S-Methyl-1-thio-D-xylulose 5-phosphate
• C00623 sn-Glycerol 1-phosphate
• C00093 sn-Glycerol 3-phosphate
• C08250 Sophorose
• C03539 S-Ribosyl-L-homocysteine
• C05824 S-Sulfo-L-cysteine
• C03641 Sterol 3-beta-D-glucoside
• C01138 Streptomycin 6-phosphate
• C00059 Sulfate
• C02084 Tetrathionate
• C03541 THF-polyglutamate
• C01081 Thiamin monophosphate
• C00378 Thiamine
• C15814 Thiocarboxy-[sulfur-carrier protein]
• C01755 Thiocyanate
• C00145 Thiol
• C00343 Thioredoxin disulfide
• C20369 trans,octacis-Decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose
• C00448 trans,trans-Farnesyl diphosphate
• C00422 Triacylglycerol
• C00066 tRNA
• C04728 tRNA containing 5-[(methylamino)methyl]-2-thiouridylate
• C19080 tRNA with a 3′ CC end
• C19085 tRNA with a 3′ CCA end
• C01635 tRNA(Ala)
• C01642 tRNA(Gly)
• C01645 tRNA(Leu)
• C00390 Ubiquinol
• C00015 UDP
• C19725 UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate
• C19745 UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronate
• C19823 UDP-2-acetamido-2,6-dideoxy-beta-L-arabino-hexos-4-ulose
• C20395 UDP-2-acetamido-2-deoxy-alpha-D-ribo-hex-3-uluronate
• C20849 UDP-2-acetamido-3-dehydro-2-deoxy-alpha-D-glucopyranose
• C04613 UDP-2-acetamido-4-dehydro-2,6-dideoxyglucose
• C03733 UDP-alpha-D-galactofuranose
• C00052 UDP-alpha-D-galactose
• C00190 UDP-D-xylose
• C00167 UDP-glucuronate
• C04702 UDPMurNAc(oyl-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala)
• C20357 UDP-N,N’-diacetylbacillosamine
• C04631 UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine
• C00043 UDP-N-acetyl-alpha-D-glucosamine
• C22053 UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate
• C00203 UDP-N-acetyl-D-galactosamine
• C01212 UDP-N-acetylmuramoyl-L-alanine
• C00692 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
• C00105 UMP
• C00106 Uracil
• C05326 Uridylyl-[protein-PII]
• C00001 Water
• C00385 Xanthine
• C00655 Xanthosine 5′-phosphate

