Month: August 2025

Mast Cell Activation Syndrome: A New Perspective

Mast Cell Activation Syndrome (MCAS) has been a frustrating condition to deal with. It is likely that the microbiome is a factor but finding bacteria patterns has had poor results. Recently I did a post One Consistent Pattern Across Different Vendors Results where the agreement from different lab tests on the bacteria involved simply had not agreement (see this page to illustrate). Using  estimates on compounds and enzymes using KEGG: Kyoto Encyclopedia of Genes and Genomes went two ways:

  • enzymes associations was worse than bacteria
  • compound produced was far better than bacteria, 31x better

I decided to drill into these associations restricted it to associations seen in ALL of uBiome, Biomesight and Ombre dataset. The goal is to do a manual walkthrough of using this data to identify issues and potential solutions.

Logic Flow

  1. Obtain a large collection of microbiome samples process through different labs (in our case 3)
  2. Estimate the net amount of compound produce from each sample
  3. Using the symptom annotation, determine which compound are significant using chi2
  4. Identify the compounds that are significant for all three labs (concurrent)
  5. Remove the compounds that only occur in a few labs. Assume they are probable noise
  6. Take a shotgun sample from an individual and compute the compounds
  7. Identify where we have compound matching 5 (same direction)
  8. Ignore/discard compound that are not produced/substrate by the bacteria in sample
  9. Create a list by reversing taxa->Compound to compound->Taxa that are present in sample
  10. Pass the bacteria list with desired shift(increase/decrease) to the Fuzzy Logic Expert System to generate suggestions
  11. List the suggestions

[Step 4 Above] The compounds identified are below with ALL OF THEM BEING LOW:

KEGG IdentifierName (linked to KEGG site)
C04030(2,3-Dihydroxybenzoyl)adenylate
C04236(2S)-2-Isopropyl-3-oxosuccinate
C20844(2Z,4S,5R)-2-Amino-4,5,6-trihydroxyhex-2-enoate
C01186(3S,5S)-3,5-Diaminohexanoate
C20845(4S,5R)-4,5,6-Trihydroxy-2-iminohexanoate
C22385(L-Cysteinyl)adenylate
C01143(R)-5-Diphosphomevalonate
C00810(R)-Acetoin
C01769(S)-Acetoin
C11826[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-g-D-Glu-L-Lys-D-Ala-D-Ala)]n-diphosphoundecaprenol
C01281[L-Glutamate:ammonia ligase (ADP-forming)]
C218791-(5-O-Phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate
C011592,3-Bisphospho-D-glycerate
C172342-Aminobut-2-enoate
C026312-Isopropylmaleate
C058484-Hydroxy-3-polyprenylbenzoate
C218775-Carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate
C222675-Methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA
C222665-Methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA
C01299Adenylyl-[L-glutamate:ammonia ligase (ADP-forming)]
C05414all-trans-Phytofluene
C05430all-trans-zeta-Carotene
C19875alpha-Kdo-(2->8)-alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA
C01563Carbamate
C20969Carboxyphosphate
C00417cis-Aconitate
C19724Cobyrinate c-monamide
C02218Dehydroalanine
C15853Dehydrospermidine
C06040Diglucosyldiacylglycerol
C11930dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose
C05359e- (electron)
C05730Glutathionylspermidine
C22173Harderoheme III
C02985L-Fucose 1-phosphate
C16238Lipoyl-AMP
C19611Manganese(3+)
C15854N-(4-Aminobutylidene)-[eIF5A-precursor]-lysine
C03406N-(L-Arginino)succinate
C21009N4-Aminopropylspermidine
C03794N6-(1,2-Dicarboxyethyl)-AMP
C18060N-Acetyl-alpha-D-galactosamine 1-phosphate
C05379Oxalosuccinate
C01241Phosphatidyl-N-methylethanolamine
C00404Polyphosphate
C15527Precorrin 1
C03427Prephytoene diphosphate
C21177Prokaryotic ubiquitin-like protein
C21878Pyridinium-3-carboxy-5-thiocarboxylic acid mononucleotide
C03541THF-polyglutamate
C19080tRNA with a 3′ CC end
C22409UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine

The numbers could be low due to either:

  • Not enough being produced
  • More being consumed than being produced
  • Severe skewness combined with low occurance

Bacteria produces and consumes the above metabolites/compounds.

We are able to compute the impact of probiotics on the above, these are listed under Probiotics modeled on Compounds on this link. None makes it better, in fact all are predicted to make things worse. Checking PubMed (while some probiotics may help), the number of studies are surprisingly sparse. Sparse studies for something like this suggests that there may be a large number of unpublished studies showing no effect or a negative effect. These unfavorable studies are very rarely published, especially when funded by someone owning the patent of the probiotic being tested.

Trying this approach on a Shotgun Sample of someone with MCAS [Step 5]

There are 52 compounds identified above. I have a Thorne sample. 42 of the compounds were less than 1%ile, 6 were over 50%ile. The pattern was obtained using this trio of 16s-labs (ubiome, biomesight and ombre) and the pattern appears to hold true for a sample from a shotgun analysis. We have 80% agreement when randomness would suggest < 2% agreement.

Looking at the details, we see that most of the 42 had no bacteria producing these compounds. This suggests that we are dealing with sparse data and possible false identification. Restricting to those reported as > 0%ile with over 200 samples we ended up with just 11 compounds.

CompoundSamples
cis-Aconitate3860
N-(L-Arginino)succinate5806
Oxalosuccinate3613
4-Hydroxy-3-polyprenylbenzoate6042
UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine5407
N6-(1,2-Dicarboxyethyl)-AMP6216
N-Acetyl-alpha-D-galactosamine 1-phosphate6118
Prokaryotic ubiquitin-like protein5072
(R)-5-Diphosphomevalonate5996
2,3-Bisphospho-D-glycerate6115
(L-Cysteinyl)adenylate5028

[Step 7 Above] Returning to our Shotgun sample above, we found the following are low.

Working backwards from these 4, we end up with 3,953 taxa on our first pass. For many of these bacteria there were none reported hence the challenge of encouraging bacteria that are not there!!!

Working from what is there! [Step 9/10]

Using cis-Aconitate and N-Acetyl-alpha-D-galactosamine 1-phosphate , we want to reduce consumers and increase producers. The result is that we want to:

  • Increase these bacteria (most significant is at top)
    • Corynebacterium diphtheriae
    • Streptococcus anginosus
    • Rhodopseudomonas palustris
    • Ralstonia solanacearum
    • Pseudomonas oryzihabitans
    • Sorangium cellulosum
    • Pseudomonas putida
  • Decrease these bacteria ((most significant is at bottom)
    • Cupriavidus necator
    • Cupriavidus basilensis
    • Thermaerobacter sp. FW80

Note we are talking species here. KEGG is actually at the strain level and we extrapolated to species. Passing this data to the fuzzy logic expert system we get as suggestions [Step 11]:

  • henopodium quinoa {Quinoa}
  • hydromorphone – an addictive pain killer
  • proton-pump inhibitors (prescription)
  • synthetic disaccharide derivative of lactose {Lactulose}
  • Moringa Oleifera {Moringa}
  • Limosilactobacillus fermentum {L. fermentum}
  • Heyndrickxia coagulans {B. coagulans}
  • Latilactobacillus sakei {Lactobacillus sakei}

Bottom line, it is possible to get suggestions. The route is not direct. The suggestions above are typically viewed as safe (except the one crossed out), and thus I will pass it along to the person whose sample I used. At the end of multiple steps, we ended up with four (4) compounds that mapped to some 10 bacteria to shift. Those bacteria resulted in just 7 suggestions. We are travelling well outside of the mapped world.

From Perplexity AI

To increase or decrease the abundance of the listed bacteria, specific strategies should be considered, but many target species are not commonly sought for probiotic modulation due to their environmental, pathogenic, or niche-specific nature. Below, approaches to influence each are summarized when evidence is available.

Increase These Bacteria

  • Corynebacterium diphtheriae: There is no safe or recommended method to purposely increase C. diphtheriae, as it is a human pathogen responsible for diphtheria, a serious disease. Laboratory studies using animal models suggest that general Actinobacteria (the phylum to which Corynebacterium belongs) can be modulated using certain yeast probiotics or lactic acid bacteria in animal models, but these findings are not intended or safe for human manipulation targeting pathogenic species. Increasing this bacterium is not medically advised.
  • Streptococcus anginosus: This member of the Streptococcus anginosus group is a commensal found mainly in the mouth, throat, and gut but is also opportunistically pathogenic. There is currently no evidence-based supplement or intervention to selectively increase S. anginosus in humans; it can be affected by local tissue conditions, diet, and the existing microbiome, but any intervention to increase such bacteria outside of medical settings is not recommended.
  • Rhodopseudomonas palustris: This bacterium is environmental and photosynthetic, rarely present in the human body. In agricultural or industrial settings, it is cultured using media containing carbon (like molasses), nitrogen (like corn steep liquor), and trace minerals, kept at slightly acidic to neutral pH and moderate temperatures (around 37°C). There is no role for increasing this bacteria in humans; it is used as a soil and water probiotic for plants.
  • Ralstonia solanacearum, Pseudomonas oryzihabitans, Sorangium cellulosum, Pseudomonas putida: These are mainly environmental, soil, or water-dwelling microbes. There is no supplement or dietary approach to increase these in the human gut or on human mucosa, and such actions are not studied for human health.

Decrease These Bacteria

  • Cupriavidus necator: This environmental bacterium can be suppressed in biotechnological fermentations by nutrient limitation (especially removing nitrogen or phosphorus), but there is no guidance for targeting this in the human body, as it is not a usual component of the human microbiome. In environmental settings, its growth is limited by removing accessible carbon, nitrogen, or phosphate sources.
  • Cupriavidus basilensis: Similar to C. necator, mainly handled in environmental and fermentation settings; standard medical interventions if infection occurs would use specific antibiotics based on sensitivity.
  • Thermaerobacter sp. FW80: This is a thermophilic (heat-loving) environmental bacterium not typically present in or relevant to humans. Methods to decrease it would involve lowering environmental temperatures, not relevant to dietary or supplement choices.

Practical Notes

  • Most of the bacteria on your list are not normal human microbiome residents and manipulating them carries significant health risks or is not practically or ethically possible.
  • For environmental and plant-associated bacteria (such as R. palustris, P. putida, Ralstonia, etc.), enrichment is done in laboratory or agricultural settings with nutrient and temperature controls but is not safe or meaningful for humans.
  • For bacteria that are pathogens or opportunists (C. diphtheriae, S. anginosus), intentional enrichment is never recommended.
  • For reducing rare environmental or opportunistic bacteria in humans, general good hygiene and avoiding immunosuppression help, while in clinical cases, antibiotics may be used based on sensitivity.

One Consistent Pattern Across Different Vendors Results

In my prior post, Patterns of Microbiome Distributions Across Different Vendors, we saw that the distribution patterns were not consistent. With annotated samples from several different vendors, it was logical to see if there was consistency of bacteria identified across vendors for specific symptoms. This question was directed to me by Chidozie Ojobor, Ph.D.   The results can be viewed on my Special Studies page.

This page hunts for statistical association with P < 0.001. The results shown are not only for bacteria, but estimates on compounds and enzymes using KEGG: Kyoto Encyclopedia of Genes and Genomes.

  • Definitions:
    • Singleton: only found in one of the labs
    • Pair: two labs reported the same
    • Triplet: all three labs reported the same

Given the difference of sample sizes and thus significance levels, some lack of consensus is expected.

