Special Studies Percentage Matches

I have recently changed the display below to show the percentage of matched instead of just the number of bacteria matches (the number will appear if you hover over the link as a tool tip). The numbers may be prone to misinterpretation, hence this technical page.

The candidate bacteria comes from special studies — it is important to note that often these bacteria are rarely seen, so having a 100% match is effectively impossible. We also have the dilemma of a single sample versus a collection of samples.

The rule that I am using is simple, a match must:

  • Have the bacteria (if it is missing, it is not deemed a match)
  • The bacteria count must be either:
    • below the study mean – 3 standard deviations of the mean if the study found it to be a low mean value against the reference population
    • above the study mean + 3 standard deviations of the mean if the study found it to be a high mean value against the reference population

Naively, assuming a normal distribution, the odds of a single match is around 1%, so with 200 items to check, we would expect 1% for a random person.

You should NOT view these as predictive, for example both ME/CFS with IBS and ME/CFS without IBS are on the list with the same value!!! Instead, your existing condition(s) should be used to select only the ones that apply to you. You could arbitrarily do all of the high ones — I do have a concern about that approach, you are creating noise that may make suggestions less effective.

One last item is the quality of the read (i.e. how many bacteria was actually detected in the sample). Since we are dealing with rare bacteria, bacteria (that are actually there) may not be detected and thus you have a lower percentage match. So do not view the percentage as absolute. but relative to others in the sample.

Special Studies: General Fatigue

This is a common symptom for many people. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does. We are not being specific about the type of fatigue. Each person use their own subject definition of fatigue, thus we do not expect strong statistical associations (and do not get it!)

Study Populations:

I include values for Special Studies: General ME/CFS below

SymptomReferenceStudy
General Fatigue1095134
  • Bacteria Detected with z-score > 2.6: found 158 items, highest value was 5.3 (ME/CFS was 6.6)
  • Enzymes Detected with z-score > 2.6: found 410 items, highest value was 6.0 (ME/CFS was 4.5)
  • Compound Detected with z-score > 2.6: found 67 items, highest values was -4/4 (ME/CFS was 3.1)

So we have a weaker bacteria signature but stronger enzymes and compound signature than ME/CFS. Many people marking one will mark the other… so get your sodium chloride crystals out!

Interesting Significant Bacteria

All bacteria found significant had too low levels. The list of those with a z-score over 5 is small. Low Prevotella copri and Escherichia coli which appears on special studies on many co-morbid symptoms. The good news, is that there is work ongoing to produce a prevotella copri probiotic and several Escherichia coli probiotics are available.

We do see a few overgrowth These are seen only in some subsets.

BacteriaReference MeanStudyZ-Score
Lactiplantibacillus pentosus (species)114225.3
Prevotella copri (species)68098218645.2
Gammaproteobacteria (class)1438259445.2
Veillonella (genus)402223245.1
Escherichia coli (species)8291965

Interesting Enzymes

Most enzymes found significant had too low levels. A few were higher (12 of 410), which are listed in a second table below

EnzymeReference MeanStudy MeanZ-Score
[cysteine desulfurase]-S-sulfanyl-L-cysteine:[molybdopterin-synthase sulfur-carrier protein]-Gly-Gly sulfurtransferase (2.8.1.11)540724206
3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate:NAD+ oxidoreductase (1.3.1.87)5971445.5
3-phenylpropanoate,NADH:oxygen oxidoreductase (2,3-hydroxylating) (1.14.12.19)6111485.5
deoxyribocyclobutadipyrimidine pyrimidine-lyase (4.1.99.3)431116685.5
tRNA-uridine65 uracil mutase (5.4.99.26)420117335.4
S-adenosyl-L-methionine:23S rRNA (guanine2069-N7)-methyltransferase (2.1.1.264)585030675.3
propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming) (2.3.3.5)15755015.2
N4-acetylcytidine amidohydrolase (3.5.1.135)308312795.2
ATP:D-tagatose 6-phosphotransferase (2.7.1.101)4151125.1
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming) (4.1.3.30)15244845.1
acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase (2.3.1.15)338514385.1
S-adenosyl-L-methionine:tRNA (cytidine32/uridine32-2′-O)-methyltransferase (2.1.1.200)343713905.1
2-(glutathione-S-yl)-hydroquinone:glutathione oxidoreductase (1.8.5.7)326310995.1
galactitol-1-phosphate:NAD+ oxidoreductase (1.1.1.251)10422925
acetyl-CoA:[elongator tRNAMet]-cytidine34 N4-acetyltransferase (ATP-hydrolysing) (2.3.1.193)343013875
S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase (2.1.1.189)337913855
ATP phosphohydrolase (ABC-type, thiamine-importing) (7.6.2.15)363714545
[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3R-hydroxylating) (1.14.11.47)344814405
7,8-dihydroneopterin 3′-triphosphate diphosphohydrolase (3.6.1.67)371916345
ATP:N-acetyl-D-glucosamine 6-phosphotransferase (2.7.1.59)338313695
Most Significant (all LOW)
EnzymeReference MeanStudy MeanZ-Score
CTP:N,N’-diacetyllegionaminate cytidylyltransferase (2.7.7.82)5956876504-2.9
1-phosphatidyl-1D-myo-inositol:a very-long-chain (2’R)-2′-hydroxy-phytoceramide phosphoinositoltransferase (2.7.1.227)3914450749-2.9
1,5-anhydro-D-mannitol:NADP+ oxidoreductase (1.1.1.292)6501081029-2.9
alginate oligosaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronate-(1->4)-hexananopyranuronate lyase (4.2.2.26)7972599196-2.8
phosphatidylglycerophosphate phosphohydrolase (3.1.3.27)87820105463-2.7
chondroitin-sulfate-ABC endolyase (4.2.2.20)7177388107-2.7
chondroitin-sulfate-ABC exolyase (4.2.2.21)7177388107-2.7
arabinogalactan 4-beta-D-galactanohydrolase (3.2.1.89)107701128121-2.7
cephalosporin-C acetylhydrolase (3.1.1.41)86153104494-2.7
UDP-N-acetyl-alpha-D-glucosamine 4-epimerase (5.1.3.7)83349100761-2.6
N-sulfo-D-glucosamine sulfohydrolase (3.10.1.1)5963473685-2.6
6-alpha-D-glucan 6-glucanohydrolase (3.2.1.11)6403578529-2.6
GDP-alpha-D-mannose:2-O-alpha-D-mannosyl-1-phosphatidyl-1D-myo-inositol 6-alpha-D-mannosyltransferase (configuration-retaining) (2.4.1.346)4374455284-2.6
The enzymes that are in excess.

Interesting Compound

Unlike most of the special studies we have many compounds that are significant. I have listed the high and low in separate tables below. Spot checking most of these found no useful information. For Maltodextrin which becomes  glucose would fit with fatigue — i.e. low sugar being produced.

Of the low items, the following appear to be available as supplements and potentially could help with fatigue

NamesZ-Score
beta-D-Ribofuranose (C16639)4
1,2-Diacyl-3-alpha-D-glucosyl-sn-glycerol (C06364)3.8
Coproporphyrin III (C05770)3.3
Cys-Gly (C01419)3.2
Deoxyinosine (C05512)3.2
UDP-N-acetyl-alpha-D-glucosamine 3′-phosphate (C20245)3.2
Inosine (C00294)3.1
Carboxylate (C00060)3.1
Thymine (C00178)2.9
3-(4-Hydroxyphenyl)pyruvate (C01179)2.9
Acetoacetyl-CoA (C00332)2.8
beta-D-Galactosyl-(1->3)-N-acetyl-D-galactosamine (C07278)2.8
Prokaryotic ubiquitin-like protein (C21177)2.8
dTDP (C00363)2.7
tRNA with a 3′ CCA end (C19085)2.7
Cytosine (C00380)2.7
alpha-D-Aldose 1-phosphate (C00991)2.7
5′-O-Phosphonoadenylyl-(3′->5′)-adenosine (C22092)2.7
Hexadecanoic acid (C00249)2.6
Maltodextrin (C01935)2.6
Hydroquinone (C15603)2.6
Chemical that have low production
NamesZ-Score
beta-D-Ribopyranose (C08353)-4
Chitobiose (C01674)-3.6
Deoxyadenosine (C00559)-3.5
Glutaredoxin (C07292)-3
tRNA(Leu) (C01645)-3
Lacto-N-biose (C06372)-3
alpha-D-Glucosamine 1-phosphate (C06156)-3
Pantetheine 4′-phosphate (C01134)-2.9
UDP-N-acetylmuramate (C01050)-2.9
L-Formylkynurenine (C02700)-2.9
tRNA uridine (C00868)-2.9
(S)-3-Hydroxybutanoyl-CoA (C01144)-2.9
Amino acid (C00045)-2.8
1,2-Diacyl-sn-glycerol (C00641)-2.8
L-Glutamate 5-semialdehyde (C01165)-2.8
Taurine (C00245)-2.8
tRNA with a 3′ cytidine (C19078)-2.8
tRNA precursor (C02211)-2.8
Sucrose (C00089)-2.8
UTP (C00075)-2.8
beta-D-Glucose 1-phosphate (C00663)-2.8
UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine (C05892)-2.7
tRNA(Lys) (C01646)-2.7
L-Threonine (C00188)-2.7
2-Succinylbenzoate (C02730)-2.7
Oxygen (C00007)-2.7
UDP-sugar (C05227)-2.7
Phenyl acetate (C15583)-2.7
Isopentenyl diphosphate (C00129)-2.7
Cyclomaltodextrin (C00973)-2.7
Chemical that have high production

Similarly, items that are too high are likely to be avoided, including the following

  • Sucrose
  • Taurine
  • Threonine

All of these suggestions are theoretical based in the model. Some literature to consider that appears to confirm the above (a.k.a. cross-validation)

Bottom Line

II was not expecting much from this special study. I was pleased to see some suggestions being generated that can be implemented (or soon will be)

In looking at the suggestions below, remember we are using two very different models. Above we use KEGG data to identify what the bacteria are producing (the items going to the farmer’s market). Below, we use what has been reported to influence the population of the bacteria that we are too low in (i.e. “Fertilizer”)

Pro forma Suggestions

Special Study: Poor gut motility

This is a common symptom for many people. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does.