For Metabolite Substrate/Consumers

• C05366 (+)-Pinoresinol
• C04411 (2R,3S)-3-Isopropylmalate
• C06326 (2S)-2-{[1-(R)-Carboxyethyl]amino}pentanoate
• C04236 (2S)-2-Isopropyl-3-oxosuccinate
• C04593 (2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylate
• C01142 (3S)-3,6-Diaminohexanoate
• C01186 (3S,5S)-3,5-Diaminohexanoate
• C05786 (3Z)-Phycocyanobilin
• C20485 (4S)-4-Hydroxy-2-oxoglutarate
• C20954 (5-Formylfuran-3-yl)methyl phosphate
• C04856 (6S)-6beta-Hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide
• C04899 (6S)-6beta-Hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate
• C02214 (E)-Glutaconate
• C22385 (L-Cysteinyl)adenylate
• C03195 (R)-10-Hydroxystearate
• C04272 (R)-2,3-Dihydroxy-3-methylbutanoate
• C01087 (R)-2-Hydroxyglutarate
• C02612 (R)-2-Methylmalate
• C04352 (R)-4′-Phosphopantothenoyl-L-cysteine
• C00810 (R)-Acetoin
• C16241 (R)-Lipoate
• C02912 (R)-Propane-1,2-diol
• C03044 (R,R)-Butane-2,3-diol
• C00898 (R,R)-Tartaric acid
• C02103 (S)-2-Haloacid
• C15565 (S)-2-Hydroxyacid
• C11499 (S)-3-Sulfolactate
• C00337 (S)-Dihydroorotate
• C02917 (S)-Propane-1,2-diol
• C07281 [eIF5A-precursor]-lysine
• C15811 [Enzyme]-cysteine
• C15812 [Enzyme]-S-sulfanylcysteine
• C22154 [Fe-S] cluster scaffold protein carrying a [4Fe-4S]2+ cluster
• C01281 [L-Glutamate:ammonia ligase (ADP-forming)]
• C16240 [Lipoyl-carrier protein]-L-lysine
• C21179 [Prokaryotic ubiquitin-like protein]-L-glutamine
• C02743 [Protein]-L-cysteine
• C19803 [Protein]-L-threonine
• C16236 [Protein]-N6-(octanoyl)-L-lysine
• C01242 [Protein]-S8-aminomethyldihydrolipoyllysine
• C21440 [Protein]-S-sulfanyl-L-cysteine
• C05250 [Protein-PII]
• C21879 1-(5-O-Phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate
• C04751 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate
• C02739 1-(5-Phospho-D-ribosyl)-ATP
• C04823 1-(5′-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole
• C04677 1-(5′-Phosphoribosyl)-5-amino-4-imidazolecarboxamide
• C02490 1,2-beta-D-Glucan
• C21335 1,2-beta-Oligomannan
• C06364 1,2-Diacyl-3-alpha-D-glucosyl-sn-glycerol
• C00641 1,2-Diacyl-sn-glycerol
• C19776 1,2-Diacyl-sn-glycerol 3-diphosphate
• C17207 1,4-beta-D-Mannooligosaccharide
• C16538 1,5-Anhydro-D-mannitol
• C19769 1,6-Anhydro-N-acetyl-beta-muramate
• C00234 10-Formyltetrahydrofolate
• C00681 1-Acyl-sn-glycerol 3-phosphate
• C01234 1-Aminocyclopropane-1-carboxylate
• C11811 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate
• C19703 1-O-[2-(L-Cysteinamido)-2-deoxy-alpha-D-glucopyranosyl]-1D-myo-inositol
• C01194 1-Phosphatidyl-D-myo-inositol
• C04637 1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate
• C20247 2-(2-Carboxy-4-methylthiazol-5-yl)ethyl phosphate
• C19771 2′-(5-Triphosphoribosyl)-3′-dephospho-CoA
• C04640 2-(Formamido)-N1-(5′-phosphoribosyl)acetamidine
• C03972 2,3,4,5-Tetrahydrodipicolinate
• C01159 2,3-Bisphospho-D-glycerate
• C01240 2′,3′-Cyclic nucleotide
• C04039 2,3-Dihydroxy-3-methylbutanoate
• C20246 2-[(2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
• C21895 2-Acetylphloroglucinol
• C17234 2-Aminobut-2-enoate
• C22039 2-Carboxy-1,4-naphthoquinone
• C11434 2-C-Methyl-D-erythritol 4-phosphate
• C04442 2-Dehydro-3-deoxy-6-phospho-D-gluconate
• C04691 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
• C03826 2-Dehydro-3-deoxy-D-xylonate
• C19969 2-Hydroxy-dATP
• C05123 2-Hydroxyethanesulfonate
• C06451 2-Hydroxyethylphosphonate
• C20905 2-Iminobutanoate
• C20904 2-Iminopropanoate
• C02631 2-Isopropylmaleate
• C19858 2-Methoxy-6-all-trans-polyprenyl-1,4-benzoquinol
• C15882 2-Methyl-6-phytylquinol
• C17570 2-Methyl-6-solanyl-1,4-benzoquinol
• C21609 2-O-(6-O-Acyl-alpha-D-mannosyl)-1-phosphatidyl-1D-myo-inositol
• C19791 2-O-(alpha-D-Glucopyranosyl)-3-phospho-D-glycerate
• C00026 2-Oxoglutarate
• C11436 2-Phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol
• C00631 2-Phospho-D-glycerate
• C00988 2-Phosphoglycolate
• C13309 2-Phytyl-1,4-naphthoquinone
• C20772 3-[(1-Carboxyvinyl)oxy]benzoate
• C11638 3-Amino-2-oxopropyl phosphate
• C04287 3D-3,5/4-Trihydroxycyclohexane-1,2-dione
• C00944 3-Dehydroquinate
• C21383 3-Deoxy-D-glycero-D-galacto-non-2-ulopyranosonate 9-phosphate
• C02514 3-Fumarylpyruvate
• C00141 3-Methyl-2-oxobutanoic acid
• C02939 3-Methylbutanoyl-CoA
• C22131 3”-O-Acetyl-ADP-D-ribose
• C02940 3-Oxo-5alpha-steroid
• C01876 3-Oxosteroid
• C00197 3-Phospho-D-glycerate
• C02798 3-Phosphonopyruvate
• C02508 3′-Ribonucleotide
• C22312 3-Sulfanylpropanoate
• C06118 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
• C20559 4-(beta-D-Ribofuranosyl)aniline 5′-phosphate
• C11435 4-(Cytidine 5′-diphospho)-2-C-methyl-D-erythritol
• C04556 4-Amino-2-methyl-5-(phosphooxymethyl)pyrimidine
• C20267 4-Amino-5-aminomethyl-2-methylpyrimidine
• C01279 4-Amino-5-hydroxymethyl-2-methylpyrimidine
• C04752 4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate
• C05848 4-Hydroxy-3-polyprenylbenzoate
• C00989 4-Hydroxybutanoic acid
• C13635 4-Hydroxyphenacyl alcohol
• C04327 4-Methyl-5-(2-phosphooxyethyl)thiazole
• C20236 4-O-beta-D-Mannopyranosyl-D-glucopyranose
• C20749 4-Trimethylammoniobutanoyl-CoA
• C04294 5-(2-Hydroxyethyl)-4-methylthiazole
• C04896 5-(5-Phospho-D-ribosylaminoformimino)-1-(5-phosphoribosyl)-imidazole-4-carboxamide
• C00445 5,10-Methenyltetrahydrofolate
• C00143 5,10-Methylenetetrahydrofolate
• C04454 5-Amino-6-(5′-phospho-D-ribitylamino)uracil
• C00990 5-Aminopentanamide
• C21877 5-Carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate
• C15667 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole
• C05198 5′-Deoxyadenosine
• C16737 5-Deoxy-D-glucuronate
• C00664 5-Formiminotetrahydrofolate
• C00170 5′-Methylthioadenosine
• C01269 5-O-(1-Carboxyvinyl)-3-phosphoshikimate
• C01879 5-Oxoproline
• C03090 5-Phosphoribosylamine
• C04376 5′-Phosphoribosyl-N-formylglycinamide
• C02520 5′-Ribonucleotide
• C20773 6-Amino-6-deoxyfutalosine