  • uBiome: 790
  • Thryve: 1542
  • Biomesight: 4604

Over P < 0.001 data, we had the following

  • Looking at bacteria to symptom agreement
    • 19558 singleton relationships
    • 1914 pair relationships
    • 94 triplet relationship. or 0.436%
  • Looking at enzymes to symptom agreement
    • 74159 singleton relationships
    • 1629 pair relationships
    • 3 triplet relationship or 0.004%
  • Looking at compound to symptom agreement
    • 69147 singleton relationships
    • 9364 pair relationships
    • 6189 triplet relationships or 7.3%

Of special interest is when we went to P < 0.0001 for compound to symptom , we got significantly better results for compounds

  • 5952 singleton
  • 45439 pair relationships
  • 8153 triplet relationships or 13.7%

Bottom Line

While I am doing a naive estimate for compounds using KEGG data, the results support the model:

It is not the bacteria that causes the symptoms, it is the net amount of compounds produced by the bacteria that causes the symptoms. Surplus or deficiency of compounds can come from a vast array of different collections of bacteria. The bacteria may just be noise!!

This shifts any model to generate suggestions for a symptom to one further and significant indirection.

All of the date used is available as CSV files at Citizen Science Data Share.

Patterns of Microbiome Distributions Across Different Vendors

This week I had some discussion with several CEOs of various microbiome testing companies and the question came up:

Can we take the percentile threshold from the Kaltoft-Møldrup(KM) Range computation and apply it to other tests?

If this is likely true, then we reduce the impact of the Blue “Whale in the Room”

Fortunately, I have the data to reasonably answer that (for the common good) and show charts from some of the 60+ providers that have had samples uploaded. Most people in this area are very siloed into one lab, one way and cannot see the forest, only the leaf that they are on.

Lactobacillus

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bifidobacterium Longum

Biomesight

Ubiome

Ombre

Not sufficient data (3 samples had it)

PrecisionBiome

Vitract

Not sufficient data (3 samples had it)

Thorne

Faecalibacterium prausnitzii

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bottom Line

The first item of note: Two labs will typically (99% odds!!) report no Bifidobacterium Longum! In both cases, they do report it, but rarely detect any. Some medical practitioners (not knowing better about the test) will advocate this strongly as a probiotic with no safe evidence support that. This returns us to Scott’s quotation cited above, the blue whale!

While conceptually, the ability to transfer percentile ranges between labs is very appealing, it appears to be unsafe. Looking at the lower bounds for Faecalibacterium prausnitzii we see the following suggested (eye balling – make your own estimates):

  • Biomesight: 18%ile
  • uBiome: 30%ile
  • Ombre: 12%ile
  • PrecisionBiome: 30%ile
  • Vitract: 12%ile
  • Thorne: 20%ile

To me, this settles the issues. The KM percentile estimates for ranges cannot be transfered across labs. They are lab specific (and unlike the naive mean and standard deviation approach that ignores the high skews) require significant sample size.

The hidden Minefield in Microbiome Data and AI

Most contemporary AI models has a quiet unspoken assumption: data is a near normal distribution or Bayesian. This translate into assuming the data distribution has a statistical SKEWNESS of near zero(0). Often these models improve when the data is transformed to reduced skewness (often a log function is used). If a model improves with data normalization, it is skew sensitive.

A skew near zero is true for a very small percentage of taxa as shown by this table based on shotgun analysis of 1000 healthy individuals. This issue often has huge impacts for reference range computation.