  • “Motility” is a term used to describe the contraction of the muscles that mix and propel contents in the gastrointestinal (GI) tract. [Src] thus it has similarity to constipation (See Special Studies: Constipation)
  • “An excess of intracolonic saturated long-chain fatty acids (SLCFAs) was associated with enhanced bowel motility in NMS rats. Heptadecanoic acid (C17:0) and stearic acid (C18:0), as the most abundant odd- and even-numbered carbon SLCFAs in the colon lumen, can promote rat colonic muscle contraction and increase stool frequency” [2018]

Study Populations:

SymptomReferenceStudy
Poor gut motility117155
  • Bacteria Detected with z-score > 2.6: found 170 items, highest z-score value was 8.8
  • Enzymes Detected with z-score > 2.6: found 336 items, highest z-score value was 6.4
  • Compound Detected with z-score > 2.6: found No items

Interesting Significant Bacteria

All bacteria that was found significant are too low. This is a common pattern for most of the special studies and really challenge the internet myth of the cause being too many bad bacteria. One bacteria really stands out — and there is ongoing work on making this one bacteria, Prevotella copri , available as a probiotics!

BacteriaReference MeanStudyZ-Score
Prevotella copri (species)6456854988.8
Sutterella stercoricanis (species)30984107.5
Prevotella paludivivens (species)144267.1
Prevotella (genus)72220205876.2
Alkalibacterium (genus)102216
Prevotellaceae (family)79801325495.2
Leptospiraceae (family)67245.2
Leptospira (genus)67245.2
Leptospirales (order)67245.2
Leptospira licerasiae (species)67245.2
Ruminiclostridium (genus)10003485.1
Phocaeicola sartorii (species)8073755.1
  • “For example, abundances of LactobacillusPrevotella and Alistipes spp. are significantly decreased in patients with constipation ” [2018]

Interesting Enzymes

Most of the enzymes are too low, however a few are too high which is not the usual pattern seen in other of these special studies.

S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)374013736.4
n/a (3.4.14.13)12702485.9
D-alanine:2-oxoglutarate aminotransferase (2.6.1.21)26879595.9
1-aminocyclopropane-1-carboxylate aminohydrolase (isomerizing) (3.5.99.7)14283375.9
succinyl-CoA:3-oxo-acid CoA-transferase (2.8.3.5)13072915.8
N-acyl-D-amino acid amidohydrolase (3.5.1.81)17773965.8
4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) (1.13.11.27)14462255.6
carotenoid beta-end group lyase (ring-opening) (5.5.1.19)14501345.6
ATP:L-threonine O3-phosphotransferase (2.7.1.177)23204865.6
n/a (3.4.15.6)15853915.6
hydrogen-sulfide:flavocytochrome c oxidoreductase (1.8.2.3)11641085.5
15-cis-phytoene:acceptor oxidoreductase (lycopene-forming) (1.3.99.31)22339025.5
all-trans-zeta-carotene:acceptor oxidoreductase (1.3.99.26)22339025.5
15-cis-phytoene:acceptor oxidoreductase (zeta-carotene-forming) (1.3.99.29)22339025.5
15-cis-phytoene:acceptor oxidoreductase (neurosporene-forming) (1.3.99.28)22339025.5
[SoxY protein]-S-sulfosulfanyl-L-cysteine sulfohydrolase (3.1.6.20)11831065.5
CTP:5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-nonulosonic acid cytidylyltransferase (2.7.7.81)11391195.5
medium-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (1.3.8.7)13003255.4
2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (ring-opening) (5.5.1.2)13321985.3
sulfite:oxygen oxidoreductase (1.8.3.1)11991075.3
alkane,reduced-rubredoxin:oxygen 1-oxidoreductase (1.14.15.3)10871075.3
4-hydroxybenzoate,NADPH:oxygen oxidoreductase (3-hydroxylating) (1.14.13.2)13192035.2
protocatechuate:oxygen 3,4-oxidoreductase (ring-opening) (1.13.11.3)13191995.2
dihydro-NAD(P):oxygen oxidoreductase (H2O2-forming) (1.6.3.5)12901455.2
glutaryl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (decarboxylating) (1.3.8.6)12572585.2
3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming) (6.4.1.4)11142055.1
N-acyl-L-homoserine-lactone amidohydrolase (3.5.1.97)10441265.1
4a-hydroxytetrahydrobiopterin hydro-lyase (6,7-dihydrobiopterin-forming) (4.2.1.96)13142235.1
Too Low Enzymes

Too High Enzymes

EnzymeReference MeanStudy MeanZ-Score
L-leucyl-tRNALeu:[protein] N-terminal L-lysine/L-arginine leucyltransferase (2.3.2.6)130285170931-2.9
polyphosphate phosphohydrolase (3.6.1.11)171217211918-2.8
guanosine-5′-triphosphate-3′-diphosphate 5′-phosphohydrolase (3.6.1.40)171217211918-2.8
1-deoxy-D-xylulose 5-phosphate:thiol sulfurtransferase (2.8.1.10)198195242062-2.7
(R)-2-carboxy-2,5-dihydro-5-oxofuran-2-acetate carboxy-lyase (4,5-dihydro-5-oxofuran-2-acetate-forming) (4.1.1.44)199133242528-2.7
ATP phosphohydrolase (P-type, Ca2+-transporting) (7.2.2.10)234154280063-2.7
acetyl-CoA:maltose O-acetyltransferase (2.3.1.79)206724252634-2.7
3-methylbut-3-en-1-yl-diphosphate:ferredoxin oxidoreductase (1.17.7.4)239452285669-2.7
L-aspartate:tRNAAsp ligase (AMP-forming) (6.1.1.12)244534289637-2.6
5,10-methylenetetrahydrofolate:dUMP C-methyltransferase (2.1.1.45)245078290417-2.6
D-arabinose aldose-ketose-isomerase (5.3.1.3)188214231505-2.6
L-fucose aldose-ketose-isomerase (5.3.1.25)188214231505-2.6
5,6,7,8-tetrahydrofolate:NADP+ oxidoreductase (1.5.1.3)247230291626-2.6

Bottom Line

While poor gut motility is often assumed to be due too many of some bacteria, the evidence suggestions that not enough is the more likely cause. There appears to be no simple model or answer.

Prevotella copri will hopefully be available as a probiotic in a few year. There are two natural sources for P.Copri : Beer and Sauerkraut [2020], which may be an experiment for those that are prone to poor gut motility..

  • “This species is more prevalent in non-Western populations likely due to its association with high fibre low fat diets” [2022]
  • “Across all ethnicities, only coffee consumption was associated with an increased Prevotella relative abundance ” [2022]
  • “Ancient stool samples suggest Westernization leads to P. copri underrepresentation” [2019]
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations [2019]

The real bottom line is changing diet significantly. Consider some Indian style of food as part of supper every day, some examples ready to heat are here.

https://microbiomeprescription.com/Library/CitizenScience

It should be noted that the B-Vitamins below are likely in the avoid list because they are usually provided thru meat in traditional diet.

Proforma Suggestions

Cure Root Caus-icitis

This is a devastating mental infection of many people suffering severe ongoing health issues. The mythology is simple “Fix the root cause, and you will get better!” For acute, send yourself to the hospital, diseases this may be true, but there is another class of conditions where it is false.

Example, you developed rickets and developed skeletal deformities such as:

  • Bowed legs or knock knees
  • Thickened wrists and ankles
  • Breastbone projection.

We know the root cause, not sufficient vitamin D. Will taking vitamin-D correct the skeletal deformities? No. Treatment will slow progression. You have lung cancer because you are a heavy smoker, will stop smoking cure lung cancer? You have Long COVID, ah the cure is to always wear a N95 mask?

Yes There was a Cause likely, but…

For items dealing with the microbiome, the cause starts a microbiome cascade that keeps going onwards. Think of a land slide, things are changed. There are side-effects like impact on fish or even getting into towns. So people start trying to cure the landslide by clearing the river or building a new road or…. and those attempt at curing, could cause more problems.

The best example that is well documented is the Bergen’s Giardia Infection. The root cause was Giardia infection. They eliminated the giardia — but the IBS, ME/CFS issues remained. They very well documented the root cause and dealt with it. No magical recovery.