• C20737 6-Geranylgeranyl-2-methylbenzene-1,4-diol
• C03847 6-Phospho-beta-D-galactoside
• C15858 7,9,7′,9′-tetracis-Lycopene
• C19759 7,9,9′-tricis-Neurosporene
• C01092 8-Amino-7-oxononanoate
• C19967 8-Oxo-dGTP
• C22234 8-Oxo-GTP
• C15857 9,9′-dicis-zeta-Carotene
• C00033 Acetate
• C00024 Acetyl-CoA
• C00173 Acyl-[acyl-carrier protein]
• C00040 Acyl-CoA
• C06506 Adenosyl cobyrinate a,c diamide
• C01299 Adenylyl-[L-glutamate:ammonia ligase (ADP-forming)]
• C15813 Adenylyl-[sulfur-carrier protein]
• C00008 ADP
• C00498 ADP-glucose
• C00301 ADP-ribose
• C03687 Alkane-alpha,omega-diamine
• C05847 all-trans-Polyprenyl diphosphate
• C04218 alpha,alpha’-Trehalose 6-mycolate
• C00984 alpha-D-Galactose
• C00446 alpha-D-Galactose 1-phosphate
• C06156 alpha-D-Glucosamine 1-phosphate
• C00267 alpha-D-Glucose
• C00668 alpha-D-Glucose 6-phosphate
• C20440 alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate
• C00620 alpha-D-Ribose 1-phosphate
• C20237 alpha-Maltose 1-phosphate
• C03373 Aminoimidazole ribotide
• C00014 Ammonia
• C00020 AMP
• C20144 Androsta-1,4-diene-3,17-dione
• C06249 Apo-[carboxylase]
• C11215 Arsenate ion
• C00002 ATP
• C11242 Bacteriochlorophyll a
• C21336 beta-1,2-Mannobiose
• C21454 beta-1,2-Mannotriose
• C00099 beta-Alanine
• C00602 beta-D-Galactoside
• C00663 beta-D-Glucose 1-phosphate
• C20887 beta-D-Mannosyl-1,4-N-acetyl-D-glucosamine
• C20568 beta-L-Arabinofuranosyl-(1->2)-beta-L-arabinofuranose
• C00486 Bilirubin
• C00120 Biotin
• C00323 Caffeoyl-CoA
• C01563 Carbamate
• C00169 Carbamoyl phosphate
• C01353 Carbonic acid
• C04419 Carboxybiotin-carboxyl-carrier protein
• C20969 Carboxyphosphate
• C00513 CDP-glycerol
• C00185 Cellobiose
• C00916 Cephalosporin C
• C00695 Cholic acid
• C00588 Choline phosphate
• C00919 Choline sulfate
• C04431 cis-4-Carboxymethylenebut-2-en-4-olide
• C00417 cis-Aconitate
• C00158 Citrate
• C00128 CMP-N-acetylneuraminate
• C00011 CO2
• C17401 Cobalt-factor III
• C11540 Cobalt-precorrin 4
• C11545 Cobalt-precorrin 8
• C11538 Cobalt-sirohydrochlorin
• C05773 Cobyrinate
• C19724 Cobyrinate c-monamide
• C04628 Coenzyme B
• C00876 Coenzyme F420
• C03576 Coenzyme M
• C00791 Creatinine
• C00063 CTP
• C00177 Cyanide ion
• C00973 Cyclomaltodextrin
• C00475 Cytidine
• C00380 Cytosine
• C03492 D-4′-Phosphopantothenate
• C00239 dCMP
• C00857 Deamino-NAD+
• C02970 Decaprenol phosphate
• C15494 Decylubiquinone
• C15853 Dehydrospermidine
• C17010 Dehypoxanthine futalosine
• C19847 Demethylmenaquinol
• C21084 Demethylphylloquinol
• C00677 Deoxynucleoside triphosphate
• C00882 Dephospho-CoA
• C04666 D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate
• C00279 D-Erythrose 4-phosphate
• C00095 D-Fructose
• C00354 D-Fructose 1,6-bisphosphate
• C00085 D-Fructose 6-phosphate
• C01113 D-Galactose 6-phosphate
• C00257 D-Gluconic acid
• C00198 D-Glucono-1,5-lactone
• C01236 D-Glucono-1,5-lactone 6-phosphate
• C00031 D-Glucose
• C00103 D-Glucose 1-phosphate
• C00217 D-Glutamate
• C00118 D-Glyceraldehyde 3-phosphate
• C00258 D-Glycerate
• C19880 D-glycero-alpha-D-manno-Heptose 1-phosphate
• C19878 D-glycero-alpha-D-manno-Heptose 7-phosphate
• C00286 dGTP
• C00738 D-Hexose
• C05196 Dihydroflavodoxin
• C00921 Dihydropteroate
• C20522 Dihydrourocanate
• C00235 Dimethylallyl diphosphate
• C00013 Diphosphate
• C01345 dITP
• C04574 di-trans,poly-cis-Undecaprenyl diphosphate
• C17556 di-trans,poly-cis-Undecaprenyl phosphate
• C03189 DL-Glycerol 1-phosphate
• C00476 D-Lyxose
• C00159 D-Mannose
• C00636 D-Mannose 1-phosphate
• C00039 DNA
• C00821 DNA adenine
• C04213 Dolichyl diphosphooligosaccharide
• C00515 D-Ornithine
• C01068 D-Ribitol 5-phosphate
• C00121 D-Ribose
• C00117 D-Ribose 5-phosphate
• C00309 D-Ribulose
• C00199 D-Ribulose 5-phosphate
• C11930 dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose
• C04346 dTDP-4-amino-4,6-dideoxy-D-galactose
• C11922 dTDP-4-oxo-2,6-dideoxy-D-glucose
• C11907 dTDP-4-oxo-6-deoxy-D-glucose
• C00842 dTDP-glucose
• C03319 dTDP-L-rhamnose
• C02143 D-threo-Aldose
• C00459 dTTP
• C00365 dUMP
• C00460 dUTP
• C00231 D-Xylulose 5-phosphate
• C05359 e-
• C15973 Enzyme N6-(dihydrolipoyl)lysine
• C02391 Ester
• C00189 Ethanolamine
• C00016 FAD
• C00125 Ferricytochrome c
• C00924 Ferrocytochrome
• C00126 Ferrocytochrome c
• C19775 Fluoroacetyl-CoA
• C00061 FMN
• C03479 Folinic acid
• C00067 Formaldehyde
• C00488 Formamide
• C00058 Formate
• C00798 Formyl-CoA
• C11439 Formyl-L-methionyl peptide
• C16999 Futalosine
• C00325 GDP-L-fucose
• C00096 GDP-mannose
• C00341 Geranyl diphosphate
• C07292 Glutaredoxin
• C00051 Glutathione
• C05730 Glutathionylspermidine
• C00116 Glycerol
• C00184 Glycerone
• C03120 Glycerophosphodiester
• C02412 Glycyl-tRNA(Gly)
• C00144 GMP
• C00044 GTP
• C01228 Guanosine 3′,5′-bis(diphosphate)
• C00080 H+
• C00288 HCO3-
• C04384 Heparan sulfate alpha-D-glucosaminide
• C00205 hn
• C06250 Holo-[carboxylase]
• C06399 Hydrogenobyrinate
• C00530 Hydroquinone
• C00168 Hydroxypyruvate
• C22226 Icosanoyl-[(phenol)carboxyphthiodiolenone synthase]
• C00130 IMP
• C00331 Indolepyruvate
• C00885 Isochorismate
• C00311 Isocitrate
• C17658 Isolithocholate
• C05557 Isopenicillin N
• C00129 Isopentenyl diphosphate
• C00081 ITP
• C00304 Kanamycin
• C03508 L-2-Amino-3-oxobutanoic acid
• C00041 L-Alanine
• C20957 L-Alanyl-D-glutamate
• C20925 L-Alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate
• C05519 L-Allothreonine
• C00259 L-Arabinose
• C16739 L-Arginyl-protein
• C00152 L-Asparagine
• C00049 L-Aspartate
• C00441 L-Aspartate 4-semialdehyde
• C21458 L-Aspartyl-protein
• C06251 Lauroyl-KDO2-lipid IV(A)
• C00318 L-Carnitine
• C00327 L-Citrulline
• C00097 L-Cysteine
• C02882 L-Cysteine-S-conjugate
• C01720 L-Fuconate
• C00025 L-Glutamate
• C01165 L-Glutamate 5-semialdehyde
• C00064 L-Glutamine
• C02986 L-Glutaminyl-peptide
• C21456 L-Glutamyl-protein
• C00860 L-Histidinol
• C01100 L-Histidinol phosphate
• C00263 L-Homoserine
• C00770 L-Idonate
• C16238 Lipoyl-AMP