NCBI
Taxon		namerankskewness
291645Bacteroides nordiispecies29.799
2759Eukaryotasuperkingdom29.558
333367Enterocloster asparagiformisspecies29.538
518636[Clostridium] asparagiforme DSM 15981strain29.538
117743Flavobacteriiaclass29.525
200644Flavobacterialesorder29.525
712633Streptococcus sp. oral taxon 431species28.849
2759692Streptococcus sp. Marseille-Q3533species28.405
712623Streptococcus sp. oral taxon 061species28.334
2972784Streptococcus sp. Marseille-Q6470species28.229
1386Bacillusgenus28.215
2005473Muribaculaceaefamily28.206
68892Streptococcus infantisspecies27.604
1736Eubacterium limosumspecies27.486
2714358Pusillibacter faecalisspecies27.285
2892397Pusillibactergenus27.285
4751Fungikingdom26.227
347253Streptococcus salivarius JIM8777strain26.222
2690837Eggerthella guodeyiniispecies26.159
2762318Weeksellaceaefamily25.877
1839799Streptococcus sp. FDAARGOS_192species25.823
4890Ascomycotaphylum25.785
468Moraxellaceaefamily25.736
2887326Moraxellalesorder25.736
72274Pseudomonadalesorder25.621
2682456Veillonella nakazawaespecies25.587
135621Pseudomonadaceaefamily25.569
469Acinetobactergenus25.496
1547Thomasclavelia ramosaspecies25.361
191303Turicibactergenus25.108
2810281Turicibacteraceaefamily25.108
387661Parabacteroides johnsoniispecies25.06
2529408Schaaliagenus24.99
1918540Muribaculumgenus24.929
1683Bifidobacterium angulatumspecies24.806
4892Saccharomycetalesorder24.79
4891Saccharomycetesclass24.79
1852377Actinomyces pacaensisspecies24.588
197614Streptococcus pasteurianusspecies24.543
1297617Intestinimonas butyriciproducensspecies24.533
1392389Intestinimonasgenus24.533
28127Hoylesella buccalisspecies24.515
2610896Streptococcus sp. LPB0220species24.27
1689Bifidobacterium dentiumspecies24.136
1871022Parolsenella massiliensisspecies24.122
286Pseudomonasgenus23.772
2974257Hoylesellagenus23.703
2735723Turicibacter bilisspecies23.682
1679Bifidobacterium longum subsp. longumsubspecies23.208
1944646Phoenicibacter congonensisspecies23.137
1981050Phoenicibactergenus23.137
1329Streptococcus canisspecies22.882
1316408Streptococcus sp. HSISM1species22.835
726Haemophilus haemolyticusspecies22.752
1505Paraclostridium sordelliispecies22.63
1849828Paeniclostridiumgenus22.63
1981510Monoglobus pectinilyticusspecies22.567
2039302Monoglobusgenus22.567
2834348Caproicibacteriumgenus22.417
186804Peptostreptococcaceaefamily22.213
49546Flavobacteriaceaefamily22.14
186817Bacillaceaefamily22.035
45634Streptococcus cristatusspecies21.74
1712675Turicibacter sp. H121species21.688
838Prevotellagenus21.625
86332Mogibacterium pumilumspecies21.611
1903409Erwiniaceaefamily21.56
2606626Sodaliphilus pleomorphusspecies21.511
2815786Sodaliphilusgenus21.511
1903414Morganellaceaefamily21.495
32067Leptotrichiagenus21.272
1129771Leptotrichiaceaefamily21.258
135625Pasteurellalesorder21.187
712Pasteurellaceaefamily21.187
1433513Streptococcus gwangjuensespecies21.148
1812935Enterobacter roggenkampiispecies21.039
2842531Solibaculumgenus20.918
2780922Solibaculum mannosilyticumspecies20.918
2944914Allocoprobacillus halotoleransspecies20.909
3059504Allocoprobacillusgenus20.909
76860Streptococcus constellatusspecies20.905
889201Streptococcus cristatus ATCC 51100strain20.893
206351Neisserialesorder20.791
199Campylobacter concisusspecies20.784
195Campylobacter colispecies20.759
724Haemophilusgenus20.749
481Neisseriaceaefamily20.706
43675Rothia mucilaginosaspecies20.655
482Neisseriagenus20.599
2598453Streptococcus sp. 116-D4species20.541
548Klebsiella aerogenesspecies20.51
39950Dialister pneumosintesspecies20.383
59201Salmonella enterica subsp. entericasubspecies20.349
133925Olsenellagenus20.343
729Haemophilus parainfluenzaespecies20.246
518635Bifidobacterium angulatum DSM 20098 = JCM 7096strain20.207
2948573Peptoniphilus sp. SAHP1species20.133
1328Streptococcus anginosusspecies20.096
2767842Lactiplantibacillusgenus20.094
1268Micrococcaceaefamily19.951
32207Rothiagenus19.951
3018741Cellulosilyticaceaefamily19.949
698776Cellulosilyticumgenus19.949
85006Micrococcalesorder19.899
2530390Muribaculum gordoncarterispecies19.888
2049Actinomycetaceaefamily19.868
2037Actinomycetalesorder19.868
53335Pantoeagenus19.864
72294Campylobacteraceaefamily19.835
194Campylobactergenus19.835
84642Aeromonadaceaefamily19.819
28037Streptococcus mitisspecies19.786
642Aeromonasgenus19.782
862965Haemophilus parainfluenzae T3T1strain19.769
158Treponema denticolaspecies19.679
162289Peptoniphilusgenus19.612
446660Adlercreutzia equolifaciensspecies19.516
33958Lactobacillaceaefamily19.511
28211Alphaproteobacteriaclass19.479
204441Rhodospirillalesorder19.456
165779Anaerococcusgenus19.293
433Acetobacteraceaefamily19.269
543314Eubacteriales Family XIII. Incertae Sedisfamily19.231
1434011Komagataeibactergenus19.071
65958Komagataeibacter oboediensspecies19.071
1485Clostridiumgenus18.944
938288Fenollaria massiliensisspecies18.89
1686313Fenollariagenus18.89
154288Turicibacter sanguinisspecies18.829
135614Lysobacteralesorder18.784
1578Lactobacillusgenus18.769
29547Campylobacterotaphylum18.752
3031852Epsilonproteobacteriaclass18.752
213849Campylobacteralesorder18.749
1686Bifidobacterium catenulatumspecies18.656
2942994Buchavirusgenus18.627
573Klebsiella pneumoniaespecies18.592
1776384Emergencia timonensisspecies18.586
1926556Emergenciagenus18.586
1639133Citrobacter portucalensisspecies18.58
1648923Bacillus paralicheniformisspecies18.559
136Spirochaetalesorder18.546
2845253Treponemataceaefamily18.545
157Treponemagenus18.545
506Alcaligenaceaefamily18.54
674529Bacteroides faecisspecies18.517
556259Bacteroides sp. D2species18.427
31979Clostridiaceaefamily18.413
365659Streptococcus mitis B6strain18.407
1266Sarcinagenus18.393
2726954Sarcina sp. JB2species18.393
1522[Clostridium] innocuumspecies18.363
150055Streptococcus lutetiensisspecies18.303
1352Enterococcus faeciumspecies18.288
556499Propionibacterium acidifaciensspecies18.151
78448Bifidobacterium pullorumspecies18.142
78344Bifidobacterium pullorum subsp. gallinarumsubspecies18.142
1903412Hafniaceaefamily18.071
1796646Muribaculum intestinalespecies18.017
2864143Adlercreutzia equolifaciens subsp. equolifacienssubspecies17.965
1384484Adlercreutzia equolifaciens DSM 19450strain17.965
292800Flavonifractor plautiispecies17.91
946234Flavonifractorgenus17.91
32033Lysobacteraceaefamily17.893
394340Adlercreutzia equolifaciens subsp. celatussubspecies17.87
1649459Hungatellagenus17.797
154046Hungatella hathewayispecies17.79
2144175Megasphaera stantoniispecies17.749
39778Veillonella disparspecies17.73
2682455Veillonella sp. S12025-13species17.715
1502Clostridium perfringensspecies17.684
544Citrobactergenus17.656
735Haemophilus parahaemolyticusspecies17.649
257758Streptococcus pseudopneumoniaespecies17.644
208962Escherichia albertiispecies17.64
1054460Streptococcus pseudopneumoniae IS7493strain17.619
1903411Yersiniaceaefamily17.596
680646Rothia mucilaginosa DY-18strain17.513
546Citrobacter freundiispecies17.495
2766537Caproicibacterium amylolyticumspecies17.401
629Yersiniagenus17.393
1114965Streptococcus parasanguinis FW213strain17.387
40323Stenotrophomonasgenus17.334
2819619Streptococcus toyakuensisspecies17.312
1590Lactiplantibacillus plantarumspecies17.249
1318Streptococcus parasanguinisspecies17.246
1343Streptococcus vestibularisspecies17.105
328812Parabacteroides goldsteiniispecies17.067
204455Rhodobacteralesorder17.018
1257Peptostreptococcusgenus16.978
1385942Bifidobacterium breve 689bstrain16.943
760570Streptococcus parasanguinis ATCC 15912strain16.903
1463165Klebsiella quasipneumoniaespecies16.89
747Pasteurella multocidaspecies16.833
203691Spirochaetotaphylum16.832
203692Spirochaetiaclass16.832
2005386Arabiibactergenus16.719
1870985Arabiibacter massiliensisspecies16.719
28901Salmonella entericaspecies16.716
105841Anaerostipes caccaespecies16.663
61645Enterobacter asburiaespecies16.658
1234680Streptococcus rubnerispecies16.63
827Campylobacter ureolyticusspecies16.573
85023Microbacteriaceaefamily16.569
31989Paracoccaceaefamily16.523
1260Finegoldia magnaspecies16.507
150022Finegoldiagenus16.507
54005Peptoniphilus hareispecies16.453
1303Streptococcus oralisspecies16.443
1918385Acutalibactergenus16.383
1796620Acutalibacter murisspecies16.383
2877527Blautia parvulaspecies16.379
1313Streptococcus pneumoniaespecies16.378
487173Dialister succinatiphilusspecies16.179
90964Staphylococcaceaefamily16.134
1847725Lawsonellagenus16.112
1528099Lawsonella clevelandensisspecies16.112
2805586Lawsonellaceaefamily16.112
438033Ruminococcus gauvreauiispecies16.111
1385Bacillalesorder16.095
1314Streptococcus pyogenesspecies16.081
590Salmonellagenus16.055
203490Fusobacteriiaclass16.054
32066Fusobacteriotaphylum16.054
203491Fusobacterialesorder16.054
2743582Peptacetobactergenus16.025
89152Peptacetobacter hiranonisspecies16.025
447020Adlercreutziagenus15.996
28126Segatella buccaespecies15.942
583Proteusgenus15.938
137591Weissella cibariaspecies15.924
1279Staphylococcusgenus15.923
1491Clostridium botulinumspecies15.889
1357Lactococcusgenus15.888
135624Aeromonadalesorder15.838
1358Lactococcus lactisspecies15.828
739Aggregatibacter segnisspecies15.766
862962Bacteroides fragilis 638Rstrain15.764
2058152Klebsiella grimontiispecies15.755
203492Fusobacteriaceaefamily15.747
44008Enterococcus cecorumspecies15.738
613Serratiagenus15.733
848Fusobacteriumgenus15.669
221027Treponema putidumspecies15.655
59732Chryseobacteriumgenus15.65
626932Alistipes indistinctusspecies15.619
564Escherichia fergusoniispecies15.553
712122Actinomyces sp. oral taxon 414species15.55
158787Bifidobacterium scardoviispecies15.539
1150461Bifidobacterium scardovii JCM 12489 = DSM 13734strain15.539
742737Hungatella hathewayi WAL-18680strain15.511
766764Debaryomycetaceaefamily15.464
839Xylanibacter ruminicolaspecies15.445
2806443Turicibacter sp. TJ11species15.413
1762Mycobacteriaceaefamily15.41
858619Corynebacterium variabile DSM 44702strain15.399
1727Corynebacterium variabilespecies15.399
727Haemophilus influenzaespecies15.393
538949uncultured Alistipes sp.species15.379
1902136Streptococcus sp. NPS 308species15.327
1470540Jeotgalibacagenus15.236
376805Phocaeicola salanitronisspecies15.193
667015Phocaeicola salanitronis DSM 18170strain15.193
544448Mycoplasmatotaphylum15.185
37734Enterococcus casseliflavusspecies15.155
3025755Thomasclaveliagenus15.148
265Paracoccusgenus15.116
1737405Tissierellalesorder15.088
33037Anaerococcus vaginalisspecies15.071
1570339Peptoniphilaceaefamily15.069
2763022Bacteroides sp. M10species14.944
582Morganella morganiispecies14.935
581Morganellagenus14.935
160674Raoultellagenus14.922
547Enterobactergenus14.904
499174Clostridioides difficile QCD-23m63strain14.886
2749267Amedibacteriumgenus14.848
2583452Amedibacterium intestinalespecies14.848
287Pseudomonas aeruginosaspecies14.848
2585117Alistipes onderdonkii subsp. vulgarissubspecies14.823
76859Fusobacterium animalisspecies14.814
28038Latilactobacillus curvatusspecies14.798
2816960Lactococcus cremoris subsp. cremorissubspecies14.767
33959Lactobacillus johnsoniispecies14.762
568Hafniagenus14.713
46867Clostridium chauvoeispecies14.685
837Porphyromonas gingivalisspecies14.682
908937Prevotella dentalis DSM 3688strain14.674
52227Prevotella dentalisspecies14.674
1104322Lactococcus cremoris subsp. cremoris A76strain14.606
2810280Coprobacillaceaefamily14.602
571Klebsiella oxytocaspecies14.567
1903410Pectobacteriaceaefamily14.528
712150Aggregatibacter sp. oral taxon 513species14.524
2497860Cellulosilyticum sp. WCF-2species14.522
538Eikenellagenus14.517
2966552Thermocaproicibacter melissaespecies14.504
3048127Thermocaproicibactergenus14.504
579Kluyveragenus14.489
76892Caulobacteraceaefamily14.485
204458Caulobacteralesorder14.485
85009Propionibacterialesorder14.472
31957Propionibacteriaceaefamily14.471
1335Streptococcus equinusspecies14.462
745Pasteurellagenus14.445
4893Saccharomycetaceaefamily14.398
97138Clostridium sp. MD294species14.388
1868794Jeotgalibaca arthritidisspecies14.37
1504Clostridium septicumspecies14.357
4930Saccharomycesgenus14.354
158847Megamonas hypermegalespecies14.331
205913Bifidobacterium longum DJO10Astrain14.315
72407Klebsiella pneumoniae subsp. pneumoniaesubspecies14.283
423211Streptococcus suis GZ1strain14.272
584Proteus mirabilisspecies14.269
31969Mollicutesclass14.254
1499973Escherichia marmotaespecies14.215
999416Parabacteroides distasonis CL03T12C09strain14.203
84162Cryptobacteriumgenus14.188
469378Cryptobacterium curtum DSM 15641strain14.188
84163Cryptobacterium curtumspecies14.188
95818Candidatus Saccharibacteriaphylum14.17
208479Enterocloster bolteaespecies14.165
1229621Anaerostipes rhamnosivoransspecies14.158
1322Blautia hanseniispecies14.125