Going Forward

I view many conditions as being supported (in a few cases totally caused) by the microbiome. Finding the root cause is very very unlikely to impact treatment and the way back to health. Focus on what is contributing to your current state and not ancient history!

I just banned someone called Ross Walter

Why? he has twice attacked me ad hominem (i.e. an attack on the person). I have made no secret that I am a high functioning ASD person (functioning in terms of mathematics), and that I did not learn to speak or form sentences until I was 9 y.o. I know that items like grammar are a great weakness. To attack a person with a recognized disability, for a disability is neither polite nor acceptable.
I apologize if my grammar is not perfect — my blog is not intended to be a literary masterpiece, but to convey data!

Special Study: Intolerance of Extremes of Heat and Cold

Alternative Title: Climate Change and your guts!

This is a common symptom for both ME/CFS and Long COVID. This is reported often in samples uploaded. We examine if the data reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does.

My default view is that this symptom is likely due to vesicular constriction/inflammation or “sticky blood” (which contains many possible coagulation issues). This results in slow blood flow causing issues with transferring heat to and from the body.

  • temperature intolerance is generally placed under dysautonomia
On Change Microbiome Tab

Study Populations:

SymptomReferenceStudy
Intolerance of extremes of heat and cold115954
  • Bacteria Detected with z-score > 2.6: found 247 items, highest value was 8.8
  • Enzymes Detected with z-score > 2.6: found 501 items, highest value was 6.7
  • Compound Detected with z-score > 2.6: found No items

The number of bacteria and enzymes that are significant hints that it is a complex scenario, possibly with different subsets.

Interesting Significant Bacteria

All bacteria found significant had too low levels. The dominant order is Anaeroplasmatales and three significant genus are Holdemanella, Eubacterium, and Escherichia. Every one of the 247 bacteria found significant was LOW.

BacteriaReference MeanStudyZ-Score
Holdemanella biformis (species)33703508.8
Holdemanella (genus)33793508.8
Eubacterium (genus)25075867.8
Lysobacter deserti (species)29116.5
Anaerolineae (class)87355.7
Opitutae (class)163465.5
Puniceicoccaceae (family)158445.5
Legionellales (order)82415.4
Leptospiraceae (family)67225.4
Leptospira (genus)67225.4
Leptospirales (order)67225.4
Leptospira licerasiae (species)67225.4
Bifidobacterium cuniculi (species)79265.3
Lactiplantibacillus pentosus (species)116225.3
Puniceicoccales (order)110375.3
Legionellaceae (family)81415.2
Legionella (genus)81415.2
Anaeroplasmataceae (family)8102205.2
Anaeroplasma (genus)8102205.2
Anaeroplasmatales (order)8102205.2
Chloroflexi (phylum)128555.1
Cerasicoccus arenae (species)537805.1
Caldilineaceae (family)90355.1
Caldilinea (genus)90355.1
Caldilineales (order)90355.1
Caldilinea tarbellica (species)90355.1
Caldilineae (class)90355.1
Escherichia (genus)601613675.1
Cerasicoccus (genus)312605

Interesting Enzymes

Atypical distribution for enzymes in these studies, the number of highs and lows were of the same magnitude. 268 enzymes were low and 233 enzymes were high (see 2nd table) but none above our listing threshold of 5.0.

EnzymeReference MeanStudy MeanZ-Score
(S)-2-hydroxyglutarate:quinone oxidoreductase (1.1.5.13)22143986.7
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming) (4.1.3.30)14443606.3
propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming) (2.3.3.5)14913876.3
propanoate:CoA ligase (AMP-forming) (6.2.1.17)18944836.1
D-galactaro-1,4-lactone lyase (ring-opening) (5.5.1.27)16983935.8
thiosulfate:ferricytochrome-c oxidoreductase (1.8.2.2)13812725.4
gamma-butyrobetainyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (1.3.8.13)14004415.4
glutarate, 2-oxoglutarate:oxygen oxidoreductase ((S)-2-hydroxyglutarate-forming) (1.14.11.64)12992975.4
(E)-4-(trimethylammonio)but-2-enoyl-CoA:L-carnitine CoA-transferase (2.8.3.21)13864405.4
L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming] (4.2.1.149)14443215.4
2-dehydrotetronate isomerase (5.3.1.35)14064825.3
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming] (4.2.1.79)12974395.2
3-phenylpropanoate,NADH:oxygen oxidoreductase (2,3-hydroxylating) (1.14.12.19)5811425.2
1-aminocyclopropane-1-carboxylate aminohydrolase (isomerizing) (3.5.99.7)14314165.2
n/a (3.4.23.49)13073265.2
3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate:NAD+ oxidoreductase (1.3.1.87)5681405.2
ATP:2′-deoxyadenosine 5′-phosphotransferase (2.7.1.76)19743445.2
carotenoid beta-end group lyase (ring-opening) (5.5.1.19)14522015.1
RNA-3′-phosphate:RNA ligase (cyclizing, AMP-forming) (6.5.1.4)12203165.1
NTP:deoxycytidine 5′-phosphotransferase (2.7.1.74)18852875.1
L-threonate:NAD+ 2-oxidoreductase (1.1.1.411)14104925.1
succinyl-CoA:3-oxo-acid CoA-transferase (2.8.3.5)13073635.1
acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (6,7 cis-dehydrogenating) (1.14.19.3)10632775
L-carnitine:CoA ligase (AMP-forming) (6.2.1.48)13735175
hydrogen-sulfide:flavocytochrome c oxidoreductase (1.8.2.3)11651615
L-methionine methanethiol-lyase (deaminating; 2-oxobutanoate-forming) (4.4.1.11)12722885
L-carnitine,NAD(P)H:oxygen oxidoreductase (trimethylamine-forming) (1.14.13.239)11863205
4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming) (4.1.3.16)2995
https://microbiomeprescription.com/Library/CitizenScience

Bottom Line

Temperature intolerance is not an independently study topic. Existing studies are usually in the context of some other condition. This suggests that this is the first study on it’s microbiome.

  •  “Diabetes is often associated with orthostatic hypotension and temperature intolerance.” [2005]

The suggestions below has some surprises on the to avoid list: Vitamins B-3, B-12, Curcumin,  N-Acetyl Cysteine (NAC) sitting high in the list with antibiotics. The absence of probiotics in the to take suggestions is note worthy for those that view probiotics as ‘cure all’. Not listed, but conceptually worth considering, are the E.Coli probiotics (Symbioflor-2 or Mutaflor).

Recently I have see pea appear often and I recall that peas were served with most meals as a child. Peas has largely disappear from the western menu. I am starting to wonder if having pea soup 3 times a week would help a lot of people.

Special Studies: Constipation

This is a common symptom for many people. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does. We are not being specific about the type of constipation.

Study Populations:

We have 2 symptom annotations that could be included

  • Comorbid: Constipation and diarrhea (not explosions) – 29 only
  • Comorbid: Constipation and Explosions (not diarrhea) – 11 only
  • Immune Manifestations: Constipation – 9.7 max z-score (70)
    • All of the above Constipation – 9.9 max z-score (83)

Taking all together we get 83 samples with an max z-score of 9.9

SymptomReferenceStudy
Constipation112383
  • Bacteria Detected with z-score > 2.6: found 123 items, highest value was 9.9
  • Enzymes Detected with z-score > 2.6: found 511 items, highest value was 5.2
  • Compound Detected with z-score > 2.6: found No items

Clearly some bacteria have strong associations, but the number of enzymes that are significant suggests that they may be more dimensions to the issue.

Previous studies have shown that the gut microbiota of constipated patients differs from healthy controls; however, many discrepancies exist in the findings, and no clear link has been confirmed between chronic constipation and changes in the gut microbiota.

Gut Microbiota Composition Changes in Constipated Women of Reproductive Age [2021]

The reason that I do not have Constipation on my US National Library of Medicine Studies list is that the studies are usually in the context of another microbiome altering condition. For example: Effects of Fermented Milk Containing Lacticaseibacillus paracasei Strain Shirota on Constipation in Patients with Depression [2021]

Interesting Significant Bacteria

Unusually bacteria was found significant with both high (13) and low (110). This far exceed the count expected as the false detection rate, so we should include and cite them.

BacteriaReference MeanStudyZ-Score
Prevotella copri (species)6708771509.9
Prevotella (genus)74786177558
Prevotellaceae (family)82267292196.8
Veillonella (genus)400321025
Lactiplantibacillus pentosus (species)117265

UNLIKE most of the other studies, we had a significant number of too many bacteria (far more than expected with a False Detection Rate).

BacteriaReference MeanStudyZ-Score
Tannerellaceae (family)2459234890-3.6
Parabacteroides (genus)2458734665-3.6
Porphyromonadaceae (family)2658436605-3.4
Bacteroides uniformis (species)2568242170-3.2
Bacteroidaceae (family)281711337344-3.1
Desulfosporosinus auripigmenti (species)1828-3
Hathewaya histolytica (species)26074093-2.8
Bacteroides (genus)232904276348-2.8
Oscillospira (genus)2283628653-2.8
Anaerotruncus colihominis (species)17392436-2.8
Anaerotruncus (genus)18342520-2.7
Hathewaya (genus)26184058-2.7
Parabacteroides merdae (species)724911459-2.6

There is some agreement with studies on these findings, but as cited above — results are not consistent in studies.