• C02051 Lipoylprotein
• C00666 LL-2,6-Diaminoheptanedioate
• C00123 L-Leucine
• C02047 L-Leucyl-tRNA
• C00047 L-Lysine
• C21388 L-Lysyl-protein
• C00073 L-Methionine
• C00638 Long-chain fatty acid
• C00077 L-Ornithine
• C00079 L-Phenylalanine
• C00148 L-Proline
• C00508 L-Ribulose
• C05688 L-Selenocysteine
• C00065 L-Serine
• C00188 L-Threonine
• C12147 L-Threonine O-3-phosphate
• C20641 L-Threonylcarbamoyladenylate
• C00183 L-Valine
• C03516 Magnesium protoporphyrin
• C00083 Malonyl-CoA
• C04566 Membrane-derived-oligosaccharide D-glucose
• C00409 Methanethiol
• C17530 Methyl acetate
• C03620 Monocarboxylic acid amide
• C15585 myo-Inositol phosphate
• C15854 N-(4-Aminobutylidene)-[eIF5A-precursor]-lysine
• C04916 N-(5′-Phospho-D-1′-ribulosylformimino)-5-amino-1-(5”-phospho-D-ribosyl)-4-imidazolecarboxamide
• C03406 N-(L-Arginino)succinate
• C20418 N,N’-Diacetyllegionaminate
• C22293 N4-Acetylcytidine
• C21009 N4-Aminopropylspermidine
• C21785 N5-Phospho-L-glutamine
• C03794 N6-(1,2-Dicarboxyethyl)-AMP
• C04501 N-Acetyl-alpha-D-glucosamine 1-phosphate
• C00140 N-Acetyl-D-glucosamine
• C00357 N-Acetyl-D-glucosamine 6-phosphate
• C00645 N-Acetyl-D-mannosamine
• C00624 N-Acetyl-L-glutamate
• C01250 N-Acetyl-L-glutamate 5-semialdehyde
• C03708 N-Acetyl-O-acetylneuraminate
• C00437 N-Acetylornithine
• C03000 N-Acyl-D-glucosamine
• C00625 N-Acyl-D-mannosamine
• C00003 NAD+
• C00004 NADH
• C00006 NADP+
• C00005 NADPH
• C15586 N-D-Ribosylpurine
• C21769 Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide
• C00455 Nicotinamide D-ribonucleotide
• C00244 Nitrate
• C00533 Nitric oxide
• C00697 Nitrogen
• C00887 Nitrous oxide
• C03880 N-Substituted aminoacyl-tRNA
• C04421 N-Succinyl-LL-2,6-diaminoheptanedioate
• C01075 N-Sulfo-D-glucosamine
• C21158 Nucleoside 3′,5′-bisphosphate
• C00201 Nucleoside triphosphate
• C01077 O-Acetyl-L-homoserine
• C00979 O-Acetyl-L-serine
• C05752 Octanoyl-[acp]
• C06055 O-Phospho-4-hydroxy-L-threonine
• C01102 O-Phospho-L-homoserine
• C01005 O-Phospho-L-serine
• C01103 Orotidine 5′-phosphate
• C00009 Orthophosphate
• C01118 O-Succinyl-L-homoserine
• C00209 Oxalate
• C00036 Oxaloacetate
• C00313 Oxalyl-CoA
• C22151 Oxidized [2Fe-2S] ferredoxin
• C02869 Oxidized flavodoxin
• C22335 Oxidized hydrogenase
• C01134 Pantetheine 4′-phosphate
• C00864 Pantothenate
• C00472 p-Benzoquinone
• C00395 Penicillin
• C03798 Peptidylproline (omega=180)
• C07086 Phenylacetic acid
• C00416 Phosphatidate
• C00350 Phosphatidylethanolamine
• C00344 Phosphatidylglycerol
• C03892 Phosphatidylglycerophosphate
• C01241 Phosphatidyl-N-methylethanolamine
• C00074 Phosphoenolpyruvate
• C02741 Phosphoribosyl-AMP
• C05427 Phytyl diphosphate
• C00653 Poly(ribitol phosphate)
• C00404 Polyphosphate
• C19692 Polysulfide
• C02463 Precorrin 2
• C06406 Precorrin 3B
• C06407 Precorrin 4
• C06319 Precorrin 6Y
• C06408 Precorrin 8X
• C18239 Precursor Z
• C00254 Prephenate
• C03428 Presqualene diphosphate
• C21177 Prokaryotic ubiquitin-like protein
• C01845 Propan-2-ol
• C00017 Protein
• C00615 Protein histidine
• C02188 Protein lysine
• C04261 Protein N(pi)-phospho-L-histidine
• C20743 Protein N6-acetyl-L-lysine
• C01167 Protein tyrosine phosphate
• C02880 Protochlorophyllide
• C02067 Pseudouridine
• C21851 Pyridinium-3,5-biscarboxylic acid mononucleotide
• C21878 Pyridinium-3-carboxy-5-thiocarboxylic acid mononucleotide
• C00250 Pyridoxal
• C00647 Pyridoxamine phosphate
• C00314 Pyridoxine
• C00627 Pyridoxine phosphate
• C00022 Pyruvate
• C15602 Quinone
• C00030 Reduced acceptor
• C01080 Reduced coenzyme F420
• C00138 Reduced ferredoxin
• C01847 Reduced FMN
• C00473 Retinol
• C00255 Riboflavin
• C03802 Ribonucleoside triphosphate
• C00046 RNA
• C05729 R-S-Cysteinylglycine
• C18235 S-(Hydroxymethyl)mycothiol
• C00019 S-Adenosyl-L-methionine
• C06153 scyllo-Inositol
• C00447 Sedoheptulose 1,7-bisphosphate
• C05382 Sedoheptulose 7-phosphate
• C00493 Shikimate
• C00315 Spermidine
• C03539 S-Ribosyl-L-homocysteine
• C00370 Sterol
• C00232 Succinate semialdehyde
• C00089 Sucrose
• C06125 Sulfatide
• C20829 Sulfoquinovose
• C05761 Tetradecanoyl-[acp]
• C03541 THF-polyglutamate
• C00378 Thiamine
• C00342 Thioredoxin
• C00214 Thymidine
• C20370 trans,octacis-Decaprenylphospho-beta-D-arabinofuranose
• C20368 trans,octacis-Decaprenylphospho-beta-D-ribofuranose
• C20420 tritrans,heptacis-Undecaprenyl phosphate
• C17324 tRNA adenine
• C11478 tRNA containing 5-(aminomethyl)-2-thiouridine
• C02211 tRNA precursor
• C00868 tRNA uridine
• C19080 tRNA with a 3′ CC end
• C19078 tRNA with a 3′ cytidine
• C01635 tRNA(Ala)
• C01636 tRNA(Arg)
• C01639 tRNA(Cys)
• C01641 tRNA(Glu)
• C01642 tRNA(Gly)
• C01643 tRNA(His)
• C01645 tRNA(Leu)
• C01646 tRNA(Lys)
• C01647 tRNA(Met)
• C01648 tRNA(Phe)
• C01649 tRNA(Pro)
• C01650 tRNA(Ser)
• C01651 tRNA(Thr)
• C01652 tRNA(Trp)
• C00787 tRNA(Tyr)
• C01653 tRNA(Val)
• C00399 Ubiquinone
• C19725 UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate
• C20359 UDP-2-acetamido-3-amino-2,3-dideoxy-alpha-D-glucuronate
• C04630 UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-D-glucose
• C19961 UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine
• C00052 UDP-alpha-D-galactose
• C00029 UDP-glucose
• C00167 UDP-glucuronate
• C20357 UDP-N,N’-diacetylbacillosamine
• C04573 UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate
• C00043 UDP-N-acetyl-alpha-D-glucosamine
• C22053 UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate
• C00203 UDP-N-acetyl-D-galactosamine
• C01050 UDP-N-acetylmuramate
• C01212 UDP-N-acetylmuramoyl-L-alanine
• C00692 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
• C05892 UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine
• C00105 UMP
• C01968 Undecaprenol
• C05893 Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine
• C00086 Urea
• C01051 Uroporphyrinogen III
• C00075 UTP
• C00001 Water
• C00655 Xanthosine 5′-phosphate
• C00700 XTP
• C00379 Xylitol

