Long COVID – an update

First, there is a body of literature indicating that the microbiome plays an important part in many conditions. The last one in this list of citations agrees with my hypothesis for the last 7 years: “Multi-kingdom gut microbiota analyses define CONDITION-X severity and in some case the syndrome.“

Citation
đź““ Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study.
Microorganisms (Microorganisms ) Vol: 9 Issue 6 Pages:
Pub: 2021 Jun 7 Epub: 2021 Jun 7 Authors Kim HN , Joo EJ , Lee CW , Ahn KS , Kim HL , Park DI , Park SK ,
Summary Html Article Publication
đź““ The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort.
Gut microbes (Gut Microbes ) Vol: 13 Issue 1 Pages: 1-15
Pub: 2021 Jan-Dec Epub: Authors Newsome RC , Gauthier J , Hernandez MC , Abraham GE , Robinson TO , Williams HB , Sloan M , Owings A , Laird H , Christian T , Pride Y , Wilson KJ , Hasan M , Parker A , Senitko M , Glover SC , Gharaibeh RZ , Jobin C ,
Summary Html Article Publication
đź““ Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery.
Frontiers in nutrition (Front Nutr ) Vol: 8 Issue Pages: 638825
Pub: 2021 Epub: 2021 May 13 Authors Tian Y , Sun KY , Meng TQ , Ye Z , Guo SM , Li ZM , Xiong CL , Yin Y , Li HG , Zhou LQ ,
Summary Html Article Publication
đź““ Gut Microbiota Interplay With COVID-19 Reveals Links to Host Lipid Metabolism Among Middle Eastern Populations.
Frontiers in microbiology (Front Microbiol ) Vol: 12 Issue Pages: 761067
Pub: 2021 Epub: 2021 Nov 5 Authors Al Bataineh MT , Henschel A , Mousa M , Daou M , Waasia F , Kannout H , Khalili M , Kayasseh MA , Alkhajeh A , Uddin M , Alkaabi N , Tay GK , Feng SF , Yousef AF , Alsafar HS ,
Summary Publication
đź““ Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome.
Gut (Gut ) Vol: Issue Pages:
Pub: 2022 Jan 26 Epub: 2022 Jan 26 Authors Liu Q , Mak JWY , Su Q , Yeoh YK , Lui GC , Ng SSS , Zhang F , Li AYL , Lu W , Hui DS , Chan PK , Chan FKL , Ng SC ,
Summary Publication
đź““ Alterations in microbiota of patients with COVID-19: potential mechanisms and therapeutic interventions.
Signal transduction and targeted therapy (Signal Transduct Target Ther ) Vol: 7 Issue 1 Pages: 143
Pub: 2022 Apr 29 Epub: 2022 Apr 29 Authors Wang B , Zhang L , Wang Y , Dai T , Qin Z , Zhou F , Zhang L ,
Summary Publication
đź““ Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization.
Gastroenterology (Gastroenterology ) Vol: 159 Issue 3 Pages: 944-955.e8
Pub: 2020 Sep Epub: 2020 May 20 Authors Zuo T , Zhang F , Lui GCY , Yeoh YK , Li AYL , Zhan H , Wan Y , Chung ACK , Cheung CP , Chen N , Lai CKC , Chen Z , Tso EYK , Fung KSC , Chan V , Ling L , Joynt G , Hui DSC , Chan FKL , Chan PKS , Ng SC ,
Summary Publication
đź““ Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge.
Gastroenterology (Gastroenterology ) Vol: 159 Issue 4 Pages: 1302-1310.e5
Pub: 2020 Oct Epub: 2020 Jun 26 Authors Zuo T , Zhan H , Zhang F , Liu Q , Tso EYK , Lui GCY , Chen N , Li A , Lu W , Chan FKL , Chan PKS , Ng SC ,
Summary Publication
đź““ Challenges in the Management of SARS-CoV2 Infection: The Role of Oral Bacteriotherapy as Complementary Therapeutic Strategy to Avoid the Progression of COVID-19.
Frontiers in medicine (Front Med (Lausanne) ) Vol: 7 Issue Pages: 389
Pub: 2020 Epub: 2020 Jul 7 Authors d`Ettorre G , Ceccarelli G , Marazzato M , Campagna G , Pinacchio C , Alessandri F , Ruberto F , Rossi G , Celani L , Scagnolari C , Mastropietro C , Trinchieri V , Recchia GE , Mauro V , Antonelli G , Pugliese F , Mastroianni CM ,
Summary Publication
đź““ It Ain`t Over `Til It`s Over: SARS CoV-2 and Post-infectious Gastrointestinal Dysmotility.
Digestive diseases and sciences (Dig Dis Sci ) Vol: Issue Pages:
Pub: 2022 Mar 30 Epub: 2022 Mar 30 Authors Coles MJ , Masood M , Crowley MM , Hudgi A , Okereke C , Klein J ,
Summary Publication
đź““ Integrated analysis of gut microbiome and host immune responses in COVID-19.
Frontiers of medicine (Front Med ) Vol: 16 Issue 2 Pages: 263-275
Pub: 2022 Apr Epub: 2022 Mar 8 Authors Xu X , Zhang W , Guo M , Xiao C , Fu Z , Yu S , Jiang L , Wang S , Ling Y , Liu F , Tan Y , Chen S ,
Summary Publication
đź““ Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations.
Journal of internal medicine (J Intern Med ) Vol: 291 Issue 6 Pages: 801-812
Pub: 2022 Jun Epub: 2022 Mar 17 Authors Vestad B , Ueland T , Lerum TV , Dahl TB , Holm K , Barratt-Due A , KĂĄsine T , Dyrhol-Riise AM , Stiksrud B , Tonby K , Hoel H , Olsen IC , Henriksen KN , Tveita A , Manotheepan R , Haugli M , Eiken R , Berg Ă… , Halvorsen B , Lekva T , Ranheim T , Michelsen AE , Kildal AB , Johannessen A , Thoresen L , Skudal H , Kittang BR , Olsen RB , Ystrøm CM , Skei NV , Hannula R , Aballi S , KvĂĄle R , Skjønsberg OH , Aukrust P , Hov JR , Trøseid M , NOR-Solidarity study group. ,
Summary Publication
đź““ Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.
Nature communications (Nat Commun ) Vol: 13 Issue 1 Pages: 5235
Pub: 2022 Sep 6 Epub: 2022 Sep 6 Authors Ke S , Weiss ST , Liu YY ,
Summary Publication
đź““ Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome.
Nature communications (Nat Commun ) Vol: 13 Issue 1 Pages: 6806
Pub: 2022 Nov 10 Epub: 2022 Nov 10 Authors Liu Q , Su Q , Zhang F , Tun HM , Mak JWY , Lui GC , Ng SSS , Ching JYL , Li A , Lu W , Liu C , Cheung CP , Hui DSC , Chan PKS , Chan FKL , Ng SC ,
Summary Publication