Interesting Enzymes

As with bacteria we had both too few and too many.

EnzymeReference MeanStudy MeanZ-Score
UDP-N-acetyl-alpha-D-mannosamine:NAD+ 6-oxidoreductase (1.1.1.336)121077167870-4.1
GDP-alpha-D-mannose:2-O-alpha-D-mannosyl-1-phosphatidyl-1D-myo-inositol 6-alpha-D-mannosyltransferase (configuration-retaining) (2.4.1.346)4325768972-4.1
UDP-2-acetamido-3-amino-2,3-dideoxy-alpha-D-glucuronate:2-oxoglutarate aminotransferase (2.6.1.98)4494268064-4.1
acetyl-CoA:UDP-2-acetamido-3-amino-2,3-dideoxy-alpha-D-glucuronate N-acetyltransferase (2.3.1.201)6786398332-4
chondroitin AC lyase (4.2.2.5)6278590081-3.8
alpha-N-acetyl-D-glucosaminide N-acetylglucosaminohydrolase (3.2.1.50)170810221135-3.7
glycine:H-protein-lipoyllysine oxidoreductase (decarboxylating, acceptor-amino-methylating) (1.4.4.2)188544239012-3.7
L-leucyl-tRNALeu:[protein] N-terminal L-lysine/L-arginine leucyltransferase (2.3.2.6)129313167839-3.7
5-phospho-alpha-D-ribose 1,2-cyclic phosphate 2-phosphohydrolase (alpha-D-ribose 1,5-bisphosphate-forming) (3.1.4.55)185457234894-3.7
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 5 isopentenyl units) (2.5.1.90)195115245998-3.6
The top 10 that are too high
EnzymeReference MeanStudy MeanZ-Score
propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming) (2.3.3.5)15095005.2
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming) (4.1.3.30)14585004.9
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (3.5.1.18)101418727624.7
ADP-alpha-D-glucose:alpha-D-glucose-1-phosphate 4-alpha-D-glucosyltransferase (configuration-retaining) (2.4.1.342)77187491894.6
3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate:NAD+ oxidoreductase (1.3.1.87)5801834.5
3-phenylpropanoate,NADH:oxygen oxidoreductase (2,3-hydroxylating) (1.14.12.19)5931894.4
D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming) (4.1.2.40)89078626864.4
UDP-N-acetyl-alpha-D-glucosamine:lipopolysaccharide N-acetyl-D-glucosaminyltransferase (2.4.1.56)10773764.3
D-aspartate:[beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n ligase (ADP-forming) (6.3.1.12)87698617354.3
penicillin amidohydrolase (3.5.1.11)83364577214.3
Top top 10 that are too low

Bottom Line

While constipation is often assumed to be due too many of some bacteria, the evidence suggestions that not enough is the more likely cause. There appears to be no simple model or answer.

Prevotella copri will hopefully be available as a probiotic in a few year. There are two natural sources for P.Copri : Beer and Sauerkraut [2020], which may be an experiment for those that are prone to constipation..

https://microbiomeprescription.com/Library/CitizenScience

Looking at the suggestions — Constipation caused by Antibiotics!

This is not a “new discovery” — rather it appears to confirm that the mathematic model being used is reasonable and thus Dr. Artificial Intelligence suggestions are reasonable!

Special Studies: Allergic Rhinitis (Hay Fever)

This is a common symptom for many people. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does. We are not being specific about the type of allergy.

Sub-Series Study Populations:

We have 5 symptom annotations that this sub-series are examining, I tried different combination to see which resulted in a higher z-score to identify probable siblings (in a statistical sense)

  • New food sensitivities – 12.1 z-score
  • Medication sensitivities -8.8 z-score
    • Combined, dropped to 6.4
  • Alcohol intolerance – 8.6 z-score
    • with Medication sensitivities 9.9 z-score and less bacteria
  • Allergic Rhinitis (Hay Fever) – 8.6 z-score
    • When combined with any of the above, a major drop of z-scores
  • Allergies – 9.2 z-score
    • With new food sensitivities – 9.9 z-score
    • When combined with any of the other, a major drop of z-scores

We have broken this down into 3 sub-groups of microbiome shifts:

SymptomReferenceStudy
Allergic Rhinitis (Hay Fever)116142
  • Bacteria Detected with z-score > 2.6: found 222 items, highest value was 8.6
  • Enzymes Detected with z-score > 2.6: found 250 items, highest value was 6.8
  • Compound Detected with z-score > 2.6: found No items

Interesting Significant Bacteria

All bacteria found significant (except 1) had too low levels. This is a common pattern found with these studies, it is not “bad bacteria bogie man bacteria” but an absence of “upstanding citizens bacteria”.

The key bacteria are very different from the other two studies in this sub-series. We do see one retail level probiotic in the list: Bifidobacterium animalis (species)

BacteriaReference MeanStudyZ-Score
Desulfovibrio (genus)27706258.6
Bacteroides stercoris (species)1418521697.8
Desulfovibrio simplex (species)213276.9
Phocaeicola sartorii (species)8072766.4
Opitutae (class)164406.1
Actinobacillus pleuropneumoniae (species)56166
Planifilum (genus)80345.9
Planifilum fimeticola (species)80345.9
Puniceicoccaceae (family)159405.9
Cerasicoccus (genus)313365.8
Actinobacillus porcinus (species)182625.4
Veillonella (genus)393519275.3
Desulfurispora thermophila (species)68355.3
Desulfurispora (genus)68355.3
Tepidanaerobacteraceae (family)55245.3
Thermoactinomycetaceae (family)81375.3
Rhodanobacteraceae (family)8382495.3
Eggerthella sinensis (species)179455.2
Lactiplantibacillus pentosus (species)120255.2
Tepidanaerobacter (genus)54245.1
Tepidanaerobacter syntrophicus (species)54245.1
Absiella (genus)728745.1
delta/epsilon subdivisions (subphylum)612231745.1
Veillonellales (order)17250116495
Bifidobacterium animalis (species)11601245

Looking at published studies we see many close matches, with most of the species cited in those studies being too low.

Note: This study and published studies suffer from the issues described in The taxonomy nightmare before Christmas…

Interesting Enzymes

All 250 enzymes found significant had too low levels.

EnzymeReference MeanStudy MeanZ-Score
chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming) (4.2.1.151)16543606.8
dolichyl-diphosphooligosaccharide:protein-L-asparagine N-beta-D-oligopolysaccharidotransferase (2.4.99.18)16113186.8
S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (HCO3–hydrolysing, 6-amino-6-deoxyfutalosine-forming) (2.5.1.120)16243636.8
dehypoxanthine futalosine:S-adenosyl-L-methionine oxidoreductase (cyclizing) (1.21.98.1)16153636.7
2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate:NAD+ oxidoreductase (deaminating) (1.4.1.24)15483456.6
ATP phosphohydrolase (ABC-type, tungstate-importing) (7.3.2.6)13783026.6
hydrogen:ferricytochrome-c3 oxidoreductase (1.12.2.1)13883206.6
[TtuB sulfur-carrier protein]-Gly-NH-CH2-C(O)SH:tRNA (5-methyluridine54-2-O)-sulfurtransferase (2.8.1.15)13593076.5
isethionate sulfite-lyase (4.4.1.38)15243186.5
ATP phosphohydrolase (ABC-type, capsular-polysaccharide-exporting) (7.6.2.12)9492396.5
6-amino-6-deoxyfutalosine deaminase (3.5.4.40)16674596.3
hydrogen-sulfide:[DsrC sulfur-carrier protein],acceptor oxidoreductase (1.8.99.5)13043236.2
futalosine ribohydrolase (3.2.2.26)12413116.1
siroheme carboxy-lyase (4.1.1.111)13405316
propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming) (2.3.3.5)14793665.9
S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)364615325.8
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming) (4.1.3.30)14303795.6
2-dehydrotetronate isomerase (5.3.1.35)13994475.4
L-threonate:NAD+ 2-oxidoreductase (1.1.1.411)14054465.3
5-aminopentanoate:2-oxoglutarate aminotransferase (2.6.1.48)23637975.2
(S)-3-amino-2-methylpropanoate:2-oxoglutarate aminotransferase (2.6.1.22)23567965.2
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming] (4.2.1.79)12903835.1
3-deoxy-alpha-D-manno-octulopyranosonate:oxygen 8-oxidoreductase (1.1.3.48)6991965
GTP:molybdenum cofactor guanylyltransferase (2.7.7.77)1741196625
1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase (3.1.3.78)19123265

Bottom Line

We appear to have general agreement with published studies. The purpose of this series is to identify the shifts using a lab/analysis that is available to anyone world wide with the ability to identify the bacteria causing the issue with reliability and higher statistical significance than most studies.

Special Study: Alcohol intolerance + Medication sensitivities

This is a common symptom for many people with Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does. We are not being specific about the type of allergy.