This post deals with lab results that can not be uploaded for anyone of dozens of reasons. the current list is shown below. I am going to do a walkthru in 3 manners for the latest addition SynLab (EU):

• Written Description
• Video using a PC

Test Name	Bacteria Reported
All Bacteria [Family] Reported	128 Bacteria
All Bacteria [Genus] Reported	720 Bacteria
All Taxonomies from tests	178 Bacteria
Biomefx	79 Bacteria
Bioscreen (cfu/gm)	30 Bacteria
Biovis Microbiome Plus (cfu/g)	40 Bacteria
Chuckling Goat	40 Bacteria
DayTwo	76 Bacteria
Diagnostic Solution GI-Map (cfu/gm)	72 Bacteria
Estudio de Disbiosis: Intestinal + Parasitos	13 Bacteria
GanzImmun Diagnostic A6 (cfu/gm)	76 Bacteria
GanzImmun Diagnostics AG Befundbericht	25 Bacteria
Genova Gi Effects (cfu/g)	69 Bacteria
Genova Parasitology (cfu/g)	7 Bacteria
GI EcologiX (Invivo)	55 Bacteria
GI360 Stool (UK)	66 Bacteria
Gut Zoomer (vibrant-wellness)	152 Bacteria
HealthPath	60 Bacteria
InVitaLab (cfu/gm)	23 Bacteria
Kyber Kompakt (cfu/g)	11 Bacteria
Laboratorio Teletest	202 Bacteria
Medivere Mikrobiom Plus Stuhlanalyse	55 Bacteria
Medivere: Darm Mikrobiom Stuhltest (16s limited)	16 Bacteria
Medivere: Darn Magen Diagnostik (16s Limited)	16 Bacteria
Medivere: Gesundsheitscheck Darm (16s Limited)	17 Bacteria
Metagenomics Stool (De Meirleir) (16s Limited)	53 Bacteria
Microbiome Healthpath Maxi	73 Bacteria
MyBiota (Austria)	133 Bacteria
Nordic Laboratories	56 Bacteria
NutriPATH	51 Bacteria
Randox Health	33 Bacteria
Smart Gut (16s – Limited Taxonomy)	23 Bacteria
SynLab (EU)	111 Bacteria
Tarmkollen Mega	50 Bacteria
TinyHealth	140 Bacteria
Verisana (cfu/ml) aka (kbe/ml)	11 Bacteria
Viome (Latest Reports Fail to provide ANY measurements)	30 Bacteria

Written Description

The usual best practice is to PRINT the report from the lab and have a pen handy.

• First step is to go thru and circle the high and low.

• For High, if you are more than DOUBLE the high of the range, put 2 up arrow
• For Low, if you are less than HALF the high of the range, put 2 up arrow

The next step can become a little confusing because the same bacteria may have multiple names – your lab uses one, Microbiome Prescription uses another name. We use the standardized names from the NCBI Taxonomy Browser because those names are used by most labs.

To help resolve this issue, we often list the bacteria in the same sequence as on the report.

• Some Reports will list one bacteria at many places which can add to confusion
• Some bacteria do not have matches…
  • CAG names are produced by an alternative naming schema that do not map to any NCBI Ids
  • Often strains are given, since they do not precisely match, we ignore them and go with the species or genus instead (“closest match”)
  • For some genus, the alternative schema breaks things down into _A, _B, _C, _D subgroups. We ignore those
  • Since we are entering ONLY abnormal, then use an that are abnormal when there are many to choose from!

We also give some of the alternative names to the right side. If it is a 2 part name, the second part is usually key to making a match

Next we indicate whether the lab says too high or too low. If normal, do nothing. This is made easier if you have a printed copy that has been marked up.

Once you finished entering the data, fill in the bottom. and then clock Do Analysis. You do not need to enter any emails if you wish, but if you want to explore options later, it saves having to re-enter the data.

The Do Analysis will take you to a page to select what type of modifiers you want, etc.

Video using a PC

This is a long video (40 minutes) that does the entire long test results.

We have two self reported symptoms with sufficient samples to explore associations:

• Comorbid: Histamine or Mast Cell issues
• Official Diagnosis: Mast Cell Dysfunction

I have done simplified tables below. One item that was very interesting is that some Bifidobacterium was too high and others too low. Of the four low bacteria, only Bifidobacterium breve is available commercially. Low Lactobacillus was not reported anywhere and high Lactobacillales is reported

• Too High
  • Bifidobacteriaceae
  • Bifidobacteriales
  • Bifidobacterium
  • Bifidobacterium adolescentis
  • Bifidobacterium adolescentis JCM 15918
  • Bifidobacterium angulatum
  • Bifidobacterium gallicum
• Too Low
  • Bifidobacterium breve
  • Bifidobacterium catenulatum PV20-2
  • Bifidobacterium catenulatum subsp. kashiwanohense
  • Bifidobacterium cuniculi

Everything below is P < 0.005 (or 1 in 200 of happening at random).

Official Diagnosis: Mast Cell Dysfunction

Biomesight

Bacteria	Rank	Shift
Anaerofustis	genus	Too High
Anaerofustis stercorihominis	species	Too High
Luteibacter	genus	Too Low
Luteibacter anthropi	species	Too Low

Ombre

Bacteria	Rank	Shift
Actinomycetes incertae sedis	no rank	Too High
Comamonadaceae	family	Too High
Deinococci	class	Too High
Deinococcota	phylum	Too High
Desulfocella	genus	Too High
Desulfocella halophila	species	Too High
Emticicia	genus	Too High
Hungateiclostridiaceae	family	Too High
Hungateiclostridium	genus	Too High
Limosilactobacillus	genus	Too High
Limosilactobacillus fermentum	species	Too High
Listeria	genus	Too High
Listeriaceae	family	Too High
Methylococcaceae	family	Too High
Methylococcales	order	Too High
Microbacter	genus	Too High
Neisseriaceae	family	Too High
Neisseriales	order	Too High
Oscillatoriales incertae sedis	no rank	Too High
Paracoccaceae	family	Too High
Pseudoscillatoria	genus	Too High
Pseudoscillatoria coralii	species	Too High
Rickettsia	genus	Too High
Slackia heliotrinireducens	species	Too High
Sphingobacterium	genus	Too High
Staphylococcus	genus	Too High
unclassified Burkholderiales	family	Too High
unclassified Clostridiales	family	Too High
Varibaculum	genus	Too High

Comorbid: Histamine or Mast Cell issues

We have a lot more annotated samples on this self-reported symptoms. There is fuzziness between a pure histamine issue and a mast cell issue