Looking at what is statistically significant in samples uploaded to the citizen science site, we see that only BiomeSight has sufficient data. It identifies 36 taxa/bacteria at present. With more samples coming in, this may increase. Before looking at the bacteria, I like to look at the enzymes — why? different bacteria produce the same enzymes so it is an elegant way of clustering bacteria by what they produce.

KEGG Enzyme data

In this case, I am blown away on the number of statistically significant shifts! If you want more information about these enzymes, see BRENDA or/and Kyoto Encyclopedia of Genes and Genomes.

There are 197 with P < 0.001. Give there is 8000+ enzymes, that suggests around 8 may be false positives.

Enzyme NameECKEYWith
Long COVID		Without
Long
COVID		T-ScoreDFProbability
(S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase (acetyl-CoA-forming)4.1.3.41303575207613.57666P < 0.001
4-amino-5-aminomethyl-2-methylpyrimidine aminohydrolase3.5.99.21516936912613.48666P < 0.001
dihydrourocanate:acceptor oxidoreductase1.3.99.331351335592113.44666P < 0.001
nucleoside-triphosphate diphosphohydrolase3.6.1.91455286352313.38666P < 0.001
poly(deoxyribonucleotide)-3′-hydroxyl:5′-phospho-poly(deoxyribonucleotide) ligase (ATP or NAD+)6.5.1.61294755177913.34666P < 0.001
poly(deoxyribonucleotide)-3′-hydroxyl:5′-phospho-poly(deoxyribonucleotide) ligase (ATP, ADP or GTP)6.5.1.71294755177913.34666P < 0.001
acetyl-CoA:kanamycin-B N6′-acetyltransferase2.3.1.821286735166213.32666P < 0.001
acetyl-CoA:2-deoxystreptamine-antibiotic N3-acetyltransferase2.3.1.811302005310413.28666P < 0.001
(1->4)-alpha-D-galacturonan reducing-end-disaccharide-lyase4.2.2.91280385098913.28666P < 0.001
alpha-maltose-6′-phosphate 6-phosphoglucohydrolase3.2.1.1221304965395113.28666P < 0.001
D-serine ammonia-lyase (pyruvate-forming)4.3.1.181285765198713.23666P < 0.001
ATP phosphohydrolase (ABC-type, iron(III) enterobactin-importing)7.2.2.171303735418013.15666P < 0.001
protein-Npi-phospho-L-histidine:D-mannose Npi-phosphotransferase2.7.1.1911407016280713.14666P < 0.001
protein-Npi-phospho-L-histidine:D-mannitol Npi-phosphotransferase2.7.1.1971292845372313.06666P < 0.001
ADP-alpha-D-glucose:alpha-D-glucose-1-phosphate 4-alpha-D-glucosyltransferase (configuration-retaining)2.4.1.3421346545802813.04665P < 0.001
aryl-ester hydrolase3.1.1.21511717237713.02666P < 0.001
ATP phosphohydrolase (ABC-type, Fe3+-transporting)7.2.2.71421526611112.86666P < 0.001
palmitoyl-CoA hydrolase3.1.2.21494997172812.83666P < 0.001
ATP:[protein]-L-tyrosine O-phosphotransferase (non-specific)2.7.10.21319255736012.75666P < 0.001
D-psicose 3-epimerase5.1.3.301434166828412.74666P < 0.001
D-tagatose 3-epimerase5.1.3.311434166828412.74666P < 0.001
penicillin amidohydrolase3.5.1.111391386616512.62666P < 0.001
D-aspartate:[beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n ligase (ADP-forming)6.3.1.121453567026112.57666P < 0.001
2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase2.7.7.611491967469712.46666P < 0.001
ATP:3′-dephospho-CoA 5-triphospho-alpha-D-ribosyltransferase2.4.2.521499577578112.39666P < 0.001
2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase5.3.99.111462547353812.37666P < 0.001
acetyl-CoA:citrate CoA-transferase2.8.3.101503677631812.36666P < 0.001
L-aspartate:tRNAAsx ligase (AMP-forming)6.1.1.231329396172012.22666P < 0.001
4-phospho-D-erythronate:NAD+ 3-oxidoreductase1.1.1.4091340736291412.19666P < 0.001
4-phospho-D-threonate:NAD+ 3-oxidoreductase1.1.1.4081340736291412.19666P < 0.001
poly(deoxyribonucleotide)-3′-hydroxyl:5′-phospho-poly(deoxyribonucleotide) ligase (ATP)6.5.1.11438836812812.15666P < 0.001
ATP:D-erythronate 4-phosphotransferase2.7.1.2201336316269612.13666P < 0.001
ATP:D-threonate 4-phosphotransferase2.7.1.2191336316269612.13666P < 0.001
ATP:D-glycero-alpha-D-manno-heptose 7-phosphate 1-phosphotransferase2.7.1.1681561577849111.99666P < 0.001
2-lysophosphatidylcholine acylhydrolase3.1.1.51608748681411.71666P < 0.001
UDP-alpha-D-glucose:1,2-diacyl-sn-glycerol 3-alpha-D-glucosyltransferase2.4.1.3371599608724811.57666P < 0.001
N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase3.5.1.181514828284911.49666P < 0.001
acetate:holo-[citrate-(pro-3S)-lyase] ligase (AMP-forming)6.2.1.221632459049311.44666P < 0.001
D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)4.1.2.401408147287911.44666P < 0.001
L-iditol:NAD+ 2-oxidoreductase1.1.1.1418152410988611.34666P < 0.001
alkylated-DNA glycohydrolase (releasing methyladenine and methylguanine)3.2.2.211721698902811.33666P < 0.001
oligosaccharide 6-alpha-glucohydrolase3.2.1.101616289371211.12666P < 0.001