537007Blautia hansenii DSM 20583strain14.125
981540Streptococcus pasteurianus ATCC 43144strain14.114
1805478Olsenella timonensisspecies14.114
28128Prevotella corporisspecies14.058
135623Vibrionalesorder14.053
641Vibrionaceaefamily14.053
475Moraxellagenus14.035
410072Coprococcus comesspecies14.022
1805431Enterococcus saigonensisspecies14.018
53442Eubacterium callanderispecies14.007
762982Paraprevotella xylaniphila YIT 11841strain13.99
454155Paraprevotella xylaniphilaspecies13.99
411459Blautia obeum ATCC 29174strain13.974
186827Aerococcaceaefamily13.966
1508657Ruminiclostridiumgenus13.926
122277Pectobacteriumgenus13.907
2942991Cohcovirusgenus13.901
5475Candidagenus13.862
208224Enterobacter kobeispecies13.837
171551Porphyromonadaceaefamily13.802
2093857Dysosmobacter welbionisspecies13.801
2591381Dysosmobactergenus13.801
836Porphyromonasgenus13.794
76857Fusobacterium polymorphumspecies13.755
1891914Streptococcus oralis subsp. oralissubspecies13.751
1134687Klebsiella michiganensisspecies13.734
237Flavobacteriumgenus13.709
1912216Cutibacteriumgenus13.686
1287640Anaerococcus obesiensisspecies13.685
539Eikenella corrodensspecies13.674
305719Segatella baroniaespecies13.643
46255Weissellagenus13.628
34062Moraxella osloensisspecies13.621
1776379Leyella lascolaiispecies13.605
1122992Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640strain13.593
386414Hoylesella timonensisspecies13.593
1582879Ezakiellagenus13.574
2715212Bacteroides faeciumspecies13.561
206389Rhodocyclalesorder13.559
1529Clostridium cadaverisspecies13.535
553973[Clostridium] hylemonae DSM 15053strain13.532
1217282Parabacteroides faecisspecies13.519
315405Streptococcus gallolyticusspecies13.508
41275Brevundimonasgenus13.484
80865Delftiagenus13.454
39777Veillonella atypicaspecies13.436
2942965Steigviridaefamily13.434
1282Staphylococcus epidermidisspecies13.421
2942980Kehishuvirusgenus13.411
2719313Enteroclostergenus13.394
879243Porphyromonas asaccharolytica DSM 20707strain13.371
28123Porphyromonas asaccharolyticaspecies13.371
2576376Streptococcus sp. 1643species13.366
1305Streptococcus sanguinisspecies13.345
2692118Winkiagenus13.338
33007Winkia neuiispecies13.338
2650157Bacteroides zhangwenhongiispecies13.304
28133Prevotella nigrescensspecies13.268
46507Ezakiella coagulansspecies13.26
2899133Candidatus Nanosynbacter sp. HMT-352species13.255
1283Staphylococcus haemolyticusspecies13.245
662Vibriogenus13.232
4932Saccharomyces cerevisiaespecies13.218
1490Paraclostridium bifermentansspecies13.198
1849822Paraclostridiumgenus13.198
1309Streptococcus mutansspecies13.179
2026240Klebsiella quasivariicolaspecies13.176
51288Kluyvera ascorbataspecies13.172
742725Alistipes indistinctus YIT 12060strain13.169
1918454Flintibactergenus13.156
2610895Flintibacter sp. KGMB00164species13.156
5476Candida albicansspecies13.141
3036302Mobiluncus massiliensisspecies13.091
33043Coprococcus eutactusspecies13.038
33208Metazoakingdom13.029
7711Chordataphylum13.029
9443Primatesorder13.029
9604Hominidaefamily13.029
9605Homogenus13.029
9606Homo sapiensspecies13.029
40674Mammaliaclass13.029
28025Bifidobacterium animalisspecies13.025
561Escherichiagenus13.014
2584944Sutterella faecalisspecies13.012
575Raoultella planticolaspecies12.997
2779518Blautia liquorisspecies12.994
2050Mobiluncusgenus12.966
1385939Bifidobacterium breve JCM 7017strain12.917
1330545Lelliottiagenus12.91
204457Sphingomonadalesorder12.863
2093818Candidatus Saccharimonadiaclass12.854
2093822Candidatus Nanosynbacteraceaefamily12.853
2093823Candidatus Nanosynbactergenus12.853
2093819Candidatus Nanosynbacteralesorder12.853
526525Erysipelotrichalesorder12.849
526524Erysipelotrichiaclass12.849
1622Ligilactobacillus murinusspecies12.847
1737404Tissierelliaclass12.831
33945Enterococcus aviumspecies12.735
28130Prevotella disiensspecies12.698
2763669Qiania dongpingensisspecies12.681
2944195Qianiagenus12.681
89153[Clostridium] hylemonaespecies12.679
400634Lysinibacillusgenus12.654
712310Haemophilus sp. oral taxon 036species12.645
322095Porphyromonas someraespecies12.621
28449Neisseria subflavaspecies12.616
423477Veillonella rogosaespecies12.607
158836Enterobacter hormaecheispecies12.604
178339Pauljensenia hongkongensisspecies12.598
2740557Pauljenseniagenus12.598
131110Schaalia radingaespecies12.587
2772059uncultured phage cr50_1no rank12.573
2955711Cohcovirus hiberniaespecies12.573
29466Veillonella parvulaspecies12.556
1359Lactococcus cremorisspecies12.521
824Campylobacter gracilisspecies12.501
137838Clostridium neonatalespecies12.417
1046629Streptococcus salivarius 57.Istrain12.394
565040Bifidobacterium longum subsp. infantis 157Fstrain12.379
1647Erysipelothrixgenus12.37
43769Corynebacterium propinquumspecies12.369
1016Capnocytophagagenus12.337
238749Diaphorobactergenus12.321
248744Marvinbryantiagenus12.311
168384Marvinbryantia formatexigensspecies12.311
478749Marvinbryantia formatexigens DSM 14469strain12.311
1747Cutibacterium acnesspecies12.273
1531Enterocloster clostridioformisspecies12.266
411490Anaerostipes caccae L1-92strain12.256
615Serratia marcescensspecies12.245
1492Clostridium butyricumspecies12.244
905Acidaminococcus fermentansspecies12.231
591001Acidaminococcus fermentans DSM 20731strain12.231
2702Gardnerella vaginalisspecies12.225
1200793Streptococcus salivarius K12strain12.194
2701Gardnerellagenus12.194
2901164Stutzerimonasgenus12.188
1348Streptococcus parauberisspecies12.187
1796635Longicatena caecimurisspecies12.186
1918536Longicatenagenus12.186
61646Lelliottia amnigenaspecies12.182
137732Granulicatella elegansspecies12.177
1769710Sellimonasgenus12.175
1653434Sellimonas intestinalisspecies12.175
2948688Delmidovirusgenus12.147
3029088Dethiosulfovibrionaceaefamily12.147
81852Enterococcaceaefamily12.113
2093824Candidatus Nanosynbacter lyticusspecies12.113
1350Enterococcusgenus12.107
40324Stenotrophomonas maltophiliaspecies12.079
40520Blautia obeumspecies12.06
638847Pyramidobactergenus12.04
638849Pyramidobacter piscolensspecies12.04
1334Streptococcus dysgalactiaespecies12.023
1316254Veillonella parvula HSIVP1strain12.021
2905967Candidatus Minimicrobiagenus11.998
2841264Candidatus Minimicrobia vallesaespecies11.998
1643824Atopobiaceaefamily11.997
1912897Blautia argispecies11.99
82115Rhizobiaceaefamily11.981
657309Bacteroides xylanisolvens XB1Astrain11.961
2942966Suoliviridaefamily11.948
645Aeromonas salmonicidaspecies11.931
1750Arachnia propionicaspecies11.924
1871025Ndongobacter massiliensisspecies11.9
1930845Ndongobactergenus11.9
2734150Toutatisvirus toutatisspecies11.891
2733138Toutatisvirusgenus11.891
2070187Faecalibacterium phage FP_Toutatisno rank11.891
1351Enterococcus faecalisspecies11.885
1598Limosilactobacillus reuterispecies11.871
1653Corynebacteriaceaefamily11.858
1716Corynebacteriumgenus11.858
713Actinobacillusgenus11.836
2027293Escherichia coli O8:H8serotype11.82
1613Limosilactobacillus fermentumspecies11.785
1035817Bifidobacterium longum subsp. longum KACC 91563strain11.762
85025Nocardiaceaefamily11.735
2650158Bacteroides luhongzhouiispecies11.726
1308Streptococcus thermophilusspecies11.694
2772085crAssphage cr6_1RUCEZ87711.691
419005Prevotella amniispecies11.667
2742598Limosilactobacillusgenus11.652
1177574Prevotella jejunispecies11.643
388919Streptococcus sanguinis SK36strain11.551
41297Sphingomonadaceaefamily11.516
53345Enterococcus duransspecies11.511
1077464Streptococcus oralis subsp. tigurinussubspecies11.495
850Fusobacterium mortiferumspecies11.478
469616Fusobacterium mortiferum ATCC 9817strain11.478
626940Phascolarctobacterium succinatutensspecies11.459
657308Gordonibacter pamelaeae 7-10-1-bstrain11.445
471189Gordonibacter pamelaeaespecies11.445
84566Sphingobacteriaceaefamily11.41
200666Sphingobacterialesorder11.41
117747Sphingobacteriiaclass11.41
416916Aggregatibactergenus11.408
428126Thomasclavelia spiroformis DSM 1552strain11.407
29348Thomasclavelia spiroformisspecies11.407
3047432Maliibacteriaceaefamily11.388
3047433Maliibacteriumgenus11.388
2086585Maliibacterium massiliensespecies11.388
99822Streptococcus dysgalactiae subsp. dysgalactiaesubspecies11.363
47678Bacteroides caccaespecies11.339
2767893Lentilactobacillusgenus11.314
1396Bacillus cereusspecies11.311
1155388Clostridium sp. C1species11.281
12916Acidovoraxgenus11.279
2847299Bacteroides sp. DH3716Pspecies11.274
1364Lactococcus pisciumspecies11.272
28135Segatella orisspecies11.258
1292Staphylococcus warnerispecies11.248
1827Rhodococcusgenus11.244
2767885Latilactobacillusgenus11.24
186818Planococcaceaefamily11.231
630Yersinia enterocoliticaspecies11.224
1624Ligilactobacillus salivariusspecies11.219
48736Ralstoniagenus11.206
2692113Gleimiagenus11.191
883062Bifidobacterium bifidum S17strain11.176
186532Ceduovirusgenus11.163
28453Sphingobacteriumgenus11.159
222Achromobactergenus11.156
927666Streptococcus oralis Uo5strain11.111
1433288Streptococcus thermophilus MTH17CL396strain11.106
32257Kingellagenus11.101
1074494Streptococcus salivarius M18strain11.053
876Desulfovibrio desulfuricansspecies11.052
1363Lactococcus garvieaespecies11.044
85007Mycobacterialesorder11.021
830Butyrivibriogenus11.009
118882Brucellaceaefamily11.004
66228Gleimia europaeaspecies11.003
45851Butyrivibrio crossotusspecies10.992
1501662Streptococcus parasuisspecies10.988
570Klebsiellagenus10.959
2801844Arachniagenus10.94
990721Christensenellagenus10.924
990719Christensenellaceaefamily10.924
626937Christensenella minutaspecies10.924
544580Actinomyces orisspecies10.885
1156431Streptococcus ileispecies10.879
712362Leptotrichia sp. oral taxon 221species10.863
1643822Eggerthellalesorder10.854
1643826Eggerthellaceaefamily10.854
2763062Roseburia rectibacterspecies10.835
1161942Ruminococcus champanellensisspecies10.82
234Brucellagenus10.812
1623Ligilactobacillus ruminisspecies10.81
1259973Klebsiella electricaspecies10.807
2709390Bacteroides sp. ZJ-18species10.755
712411Olsenella sp. oral taxon 807species10.754
190721Ralstonia insidiosaspecies10.752
1353Enterococcus gallinarumspecies10.719
82135Fannyhessea vaginaespecies10.717
2767327Fannyhesseagenus10.717
29430Acinetobacter haemolyticusspecies10.716
413496Cronobactergenus10.703
2047Rothia dentocariosaspecies10.7
1599Latilactobacillus sakeispecies10.697
1654Actinomycesgenus10.683
697329Ruminococcus albus 7 = DSM 20455strain10.675
1264Ruminococcus albusspecies10.675
732Aggregatibacter aphrophilusspecies10.667
29491Aeromonas salmonicida subsp. salmonicidasubspecies10.665
182773Clostridium isatidisspecies10.633
1348911Coprobactergenus10.63
2092Mycoplasmataceaefamily10.607
2085Mycoplasmatalesorder10.607
2005519Barnesiellaceaefamily10.606
1099853Coprobacter fastidiosusspecies10.603
407Methylobacteriumgenus10.597
1379Gemella haemolysansspecies10.597
33034Anaerococcus prevotiispecies10.573
525919Anaerococcus prevotii DSM 20548strain10.573
29465Veillonellagenus10.559
2820817Aggregatibacter sp. 2125159857species10.549
5794Apicomplexaphylum10.54
1301Streptococcusgenus10.522
2767886Levilactobacillusgenus10.5
1675036Megasphaera hexanoicaspecies10.495
2893057Shouchellagenus10.479
54291Raoultella ornithinolyticaspecies10.475
1796652Turicimonas murisspecies10.474
1918598Turicimonasgenus10.474
862970Streptococcus anginosus C1051strain10.473
1032069Campylobacter ureolyticus RIGS 9880strain10.462
1300Streptococcaceaefamily10.457
2848145Escherichia coli O170:H18no rank10.428
577Raoultella terrigenaspecies10.426
1280412Conoidasidaclass10.425
75739Eucoccidioridaorder10.425
861906Escherichia coli O44:H18serotype10.423
216592Escherichia coli 042strain10.423
114527Mogibacterium diversumspecies10.421
360104Campylobacter concisus 13826strain10.418
5809Sarcocystidaefamily10.407
255248Leuconostoc garlicumspecies10.401
29389Streptococcus alactolyticusspecies10.398
1580Levilactobacillus brevisspecies10.396
244366Klebsiella variicolaspecies10.395
5811Toxoplasma gondiispecies10.388
5810Toxoplasmagenus10.388
1633Limosilactobacillus vaginalisspecies10.373
2942990Canhaevirusgenus10.354
2488810Ruminiclostridium herbifermentansspecies10.349
1506577Tyzzerellagenus10.34
36835[Clostridium] colinumspecies10.34
704125Clostridium gelidumspecies10.339
502Kingella denitrificansspecies10.328
1637Listeriagenus10.318
28216Betaproteobacteriaclass10.312
80840Burkholderialesorder10.305
2603836Escherichia coli O10:H32serotype10.3
702459Bifidobacterium bifidum PRL2010strain10.286
58231Treponema mediumspecies10.286
2866570Aggregatibacter sp. Marseille-P9115species10.278
1252Leuconostoc carnosumspecies10.273
1243Leuconostocgenus10.267
28129Prevotella denticolaspecies10.241
2382163Streptococcus koreensisspecies10.22
2572088Candidatus Nanosynbacter featherlitesspecies10.208