Ombre

Bacteria	Rank	Shift
Absiella tortuosum	species	Too High
Actinomycetes incertae sedis	no rank	Too High
Actinopolysporales	order	Too High
Agaribacter	genus	Too High
Agaribacter marinus	species	Too High
Anaeromicropila	genus	Too High
Anaeromicropila populeti	species	Too High
Blastocatellia	class	Too High
Cerasicoccus frondis	species	Too High
Clostridium grantii	species	Too High
Comamonadaceae	family	Too High
Cryomorphaceae	family	Too High
Deinococci	class	Too High
Deinococcota	phylum	Too High
Desulfitobacteriaceae	family	Too High
Desulfitobacterium	genus	Too High
Desulfobacteriaceae	family	Too High
Desulfocella	genus	Too High
Desulfocella halophila	species	Too High
Desulfofarcimen acetoxidans	species	Too High
Desulfosporosinus	genus	Too High
Desulfuromonadaceae	family	Too High
Desulfuromonadia	class	Too High
Emticicia	genus	Too High
Fusibacter	genus	Too High
Gammaproteobacteria incertae sedis	no rank	Too High
Halopolyspora	genus	Too High
Halopolyspora alba	species	Too High
Holdemania massiliensis	species	Too High
Hydrogenibacillus	genus	Too High
Hydrogenibacillus schlegelii	species	Too High
Limosilactobacillus	genus	Too High
Limosilactobacillus fermentum	species	Too High
Listeria	genus	Too High
Listeriaceae	family	Too High
Mesomycoplasma conjunctivae	species	Too High
Methylococcaceae	family	Too High
Microbacter	genus	Too High
Microbacter margulisiae	species	Too High
Mzabimycetaceae	family	Too High
Neisseriaceae	family	Too High
Neisseriales	order	Too High
Nostocales	order	Too High
Odoribacter laneus	species	Too High
Oscillatoriales incertae sedis	no rank	Too High
Oscillibacter valericigenes	species	Too High
Paracoccaceae	family	Too High
Parasporobacterium	genus	Too High
Pedobacter	genus	Too High
Planctomycetales	order	Too High
Planctomycetia	class	Too High
Planctomycetota	phylum	Too High
Pontibacillus	genus	Too High
Pontibacillus halophilus	species	Too High
Porphyromonas somerae	species	Too High
Propioniferax	genus	Too High
Propioniferax innocua	species	Too High
Proteinivorax tanatarense	species	Too High
Pseudoramibacter	genus	Too High
Pseudoramibacter alactolyticus	species	Too High
Pseudorhodobacter	genus	Too High
Pseudoscillatoria	genus	Too High
Pseudoscillatoria coralii	species	Too High
Rhodocyclaceae	family	Too High
Rhodocyclales	order	Too High
Rickettsia	genus	Too High
Rickettsiaceae	family	Too High
Rickettsiales	order	Too High
Rickettsieae	tribe	Too High
Saccharofermentans	genus	Too High
Saccharofermentans acetigenes	species	Too High
Sedimentibacter	genus	Too High
Sphingobacterium	genus	Too High
spotted fever group	species group	Too High
Stackebrandtia nassauensis	species	Too High
Stomatobaculum	genus	Too High
Texcoconibacillus	genus	Too High
Texcoconibacillus texcoconensis	species	Too High
Thiohalobacter	genus	Too High
Thiohalobacter thiocyanaticus	species	Too High
Thiohalobacteraceae	family	Too High
Thiohalobacterales	order	Too High
Thiohalorhabdaceae	family	Too High
Thiohalorhabdales	order	Too High
Verrucomicrobiaceae	family	Too High
Weeksellaceae	family	Too High

Biomesight

Bacteria	Rank	Shift
Acidaminococcus	genus	Too Low
Acidaminococcus fermentans	species	Too Low
Actinomycetes	class	Too High
Actinomycetota	phylum	Too High
Amedibacillus	genus	Too High
Amedibacillus dolichus	species	Too High
Anaerobranca	genus	Too High
Anaerobranca zavarzinii	species	Too High
Anaerolinea	genus	Too High
Anaerolinea thermolimosa	species	Too High
Anaerolineaceae	family	Too High
Anaerolineales	order	Too High
Anaerotruncus	genus	Too Low
Anaerotruncus colihominis	species	Too Low
Archaea	superkingdom	Too Low
Atopobium fossor	species	Too Low
Azoarcus	genus	Too High
Bacteroidaceae	family	Too Low
Bacteroides	genus	Too Low
Bacteroides acidifaciens	species	Too Low
Bacteroides cellulosilyticus	species	Too Low
Bacteroides fluxus	species	Too Low
Bacteroides uniformis	species	Too Low
Bifidobacteriaceae	family	Too High
Bifidobacteriales	order	Too High
Bifidobacterium	genus	Too High
Bifidobacterium adolescentis	species	Too High
Bifidobacterium adolescentis JCM 15918	strain	Too High
Bifidobacterium angulatum	species	Too High
Bifidobacterium breve	species	Too Low
Bifidobacterium catenulatum PV20-2	strain	Too Low
Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	Too Low
Bifidobacterium cuniculi	species	Too Low
Bifidobacterium gallicum	species	Too High
Bilophila	genus	Too Low
Bilophila wadsworthia	species	Too Low
Blautia	genus	Too Low
Caloramator mitchellensis	species	Too High
Candidatus Tammella caduceiae	species	Too High
Catenibacterium	genus	Too High
Catenibacterium mitsuokai	species	Too High
Cetobacterium	genus	Too High
Chloroflexota	phylum	Too High
Coprococcus	genus	Too High
Coprococcus eutactus	species	Too High
Coraliomargarita	genus	Too High
Coraliomargarita	genus	Too Low
Coraliomargarita akajimensis	species	Too High
Coraliomargarita akajimensis	species	Too Low
Coraliomargaritaceae	family	Too High
Coraliomargaritaceae	family	Too Low
Deferribacter	genus	Too High
Deferribacter autotrophicus	species	Too High
Deferribacteraceae	family	Too High
Deferribacterales	order	Too High
Deferribacteres	class	Too High
Deferribacterota	phylum	Too High
Desulfitobacterium	genus	Too Low
Desulfomonilaceae	family	Too High
Desulfomonilales	order	Too High
Desulfomonilia	class	Too High
Desulforamulus	genus	Too High
Ectothiorhodospira imhoffii	species	Too High
Entomoplasmataceae	family	Too Low
Entomoplasmatales	order	Too Low
Eubacterium limosum	species	Too High
Euryarchaeota	phylum	Too Low
Faecalibacterium	genus	Too High
Fusobacterium nucleatum	species	Too High
Hathewaya	genus	Too Low
Hathewaya histolytica	species	Too Low
Helicobacter	genus	Too High
Helicobacter	genus	Too Low
Helicobacteraceae	family	Too High
Helicobacteraceae	family	Too Low
Holdemanella	genus	Too High
Holdemanella biformis	species	Too High
Holdemania	genus	Too Low
Hoylesella loescheii	species	Too High
Hyphomicrobiales	order	Too High
Hyphomicrobiales	order	Too Low
Johnsonella	genus	Too Low
Johnsonella ignava	species	Too Low
Lachnobacterium	genus	Too High
Lactobacillales	order	Too High
Lactococcus	genus	Too High
Limosilactobacillus	genus	Too Low
Luteibacter	genus	Too High
Luteibacter anthropi	species	Too High
Lysobacter deserti	species	Too High
Mesoplasma	genus	Too Low
Mesoplasma entomophilum	species	Too Low
Methanobacteria	class	Too Low
Methanobacteriaceae	family	Too Low
Methanobacteriales	order	Too Low
Methanobrevibacter	genus	Too Low
Methanobrevibacter smithii	species	Too Low
Methanomada group	clade	Too Low
Mogibacterium vescum	species	Too High
Mollicutes	class	Too High
Mycobacteriaceae	family	Too High
Mycobacterium	genus	Too High
Mycoplasmatota	phylum	Too High
Myxococcales	order	Too High
Myxococcia	class	Too High
Myxococcota	phylum	Too High
Natranaerobiales	order	Too High
Pedobacter	genus	Too Low
Phascolarctobacterium faecium	species	Too Low
Phocaeicola	genus	Too Low
Phocaeicola massiliensis	species	Too High
Phocaeicola paurosaccharolyticus	species	Too Low
Polyangia	subclass	Too High
Prevotella dentasini	species	Too High
Prevotellaceae	family	Too High
Prosthecobacter	genus	Too High
Proteinivoraceae	family	Too High
Ruminococcus callidus	species	Too High
Schaalia naturae	species	Too High
Segatella	genus	Too High
Segatella copri	species	Too High
Segatella paludivivens	species	Too High
Shewanella upenei	species	Too High
Slackia	genus	Too High
Slackia isoflavoniconvertens	species	Too Low
Sphingobium	genus	Too High
Sutterella stercoricanis	species	Too High
Syntrophales	order	Too High
Syntrophia	class	Too High
Syntrophomonadaceae	family	Too High
Thermus	genus	Too High
Thiothrix ramosa	species	Too High