(3S)-citryl-CoA oxaloacetate-lyase (acetyl-CoA-forming)4.1.3.3418537510500910.73666P < 0.001
S-adenosyl-L-methionine:tRNA (adenine22-N1)-methyltransferase2.1.1.2171579389281710.69666P < 0.001
S-adenosyl-L-methionine:16S rRNA (cytidine1409-2′-O)-methyltransferase2.1.1.22718368911402710.56666P < 0.001
S-adenosyl-L-methionine:23S rRNA (cytidine1920-2′-O)-methyltransferase2.1.1.22618368911402710.56666P < 0.001
sn-glycerol 3-phosphate:quinone oxidoreductase1.1.5.317706411048610.54666P < 0.001
L-glutamate:tRNAGlx ligase (AMP-forming)6.1.1.241654489740210.38666P < 0.001
D-glycero-D-manno-heptose 7-phosphate aldose-ketose-isomerase5.3.1.2821347513524810.25666P < 0.001
beta-D-glucose 1,6-phosphomutase5.4.2.62533831699338.98666P < 0.001
type II site-specific deoxyribonuclease3.1.21.42458641652668.77666P < 0.001
uroporphyrinogen-III carboxy-lyase (coproporphyrinogen-III-forming)4.1.1.372665621844178.59666P < 0.001
ATP phosphohydrolase (ABC-type, Ni2+-importing)7.2.2.11141054863678.56666P < 0.001
acetyl-CoA:oxalate CoA-transferase2.8.3.19133160801498.41666P < 0.001
5-phospho-alpha-D-ribose 1,2-cyclic phosphate 1,2-diphosphophosphohydrolase3.1.4.57134813821838.33666P < 0.001
Carboxypeptidase Taq3.4.17.19136153840748.31666P < 0.001
(2E)-2-enoyl-CoA:NADP+ 4-oxidoreductase1.3.1.34134146819358.31666P < 0.001
2′-deoxyribonucleoside 5′-monophosphate phosphohydrolase3.1.3.89136444842518.19666P < 0.001
cellobiose 2-epimerase5.1.3.112249331476858.17666P < 0.001
type III site-specific deoxyribonuclease3.1.21.52001551416578.10666P < 0.001
D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)4.2.1.6138933881818.02666P < 0.001
protein-Npi-phospho-L-histidine:maltose Npi-phosphotransferase2.7.1.208138609883257.98666P < 0.001
L-aspartate:NAD(P)+ oxidoreductase (deaminating)1.4.1.212451501694717.90666P < 0.001
protein-Npi-phospho-L-histidine:sucrose Npi-phosphotransferase2.7.1.211144741960847.85666P < 0.001
protein-Npi-phospho-L-histidine:N-acetyl-D-glucosamine Npi-phosphotransferase2.7.1.1931520881039707.64666P < 0.001
N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 4-epimerase5.1.3.262594341823877.64666P < 0.001
UDP-sugar sugarphosphohydrolase3.6.1.451563031089447.63666P < 0.001
rubredoxin:superoxide oxidoreductase1.15.1.21475721016997.40666P < 0.001
UDP-2-acetamido-2,6-dideoxy-L-talose:NADP+ oxidoreductase1.1.1.3672447901762967.33666P < 0.001
(4-O-methyl)-D-glucuronate—lignin ester hydrolase3.1.1.1172657631906857.31666P < 0.001
alkylated-DNA glycohydrolase (releasing methyladenine and methylguanine)3.2.2.203069512314077.30666P < 0.001
S-adenosyl-L-methionine:16S rRNA (cytosine967-C5)-methyltransferase2.1.1.1761923481439787.28666P < 0.001
ATP:molybdopterin-synthase adenylyltransferase2.7.7.802979932187887.25666P < 0.001
UDP-N-acetyl-alpha-D-glucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-beta-L-arabino-hex-4-ulose-forming)4.2.1.1152877172119847.24666P < 0.001
UDP-2-acetamido-2,6-dideoxy-beta-L-talose 2-epimerase5.1.3.282458571783087.23666P < 0.001
ATP phosphohydrolase (ABC-type, molybdate-importing)7.3.2.51578151119027.18666P < 0.001
sucrose:(1->4)-alpha-D-glucan 4-alpha-D-glucosyltransferase2.4.1.41480951022847.16666P < 0.001
UDP-N-acetyl-2-amino-2-deoxy-alpha-D-glucuronate:NAD+ 3-oxidoreductase1.1.1.3351722091248417.08666P < 0.001
an acyl-[acyl-carrier protein]:phosphate acyltransferase2.3.1.2741854451390907.05666P < 0.001
FMNH2:NAD(P)+ oxidoreductase1.5.1.391564781071797.02666P < 0.001
cellobiose:phosphate alpha-D-glucosyltransferase2.4.1.201657951177856.98666P < 0.001
4-beta-D-xylan xylohydrolase3.2.1.373084122336676.87666P < 0.001
crossover junction endodeoxyribonuclease3.1.21.103411162607196.82666P < 0.001
nucleoside-2′,3′-cyclic-phosphate 3′-nucleotidohydrolase3.1.4.163214642428306.82666P < 0.001
UDP-glucuronate 4-epimerase5.1.3.62806502075016.80666P < 0.001
S-adenosyl-L-methionine:precorrin-2 C20-methyltransferase2.1.1.1302932712275486.79666P < 0.001
S-adenosyl-L-methionine:cobalt-factor-II C20-methyltransferase2.1.1.1512931242274086.78666P < 0.001
dipeptidase E3.4.13.212042901495036.73666P < 0.001
GTP:alpha-D-mannose-1-phosphate guanylyltransferase2.7.7.133314622529986.69666P < 0.001
ATP:1,2-diacyl-sn-glycerol 3-phosphotransferase2.7.1.1073332912596976.61666P < 0.001
L-selenocysteine selenide-lyase (L-alanine-forming)4.4.1.163371722606226.56666P < 0.001
1,4-beta-D-mannooligosaccharide:phosphate alpha-D-mannosyltransferase2.4.1.3193004272273526.54666P < 0.001
4-O-beta-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate alpha-D-mannosyltransferase2.4.1.3203004272273526.54666P < 0.001
sortase B3.4.22.711613581193636.52666P < 0.001
cobalt-precorrin 5A acylhydrolase3.7.1.121607311189006.48666P < 0.001