Sub-Series Study Populations:

We have 5 symptom annotations that this sub-series are examining, I tried different combination to see which resulted in a higher z-score to identify probable siblings (in a statistical sense)

  • New food sensitivities – 12.1 z-score
  • Medication sensitivities -8.8 z-score
    • Combined, dropped to 6.4
  • Alcohol intolerance – 8.6 z-score
    • with Medication sensitivities 8.6 z-score and less bacteria
  • Allergic Rhinitis (Hay Fever) – 8.6 z-score
    • When combined with any of the above, a major drop of z-scores
  • Allergies – 9.2 z-score
    • With new food sensitivities – 9.9 z-score
    • When combined with any of the other, a major drop of z-scores

We have broken this down into 3 sub-groups of microbiome shifts:

SymptomReferenceStudy
Alcohol intolerance + Medication sensitivities114459
  • Bacteria Detected with z-score > 2.6: found 130 items, highest value was 8.6
  • Enzymes Detected with z-score > 2.6: found 507 items, highest value was 7.9
  • Compound Detected with z-score > 2.6: found No items

The bacteria that was most significant was NOT Prevotella copri (species) which we saw with Special Studies: Allergies And Food Sensitivity.

Interesting Significant Bacteria

All bacteria found significant (except 1) had too low levels. This is a common pattern found with these studies, it is not “bad bacteria bogie man bacteria” but an absence of “upstanding citizens bacteria”. The signature is very interesting because it is specific Bifidobacterium species — despite this, the Bifidobacterium genus was not found to be statistically significant. This drops us into the odd space of general Bifidobacterium probiotics likely not be effective, but specific strains may be(unfortunately those strains are not available as probiotics). There is one retail probiotics that contains Enterbacter, General Biotics/Equilibrium which give an experiment to try.

BacteriaReference MeanStudyZ-Score
Bifidobacterium gallicum (species)36981368.6
Bifidobacterium catenulatum subsp. kashiwanohense (subspecies)316556.9
Bifidobacterium kashiwanohense PV20-2 (strain)315556.8
Enterobacter (genus)13611275.6
Bifidobacterium angulatum (species)183205.2
Gammaproteobacteria (class)1401056365
Aeromonadaceae (family)157255

Interesting Enzymes

All 507 enzymes found significant had too low levels. This places it into the same class of massive enzyme disruptions as seen in Special Studies: Depression . As with that one, apologies for the massive list — I am keeping to my practice for these studies of listing everything with 5.0 z-score or higher.