Bottom Line

The above data will eventually be incorporated into the expert system suggestions on Microbiome Prescription.

The process is very simple, for a condition like ME/CFS, we compute the expected number of samples reporting this bacteria (based on people without Long COVID) and compare it to the actual number seen. This can be used to compute a statistical value called Chi-Square (χ²), This is then used to compute the chance of it happening at random. This is possible because we have over 3600 samples from some labs and thus able to detect things better.

Actual example:

• Tetragenococcus halophilus – Species reported by Biomesight
  • Expected to see 15
  • Actually seen 59
• In other words almost 4x more common than expected. The probability is
  • 1.68054690853052E-30
  • or 1 chance in 600,000,000,000,000,000,000,000,000,000 of happening at random.
• This suggests that we should reduce it to remedy Long COVID [with the other 92 bacteria involved]
  • Bacteria Shifts that are Statistically Significant for ME/CFS

Biomesight and Ombre identifies bacteria using different methodologies so often give different names and amounts. For background on this lack of standardization, see The taxonomy nightmare before Christmas…

The data below is for samples marked with “Official Diagnosis: COVID19 (Long Hauler)”. Only Biomesight had sufficient data to get patterns.

Long COVID appears similar to ME/CFS, so comparing results below to those in this post: Bacteria Shifts that are Statistically Significant for ME/CFS, may provide further insight.

Unlike some conditions shown below, it is not just one bacteria involved but combinations.

• Peptic ulcer disease: Helicobacter pylori
• Tetanus: Clostridium tetani
• Typhoid fever: Salmonella typhi
• Diphtheria: Corynebacterium diphtheriae
• Syphilis: Treponema pallidum
• Cholera: Vibrio cholerae
• Leprosy: Mycobacterium leprae
• Tuberculosis: Mycobacterium tuberculosis
• Sinusitis: Corynebacterium tuberculostearicum

Biomesight Data

We have more data from Biomesight which means better (more) detection of significant bacteria. The data is very different from ME/CFS. We have 16 bacteria too high and 61 bacteria too low. With ME/CFS and the same lab, we have 12 bacteria that are too low and 116 bacteria that are too high.

We have some commonalities

• Bifidobacterium adolescentis is too low for both Long COVID and ME/CFS
• Lactobacillus crispatus is too high
• Another probiotic genus, Lactococcus, is also too high