6-carboxy-5,6,7,8-tetrahydropterin ammonia-lyase4.3.99.33290102533286.47666P < 0.001
precorrin-8 11,12-methylmutase5.4.99.601613591198066.46666P < 0.001
precorrin-8X 11,12-methylmutase5.4.99.611613591198066.46666P < 0.001
UDP-alpha-D-glucose:NAD+ 6-oxidoreductase1.1.1.223418772679686.45666P < 0.001
4-O-beta-D-mannopyranosyl-D-glucopyranose:phosphate alpha-D-mannosyltransferase2.4.1.2812945632215466.44666P < 0.001
O-acetyl-ADP-D-ribose carboxylesterase3.1.1.1062327551783806.39666P < 0.001
2′-deoxyribonucleoside-5′-diphosphate:thioredoxin-disulfide 2′-oxidoreductase1.17.4.13550182812246.39666P < 0.001
3′-ribonucleotide phosphohydrolase3.1.3.63032022295686.38666P < 0.001
acetyl-CoA:alkane-alpha,omega-diamine N-acetyltransferase2.3.1.573418062694666.32666P < 0.001
5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase2.1.2.13566062832416.30666P < 0.001
carbonic acid hydro-lyase (carbon-dioxide-forming)4.2.1.13212952489576.29666P < 0.001
L-isoleucine:tRNAIle ligase (AMP-forming)6.1.1.53640942922096.24666P < 0.001
DNA-6-O-methylguanine/DNA-4-O-methylthymine:[protein]-L-cysteine S-methyltransferase2.1.1.633656152939756.16666P < 0.001
NADH:hydroperoxide oxidoreductase1.11.1.263232752520456.11666P < 0.001
L-glutamate:tRNAGlu ligase (AMP-forming)6.1.1.173214962620666.08666P < 0.001
bleomycin hydrolase3.4.22.403144612431756.08666P < 0.001
L-cysteine-S-conjugate thiol-lyase (deaminating; 2-aminoprop-2-enoate-forming)4.4.1.133639632932376.08666P < 0.001
UDP-alpha-D-glucose:alpha-D-galactose-1-phosphate uridylyltransferase2.7.7.121700721296506.05666P < 0.001
peptidoglycan amidohydrolase3.5.1.283632332939645.99666P < 0.001
adenine-DNA deoxyribohydrolase (adenine-releasing)3.2.2.313551242853005.95666P < 0.001
D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-dependent)5.4.2.113195822502085.95666P < 0.001
tRNA N6-(3-methylbut-2-en-1-yl)-adenine37:sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-(methylsulfanyl)transferase2.8.4.33701153012245.93666P < 0.001
10-formyltetrahydrofolate:5′-phosphoribosylglycinamide N-formyltransferase2.1.2.23633742953585.89666P < 0.001
peptidase Do3.4.21.1072766602246375.87666P < 0.001
poly(deoxyribonucleotide)-3′-hydroxyl:5′-phospho-poly(deoxyribonucleotide) ligase (NAD+)6.5.1.23724633044125.85666P < 0.001
methionyl aminopeptidase3.4.11.183724623044265.85666P < 0.001
prenyl-diphosphate:adenine37 in tRNA prenyltransferase2.5.1.753718633039245.84666P < 0.001
ATP:pyridoxal 5′-phosphotransferase2.7.1.353290322617865.80666P < 0.001
L-rhamnose aldose-ketose-isomerase5.3.1.143073932414015.80666P < 0.001
peptide-methionine:thioredoxin-disulfide S-oxidoreductase [methionine (R)-S-oxide-forming]1.8.4.122577982039355.76666P < 0.001
deoxyribonuclease IV3.1.21.23536172874045.73666P < 0.001
alpha-L-rhamnoside rhamnohydrolase3.2.1.403180532527445.68666P < 0.001
ATP phosphohydrolase (ABC-type, Zn2+-importing)7.2.2.203312542645205.66666P < 0.001
L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)4.1.2.193076322435905.63666P < 0.001
6-deoxy-6-sulfo-D-fructose:D-glyceraldehyde-3-phosphate glyceronetransferase2.2.1.14173335.6041P < 0.001
ATP:L-rhamnulose 1-phosphotransferase2.7.1.53192572556415.50666P < 0.001
ATP:glycerol 3-phosphotransferase2.7.1.302714602239705.50666P < 0.001
(R)-S-lactoylglutathione methylglyoxal-lyase (isomerizing; glutathione-forming)4.4.1.53413792800795.36666P < 0.001
exodeoxyribonuclease V3.1.11.52247101814065.36666P < 0.001
NAD(H) phosphohydrolase3.6.1.223358982753295.26666P < 0.001
L-alanyl-D-glutamate epimerase5.1.1.202119841680655.24666P < 0.001
CTP:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase2.7.7.603422402896195.12666P < 0.001
beta-D-fructofuranoside fructohydrolase3.2.1.262048151691064.91666P < 0.001
beta-lactam hydrolase3.5.2.63288922767294.76666P < 0.001
GTP 7,8-8,9-dihydrolase (diphosphate-forming)3.5.4.253631913101734.54666P < 0.001
D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)4.1.99.123631903101734.54666P < 0.001
5-amino-6-(D-ribitylamino)uracil butanedionetransferase2.5.1.783630213100464.54666P < 0.001
5-amino-6-(5-phospho-D-ribitylamino)uracil:NADP+ 1′-oxidoreductase1.1.1.1933560703027304.53666P < 0.001
2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine 2-aminohydrolase3.5.4.263560703027304.53666P < 0.001
D-mannose-6-phosphate aldose-ketose-isomerase5.3.1.83499592980384.51666P < 0.001
5′-ribonucleotide phosphohydrolase3.1.3.53634173128184.40666P < 0.001
peptidoglycan-N-acetylglucosamine amidohydrolase3.5.1.1043340652891364.35666P < 0.001
fragilysin3.4.24.74772621374.30487P < 0.001
UTP:alpha-D-glucose-1-phosphate uridylyltransferase2.7.7.91800421468294.27666P < 0.001