160453Enterococcus gilvusspecies10.204
635Edwardsiellagenus10.185
1759399Streptococcus sp. A12species10.178
2848144Escherichia coli O158:H23no rank10.177
133448Citrobacter youngaespecies10.175
2082587Parolsenellagenus10.175
617123Lachnoanaerobaculum umeaensespecies10.152
119045Methylobacteriaceaefamily10.152
76517Campylobacter hominisspecies10.142
684066Streptococcus lactariusspecies10.132
2778655Escherichia coli O167:H26serotype10.108
831Butyrivibrio fibrisolvensspecies10.099
2929492Faecalibacterium sp. I3-3-33species10.095
702439Prevotella nigrescens F0103strain10.082
1520Clostridium beijerinckiispecies10.078
995019Sutterellaceaefamily10.075
1563222Citrobacter pasteuriispecies10.071
1433289Streptococcus thermophilus M17PTZA496strain10.059
1632Limosilactobacillus orisspecies10.049
47770Lactobacillus crispatusspecies10.036
2020965Bifidobacterium imperatorisspecies10.034
569Hafnia alveispecies10.024
906Megasphaeragenus10.023
33039[Ruminococcus] torquesspecies10.02
657313[Ruminococcus] torques L2-14strain10.02
1304Streptococcus salivariusspecies10.01
1667327Klebsiella quasipneumoniae subsp. quasipneumoniaesubspecies10.001
869209Treponema succinifaciens DSM 2489strain9.9992
167Treponema succinifaciensspecies9.9992
1253Pediococcusgenus9.9913
1246Leuconostoc lactisspecies9.9872
299766Enterobacter hormaechei subsp. steigerwaltiisubspecies9.984
1415775Clostridium baratii str. Sullivanstrain9.9732
2133944Pseudoprevotella muciniphilaspecies9.9676
2884814Pseudoprevotellagenus9.9676
201Campylobacter larispecies9.9633
1354Enterococcus hiraespecies9.9626
100886Catenibacterium mitsuokaispecies9.9443
507Alcaligenesgenus9.9429
45972Staphylococcus pasteurispecies9.9336
1280Staphylococcus aureusspecies9.915
1453988Campylobacter lari RM16712strain9.9141
35703Citrobacter amalonaticusspecies9.9078
1340Streptococcus porcinusspecies9.9071
40544Sutterellagenus9.8886
244127Anaerotruncusgenus9.8579
169435Anaerotruncus colihominisspecies9.8579
985008Aggregatibacter aphrophilus ATCC 33389strain9.849
297352Lactococcus piscium MKFS47strain9.8328
80864Comamonadaceaefamily9.8266
2585119Alistipes disparspecies9.8242
86331Mogibacteriumgenus9.8192
713030Selenomonas sp. oral taxon 136species9.812
483Neisseria cinereaspecies9.7938
604330Parafannyhessea umbonataspecies9.7778
2847312Parafannyhesseagenus9.7778
2929493Faecalibacterium sp. I3-3-89species9.7764
585397Escherichia coli ED1astrain9.7746
40545Sutterella wadsworthensisspecies9.774
1244Leuconostoc gelidumspecies9.763
29375Lacrimispora xylanolyticaspecies9.7548
2005520Dysgonomonadaceaefamily9.7493
2767890Paucilactobacillusgenus9.7489
1587Lactobacillus helveticusspecies9.7475
33035Blautia productaspecies9.7472
2955579Canhaevirus hiberniaespecies9.7076
2772066uncultured phage cr10_1no rank9.7076
649776Synergistalesorder9.6987
649775Synergistiaclass9.6987
508458Synergistotaphylum9.6987
2107999Lactobacillus paragasserispecies9.6854
1458253Streptococcus oralis subsp. dentisanisubspecies9.6652
470Acinetobacter baumanniispecies9.6416
644652Gordonibactergenus9.6373
2546350Citrobacter arsenatisspecies9.6244
28132Prevotella melaninogenicaspecies9.6058
1870884Clostridioidesgenus9.5655
539813Enterobacter morispecies9.5614
1446746Escherichia coli O6:H16serotype9.5527
1903434Atlantibactergenus9.5526
131111Schaalia turicensisspecies9.5432
631220Desulfovibrio sp. G11species9.5416
2027919Enterobacter cloacae complex sp.species9.5295
2772067uncultured phage cr11_1no rank9.5276
2955741Delmidovirus splanchnicusspecies9.5276
3022127Lancefieldella sp. Marseille-Q7238species9.5229
546367Hafnia paralveispecies9.5145
2767887Ligilactobacillusgenus9.5127
970Selenomonasgenus9.4953
1069494Trueperellagenus9.4832
155493Gallibacteriumgenus9.4761
32008Burkholderiagenus9.476
1290Staphylococcus hominisspecies9.467
1685Bifidobacterium brevespecies9.4339
1326Streptococcus acidominimusspecies9.4198
1300227Bifidobacterium longum subsp. longum GT15strain9.4145
2003188Parolsenella catenaspecies9.4127
907Megasphaera elsdeniispecies9.3998
505341Gallibacterium salpingitidisspecies9.398
565Atlantibacter hermanniispecies9.3863
1305849Enterococcus faecium Aus0085strain9.3746
1232659Haemophilus influenzae 2019strain9.3629
331111Escherichia coli O139:H28 str. E24377Astrain9.357
1603259Escherichia coli O139:H28serotype9.357
1871021Lachnoclostridium phocaeensespecies9.3261
1661Trueperella pyogenesspecies9.2778
2109686Butyricicoccus sp. GAM44species9.2646
580596Butyricicoccusgenus9.2646
67827Citrobacter werkmaniispecies9.2591
525282Finegoldia magna ATCC 53516strain9.2375
2598457Streptococcus sp. KS 6species9.2263
1335613Gordonibacter urolithinfaciensspecies9.2162
301301Roseburia hominisspecies9.2112
249188Haemophilus pittmaniaespecies9.2072
712538Selenomonas sp. oral taxon 478species9.1851
2841037Eubacterium sp. c-25species9.1726
547043Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505strain9.161
2811390Sporofaciensgenus9.1239
2681861Sporofaciens musculispecies9.1239
32003Nitrosomonadalesorder9.1194
1310Streptococcus sobrinusspecies9.1181
1302Streptococcus gordoniispecies9.0986
71452Enterococcus raffinosusspecies9.0831
1743Propionibacteriumgenus9.0806
13687Sphingomonasgenus9.0761
1245Leuconostoc mesenteroidesspecies9.0668
2051Mobiluncus curtisiispecies9.0624
28144Salmonella enterica subsp. enterica serovar Derbyno rank9.0361
1655Actinomyces naeslundiispecies9.0272
83655Leclercia adecarboxylataspecies9.0215
447792Phytobactergenus9.0141
1375Aerococcusgenus9.0125
69218Enterobacter cancerogenusspecies9.0021
33905Bifidobacterium thermophilumspecies9.0007
2937909Desulfitobacteriaceaefamily8.9984
47714Lacticaseibacillus paracasei subsp. paracaseisubspecies8.9954
1682Bifidobacterium longum subsp. infantissubspecies8.975
162Treponema phagedenisspecies8.9692
85011Kitasatosporalesorder8.9615
2062Streptomycetaceaefamily8.9615
1338Streptococcus intermediusspecies8.9432
190146Actinotignum urinalespecies8.9392
2490633Streptococcus periodonticumspecies8.9175
1311Streptococcus agalactiaespecies8.9139
28119Bacteroides zoogleoformansspecies8.8714
1470347Alistipes ihumiispecies8.8466
1211813Alistipes ihumii AP11strain8.8466
866777Bifidobacterium breve ACS-071-V-Sch8bstrain8.8371
67824Citrobacter farmerispecies8.8369
1642646Petrimonas mucosaspecies8.8241
307628Petrimonasgenus8.8241
47670Lautropiagenus8.823
47671Lautropia mirabilisspecies8.823
2041044Eubacterium maltosivoransspecies8.8028
2913614Prevotella communisspecies8.8008
1589Lactiplantibacillus pentosusspecies8.7922
248315Veillonella rodentiumspecies8.7846
33033Parvimonas micraspecies8.7761
543311Parvimonasgenus8.7761
115778Leuconostoc gasicomitatumspecies8.7657
488Neisseria mucosaspecies8.7539
1883Streptomycesgenus8.7351
2919589Vaginimicrobiumgenus8.7251
1871034Vaginimicrobium propionicumspecies8.7251
1561Clostridium baratiispecies8.7189
1583Weissella confusaspecies8.7086
2479767Blautia sp. SC05B48species8.6993
87541Aerococcus christenseniispecies8.6984
328813Alistipes onderdonkiispecies8.6973
1547448Arachnia rubraspecies8.6843
2663009Fusobacterium pseudoperiodonticumspecies8.6832
38304Corynebacterium tuberculostearicumspecies8.6822
1852381Duodenibacillus massiliensisspecies8.671
1980697Duodenibacillusgenus8.671
2787628Treponema peruensespecies8.6617
1296540Paucilactobacillus nenjiangensisspecies8.6465
890402Bifidobacterium longum subsp. longum BBMN68strain8.6424
181487Schaalia cardiffensisspecies8.6333
888050Schaalia cardiffensis F0333strain8.6333
1970189Marinilabilialesorder8.605
2714353Vescimonas fastidiosaspecies8.585
1496Clostridioides difficilespecies8.5787
2742601Limosilactobacillus portuensisspecies8.5672
1597Lacticaseibacillus paracaseispecies8.5651
1330547Kosakoniagenus8.5484
363265Leyella stercoreaspecies8.543
1122981Prevotella corporis DSM 18810 = JCM 8529strain8.5289
214856Alistipes finegoldiispecies8.5266
1255Pediococcus pentosaceusspecies8.5236
470146Coprococcus comes ATCC 27758strain8.508
2974265Leyellagenus8.5057
868129Prevotella bivia DSM 20514strain8.4966
186820Listeriaceaefamily8.4905
90371Salmonella enterica subsp. enterica serovar Typhimuriumno rank8.4744
679935Alistipes finegoldii DSM 17242strain8.4679
2086584Massilistercora timonensisspecies8.4675
2717089Massilistercoragenus8.4675
2773707Escherichia coli O19:H7no rank8.4458
2763104Escherichia coli O150:H6serotype8.4447
2803850Mammaliicoccusgenus8.4413
873513Segatella buccae ATCC 33574strain8.4355
186826Lactobacillalesorder8.4177
490Neisseria siccaspecies8.4171
1048332Streptococcus salivarius CCHSS3strain8.4076
1288121Alistipes senegalensisspecies8.3998
196081Scardoviagenus8.3914
78259Scardovia inopinataspecies8.3914
1150468Scardovia inopinata JCM 12537strain8.3914
1796616Blautia pseudococcoidesspecies8.3643
730[Haemophilus] ducreyispecies8.3473
706438Actinomyces sp. oral taxon 171species8.3329
706439Actinomyces sp. oral taxon 171 str. F0337strain8.3329
69965Macrococcusgenus8.309
85020Dermabacteraceaefamily8.2955
91061Bacilliclass8.2911
37637Corynebacterium pseudodiphtheriticumspecies8.2794
147802Lactobacillus inersspecies8.2667
632Yersinia pestisspecies8.2177
2714355Vescimonas coprocolaspecies8.2067
2494234Sutterella megalosphaeroidesspecies8.1807
113107Streptococcus australisspecies8.1803
411903Collinsella aerofaciens ATCC 25986strain8.1347
722911Bifidobacterium longum subsp. longum F8strain8.1118
57493Kocuriagenus8.1073
1436725Streptococcus thermophilus TH1477strain8.101
1926677Raoultibactergenus8.1003
1907662Raoultibacter timonensisspecies8.1003
379Rhizobiumgenus8.095
203275Tannerella forsythia 92A2strain8.0864
28134Hoylesella oralisspecies8.0598
1643686Brachyspiralesorder8.0537
29521Brachyspiragenus8.0537
143786Brachyspiraceaefamily8.0537
1336Streptococcus equispecies8.0488
1843490Sporomusaceaefamily8.0442
997873Bacteroides caccae CL03T12C61strain8.0427
693979Bacteroides helcogenes P 36-108strain8.0376
290053Bacteroides helcogenesspecies8.0376
1155385Proteiniclasticumgenus8.0255
3036945Proteiniclasticum sp. QWL-01species8.0255
33040Streptococcus millerispecies8.0219
2815775Berryellagenus7.9936
823Parabacteroides distasonisspecies7.9932
2478954Catenibacterium sp. co_0103species7.9864
157687Leptotrichia wadeispecies7.9769
119060Burkholderiaceaefamily7.973
29391Gemella morbillorumspecies7.9635
2060094Aminipilagenus7.9504
34105Streptobacillus moniliformisspecies7.9161
34104Streptobacillusgenus7.9161
1046624Lactococcus lactis subsp. lactis IO-1strain7.8953
2169621Limdunavirusgenus7.8846
2870563Methanobrevibacter sp. TLL-48-HuF1species7.8845
861Fusobacterium ulceransspecies7.88
1931217Bifidobacterium longum subsp. suillumsubspecies7.8691
83231Xylanibacter brevisspecies7.8565
299767Enterobacter ludwigiispecies7.847
135858Catenibacteriumgenus7.83
856Fusobacterium variumspecies7.798
40041Streptococcus equi subsp. zooepidemicussubspecies7.7883
1623305Skunavirusgenus7.7779
74426Collinsella aerofaciensspecies7.7776
356Hyphomicrobialesorder7.7774
1584Lactobacillus delbrueckiispecies7.7761
102106Collinsellagenus7.7633
84107Coriobacteriaceaefamily7.7624
2666138Caproicibacterium lactatifermentansspecies7.7593
2815358Leclercia pneumoniaespecies7.7471
1905344Ruthenibacteriumgenus7.746
1550024Ruthenibacterium lactatiformansspecies7.746
33011Cutibacterium granulosumspecies7.744
94869Clostridium gasigenesspecies7.7341
1330546Pluralibactergenus7.7283
283Comamonasgenus7.7169
2785531Bacteroides sp. HF-162species7.7131
84999Coriobacterialesorder7.7122
941322Escherichia coli O25b:H4-ST131no rank7.7036
1504576Pseudocitrobactergenus7.7031
2891570Pseudocitrobacter corydidarispecies7.7031
61592Corynebacterium durumspecies7.7013
338Xanthomonasgenus7.6781
186814Thermoanaerobacteraceaefamily7.6745
762210Bifidobacterium saguinispecies7.6737
1360Lactococcus lactis subsp. lactissubspecies7.6651
515620[Eubacterium] eligens ATCC 27750strain7.6619
1623304Moineauvirusgenus7.6609
671267Phocaeicola sartoriispecies7.6568
1150460Bifidobacterium catenulatum subsp. kashiwanohense JCM 15439 = DSM 21854strain7.6556
106589Cupriavidusgenus7.6486
2696063Anaerocolumna sedimenticolaspecies7.646
881260Enterobacter bugandensisspecies7.6448
375288Parabacteroidesgenus7.6353
2005525Tannerellaceaefamily7.6349
204Campylobacter showaespecies7.6239
1531429Berryella intestinalisspecies7.6229
2731643Autographiviridaefamily7.5822
1681Bifidobacterium bifidumspecies7.5668
195950Tannerellagenus7.561
253239Ethanoligenens harbinensespecies7.5595
253238Ethanoligenensgenus7.5595
186828Carnobacteriaceaefamily7.5478
445974Thomasclavelia ramosa DSM 1402strain7.5476
28026Bifidobacterium pseudocatenulatumspecies7.5419
930406Escherichia coli O157:H16strain7.5377
2854732Escherichia coli O78:H4serotype7.5209