Tax_Name	Tax_Rank	Expected	Observed	Shift	Probability
50 kb inversion clade	clade	77.3	54	Too Low	0.008002
Acinetobacter antiviralis	species	13.7	24	Too High	0.00524
Acinetobacter johnsonii	species	18.1	30	Too High	0.004944
Actinopolyspora	genus	62.3	35	Too Low	0.001477
Actinopolysporaceae	family	62.3	35	Too Low	0.001477
Actinopolysporales	order	62.3	35	Too Low	0.001477
Aeromonadaceae	family	81.8	57	Too Low	0.006169
Alkalibacterium	genus	112.5	81	Too Low	0.005041
Anaerococcus lactolyticus	species	23.2	38	Too High	0.002205
Anaerococcus prevotii	species	20.1	33	Too High	0.003987
ant, tsetse, mealybug, aphid, etc. endosymbionts	clade	82.7	58	Too Low	0.006624
Bifidobacterium adolescentis	strain	103.5	65	Too Low	0.002509
Chromatium	genus	61.3	34	Too Low	0.00355
Chromatium weissei	species	61.2	34	Too Low	0.00355
Chromobacterium group	no rank	15.3	26	Too High	0.006127
Citrobacter	genus	64.1	41	Too Low	0.003939
Clostridium neonatale	species	13.7	25	Too High	0.002196
Cohnella	genus	108.6	78	Too Low	0.005067
Coraliomargarita	genus	96.4	70	Too Low	0.00718
Coraliomargarita akajimensis	species	96.3	70	Too Low	0.007357
core genistoids	clade	77.3	54	Too Low	0.008002
Corynebacterium striatum	species	16.9	28	Too High	0.006887
Crotalarieae	tribe	77.3	54	Too Low	0.008002
Deferribacteraceae	family	98.2	71	Too Low	0.006129
Deferribacterales	order	98.2	71	Too Low	0.006129
Deferribacteres	class	98.2	71	Too Low	0.006129
Deferribacterota	phylum	98.2	71	Too Low	0.006129
Desulfallaceae	family	148.6	108	Too Low	0.001472
Enterobacter cloacae complex	species group	86.4	60	Too Low	0.004516
Enterobacter hormaechei	species	85.4	57	Too Low	0.002134
Enterobacteriaceae incertae sedis	no rank	82.7	58	Too Low	0.006624
Erysipelothrix inopinata	species	54.2	21	Too Low	4.45E-05
Fabaceae	family	77.3	54	Too Low	0.008002
Fabales	order	77.3	54	Too Low	0.008002
fabids	clade	77.3	54	Too Low	0.008002
genistoids sensu lato	clade	77.3	54	Too Low	0.008002
Granulicella	genus	16.4	29	Too High	0.001841
Granulicella tundricola	species	16.2	29	Too High	0.00148
Hallella bergensis	species	20.1	33	Too High	0.003987
Lactobacillus crispatus	species	26.5	43	Too High	0.001406
Lactococcus	genus	161.5	201	Too High	0.001877
Leptospira	genus	89.5	61	Too Low	0.002559
Leptospira licerasiae	species	89.4	61	Too Low	0.002701
Leptospiraceae	family	89.5	61	Too Low	0.002559
Leptospirales	order	89.5	61	Too Low	0.002559
Lysinibacillus	genus	51.5	32	Too Low	0.006618
Lysinibacillus parviboronicapiens	species	50.4	29	Too Low	0.002564
Macrococcus	genus	118.9	89	Too Low	0.006111
Microbacteriaceae	family	99.5	72	Too Low	0.005912
Moorella group	norank	152.6	188	Too High	0.004132
Oxalobacter	genus	130.9	99	Too Low	0.005356
Oxalobacter vibrioformis	species	94.9	65	Too Low	0.007793
Papilionoideae	subfamily	77.3	54	Too Low	0.008002
Peptoniphilus lacrimalis	species	51.8	72	Too High	0.004884
Piscirickettsiaceae	family	51.5	29	Too Low	0.007262
Psychrobacter	genus	138.9	99	Too Low	0.001332
Psychrobacter glacialis	species	75.1	51	Too Low	0.00545
rosids	clade	77.3	54	Too Low	0.008002
Rothia	genus	77.3	54	Too Low	0.008002
Rothia mucilaginosa	species	64.1	40	Too Low	0.002631
Sporotomaculum	genus	148.6	108	Too Low	0.001472
Sporotomaculum syntrophicum	species	146.7	107	Too Low	0.001751
Streptococcus massiliensis	species	53.6	34	Too Low	0.007353
Syntrophobacteraceae	family	118.3	83	Too Low	0.00291
Tetragenococcus halophilus	species	18.0	59	Too High	3.63E-22
Thiomicrospira	genus	43.7	26	Too Low	0.007396
Tolumonas	genus	80.7	55	Too Low	0.004169
Tolumonas auensis	species	79.9	54	Too Low	0.003748
Trabulsiella	genus	59.1	37	Too Low	0.004074
Vagococcus	genus	99.2	72	Too Low	0.00718
Varibaculum cambriense	species	17.3	30	Too High	0.002302

Bottom Line

My personal view is that this pattern is not unexpected. ME/CFS microbiome is typically after years of the dysbiosis microbiome evolving. With Long COVID, we have the microbiome still trying to stabilize.

• Bif. Adolescentis

And all Lactobacillus and Lactococcus probiotics should be avoided.

The above information will be eventually integrated into Microbiome Prescription suggestions expert system. The purpose is to first identify the bacteria of concern.

The following bacteria were reported by 2 or 3 of the ME/CFS analysis and the same shift seen with Long COVID.

Anaerococcus murdochii	species — sibling high in ME/CFS
Peptoniphilus lacrimalis	species – HIGH EVERYWHERE
Varibaculum	genus – HIGH EVERYWHERE

Varibaculum, particularly Varibaculum cambriense, has been identified as a potential pathogen associated with various human infections, especially in skin and soft tissues²⁶. This anaerobic, gram-positive bacterium was first described in 2003 and has since been isolated from several clinical cases².

A new species, Varibaculum timonense, has been isolated from human stool samples, indicating that the genus Varibaculum may have a broader presence in the human microbiome than previously recognized³.

While Varibaculum species are not yet widely known pathogens, their isolation from various infection sites suggests they may play a more significant role in human health than currently understood. Further research is needed to fully elucidate the pathogenic potential and clinical importance of these bacteria.

The process is very simple, for a condition like Long COVID, we compute the expected number of samples reporting this bacteria (based on people without Long COVID) and compare it to the actual number seen. This can be used to compute a statistical value called Chi-Square (χ²), This is then used to compute the chance of it happening at random. This is possible because we have over 3600 samples from some labs and thus able to detect things better.

Actual example:

• Tetragenococcus halophilus – Species reported by Biomesight
  • Expected to see 15
  • Actually seen 59
• In other words almost 4x more common than expected. The probability is
  • 1.68054690853052E-30
  • or 1 chance in 600,000,000,000,000,000,000,000,000,000 of happening at random.
• This suggests that we should reduce it to remedy Long COVID [with the other 92 bacteria involved]
  • Bacteria Shifts that are Statistically Significant for ME/CFS
  • Bacteria Shifts that are Statistically Significant for Long COVID

Not all symptoms have many bacteria associated

A few examples (using Biomesight data). All samples are P < 0.01 (1 in 1000)

• Myalgia (pain)
  • Mobiluncus — too high
  • Peptoniphilus asaccharolyticus — too high
  • Campylobacter ureolyticus — too high
• Headaches
  • Microbacterium — too high
  • Anaerococcus hydrogenalis — too high
  • Eubacterium limosum — too high
  • Peptoniphilus asaccharolyticus — too high
• Recurrent flu-like symptoms
  • Sphingomonas — too high
  • Chromatium — too high
  • Chromatium weissei — too high
• Excessive adrenaline
  • unclassified Bacteroidetes Order II — too low
  • Bifidobacterium adolescentis — too low. Implies that Bifidobacterium adolescentis probiotics may help
• Difficulty reading
  • Bifidobacterium indicum — too low
• Upset stomach
  • Streptococcus anginosus – too high
  • Viridiplantae (kingdom) – green plants! – too high (how this shows up in results, I will leave to Biomesight to explain)
• Tingling feeling
  • Bifidobacterium indicum – too high
  • Prevotella bivia – too low
• Need to nap during each day
  • Kushneria – too low
  • Prevotella bivia – too low
• Difficulty falling asleep
  • Alkalithermobacter thermoalcaliphilus – too low
  • Paraprevotella xylaniphila – too high
• Absent-mindedness
  • Corynebacterium aurimucosum — too low
  • Streptococcus gordonii — too low
  • Catenibacterium mitsuokai – too low
• Mood swings
  • Glaciecola – too high
• Acne
  • Mogibacterium vescum — too low
  • Listeria — too low
  • Listeria innocua — too low
  • Mogibacterium vescum — too low
• Dry Mouth
  • Prevotella bivia — too low
  • Prevotella disiens — too low
  • Clostridium malenominatum — too low

The reasons that there may be few bacteria associated may originate in symptoms being self-declared and there is a wide variety of actual shifts.