adenosylcobinamide-GDP:alpha-ribazole ribazoletransferase2.7.8.263361012899804.27666P < 0.001
Fe(II):oxygen oxidoreductase ([FeO(OH)]core-producing)1.16.3.23438862956424.23666P < 0.001
D-stereospecific aminopeptidase3.4.11.191467321146084.23666P < 0.001
D-glycerate:NAD+ oxidoreductase1.1.1.293047902583954.21666P < 0.001
ATP:dTMP phosphotransferase2.7.4.91827271498044.20666P < 0.001
ATP:UDP-N-acetyl-alpha-D-glucosamine 3′-phosphotransferase2.7.1.176730431214.15664P < 0.001
L-histidinol:NAD+ oxidoreductase1.1.1.233607763121294.13666P < 0.001
queuosine34 in tRNA:acceptor oxidoreductase1.17.99.63658033187094.13666P < 0.001
L-lysine:tRNALys ligase (AMP-forming)6.1.1.63728373258564.10666P < 0.001
(R)-lactate hydro-lyase (adding N-acetyl-D-glucosamine 6-phosphate; N-acetylmuramate 6-phosphate-forming)4.2.1.1263154092680454.06666P < 0.001
CoA-[4′-phosphopantetheine]:apo-[acyl-carrier protein] 4′-pantetheinephosphotransferase2.7.8.71704651397214.06666P < 0.001
D-altronate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)4.2.1.73075682628544.05666P < 0.001
(6R)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide 6-epimerase5.1.99.63737213278863.98666P < 0.001
UTP:L-glutamine amido-ligase (ADP-forming)6.3.4.23696333245263.96666P < 0.001
beta-D-4-deoxy-Delta4-GlcAp-(1->3)-beta-D-GalNAc6S hydrolase3.2.1.1803002452583913.94666P < 0.001
D-erythro-1-(imidazol-4-yl)glycerol-3-phosphate hydro-lyase [3-(imidazol-4-yl)-2-oxopropyl-phosphate-forming]4.2.1.193617923162333.94666P < 0.001
1-(5-phospho-beta-D-ribosyl)-ATP:diphosphate phospho-alpha-D-ribosyl-transferase2.4.2.173618223162713.94666P < 0.001
2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate-forming)4.6.1.123751993299063.93666P < 0.001
1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide aldose-ketose-isomerase5.3.1.163617273162613.93666P < 0.001
[poly-N-acetyl-D-glucosaminyl-(1->4)-(N-acetyl-D-muramoylpentapeptide)]-diphosphoundecaprenol:[N-acetyl-D-glucosaminyl-(1->4)-N-acetyl-D-muramoylpentapeptide]-diphosphoundecaprenol disaccharidetransferase2.4.1.1293673313223813.93666P < 0.001
5-[(5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate-lyase (L-glutamine-hydrolysing; 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide-forming)4.3.2.103631903179253.91666P < 0.001
dTDP-alpha-D-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-alpha-D-glucose-forming)4.2.1.463633853183893.90666P < 0.001
ATP:(d)CMP phosphotransferase2.7.4.253701173258013.88666P < 0.001
L-histidinol-phosphate:2-oxoglutarate aminotransferase2.6.1.93721173279343.85666P < 0.001
5,10-methylenetetrahydrofolate,FADH2:dUMP C-methyltransferase2.1.1.1481436851151123.81666P < 0.001
orotidine-5′-phosphate carboxy-lyase (UMP-forming)4.1.1.233768413330513.81666P < 0.001
N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide:L-glutamine amido-ligase (ADP-forming)6.3.5.33766903329923.80666P < 0.001
alpha-D-galactoside galactohydrolase3.2.1.223518693092623.80666P < 0.001
oligonucleotidase3.1.13.33610853184013.79666P < 0.001
ATP:pseudouridine 5′-phosphotransferase2.7.1.831431921148313.78666P < 0.001
citrate(isocitrate) hydro-lyase (cis-aconitate-forming)4.2.1.33703443270043.78666P < 0.001
adenosine-3′(2′),5′-bisphosphate 3′(2′)-phosphohydrolase3.1.3.73634183213453.74666P < 0.001
adenylyl-molybdopterin:molybdate molybdate transferase (AMP-forming)2.10.1.11558621283093.71666P < 0.001
sn-glycerol-3-phosphate:NAD(P)+ 2-oxidoreductase1.1.1.943704383286043.70666P < 0.001
isocitrate:NADP+ oxidoreductase (decarboxylating)1.1.1.423612303193823.70666P < 0.001
short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase1.3.8.11409721132313.70666P < 0.001
acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl-forming]2.3.3.13625153211953.65666P < 0.001
UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase3.6.1.57560120563.64644P < 0.001
D-mannonate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)4.2.1.83294392881353.63666P < 0.001
ribonuclease M53.1.26.81468131199613.60666P < 0.001
(S)-4-hydroxymandelate:oxygen 1-oxidoreductase1.1.3.461483081221833.58666P < 0.001
S-adenosyl-L-methionine:tRNA (carboxymethyluridine34-5-O)-methyltransferase2.1.1.22986343.5087P < 0.001
5,10-methylenetetrahydrofolate:tRNA (uracil54-C5)-methyltransferase2.1.1.741460471200063.48666P < 0.001
aldehyde:ferredoxin oxidoreductase1.2.7.51400991144743.47666P < 0.001
cobalt-precorrin-6B:NAD+ oxidoreductase1.3.1.1061501011251203.41666P < 0.001
precorrin-6B:NADP+ oxidoreductase1.3.1.541501011251203.41666P < 0.001
(3S)-3-hydroxyacyl-CoA hydro-lyase4.2.1.171462591213433.40666P < 0.001
coproporphyrinogen-III:S-adenosyl-L-methionine oxidoreductase (decarboxylating)1.3.98.31835671567503.31666P < 0.001