2748Carnobacterium divergensspecies7.5192
79603Denitrobacteriumgenus7.5137
79604Denitrobacterium detoxificansspecies7.5137
83654Leclerciagenus7.5007
2994078Caproicibacterium sp. BJN0003species7.4953
57706Citrobacter braakiispecies7.4818
72293Helicobacteraceaefamily7.4558
1505652Terrisporobactergenus7.449
2813371Terrisporobacter hibernicusspecies7.449
209Helicobactergenus7.4295
1408428Bilophila wadsworthia ATCC 49260strain7.4156
1385940Bifidobacterium breve JCM 7019strain7.4014
371601Bacteroides xylanisolvensspecies7.3943
546269Filifactor alocis ATCC 35896strain7.3853
143361Filifactor alocisspecies7.3853
44259Filifactorgenus7.3853
43768Corynebacterium matruchotiispecies7.3703
1296Mammaliicoccus sciurispecies7.3674
225991Comamonas aquaticaspecies7.3652
2304687Petroclostridiumgenus7.3651
2068655Novisyntrophococcus fermenticellaespecies7.3633
2888809Novisyntrophococcusgenus7.3633
28131Prevotella intermediaspecies7.3572
1118202Cruoricaptor ignavusspecies7.3522
1433995Cruoricaptorgenus7.3522
649777Synergistaceaefamily7.352
1197717Cloacibacillus porcorumspecies7.3467
508459Cloacibacillusgenus7.3467
33968Leuconostoc pseudomesenteroidesspecies7.3374
904Acidaminococcusgenus7.3273
5204Basidiomycotaphylum7.3243
47715Lacticaseibacillus rhamnosusspecies7.324
329854Bacteroides intestinalisspecies7.318
2507160Aminipila luticellariispecies7.3171
28111Bacteroides eggerthiispecies7.3138
2044467Escherichia sp. E4742species7.3061
2747Carnobacteriumgenus7.3044
1296536Enterobacter hormaechei subsp. xiangfangensissubspecies7.3022
165695Sphingobiumgenus7.2626
246787Bacteroides cellulosilyticusspecies7.251
46124Granulicatella adiacensspecies7.2148
244320Escherichia coli O55:H7no rank7.2102
186807Peptococcaceaefamily7.1915
3016343Peptoniphilus equinusspecies7.1807
1852374Ezakiella massiliensisspecies7.1398
33010Cutibacterium avidumspecies7.1351
871541Actinomyces oris K20strain7.1305
563008Segatella oris C735strain7.1223
1269Micrococcusgenus7.1209
2942964Intestiviridaefamily7.1129
28112Tannerella forsythiaspecies7.104
864564Parascardovia denticolens DSM 10105 = JCM 12538strain7.0854
196082Parascardoviagenus7.0854
78258Parascardovia denticolensspecies7.0854
909929Selenomonadalesorder7.0844
129337Geobacillusgenus7.0763
545Citrobacter koserispecies7.0745
1680Bifidobacterium adolescentisspecies7.0698
1579Lactobacillus acidophilusspecies7.0498
712116Actinomyces sp. oral taxon 169species7.0411
1843491Selenomonadaceaefamily7.0396
501783Cloacibacteriumgenus7.0337
1298Deinococcusgenus7.0322
118964Deinococcalesorder7.0322
183710Deinococcaceaefamily7.0322
502558Eggerthella sp. YY7918species7.0314
1281486Lactococcus formosensisspecies7.0247
1069534Ligilactobacillus ruminis ATCC 27782strain7.0092
1659Actinomyces israeliispecies7.0028
33682Euglenozoaphylum6.9992
2704949Trypanosomatidaorder6.9992
5654Trypanosomatidaefamily6.9992
5653Kinetoplasteaclass6.9992
435591Parabacteroides distasonis ATCC 8503strain6.98
68933Thermalesorder6.964
188786Thermaceaefamily6.964
521095Lancefieldella parvula DSM 20469strain6.9621
1382Lancefieldella parvulaspecies6.9621
172042Rothia aeriaspecies6.9552
5658Leishmaniagenus6.9546
1596Lactobacillus gasserispecies6.9527
1501Clostridium pasteurianumspecies6.9374
29385Staphylococcus saprophyticusspecies6.925
718252Faecalibacterium prausnitzii L2-6strain6.9208
1064535Megasphaera elsdenii DSM 20460strain6.9198
2772089uncultured phage cr115_1no rank6.9105
2955498Birpovirus hiberniaespecies6.9105
84998Coriobacteriiaclass6.9096
151276Bacteroides coprosuisspecies6.905
679937Bacteroides coprosuis DSM 18011strain6.905
61647Pluralibacter gergoviaespecies6.9039
633147Olsenella uli DSM 7084strain6.8991
133926Olsenella ulispecies6.8991
2778656Escherichia coli O20:H12no rank6.8893
622Shigella dysenteriaespecies6.8791
712710Tannerella serpentiformisspecies6.873
147206Collinsella stercorisspecies6.8677
28035Staphylococcus lugdunensisspecies6.8665
2751Carnobacterium maltaromaticumspecies6.865
97478Limosilactobacillus mucosaespecies6.8606
2848143Escherichia coli O85:H1no rank6.8604
2823317Phascolarctobacterium sp. Marseille-Q4147species6.8584
34037Rahnellagenus6.8453
1297793Lacrimispora sphenoides JCM 1415strain6.845
29370Lacrimispora sphenoidesspecies6.845
2507162Caproiciproducens sp. NJN-50species6.8446
1738645Caproiciproducensgenus6.8446
634176Aggregatibacter aphrophilus NJ8700strain6.8286
69710Treponema vincentiispecies6.8193
1380Atopobiumgenus6.8137
712157Atopobium sp. oral taxon 416species6.8137
496Neisseria macacaespecies6.7759
84112Eggerthella lentaspecies6.7669
2678885Faecalibacillusgenus6.7549
1982626Faecalibacillus intestinalisspecies6.7549
2564099Ruminococcus bovisspecies6.7505
69966Macrococcoides caseolyticumspecies6.7491
33038Mediterraneibacter gnavusspecies6.7395
2759736Lacticaseibacillusgenus6.7368
1307Streptococcus suisspecies6.7281
31977Veillonellaceaefamily6.7226
1843489Veillonellalesorder6.7226
102684Streptococcus infantariusspecies6.7157
46123Abiotrophiagenus6.7149
46125Abiotrophia defectivaspecies6.7149
10239Virusessuperkingdom6.7143
2731360Heunggongviraekingdom6.7048
2731618Uroviricotaphylum6.7048
2731619Caudoviricetesclass6.7048
84111Eggerthellagenus6.7039
1866885Mycolicibacteriumgenus6.7014
2789425Actinomyces sp. HMT 175species6.6931
1297Deinococcotaphylum6.6774
188787Deinococciclass6.6774
187327Acidaminococcus intestinispecies6.6718
2569097Anaerobutyricumgenus6.6708
39488Anaerobutyricum halliispecies6.6708
712624Streptococcus sp. oral taxon 064species6.6649
2767353Lancefieldellagenus6.6614
649757Anaerostipes hadrus ATCC 29173 = JCM 17467strain6.6558
2767881Fructilactobacillusgenus6.6508
1978007Crassviralesorder6.6435
75984Mannheimiagenus6.643
1694Bifidobacterium pseudolongumspecies6.6391
1161918Brachyspira pilosicoli WesBstrain6.6058
2070Pseudonocardiaceaefamily6.6023
85010Pseudonocardialesorder6.6023
586Providenciagenus6.574
577309Paraprevotellagenus6.5725
28113Bacteroides heparinolyticusspecies6.5688
2955997Jahgtovirus intestinihominisspecies6.5634
2772061uncultured phage cr107_1no rank6.5634
1447716Bifidobacterium catenulatum PV20-2strain6.5632
28125Prevotella biviaspecies6.5578
117563Granulicatellagenus6.5547
2364787Alistipes megagutispecies6.5427
357Agrobacteriumgenus6.5327
409322Treponema pedisspecies6.5216
550Enterobacter cloacaespecies6.5156
69823Selenomonas sputigenaspecies6.5146
479437Eggerthella lenta DSM 2243strain6.5079
29388Staphylococcus capitisspecies6.4974
225992Comamonas kerstersiispecies6.4867
1002367Leyella stercorea DSM 18206strain6.4853
76123Hoylesella enoecaspecies6.4814
295405Bacteroides fragilis YCH46strain6.4692
2995122Leptogranulimonasgenus6.469
2894156Leptogranulimonas caecicolaspecies6.469
2608867Escherichia ruysiaespecies6.4602
282402Prevotella multiformisspecies6.4572
454154Paraprevotella claraspecies6.4555
387090Phocaeicola coprophilusspecies6.4459
1232428Megasphaera massiliensisspecies6.4433
2948767Jahgtovirusgenus6.4375
862967Streptococcus intermedius B196strain6.4322
679191Prevotella amnii CRIS 21A-Astrain6.4208
28141Cronobacter sakazakiispecies6.4014
77635Bifidobacterium subtilespecies6.3808
2035811Pseudodesulfovibriogenus6.3616
200795Chloroflexotaphylum6.3564
29347[Clostridium] scindensspecies6.3545
166486Roseburia intestinalisspecies6.3404
361101Streptococcus pseudoporcinusspecies6.3338
2707299Adlercreutzia hattoriispecies6.3315
39948Dialistergenus6.3261
536231Roseburia intestinalis L1-82strain6.3257
2691580Prevotella sp. Rep29species6.3242
52584Brachyspira pilosicolispecies6.2966
2946830Birpovirusgenus6.276
186822Paenibacillaceaefamily6.2575
1216932Clostridium bornimensespecies6.249
83334Escherichia coli O157:H7serotype6.2455
44249Paenibacillusgenus6.2446
33964Leuconostoc citreumspecies6.2316
1458465Megasphaera elsdenii 14-14strain6.2267
384636Lacrimispora xylanisolvensspecies6.2198
1051631Streptococcus phage YMC-2011species6.2196
270Thermusgenus6.1948
2093856Butyricimonas faecalisspecies6.1941
2679910Intestinibaculumgenus6.1884
2487118Intestinibaculum porcispecies6.1884
84135Gemella sanguinisspecies6.1868
85019Brevibacteriaceaefamily6.1839
1696Brevibacteriumgenus6.1839
2718Cardiobacterium hominisspecies6.1641
1231072Clostridium tetani 12124569strain6.1618
2892396Vescimonasgenus6.1578
52773Schaalia meyerispecies6.1559
2081702Actinomyces sp. oral taxon 897species6.1547
818Bacteroides thetaiotaomicronspecies6.1537
1625Fructilactobacillus sanfranciscensisspecies6.1495
420247Methanobrevibacter smithii ATCC 35061strain6.1307
2929491Faecalibacterium sp. HTF-Fspecies6.1091
68295Thermoanaerobacteralesorder6.1008
291644Bacteroides salyersiaespecies6.0944
1507512Romboutsia hominisspecies6.0655
515622Butyrivibrio proteoclasticus B316strain6.0578
43305Butyrivibrio proteoclasticusspecies6.0578
69277Phyllobacteriaceaefamily6.0402
2767879Companilactobacillusgenus6.0245
161879Corynebacterium kroppenstedtiispecies6.0242
1042156Clostridium sp. SY8519species6.0184
2841528Eubacterium sp. MSJ-33species6.0089
1506553Lachnoclostridiumgenus6.0082
1660Schaalia odontolyticaspecies6.0077
216816Bifidobacterium longumspecies6.0001
1573534Faecalitaleagenus5.9918
717960Faecalitalea cylindroides T2-87strain5.9918
39483Faecalitalea cylindroidesspecies5.9918
59310Streptococcus macedonicusspecies5.9885
33967Leuconostoc mesenteroides subsp. mesenteroidessubspecies5.9866
5042Eurotialesorder5.977
147545Eurotiomycetesclass5.977
714Aggregatibacter actinomycetemcomitansspecies5.9456
301297Dehalococcoidiaclass5.9432
1378Gemellagenus5.9309
243164Dehalococcoides mccartyi 195strain5.9267
61434Dehalococcoidesgenus5.9031
1202464Dehalococcoidaceaefamily5.9031
1202465Dehalococcoidalesorder5.9031
61435Dehalococcoides mccartyispecies5.881
31983Helcococcusgenus5.8788
40091Helcococcus kunziispecies5.8788
3029087Aminobacteriaceaefamily5.855
651822Fretibacterium fastidiosumspecies5.855
1434006Fretibacteriumgenus5.855
2316020Mediterraneibactergenus5.8469
1366Lactococcus raffinolactisspecies5.8243
762948Rothia dentocariosa ATCC 17931strain5.8122
470565Prevotella histicolaspecies5.8068
2737Vagococcusgenus5.8051
2733199Oengusvirusgenus5.8011
2734262Oengusvirus oengusspecies5.8011
2070188Faecalibacterium phage FP_oengusno rank5.8011
128827Erysipelotrichaceaefamily5.7976
862966Streptococcus intermedius C270strain5.7869
119602Streptococcus dysgalactiae subsp. equisimilissubspecies5.7807
84108Slackiagenus5.7723
84110Slackia heliotrinireducensspecies5.7723
469617Fusobacterium ulcerans ATCC 49185strain5.7705
624Shigella sonneispecies5.7682
1501226Romboutsiagenus5.7627
1449093Lactococcus cremoris subsp. cremoris IBB477strain5.7419
158846Megamonasgenus5.7268
44742Desulfovibrio fairfieldensisspecies5.7252
768503Cytophagiaclass5.7247
768507Cytophagalesorder5.7247
997879Bacteroides fragilis CL03T12C07strain5.7183
2489014Klebsiella variicola subsp. tropicasubspecies5.6997
187101Sneathia vaginalisspecies5.6958
168808Sneathiagenus5.6958
2724150Romboutsia sp. CE17species5.6846
197Campylobacter jejunispecies5.6711
551Erwiniagenus5.6707
437897Megamonas funiformisspecies5.6624
2806552Bulleidia sp. zg-1006species5.6621
118747Bulleidiagenus5.6621
1744Propionibacterium freudenreichiispecies5.6534
1601Ligilactobacillus agilisspecies5.6514
2764325[Eubacterium] hominisspecies5.6479
89966Hymenobactergenus5.6449
1131492Aspergillaceaefamily5.6363
1852373Murdochiella vaginalisspecies5.6353
1161127Murdochiellagenus5.6353
186329Acholeplasmatalesorder5.6347
2146Acholeplasmataceaefamily5.6347
868Cardiobacteriaceaefamily5.6326
135615Cardiobacterialesorder5.6316
589437Prevotella scoposspecies5.6177
1236518Prevotella scopos JCM 17725strain5.6177
77095Segatella bryantiispecies5.5925
2717Cardiobacteriumgenus5.5818
1160721Ruminococcus bicirculans (ex Wegman et al. 2014)species5.5818
859Fusobacterium necrophorumspecies5.575
2025876Parabacteroides sp. CT06species5.5687
1585Lactobacillus delbrueckii subsp. bulgaricussubspecies5.5675
40214Acinetobacter johnsoniispecies5.5605
1115758Romboutsia ilealisspecies5.5565
751585Coprococcus sp. ART55/1species5.5551
2709410Chordicoccus furentiruminisspecies5.5376
3031933Chordicoccusgenus5.5376
495Neisseria elongataspecies5.5305
623Shigella flexnerispecies5.5099
851Fusobacterium nucleatumspecies5.5022
1853232Hymenobacteraceaefamily5.4842
433286Anaerocolumna cellulosilyticaspecies5.4546
549Pantoea agglomeransspecies5.4521
971Selenomonas ruminantiumspecies5.4355
114197Selenomonas ruminantium subsp. lactilyticasubspecies5.4355
927704Selenomonas ruminantium subsp. lactilytica TAM6421strain5.4355
46503Parabacteroides merdaespecies5.4332
2763670Wujia chipingensisspecies5.4314
2944152Wujiagenus5.4314
2490855Lachnoanaerobaculum gingivalisspecies5.3855