EnzymeReference MeanStudy MeanZ-Score
2-acetylphloroglucinol C-acetyltransferase (2.3.1.272)177287.9
[cysteine desulfurase]-S-sulfanyl-L-cysteine:[molybdopterin-synthase sulfur-carrier protein]-Gly-Gly sulfurtransferase (2.8.1.11)523118057.7
S-adenosyl-L-methionine:tellurite methyltransferase (2.1.1.265)523819387
decenoyl-[acyl-carrier protein] Delta2-trans-Delta3-cis-isomerase (5.3.3.14)601022766.9
tRNA-uridine65 uracil mutase (5.4.99.26)405212266.8
coproporphyrinogen:oxygen oxidoreductase (decarboxylating) (1.3.3.3)31637466.8
donor:hydrogen-peroxide oxidoreductase (1.11.1.21)30306726.7
2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (5.3.3.18)309710596.7
3-hydroxybutanoyl-CoA 3-epimerase (5.1.2.3)29516966.7
ATP:nicotinamide-nucleotide adenylyltransferase (2.7.7.1)507622006.7
ATP:1-(beta-D-ribofuranosyl)-nicotinamide 5′-phosphotransferase (2.7.1.22)502521876.6
isocitrate glyoxylate-lyase (succinate-forming) (4.1.3.1)29557306.6
D-amino acid:quinone oxidoreductase (deaminating) (1.4.5.1)24856866.5
L-methionine:2-oxo-acid aminotransferase (2.6.1.88)27596526.5
2-(glutathione-S-yl)-hydroquinone:glutathione oxidoreductase (1.8.5.7)31407486.5
D-glucose:ubiquinone oxidoreductase (1.1.5.2)22004626.5
methanesulfonate,FMNH2:oxygen oxidoreductase (1.14.14.34)22394896.5
alkanesulfonate,FMNH2:oxygen oxidoreductase (1.14.14.5)22394896.5
glutathione:NADP+ oxidoreductase (1.8.1.7)594724946.5
triphosphate phosphohydrolase (3.6.1.25)449420126.4
S-(hydroxymethyl)glutathione:NAD+ oxidoreductase (1.1.1.284)28627596.4
(S)-3-hydroxyacyl-CoA:NAD+ oxidoreductase (1.1.1.35)33749266.4
ferredoxin:NAD+ oxidoreductase (1.18.1.3)19924556.4
acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase (2.3.1.15)327011396.4
S-adenosyl-L-methionine:tRNA (cytidine32/uridine32-2′-O)-methyltransferase (2.1.1.200)331610936.3
[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3R-hydroxylating) (1.14.11.47)333411146.3
choline:acceptor 1-oxidoreductase (1.1.99.1)27485626.3
acetyl-CoA:glyoxylate C-acetyltransferase [(S)-malate-forming] (2.3.3.9)31169506.3
siroheme ferro-lyase (sirohydrochlorin-forming) (4.99.1.4)25655396.2
deoxyribocyclobutadipyrimidine pyrimidine-lyase (4.1.99.3)415613376.2
acetyl-CoA:[elongator tRNAMet]-cytidine34 N4-acetyltransferase (ATP-hydrolysing) (2.3.1.193)330910946.2
7,8-dihydroneopterin 3′-triphosphate diphosphohydrolase (3.6.1.67)360712996.2
n/a (3.4.11.23)331210836.2
acetyl-CoA:dTDP-4-amino-4,6-dideoxy-alpha-D-galactose N-acetyltransferase (2.3.1.210)27666736.2
ATP:N-acetyl-D-glucosamine 6-phosphotransferase (2.7.1.59)326310716.2
L-2,4-diaminobutanoate carboxy-lyase (propane-1,3-diamine-forming) (4.1.1.86)21273046.2
chorismate pyruvate-lyase (4-hydroxybenzoate-forming) (4.1.3.40)25965676.2
protein dithiol:quinone oxidoreductase (disulfide-forming) (1.8.5.9)355712766.2
fatty acyl-[acyl-carrier protein]:alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-(acyl)-[lipid IVA] O-acyltransferase (2.3.1.243)332210976.2
ATP:L-threonine O3-phosphotransferase (2.7.1.177)23583506.1
ditrans-octacis-undecaprenyl-diphosphate:alpha-D-Kdo-(2->4)-alpha-D-Kdo-(2->6)-lipid-A phosphotransferase (2.7.4.29)285210086.1
D-sorbitol-6-phosphate:NAD+ 2-oxidoreductase (1.1.1.140)24476776.1
diacylglycerol-3-phosphate phosphohydrolase (3.1.3.4)328411056.1
1,2-diacyl-sn-glycerol 3-phosphate phosphohydrolase (3.1.3.81)328411056.1
(R)-lactate:quinone 2-oxidoreductase (1.1.5.12)23285106.1
(S)-lactate:ferricytochrome-c 2-oxidoreductase (1.1.2.3)23685446.1
methyl DNA-base, 2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming) (1.14.11.33)23044756.1
ATP:D-ribulose-5-phosphate 1-phosphotransferase (2.7.1.19)24355436.1
(2S,3S)-2,3-dihydro-2,3-dihydroxybenzoate:NAD+ oxidoreductase (1.3.1.28)22404766.1
D-mannitol-1-phosphate:NAD+ 5-oxidoreductase (1.1.1.17)26727276
2-O-(alpha-D-mannopyranosyl)-D-glycerate D-mannohydrolase (3.2.1.170)12483966
S-formylglutathione hydrolase (3.1.2.12)24025546
gamma-L-glutamyl-L-cysteinyl-glycine:spermidine amidase (3.5.1.78)318910596
gamma-L-glutamyl-L-cysteinyl-glycine:spermidine ligase (ADP-forming) [spermidine is numbered so that atom N-1 is in the amino group of the aminopropyl part of the molecule] (6.3.1.8)318910596
S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase (2.1.1.189)325711126
S-adenosyl-L-methionine:uridine in tRNA 3-[(3S)-3-amino-3-carboxypropyl]transferase (2.5.1.25)17043036
succinate-semialdehyde:NAD+ oxidoreductase (1.2.1.24)24164496
Fe(II)-siderophore:NADP+ oxidoreductase (1.16.1.9)23444476
ATP phosphohydrolase (ABC-type, taurine-importing) (7.6.2.7)21855216
geraniol:NADP+ oxidoreductase (1.1.1.183)24704666
ATP:N-acyl-D-mannosamine 6-phosphotransferase (2.7.1.60)320410985.9
L-serine:[L-seryl-carrier protein] ligase (AMP-forming) (6.2.1.72)21994545.9
galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming) (4.2.1.42)30159635.9
propanoyl-CoA:phosphate propanoyltransferase (2.3.1.222)17383585.9
ATP:thiamine phosphotransferase (2.7.1.89)23724925.9
ATP phosphohydrolase (ABC-type, putrescine-importing) (7.6.2.16)23025035.9
ubiquinol:oxygen oxidoreductase (superoxide-forming) (1.10.3.17)22324755.9
S-adenosyl-L-methionine:23S rRNA (guanine1835-N2)-methyltransferase (2.1.1.174)22584855.9
riboflavin:NAD(P)+ oxidoreductase (1.5.1.41)23234915.9
D-erythrose 4-phosphate:NAD+ oxidoreductase (1.2.1.72)22674855.9
CDP-diacylglycerol phosphatidylhydrolase (3.6.1.26)22394995.9
D-glucarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming) (4.2.1.40)295311255.9
6-phospho-D-gluconate hydro-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming) (4.2.1.12)22604955.8
ATP:propanoate phosphotransferase (2.7.2.15)22154695.8
isochorismate pyruvate-hydrolase (3.3.2.1)21644735.8
(3Z/3E)-alk-3-enoyl-CoA (2E)-isomerase (5.3.3.8)22254875.8
ATP phosphohydrolase (ABC-type, L-arabinose-importing) (7.5.2.12)22144735.8
n/a (3.4.24.55)22794925.8
diacylphosphatidylethanolamine:alpha-D-Kdo-(2->4)-alpha-D-Kdo-(2->6)-lipid-A 7”-phosphoethanolaminetransferase (2.7.8.42)23715005.8
2,3-dihydroxybenzoate:L-serine ligase (6.3.2.14)21796115.8
2-O-(alpha-D-glucopyranosyl)-D-glycerate:phosphate alpha-D-glucosyltransferase (configuration-retaining) (2.4.1.352)12172495.8
pyrimidine-5′-nucleotide phosphoribo(deoxyribo)hydrolase (3.2.2.10)22224955.8
6-sulfo-alpha-D-quinovosyl diacylglycerol 6-sulfo-D-quinovohydrolase (3.2.1.199)11132225.8
(9Z)-hexadec-9-enoyl-[acyl-carrier protein]:Kdo2-lipid IVA O-palmitoleoyltransferase (2.3.1.242)23565025.8
[RNA]-adenosine-cytidine 5′-hydroxy-adenosoine ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′-cytidine-2′,3′-cyclophosphate-forming and hydrolysing) (4.6.1.21)23124705.8
ATP phosphohydrolase (ABC-type, D-allose-importing) (7.5.2.8)21464315.8
6-methoxy-3-methyl-2-(all-trans-polyprenyl)-1,4-benzoquinol,acceptor:oxygen oxidoreductase (5-hydroxylating) (1.14.99.60)21805405.8
NADPH:NAD+ oxidoreductase (Si-specific) (1.6.1.1)22044905.8
taurine, 2-oxoglutarate:oxygen oxidoreductase (sulfite-forming) (1.14.11.17)21224965.8
(deoxy)cytidine 5′-triphosphate diphosphohydrolase (3.6.1.65)23075005.7
2-(all-trans-polyprenyl)phenol,NADPH:oxygen oxidoreductase (6-hydroxylating) (1.14.13.240)21785355.7
dTDP-N-acetyl-alpha-D-fucose:N-acetyl-beta-D-mannosaminouronyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol N-acetylfucosaminyltransferase (2.4.1.325)23085075.7
ATP:[isocitrate dehydrogenase (NADP+)] phosphotransferase (2.7.11.5)21425165.7
2,3-dihydroxybenzoate:[aryl-carrier protein] ligase (AMP-forming) (6.2.1.71)21186045.7
5,6,7,8-tetrahydromonapterin:NADP+ oxidoreductase (1.5.1.50)21594765.7
glutathione gamma-glutamyl cyclotransferase (5-oxo-L-proline producing) (4.3.2.7)21585005.7
iron(III)-enterobactin hydrolase (3.1.1.108)22044915.7
N,N’-diacetylchitobiose acetylhydrolase (3.5.1.105)23045085.7
N-succinyl-L-glutamate amidohydrolase (3.5.1.96)21725185.7
protein-Npi-phospho-L-histidine:N-acetyl-D-muramate Npi-phosphotransferase (2.7.1.192)22834745.7
4-alpha-D-[(1->4)-alpha-D-glucano]trehalose glucanohydrolase (trehalose-producing) (3.2.1.141)13351815.7
acetyl-CoA:N6-hydroxy-L-lysine 6-acetyltransferase (2.3.1.102)7081595.6
4-aminobutanoate:2-oxoglutarate aminotransferase (2.6.1.19)360011555.6
ATP:(S)-4,5-dihydroxypentane-2,3-dione 5-phosphotransferase (2.7.1.189)14152205.6
inosine/xanthosine 5′-triphosphate phosphohydrolase (3.6.1.73)20714965.6
6-deoxy-6-sulfofructose-1-phosphate 2-hydroxy-3-oxopropane-1-sulfonate-lyase (glycerone-phosphate-forming) (4.1.2.57)13462955.6
protein-Npi-phospho-L-histidine:2-O-alpha-mannopyranosyl-D-glycerate Npi-phosphotransferase (2.7.1.195)11632345.6
2,3-dihydroxypropane-1-sulfonate:NAD+ 3-oxidoreductase (1.1.1.373)13412955.6
4-aminobutanal:NAD+ 1-oxidoreductase (1.2.1.19)22374915.6
N-succinyl-L-glutamate 5-semialdehyde:NAD+ oxidoreductase (1.2.1.71)21355355.6
protein-dithiol:NAD(P)+ oxidoreductase (1.8.1.8)21515405.6
succinyl-CoA:acetyl-CoA C-succinyltransferase (2.3.1.174)14452055.6
succinyl-CoA:L-arginine N2-succinyltransferase (2.3.1.109)21355365.6
3-oxo-5,6-dehydrosuberyl-CoA semialdehyde:NADP+ oxidoreductase (1.2.1.91)14612215.6
2-oxepin-2(3H)-ylideneacetyl-CoA hydrolase (3.3.2.12)14612215.6
N2-succinyl-L-arginine iminohydrolase (decarboxylating) (3.5.3.23)21345365.6
ATP phosphohydrolase (ABC-type, nitrate-importing) (7.3.2.4)15231425.6
7,8-dihydroneopterin 3′-triphosphate 2′-epimerase (5.1.99.7)19284685.5
N4-acetylcytidine amidohydrolase (3.5.1.135)296610965.5
N2-succinyl-L-ornithine:2-oxoglutarate 5-aminotransferase (2.6.1.81)22546775.5
(1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase (5.4.99.15)13191835.5
ATP:2-dehydro-3-deoxy-D-galactonate 6-phosphotransferase (2.7.1.58)15362995.5
2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phospho-lyase (pyruvate-forming) (4.1.2.21)15382995.5
(S)-ureidoglycolate:NAD+ oxidoreductase (1.1.1.350)17294365.5
ATP:D-glyceraldehyde 3-phosphotransferase (2.7.1.28)15121155.5
ATP:glycerone phosphotransferase (2.7.1.29)15121155.5
FAD AMP-lyase (riboflavin-cyclic-4′,5′-phosphate-forming) (4.6.1.15)15121155.5
tRNA 2-(methylsulfanyl)-N6-prenyladenosine37,donor:oxygen 4-oxidoreductase (trans-hydroxylating) (1.14.99.69)15651585.5
S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)367315435.4
primary-amine:oxygen oxidoreductase (deaminating) (1.4.3.21)14952175.4
UDP-4-amino-4-deoxy-alpha-L-arabinose:ditrans,octacis-undecaprenyl phosphate 4-amino-4-deoxy-alpha-L-arabinosyltransferase (2.4.2.53)21075735.4
(2S)-2-hydroxy-3,4-dioxopentyl phosphate aldose-ketose-isomerase (5.3.1.32)15292595.4
acyl-CoA:acetyl-CoA C-acyltransferase (2.3.1.16)386918765.4
2,3-didehydroadipoyl-CoA:acetyl-CoA C-didehydroadipoyltransferase (double bond migration) (2.3.1.223)15162245.4
10-formyltetrahydrofolate:UDP-4-amino-4-deoxy-beta-L-arabinose N-formyltransferase (2.1.2.13)20484705.4
UDP-alpha-D-glucuronate:NAD+ oxidoreductase (decarboxylating) (1.1.1.305)20484705.4
4-amino-4-deoxy-alpha-L-arabinopyranosyl ditrans,octacis-undecaprenyl-phosphate:lipid IVA 4-amino-4-deoxy-L-arabinopyranosyltransferase (2.4.2.43)20444735.4
5-(methylsulfanyl)-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylsulfanyl)-2,3-dioxopentyl-phosphate-forming] (4.2.1.109)15521815.3
UDP-4-amino-4-deoxy-beta-L-arabinose:2-oxoglutarate aminotransferase (2.6.1.87)20704805.3
phenylacetyl-CoA:oxygen oxidoreductase (1,2-epoxidizing) (1.14.13.149)13752785.3
ATP phosphohydrolase (ABC-type, D-xylose-transporting) (7.5.2.10)14733085.3
5-(methylsulfanyl)-2,3-dioxopentyl-phosphate phosphohydrolase (isomerizing) (3.1.3.77)16891215.3
N-benzoylamino-acid amidohydrolase (3.5.1.32)17124085.3
phenylacetaldehyde:NAD+ oxidoreductase (1.2.1.39)13912715.3
L-glutamate:putrescine ligase (ADP-forming) (6.3.1.11)19024485.3
iron(III)-salmochelin complex hydrolase (3.1.1.109)7271595.3
2-O-(alpha-D-mannosyl)-3-phosphoglycerate phosphohydrolase (3.1.3.70)20614985.3
4-(gamma-L-glutamylamino)butanoate amidohydrolase (3.5.1.94)19144455.3
GDP-alpha-D-mannuronate:mannuronan D-mannuronatetransferase (2.4.1.33)154395.2
[mannuronan]-beta-D-mannuronate 5-epimerase (5.1.3.37)154395.2
3-(indol-3-yl)pyruvate carboxy-lyase [(2-indol-3-yl)acetaldehyde-forming] (4.1.1.74)18021385.2
quinate:quinol 3-oxidoreductase (1.1.5.8)15231245.2
betaine-aldehyde:NAD+ oxidoreductase (1.2.1.8)20574345.2
catechol:oxygen 2,3-oxidoreductase (ring-opening) (1.13.11.2)324014165.2
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming) (1.13.11.53)17142835.2
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate-forming) (1.13.11.54)17142835.2
ATP phosphohydrolase (ABC-type, thiamine-importing) (7.6.2.15)350313005.2
citrate:N6-acetyl-N6-hydroxy-L-lysine ligase (AMP-forming) (6.3.2.38)7971935.1
RX:glutathione R-transferase (2.5.1.18)296810255.1
N2-citryl-N6-acetyl-N6-hydroxy-L-lysine:N6-acetyl-N6-hydroxy-L-lysine ligase (AMP-forming) (6.3.2.39)7951935.1
putrescine:2-oxoglutarate aminotransferase (2.6.1.82)316814905.1
UDP-alpha-D-glucose:enterobactin 5′-C-beta-D-glucosyltransferase (configuration-inverting) (2.4.1.369)8072005.1
4-hydroxybutanoate:NAD+ oxidoreductase (1.1.1.61)23226075.1
D-xylonate hydro-lyase (2-dehydro-3-deoxy-D-arabinonate-forming) (4.2.1.82)6211785
D-glycerate:NAD(P)+ oxidoreductase (1.1.1.60)18885165
galactitol-1-phosphate:NAD+ oxidoreductase (1.1.1.251)9972775
alkylmercury mercury(II)-lyase (alkane-forming) (4.99.1.2)5771155
(S)-2-hydroxyglutarate:quinone oxidoreductase (1.1.5.13)21926705
(R)-3-hydroxyacyl-CoA:NADP+ oxidoreductase (1.1.1.36)5231545