Looking at the weaker statistical significance (where we expect 80 to be false positive) we have just 87 items. In other words, the ones below should likely be excluded from any analysis

Enzyme NameECKEYWith Long COVIDWithout
Long
COVID		T-ScoreDFProbability
protein-Npi-phospho-L-histidine:D-glucose Npi-phosphotransferase2.7.1.1991503951260463.30666P < 0.01
ATP:4-methyl-5-(2-hydroxyethyl)thiazole 2-phosphotransferase2.7.1.501893601640623.30666P < 0.01
D-glucose-6-phosphate:NAD+ oxidoreductase1.1.1.361368883.26359P < 0.01
ATP:alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase2.7.1.181386913.26346P < 0.01
S-adenosyl-L-methionine:3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase2.1.1.294386913.26346P < 0.01
S-adenosyl-L-methionine:23S rRNA (guanine745-N1)-methyltransferase2.1.1.1871477221232113.25666P < 0.01
kanosamine-6-phosphate phosphohydrolase3.1.3.92364883.25363P < 0.01
kanosamine 6-phosphate:2-oxoglutarate aminotransferase2.6.1.104368923.24365P < 0.01
ATP:L-glutamine N5-phosphotransferase2.7.3.13241333.2354P < 0.01
GDP-beta-L-fucose:beta-D-Gal-(1->3)-alpha-D-GalNAc-(1->3)-alpha-D-GalNAc-diphospho-ditrans,octacis-undecaprenol alpha-1,2-fucosyltransferase2.4.1.308390893.22326P < 0.01
UDP-alpha-D-galactose:N-acetyl-alpha-D-galactosaminyl-R beta-1,3-galactosyltransferase (configuration-inverting)2.4.1.122390893.22326P < 0.01
UDP-alpha-D-glucose:N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol beta-1,3-glucosyltransferase2.4.1.305390893.22326P < 0.01
UDP-N-acetyl-alpha-D-galactosamine:N-acetyl-alpha-D-galactosaminyl-diphospho-ditrans,octacis-undecaprenol alpha-1,3-N-acetyl-D-galactosyltransferase2.4.1.306390893.22326P < 0.01
fluoroacetyl-CoA hydrolase3.1.2.292428212110223.20666P < 0.01
GDP-alpha-D-mannose:alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]n-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 2,3-alpha-mannosyltransferase (configuration-retaining)2.4.1.371387973.20347P < 0.01
GDP-alpha-D-mannose:alpha-D-mannosyl-(1->3)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-alpha-mannosyltransferase (configuration-retaining)2.4.1.349387973.20347P < 0.01
carbamoyl-phosphate:L-ornithine carbamoyltransferase2.1.3.31936661690293.19666P < 0.01
ATP:L-homoserine O-phosphotransferase2.7.1.391694241444043.19666P < 0.01
GDP-alpha-D-mannose:N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-alpha-mannosyltransferase (configuration-retaining)2.4.1.348386983.18346P < 0.01
16S rRNA-uridine516 uracil mutase5.4.99.191912281672103.17666P < 0.01
2,3-dihydroxybenzoate:oxygen 3,4-oxidoreductase (ring-opening)1.13.11.1456243.1772P < 0.01
ATP:molybdopterin adenylyltransferase2.7.7.751509831278383.16666P < 0.01
GDP-beta-L-colitose:beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine L-colitosyltransferase (configuration-inverting)2.4.1.341391963.16326P < 0.01
pyrimidine-nucleoside:phosphate (2′-deoxy)-alpha-D-ribosyltransferase2.4.2.21609661377553.13666P < 0.01
ATP phosphohydrolase (ABC-type, D-galactose-importing)7.5.2.111501901266613.13666P < 0.01
protein-Npi-phospho-L-histidine:D-fructose Npi-phosphotransferase2.7.1.2021501701271513.12666P < 0.01
diphosphate phosphohydrolase3.6.1.12049021807743.10666P < 0.01
2-oxo-acid carboxy-lyase (aldehyde-forming)4.1.1.1356953.09358P < 0.01
NAD+:diphthamide-[translation elongation factor 2] N-(ADP-D-ribosyl)transferase2.4.2.363911033.08326P < 0.01
GDP-4-dehydro-alpha-D-rhamnose 3-hydro-lyase4.2.1.1683911033.08326P < 0.01
acetyl-CoA:L-glutamate N-acetyltransferase2.3.1.11982821745523.07666P < 0.01
(8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate lyase (cyclic pyranopterin phosphate-forming)4.6.1.171648161420923.06666P < 0.01
GTP 3′,8-cyclase [(8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate-forming]4.1.99.222072831801493.05666P < 0.01
ADP-L-glycero-D-manno-heptose 6-epimerase5.1.3.2033154226353.03666P < 0.01
malonyl-CoA:malonyl-CoA malonyltransferase (decarboxylating, phloroglucinol-forming)2.3.1.2535693.0347P < 0.01
N2-acetyl-L-ornithine:L-glutamate N-acetyltransferase2.3.1.351959171724693.03666P < 0.01
dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose:2-oxoglutarate aminotransferase2.6.1.10648253.0161P < 0.01
L-threonine ammonia-lyase (2-oxobutanoate-forming)4.3.1.192873082598803.01666P < 0.01