2528203Bacteroides sp. A1C1species5.3817
2582419Dialister hominisspecies5.3716
2662363Alistipes sp. dk3624species5.3691
1703250Citrobacter sp. CRE-46species5.3544
302911Bifidobacterium animalis subsp. lactissubspecies5.3507
41294Nitrobacteraceaefamily5.3501
1871109Neisseria sp. RH3002v2gspecies5.3386
66219Lachnoclostridium phytofermentansspecies5.3383
357809Lachnoclostridium phytofermentans ISDgstrain5.3383
40215Acinetobacter juniispecies5.3372
2161821Dialister massiliensisspecies5.3275
46205Pseudobutyrivibriogenus5.3271
185007Pseudobutyrivibrio xylanivoransspecies5.3271
1183380Campylobacter coli RM5611strain5.3228
1249Weissella paramesenteroidesspecies5.3221
484Neisseria flavescensspecies5.3157
2585118Alistipes communisspecies5.2944
649756Anaerostipes hadrusspecies5.2889
1649Kurthiagenus5.2799
2732414Petitviralesorder5.2753
2732412Phixviricotaphylum5.2753
2732091Sangerviraekingdom5.2753
2732413Malgrandaviricetesclass5.2753
10841Microviridaefamily5.2753
841Roseburiagenus5.2685
1843210Anaerocolumnagenus5.2599
817Bacteroides fragilisspecies5.2242
294702Proteiniphilumgenus5.2238
847Oxalobacter formigenesspecies5.2219
479831Clostridioides difficile QCD-63q42strain5.1847
29393Dolosigranulumgenus5.1813
29394Dolosigranulum pigrumspecies5.1813
1513Clostridium tetanispecies5.1794
79880Shouchella clausiispecies5.1644
143387Fusobacterium necrophorum subsp. funduliformesubspecies5.1549
872Desulfovibriogenus5.1511
135622Alteromonadalesorder5.1463
2733190Lughvirusgenus5.1334
2734248Lughvirus lughspecies5.1334
2070184Faecalibacterium phage FP_Lughno rank5.1334
207244Anaerostipesgenus5.1222
374Bradyrhizobiumgenus5.044
2942993Blohavirusgenus5.0409
901Desulfovibrio pigerspecies5.0326
712361Leptotrichia sp. oral taxon 218species5.0265
2708053Romboutsia sp. 13368species5.0245
1263Ruminococcusgenus5.0125
2956053Kehishuvirus primariusspecies5.0117
2301731Bacteroides phage crAss001no rank5.0117
884684Mageeibacillus indolicusspecies4.9975
699246Mageeibacillus indolicus UPII9-5strain4.9975
1637257Mageeibacillusgenus4.9975
1647988Akkermansiaceaefamily4.9733
239934Akkermansiagenus4.9733
48461Verrucomicrobialesorder4.9731
203494Verrucomicrobiiaclass4.9731
74201Verrucomicrobiotaphylum4.973
2709317Bacteroides phage crAss002no rank4.9597
2955998Jahgtovirus secundusspecies4.9597
2913621Prevotella sp. E9-3species4.9552
941323Escherichia coli VR50strain4.9255
562Escherichia colispecies4.923
568816Acidaminococcus intestini RyC-MR95strain4.9002
411470Mediterraneibacter gnavus ATCC 29149strain4.8944
28890Euryarchaeotaphylum4.8866
2734096Brigitvirus brigitspecies4.8861
2070181Faecalibacterium phage FP_Brigitno rank4.8861
2733097Brigitvirusgenus4.8861
1653174Actinotignumgenus4.8813
239935Akkermansia muciniphilaspecies4.8803
2157Archaeasuperkingdom4.8576
1583098Fusobacterium hwasookiispecies4.8541
2789424Actinomyces sp. HMT897species4.8316
38284Corynebacterium accolensspecies4.8257
85015Nocardioidaceaefamily4.8191
1796613Bacteroides caecimurisspecies4.8184
2576755Caproicibactergenus4.8161
2576756Caproicibacter fermentansspecies4.8161
630129Bifidobacterium catenulatum subsp. kashiwanohensesubspecies4.8136
589436Prevotella fuscaspecies4.8083
1236517Prevotella fusca JCM 17724strain4.8083
936351Bifidobacterium breve S27strain4.8057
2845437Skunavirus P656species4.7933
2662298Lactococcus phage P656no rank4.7933
2874051Escherichia coli O99:H6serotype4.7887
208223Kosakonia cowaniispecies4.7698
204037Dickeyagenus4.7678
2792859Bacteroides humanifaecisspecies4.7329
84030Lacrimispora saccharolyticaspecies4.7099
2719231Lacrimisporagenus4.6978
1655645Parabacteroides phage YZ-2015bspecies4.6918
657314Blautia obeum A2-162strain4.6831
1117Cyanobacteriotaphylum4.68
1051074Streptococcus thermophilus JIM 8232strain4.6739
2773705Escherichia coli O18ac:H14no rank4.6698
2751153Coprobacter secundus subsp. similissubspecies4.6668
1501392Coprobacter secundusspecies4.6668
3031451Desulfobulbiaclass4.6547
3024411Desulfobulbalesorder4.6547
33882Microbacteriumgenus4.6498
459786Oscillibactergenus4.5986
2763056Oscillibacter hominisspecies4.5986
411486Clostridium sp. M62/1species4.5983
185008Butyrivibrio hungateispecies4.5971
997877Phocaeicola dorei CL03T12C01strain4.5875
33042Coprococcusgenus4.5745
1727145Anaerocolumna chitinilyticaspecies4.5703
3028117Cyanophyceaeclass4.5658
28116Bacteroides ovatusspecies4.5602
1122979Prevotella amnii DSM 23384 = JCM 14753strain4.5417
203682Planctomycetotaphylum4.5364
411474Coprococcus eutactus ATCC 27759strain4.5352
2944198Wansuiagenus4.5336
2763667Wansuia hejianensisspecies4.5336
28137Prevotella veroralisspecies4.53
267890Shewanellaceaefamily4.5142
42817Corynebacterium argentoratensespecies4.5132
1348662Corynebacterium argentoratense DSM 44202strain4.5132
2173Methanobrevibacter smithiispecies4.5082
2159Methanobacteriaceaefamily4.5036
183925Methanobacteriaclass4.5035
2158Methanobacterialesorder4.5035
22Shewanellagenus4.4975
75682Oxalobacteraceaefamily4.4902
2944193Simiaoagenus4.4833
2763672Simiaoa suniispecies4.4833
718255Roseburia intestinalis XB6B4strain4.4785
2837504Heyndrickxiagenus4.4783
61648Kluyvera intermediaspecies4.4707
239759Alistipesgenus4.4593
171550Rikenellaceaefamily4.4593
909932Negativicutesclass4.4521
213121Desulfobulbaceaefamily4.4201
226186Bacteroides thetaiotaomicron VPI-5482strain4.4156
2172Methanobrevibactergenus4.415
2779519Thermophilibacter immobilisspecies4.3952
2847307Thermophilibactergenus4.3952
1822464Paraburkholderiagenus4.3847
236753Fastidiosipila sanguinisspecies4.3749
236752Fastidiosipilagenus4.3749
1656Actinomyces viscosusspecies4.3346
846Oxalobactergenus4.3282
46228[Ruminococcus] lactarisspecies4.3105
471875[Ruminococcus] lactaris ATCC 29176strain4.3105
2070186Faecalibacterium phage FP_Taranisno rank4.3072
2733134Taranisvirusgenus4.3072
2734146Taranisvirus taranisspecies4.3072
1729679Faecalibaculumgenus4.274
1702221Faecalibaculum rodentiumspecies4.274
46506Bacteroides stercorisspecies4.2581
620Shigellagenus4.2577
39486Dorea formicigeneransspecies4.2514
2583584Streptococcus sp. NCTC 11567species4.248
2316Methanosphaeragenus4.2035
657315Roseburia intestinalis M50/1strain4.2022
2108523Lawsonibacter asaccharolyticusspecies4.1622
2172004Lawsonibactergenus4.1622
1385938Bifidobacterium breve 12Lstrain4.1593
310298Phocaeicola coprocolaspecies4.142
470145Phocaeicola coprocola DSM 17136strain4.142
328814Alistipes shahiispecies4.1124
717959Alistipes shahii WAL 8301strain4.1124
2070182Faecalibacterium phage FP_Eponano rank4.1016
2734105Eponavirus eponaspecies4.1016
2733103Eponavirusgenus4.1016
397864Barnesiellagenus4.0951
397865Barnesiella viscericolaspecies4.0951
880074Barnesiella viscericola DSM 18177strain4.0951
2317Methanosphaera stadtmanaespecies4.091
39496Eubacterium ventriosumspecies4.0826
2899121Tannockella kyphosispecies4.0805
2943184Tannockellagenus4.0805
1398Heyndrickxia coagulansspecies4.0793
2866573Cardiobacterium sp. Marseille-Q4385species4.0783
196Campylobacter fetusspecies4.07
997890Bacteroides uniformis CL03T12C37strain4.0546
116085Coprococcus catusspecies4.032
2929490Faecalibacterium sp. I2-3-92species4.02
39485Lachnospira eligensspecies4.0161
28050Lachnospiragenus4.0161
393921Porphyromonas crevioricanisspecies4.0144
37923Rothia kristinaespecies4.0086
572511Blautiagenus3.9996
155615Fusobacterium vincentiispecies3.979
32020Campylobacter fetus subsp. venerealissubspecies3.9746
418240Blautia wexleraespecies3.9542
1121115Blautia wexlerae DSM 19850strain3.9542
2948680Diorhovirusgenus3.9512
2929494Faecalibacterium sp. I4-1-79species3.918
138851Treponema parvumspecies3.8965
2929488Faecalibacterium sp. IP-1-18species3.8962
657322Faecalibacterium prausnitzii SL3/3strain3.8736
1164882Lachnoanaerobaculumgenus3.8719
88431Dorea longicatenaspecies3.8655
2489010Klebsiella africanaspecies3.8568
1870984Anaerococcus mediterraneensisspecies3.856
853Faecalibacterium prausnitziispecies3.8524
449673Bacteroides stercoris ATCC 43183strain3.8297
1643513Treponema sp. OMZ 857species3.7909
2603322Vallitaleaceaefamily3.764
357276Phocaeicola doreispecies3.7613
2946593Oxalobacter aliiformigenesspecies3.7341
34084Riemerellagenus3.7314
2518495Duncaniellagenus3.7118
203Campylobacter rectusspecies3.6624
2029659Lactococcus phage 16802no rank3.6177
2845153Skunavirus sv16802species3.6177
28124Porphyromonas endodontalisspecies3.6127
2755405Bacteroides sp. CACC 737species3.6041
2772080uncultured phage cr53_1no rank3.6009
2955510Blohavirus americanusspecies3.6009
44283Pasteurella multocida subsp. multocidasubspecies3.5988
543Enterobacteriaceaefamily3.5941
1730Eubacteriumgenus3.5859
186806Eubacteriaceaefamily3.5857
91347Enterobacteralesorder3.5611
85004Bifidobacterialesorder3.5348
31953Bifidobacteriaceaefamily3.5348
1678Bifidobacteriumgenus3.5344
189330Doreagenus3.5324
1760Actinomycetesclass3.5314
1236Gammaproteobacteriaclass3.4912
35832Bilophilagenus3.4836
35833Bilophila wadsworthiaspecies3.4836
1224Pseudomonadotaphylum3.4676
3024823Anaeromicropilagenus3.4646
2785025Anaeromicropila herbilyticaspecies3.4646
2845434Skunavirus P4565species3.4294
2662297Lactococcus phage P4565no rank3.4294
228603Hoylesella shahiispecies3.4198
2981344Xiameniagenus3.4192
2682776Xiamenia xianingshaonisspecies3.4192
28256Halomonadaceaefamily3.4033
575614Prevotella sp. oral taxon 299 str. F0039strain3.3998
652716Prevotella sp. oral taxon 299species3.3998
574697Butyricimonasgenus3.3966
420952Paraburkholderia bryophilaspecies3.358
28264Arcanobacterium haemolyticumspecies3.3414
544645Butyricimonas virosaspecies3.3361
2162637Bacteroides sp. PHL 2737species3.3095
1534Clostridium kluyverispecies3.3081
2763068Streptococcus sp. NSJ-72species3.2893
201174Actinomycetotaphylum3.2891
13076Globicatella sanguinisspecies3.2685
13075Globicatellagenus3.2685
186823Alicyclobacillaceaefamily3.2346
2518971Duncaniella dubosiispecies3.2306
183963Halobacteriaclass3.2226
1737424Blautia massiliensis (ex Durand et al. 2017)species3.1839
717605Thermobacillus composti KWC4strain3.1738
377615Thermobacillus compostispecies3.1738
76632Thermobacillusgenus3.1738
292632Subdoligranulumgenus3.1698
214851Subdoligranulum variabilespecies3.1698
33024Phascolarctobacteriumgenus3.1137
135619Oceanospirillalesorder3.0941
165179Segatella coprispecies3.006
2974251Segatellagenus3.006
194924Desulfovibrionaceaefamily3.0022
213115Desulfovibrionalesorder3.0017
3031449Desulfovibrioniaclass3.0017
200940Thermodesulfobacteriotaphylum2.999
28263Arcanobacteriumgenus2.9903
2375Sporomusagenus2.9612
411483Faecalibacterium duncaniaespecies2.96
171552Prevotellaceaefamily2.9365
394503Ruminiclostridium cellulolyticum H10strain2.9305
1521Ruminiclostridium cellulolyticumspecies2.9305
33926Candidatus Phytoplasmagenus2.9252
1843488Acidaminococcalesorder2.9156
909930Acidaminococcaceaefamily2.9156
1853229Chitinophagalesorder2.9063
563835Chitinophagaceaefamily2.9063
1853228Chitinophagiaclass2.9063
3031651Desulfuromonadiaclass2.9025
33025Phascolarctobacterium faeciumspecies2.8972
2377Sporomusa termitidaspecies2.8942
3039116Anaerocolumna sp. AGMB13025species2.8324
3031668Geobacteralesorder2.8267
213422Geobacteraceaefamily2.8267
621Shigella boydiispecies2.8033
537011Segatella copri DSM 18205strain2.7553
1538075Malasseziomycetesclass2.7053
742845Malasseziaceaefamily2.7053
55193Malasseziagenus2.7053
162474Malassezialesorder2.7053
2734634Berryella wangjianweiispecies2.6998
76775Malassezia restrictaspecies2.6771
2929495Faecalibacterium sp. I4-3-84species2.6632
109328Leptotrichia trevisaniispecies2.6442
359110Pseudomonas extremaustralisspecies2.6212
2929489Faecalibacterium sp. IP-3-29species2.6134
213118Desulfobacteralesorder2.566
3024418Desulfobacteriaclass2.566
28118Odoribacter splanchnicusspecies2.5061
283168Odoribactergenus2.5061
820Bacteroides uniformisspecies2.4089
709991Odoribacter splanchnicus DSM 20712strain2.3887
2913616Prevotella sp. E13-17species2.3359
28446Anaerotignum propionicumspecies2.3254
2039240Anaerotignumgenus2.3254
991789Anaerotignum propionicum DSM 1682strain2.3254
1853231Odoribacteraceaefamily2.276
821Phocaeicola vulgatusspecies2.1936
2725997Escherichia sp. SCLE84species2.1911
611Salmonella enterica subsp. enterica serovar Heidelbergno rank2.1785
2818505Myxococcotaphylum2.0115
1124936Salmonella enterica subsp. enterica serovar Heidelberg str. 41578strain1.9976
216851Faecalibacteriumgenus1.9532
909656Phocaeicolagenus1.7058
592316Pantoea sp. At-9bspecies1.6002
216572Oscillospiraceaefamily1.5468
186803Lachnospiraceaefamily1.5367
1239Bacillotaphylum0.9549
816Bacteroidesgenus0.9515
186801Clostridiaclass0.9074
186802Eubacterialesorder0.9074
815Bacteroidaceaefamily0.2148
171549Bacteroidalesorder-0.482
200643Bacteroidiaclass-0.482
976Bacteroidotaphylum-0.498