Bottom Line

These two symptoms tend to be ignored by the medical establishment. There are studies on the microbiome impacting the efficiency of prescription drugs but not sensitivities or hyper-reactivity. This means that this post is likely the first study on these in existence.

Social Thread

Special Studies: Allergies And Food Sensitivity

This is a common symptom for many people. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does. We are not being specific about the type of allergy.

Sub-Series Study Populations:

We have 5 symptom annotations that this sub-series are examining, I tried different combination to see which resulted in a higher z-score to identify probable siblings (in a statistical sense)

  • New food sensitivities – 12.1 z-score
  • Medication sensitivities -8.8 z-score
    • Combined, dropped to 6.4
  • Alcohol intolerance – 8.6 z-score
    • with Medication sensitivities 9.9 z-score and less bacteria
  • Allergic Rhinitis (Hay Fever) – 8.6 z-score
    • When combined with any of the above, a major drop of z-scores
  • Allergies – 9.2 z-score
    • With new food sensitivities – 9.9 z-score
    • When combined with any of the other, a major drop of z-scores

We have broken this down into 3 sub-groups of microbiome shifts:

SymptomReferenceStudy
Allergies And Food Sensitivity113073
  • Bacteria Detected with z-score > 2.6: found 163 items, highest value was 9.9
  • Enzymes Detected with z-score > 2.6: found 364 items, highest value was 6.8
  • Compound Detected with z-score > 2.6: found No items

The bacteria that was most significant was Prevotella copri (species) which seems to occur often in these special studies.

Interesting Significant Bacteria

All bacteria found significant (except 1) had too low levels. This is a common pattern found with these studies, it is not “bad bacteria bogie man bacteria” but an absence of “upstanding citizens bacteria”. What is very striking is that with allergies, Prevotella copri is 1/10 that of the reference population, but as you move up to it’s genus (Prevotella) and family (Prevotellaceae) the ratio becomes less and less extreme. The species is where things are happening. There is one retail probiotic species listed (E.Coli – i.e. Mutaflor or Symbioflor-2) and two Bifidobacterium species which hopefully will become available one day.

” Since its discovery in 2007, the importance of the human gut bacterium Prevotella copri (P. copri) has been widely recognized with its links to diet and health status and potential as next generation probiotic” [2021]

BacteriaReference MeanStudyZ-Score
Prevotella copri (species)6619060979.9
Shuttleworthia (genus)279616.9
Prevotella (genus)73487241016.2
Tepidanaerobacter (genus)55256.2
Tepidanaerobacter syntrophicus (species)55256.2
Tepidanaerobacteraceae (family)55256.2
Prevotellaceae (family)81231331605.8
Sporolactobacillaceae (family)174605.7
Sporolactobacillus (genus)176625.6
Sporolactobacillus putidus (species)176625.6
Thermosediminibacterales (order)53185.6
Bifidobacterium catenulatum subsp. kashiwanohense (subspecies)322895.6
Bifidobacterium kashiwanohense PV20-2 (strain)321895.6
Caldilineaceae (family)91375.4
Caldilinea (genus)91375.4
Caldilineales (order)91375.4
Caldilinea tarbellica (species)91375.4
Caldilineae (class)91375.4
Lactiplantibacillus pentosus (species)119225.3
Escherichia (genus)612315495.1

Prevotella copri is called out in several studies

Interesting Enzymes

All enzymes (except 3) found significant had too low levels. Given 364 items and 99% confidence, 3 is what you would expect with False Detection Rate, so we can dismiss these one.

EnzymeReference MeanStudy MeanZ-Score
propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming) (2.3.3.5)15133696.8
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming) (4.1.3.30)14613696.5
(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming] (4.2.1.79)13173856
S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)370515415.9
L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming] (4.2.1.149)14723465.6
5-aminopentanoate:2-oxoglutarate aminotransferase (2.6.1.48)24077935.6
(S)-3-amino-2-methylpropanoate:2-oxoglutarate aminotransferase (2.6.1.22)24007905.6
2-dehydrotetronate isomerase (5.3.1.35)14245285.5
n/a (3.4.23.49)13333545.5
L-threonate:NAD+ 2-oxidoreductase (1.1.1.411)14305275.5
glutarate, 2-oxoglutarate:oxygen oxidoreductase ((S)-2-hydroxyglutarate-forming) (1.14.11.64)13193405.5
(R)-lactate hydro-lyase (4.2.1.130)15843485.4
L-carnitine,NAD(P)H:oxygen oxidoreductase (trimethylamine-forming) (1.14.13.239)12123335.4
UDP-N-acetyl-alpha-D-glucosamine:lipopolysaccharide N-acetyl-D-glucosaminyltransferase (2.4.1.56)10942935.3
protein-Npi-phospho-L-histidine:D-mannitol Npi-phosphotransferase (2.7.1.197)72060431585.3
acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (6,7 cis-dehydrogenating) (1.14.19.3)10883165.3
2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase (5.3.99.11)89479625625.3
ATP:L-threonine O3-phosphotransferase (2.7.1.177)23814635.2
alpha-maltose-6′-phosphate 6-phosphoglucohydrolase (3.2.1.122)72165443035.1
2-acetylphloroglucinol C-acetyltransferase (2.3.1.272)179635.1
L-carnitine:CoA ligase (AMP-forming) (6.2.1.48)13875725.1
RNA-3′-phosphate:RNA ligase (cyclizing, AMP-forming) (6.5.1.4)12323715.1
D-serine ammonia-lyase (pyruvate-forming) (4.3.1.18)70096428045
(E)-4-(trimethylammonio)but-2-enoyl-CoA:L-carnitine CoA-transferase (2.8.3.21)13975635
gamma-butyrobetainyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (1.3.8.13)14115665
3-dehydro-4-phosphotetronate carboxy-lyase (4.1.1.104)16986475

Bottom Line

There is an excellent article on different strains and how they are related to diet with discussion of KEGG Enzymes, Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets [2021] which states ” Interestingly, Italian V and VG clustered with Western populations, suggesting that a Western plant-based diet is still not effective in establishing a P. copri strain consortium typical of a traditional agrarian diet, and supporting the existence of a geographically based distribution of different strain patterns” — which hints how a change of diet is causing an uptick in allergies.

” Prevotella copri is a bacterium naturally present .. in sauerkraut and beer.” [2020] So the German Beer Hall Diet!! 😉

Special Studies: Depression

This is a common symptom for our times, especially with climate change and politics in some places. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does.

Depression is likely a part of a feedback loop — depression chemicals modify the microbiome resulting in more depression triggering chemicals being released.