acetyl-CoA:dTDP-4-amino-4,6-dideoxy-alpha-D-glucose N-acetyltransferase2.3.1.2093911093.01326P < 0.01
acetyl-CoA:GDP-4-amino-4,6-dideoxy-alpha-D-mannose N-acetyltransferase2.3.1.2273911093.01326P < 0.01
acetyl-CoA:polysialic-acid O-acetyltransferase2.3.1.1363911093.01326P < 0.01
UDP-alpha-D-galactose:N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-beta-galactosyltransferase (configuration-inverting)2.4.1.3033911093.01326P < 0.01
phosphoenolpyruvate:protein-L-histidine Npi-phosphotransferase2.7.3.91983271751542.99666P < 0.01
beta-D-galactopyranosyl-(1->3)-N-acetyl-D-hexosamine:phosphate galactosyltransferase2.4.1.2111572151348372.98666P < 0.01
acyl phosphoate:sn-glycerol 3-phosphate acyltransferase2.3.1.2751881801658852.97666P < 0.01
(S)-3-hydroxybutanoyl-CoA:NADP+ oxidoreductase1.1.1.1571524421306082.95666P < 0.01
prephenate:NAD+ oxidoreductase (decarboxylating)1.3.1.122092571865582.95666P < 0.01
GDP-beta-L-fucose:beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-R 4I-alpha-L-fucosyltransferase (configuration-inverting)2.4.1.6522456126482.95648P < 0.01
GDP-beta-L-fucose:beta-D-galactosyl-(1->4)-N-acetyl-D-glucosaminyl-R 3-alpha-L-fucosyltransferase (configuration-inverting)2.4.1.15222456126482.95648P < 0.01
S-adenosyl-L-methionine:tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2′-O)-methyltransferase2.1.1.2072032981803002.95666P < 0.01
Ste24 endopeptidase3.4.24.84805452702.94642P < 0.01
dTDP-4-amino-4,6-dideoxy-alpha-D-glucose:2-oxoglutarate aminotransferase2.6.1.333921162.94327P < 0.01
formate:NADP+ oxidoreductase1.17.1.10930060922.93618P < 0.01
[biotin carboxyl-carrier protein]-N6-carboxybiotinyl-L-lysine:acetyl-CoA:carboxytransferase2.1.3.153448443106162.92666P < 0.01
2-hydroxy-2H-chromene-2-carboxylate—(3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate isomerase5.99.1.448172.9288P < 0.01
acetyl-CoA:acetyl-CoA C-acetyltransferase2.3.1.91527241312472.92666P < 0.01
1H-pyrrole-2-carbonyl-[peptidyl-carrier protein]:FADH2 oxidoreductase (chlorinating)1.14.19.565782.9243P < 0.01
phosphoenolpyruvate:D-erythrose-4-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming)2.5.1.542018751790972.91666P < 0.01
SpoIVB peptidase3.4.21.1161586651370292.90666P < 0.01
ATP:adenosine 5′-phosphotransferase2.7.1.20855057452.90614P < 0.01
ATP:selenide, water phosphotransferase2.7.9.31602181390602.89666P < 0.01
CTP:molybdenum cofactor cytidylyltransferase2.7.7.761583411366622.89666P < 0.01
ATP phosphohydrolase (ABC-type, polar-amino-acid-importing)7.4.2.11991971768582.86666P < 0.01
6-phospho-beta-D-glucosyl-(1->4)-D-glucose glucohydrolase3.2.1.861513591305222.85666P < 0.01
D-mannonate:NAD+ 5-oxidoreductase1.1.1.571569421357442.83666P < 0.01
acetyl-CoA:N-terminal L-alanyl-[S5 protein of 30S ribosome] N-acetyltransferase2.3.1.2673342493050712.82666P < 0.01
23S rRNA-uridine955/2504/2580 uracil mutase5.4.99.241739821529792.79666P < 0.01
aspartyl aminopeptidase3.4.11.211748111543212.75666P < 0.01
adenine aminohydrolase3.5.4.21656891457302.73666P < 0.01
D-threo-aldose:NAD+ 1-oxidoreductase1.1.1.1223181462.72529P < 0.01
N-acyl-D-glucosamine-6-phosphate 2-epimerase5.1.3.91693111491932.71666P < 0.01
(S)-2-haloacid halidohydrolase3.8.1.21551731350182.71666P < 0.01
peptide-L-methionine:thioredoxin-disulfide S-oxidoreductase [L-methionine (S)-S-oxide-forming]1.8.4.113125462839312.71666P < 0.01
S-adenosyl-L-methionine:precorrin-3B C17-methyltransferase2.1.1.1311616831415682.70666P < 0.01
S-adenosyl-L-methionine:cobalt-factor III C17-methyltransferase (ring contracting)2.1.1.2721615481414422.69666P < 0.01
23S rRNA-uridine2605 uracil mutase5.4.99.223568493242932.69666P < 0.01
4-hydroxybenzoyl-CoA hydrolase3.1.2.23851556952.67538P < 0.01
phosphate-monoester phosphohydrolase (alkaline optimum)3.1.3.13505423178572.67666P < 0.01
aceneuramate pyruvate-lyase (N-acetyl-D-mannosamine-forming)4.1.3.33083992810172.65666P < 0.01
ADP-D-ribose ribophosphohydrolase3.6.1.133236562964522.65666P < 0.01
Repressor LexA3.4.21.881948501743702.64666P < 0.01
pectin pectylhydrolase3.1.1.112732402449082.64666P < 0.01
S-methyl-5′-thioinosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase2.4.2.44831255822.62547P < 0.01
hydrogen:ferredoxin oxidoreductase1.12.7.2824557202.61609P < 0.01
phosphonoacetate phosphonohydrolase3.11.1.2920962612.60489P < 0.01
sortase A3.4.22.701709411512982.59666P < 0.01

I will leave it to the professional microbiologists to make sense of the 190 enzymes above. I should point out that the levels with Long COVID are always higher than the control. I saw the same pattern with Salicylate sensitive – Data And Research, but not as extreme (as with much fewer significant enzymes).

Bacteria Found Significant

The strongest associations are shown below. It is interesting to note that the t-scores are lower for bacteria than for enzymes. The clustering by enzymes was beneficial. We expect less than 2 false positives in this list. Note that the degrees of freedom (Df) is reflected of frequency found. df=38 means that 40 out of 668 samples reported this bacteria.

Tax rankTaxa NameWith
Long COVID		Without
Long COVID		T-ScoreDfProbability
speciesFaecalibacterium prausnitzii1381511096733.78666P < 0.001
genusPlanococcus41253.89118P < 0.001
genusAnaeroplasma1932837663.4974P < 0.001
classMollicutes577426103.65642P < 0.001
genusCoriobacterium173325.4138P < 0.001
speciesCoriobacterium glomerans173325.4138P < 0.001
genusKushneria54283.62148P < 0.001
phylumTenericutes577426103.65642P < 0.001
orderAnaeroplasmatales1932837663.4974P < 0.001
familyAnaeroplasmataceae1932837663.4974P < 0.001
speciesPlanococcus columbae41244.85108P < 0.001

The less significant ones are shown below:

Tax rankTaxa nameWith
Long COVID		Without
Long COVID		T-ScoreDfProbability
speciesLactobacillus letivazi28113.9312P < 0.01
speciesClostridium fallax84223.5332P < 0.01
speciesCorynebacterium xerosis755903.3448P < 0.01
species groupPseudomonas syringae group60253.1746P < 0.01
speciesCorynebacterium kutscheri186343.1233P < 0.01
genusComamonas289513.1161P < 0.01
speciesPeptoniphilus indolicus150303.1167P < 0.01
speciesPrevotella oulorum87523.0672P < 0.01
orderSphingobacteriales40382316622.99667P < 0.01
classSphingobacteriia40382316622.99667P < 0.01
familyAzonexaceae60202.9860P < 0.01
genusDechloromonas60202.9860P < 0.01
familyRhodocyclaceae71502.97413P < 0.01
genusMarinospirillum42282.87156P < 0.01
speciesEuzebya tangerina64462.79370P < 0.01
classNitriliruptoria64462.79370P < 0.01
orderEuzebyales64462.79370P < 0.01
familyEuzebyaceae64462.79370P < 0.01
genusEuzebya64462.79370P < 0.01
speciesClostridium caliptrosporum26172.7237P < 0.01
genusPedobacter1291796862.72656P < 0.01
speciesSphingobacterium bambusae4803152.70579P < 0.01
speciesPrevotella corporis18836452.69315P < 0.01
speciesDechloromonas hortensis34212.6856P < 0.01
familySphingobacteriaceae35765286162.59666P < 0.01

At this point, our first set of bacteria to look at are ones with a high df (and thus most commonly seen). This is a short list when we drop parent and child with the same numbers:

Tax rankTaxa nameWith
Long COVID		Without
Long COVID		TScoreDfProbability
orderSphingobacteriales40382316622.99667P < 0.01
speciesFaecalibacterium prausnitzii1381511096733.78666P < 0.001
familySphingobacteriaceae35765286162.59666P < 0.01
genusPedobacter1291796862.72656P < 0.01
phylumTenericutes577426103.65642P < 0.001

Comparing to published studies above

We have no agreement on identification of significant bacteria. The only bacteria in common was Faecalibacterium prausnitzii. This bacteria was cited in just one Pubmed studies on Long COVID. Many studies reported on it during the active COVID infection. This study reported it was lower. We found that it was higher. That study sample size was considerable smaller than us : 106 with Long COVID and 68 Control; they did not mention the significance level but used the term often seen when there was poor significance: “were characterized by”. This study cites “Faecalibacterium prausnitzii showed the largest inverse correlations with PACS at 6 months.” We are dealing with samples with different periods since onset.

The absence of bacteria in common is not unexpected given differences in methodologies. This is often seen when multiple studies on the same condition are done, non-replication of results. I refer the reader to this story

Three blind microbiologists attempt to describe the microbiome of an elephant…

See Blind men and an elephant

Comparing Suggestions

We have suggestions generated from the US National Library of Medicine studies, and we also have suggests from this analysis. These suggestions are generated by the Fuzzy Logic Artificial Intelligence on the Microbiome Prescription site. How do they compare?

Running with everything that is suggested (including prescription items) by both sets of data we found:

  • Agreement on 1255 items that will help
  • Disagreement on 396 items (one says help, one says hurt)

This is 76% agreement on suggestions that would help. This is surprisingly good given that Faecalibacterium prausnitzii are reported in opposite directions between these two sets. The best agreement was for:

  • Drug or “Non-drug” at 90.5% – with 95 items considered
  • Prescription other at 93.8% – with 933 items considered

This was not surprising because the data density for these two is good. For many other things, the data density is sparse — for example, for Prebiotics, Amino acids and Probiotics. There is almost no literature on how they impact many of the bacteria cited.

How to Use this data?

The root problem is having insufficient data in many vectors. As a fuzzy logic engineer, this does not concern me — we will simply make the best use of available data in the belief that it is better than working from no data.

The system on Microbiome Prescription uses the consensus system for treatment suggestions. You can process a microbiome using PubMed studies, process it again with the above data, and then get a list where the suggestions are in agreement. At present, the microbiome sample must be processed thru Biomesight because that is how the items of significance were detected. In time, other labs could reach sufficient data to get results.

To illustrate this process, I have done a video below using a sample from someone with Long COVID.

Related Blog Posts for those who are interested:

Data Availability: The samples and symptoms are available at: Microbiome Prescription Citizen Science Data Share

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.