Study Populations:

We have 2 symptom annotations that could be included

  • General: Depression
  • Official Diagnosis: Depression

Taking the first two together we get 85 samples with an max z-score of 5.7

SymptomReferenceStudy
High Anxiety and Anxiety/tension114985
  • Bacteria Detected with z-score > 2.6: found 156 items, highest value was 7.8
  • Enzymes Detected with z-score > 2.6: found 508 items, highest value was 8.3
  • Compound Detected with z-score > 2.6: found No items

This hints that the enzymes being produced are likely more significant than the bacteria and the number of enzymes found significant is slightly overwhelming! (I dare not say depressing)

Interesting Significant Bacteria

All bacteria found significant (except 2) had too low levels. These two are almost expected as the false detection rate, so we can likely exclude them. This is a common pattern found with these studies, it is not “bad bacteria bogie man bacteria” but an absence of “upstanding citizens bacteria”.

BacteriaReference MeanStudyZ-Score
Shuttleworthia (genus)273427.8
Actinobacillus (genus)339806.6
Actinobacillus porcinus (species)181486
Haemophilus (genus)15984255.9
Haemophilus parainfluenzae (species)15984245.9
Pasteurellaceae (family)19735345.8
Pasteurellales (order)19735345.8
Pasteurellaceae incertae sedis (norank)143435.8
[Pasteurella] aerogenes-[Pasteurella] mairii-[Actinobacillus] rossii complex (species group)143435.8
Legionellaceae (family)80405.7
Legionella (genus)80405.7
[Actinobacillus] rossii (species)143465.6
Legionellales (order)81435.2
Thiobacillus thiophilus (species)81245.2
Veillonella dispar (species)823595.1
Thiobacillaceae (family)81255
Thiobacillus (genus)80255

Similar findings have been reported in some studies, for example: low Haemophilus, Pasteurellaceae, uncultured_Veillonellaceae_bacterium reported in Gut Microbiome Composition Associated With Major Depressive Disorder and Sleep Quality [2021].

Interesting Enzymes

All 508 enzymes found significant, had too low levels. Excuse the long list, but my practice has been to list everything with a z-score over 5.0; there are a lot with depression.

EnzymeReference MeanStudy MeanZ-Score
[cysteine desulfurase]-S-sulfanyl-L-cysteine:[molybdopterin-synthase sulfur-carrier protein]-Gly-Gly sulfurtransferase (2.8.1.11)523615178.3
tRNA-uridine65 uracil mutase (5.4.99.26)40599717.6
deoxyribocyclobutadipyrimidine pyrimidine-lyase (4.1.99.3)415611796.8
acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase (2.3.1.15)32709766.7
7,8-dihydroneopterin 3′-triphosphate diphosphohydrolase (3.6.1.67)360910846.6
(1->4)-alpha-D-galacturonan lyase (4.2.2.2)23527066.4
N4-acetylcytidine amidohydrolase (3.5.1.135)29708426.4
diacylglycerol-3-phosphate phosphohydrolase (3.1.3.4)32879206.3
1,2-diacyl-sn-glycerol 3-phosphate phosphohydrolase (3.1.3.81)32879206.3
acetyl-CoA:[elongator tRNAMet]-cytidine34 N4-acetyltransferase (ATP-hydrolysing) (2.3.1.193)33099386.3
S-adenosyl-L-methionine:tRNA (cytidine32/uridine32-2′-O)-methyltransferase (2.1.1.200)33129636.3
S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase (2.1.1.189)32609316.3
protein dithiol:quinone oxidoreductase (disulfide-forming) (1.8.5.9)355511176.3
ATP phosphohydrolase (ABC-type, thiamine-importing) (7.6.2.15)35069736.2
ATP:(Kdo)-lipid IVA 3-deoxy-alpha-D-manno-oct-2-ulopyranose 4-phosphotransferase (2.7.1.166)15143806.2
[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3R-hydroxylating) (1.14.11.47)33289786.2
D-glucarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming) (4.2.1.40)29589976.1
ATP:N-acetyl-D-glucosamine 6-phosphotransferase (2.7.1.59)32579476.1
fatty acyl-[acyl-carrier protein]:alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-(acyl)-[lipid IVA] O-acyltransferase (2.3.1.243)33189606.1
[RNA] 5′-hydroxy-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′- nucleoside-2′,3′-cyclophosphate-forming and hydrolysing) (4.6.1.19)15153906.1
ATP:N-acyl-D-mannosamine 6-phosphotransferase (2.7.1.60)32049326.1
n/a (3.4.11.23)33059666.1
coproporphyrinogen:oxygen oxidoreductase (decarboxylating) (1.3.3.3)31538246.1
D-amino acid:quinone oxidoreductase (deaminating) (1.4.5.1)24846816.1
gamma-L-glutamyl-L-cysteinyl-glycine:spermidine amidase (3.5.1.78)31859406
gamma-L-glutamyl-L-cysteinyl-glycine:spermidine ligase (ADP-forming) [spermidine is numbered so that atom N-1 is in the amino group of the aminopropyl part of the molecule] (6.3.1.8)31859406
CMP-N-acetyl-beta-neuraminate:beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-R (2->3)-N-acetyl-alpha-neuraminyltransferase (configuration-inverting) (2.4.99.6)16034066
galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming) (4.2.1.42)30148865.9
methanesulfonate,FMNH2:oxygen oxidoreductase (1.14.14.34)22375115.9
alkanesulfonate,FMNH2:oxygen oxidoreductase (1.14.14.5)22375115.9
donor:hydrogen-peroxide oxidoreductase (1.11.1.21)30197975.8
D-glucose:ubiquinone oxidoreductase (1.1.5.2)21964975.8
glutathione:hydroperoxide oxidoreductase (1.11.1.27)17534135.8
3-hydroxybutanoyl-CoA 3-epimerase (5.1.2.3)29408265.7
acetyl-CoA:glyoxylate C-acetyltransferase [(S)-malate-forming] (2.3.3.9)31099935.7
L-methionine:2-oxo-acid aminotransferase (2.6.1.88)27497455.7
S-adenosyl-L-methionine:23S rRNA (guanine2069-N7)-methyltransferase (2.1.1.264)568526085.7
ferredoxin:NAD+ oxidoreductase (1.18.1.3)19904815.6
choline:acceptor 1-oxidoreductase (1.1.99.1)27396555.6
n/a (3.1.25.1)15434425.5
isocitrate glyoxylate-lyase (succinate-forming) (4.1.3.1)29428595.5
acetyl-CoA:dTDP-4-amino-4,6-dideoxy-alpha-D-galactose N-acetyltransferase (2.3.1.210)27627455.5
(S)-3-hydroxyacyl-CoA:NAD+ oxidoreductase (1.1.1.35)336110735.5
N-acyl-D-amino acid amidohydrolase (3.5.1.81)17874125.4
2-(glutathione-S-yl)-hydroquinone:glutathione oxidoreductase (1.8.5.7)31249165.4
S-(hydroxymethyl)glutathione:NAD+ oxidoreductase (1.1.1.284)28508925.3
succinyl-CoA:3-oxo-acid CoA-transferase (2.8.3.5)13063195.3
n/a (3.4.23.51)501623115.3
L-2,4-diaminobutanoate carboxy-lyase (propane-1,3-diamine-forming) (4.1.1.86)21203825.3
formate:[oxidized hydrogenase] oxidoreductase (1.17.98.4)599029165.3
S-methyl-5-thio-D-ribulose 1-phosphate 1,3-isomerase (5.3.3.23)1135955.1
RX:glutathione R-transferase (2.5.1.18)296110215.1
n/a (3.4.24.74)427911325.1
gamma-L-glutamyl-L-cysteine:glycine ligase (ADP-forming) (6.3.2.3)28089015.1
D-glucose:NAD(P)+ 1-oxidoreductase (1.1.1.47)12433095.1
propanoyl-CoA:phosphate propanoyltransferase (2.3.1.222)17254175
(S)-2-hydroxyglutarate:quinone oxidoreductase (1.1.5.13)21906015
4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) (1.13.11.27)14372555
thiosulfate:ferricytochrome-c oxidoreductase (1.8.2.2)13613365

This high count is actually reflected in recent literature, although it was with animal models and not humans (in our case).

 Moreover, the fecal metabolomic analysis identified 468 differential expressed metabolites. Among all the differential metabolites, 11 specific pathways significantly altered, which were mainly belonged to lipid and amino acid metabolism.

Comparative analysis of gut microbiota and fecal metabolome features among multiple depressive animal models [2022]

Given the huge numbers of enzymes, I decided to see what came up from KEGG calculations for appropriate probiotics. If you have depression, the site will compute those specific for yourself. As seems to happen often, E.Coli produces a lot of different enzymes and thus at the top of the list.

Tax_NameContribution
Escherichia coli200.9
Bacillus thuringiensis70.2
Bacillus licheniformis67
Bacillus subtilis64.5
Bacillus subtilis subsp. natto63
Bacillus pumilus58
Bacillus velezensis57.8
Bacillus amyloliquefaciens56.8
Brevibacillus laterosporus45
Lactobacillus plantarum subsp. plantarum31.5
Lactiplantibacillus plantarum31.4
Clostridium beijerinckii28.3
Lacticaseibacillus rhamnosus23
Lacticaseibacillus casei23

Bottom Line

The high number of statistically significant enzymes was a surprise — but checking the literature, it appears to be in agreement with other studies. The special study suggestions engines are available now. Either via the a priori suggestion or the suggestions specific for your microbiome.

Given these facts, fixing depression may be a challenge until someone develops a Shuttleworthia and a Actinobacillus probiotic.

https://microbiomeprescription.com/Library/CitizenScience