As a FYI, my preferred transformation reduces skew to zero for everyone above. Life is good.

Vaccinations and the Microbiome

This post was triggered by the email below. They included a Biomesight microbiome test, Mosaic Organic Acid Test and a Gastric Tissue report. My expertise is solely the microbiome as a statistican so I will ignore all except the microbiome test.

Key Question: Is “vaccine injury” is a permanent condition?

  • Answer: No, the most probable cause of vaccine injury is a vaccine response triggering or worsening a microbiome dysbiosis. See the literature below.
    • A microbiome dysbiosis may self-resolve for some people (i.e. people feel off for a few days or weeks after the shot) or become stable — requiring sophisticated intervention.
    • There can be other speculated mechanism (autoimmunity induced, molecular mimicry or bystander activation) but they lack clear evidence, and are often based on ideological beliefs. I keep to Osler Principle and the simplest explanation supported by evidence.
    • Followup from reader: H1N1 Influenza Pandemrix vaccine which caused narcolepsy (autoimmune disease) due molecular mimicry, which is my worst fear..
      • Correct: Narcolepsy Associated with Pandemrix Vaccine [2018]. This is one specific vaccine, not for all vaccines (my scope). The researchers who found this in the data would have reported all vaccines with similar side effects if there was data supporting it. [Studies] It seems to be associated to H1N1 vaccines.

I wanted to give you a rundown of what’s been going on with me. On January 6, 2023, I got the third dose of the nonavalent HPV vaccine, Gardasil 9. Immediately after the shot, I felt wiped out and weird, but my symptoms subsided only to come back with vengeance two weeks later.

The symptoms I experienced were all the classic ME/CFS ones, specifically POTS, tachycardia, panic attacks, brain fog, blurred vision, shortness of breath, trouble finding words, fatigue, PEM, fasciculations, neuropathy, pins and needles, Raynaud’s phenomenon, joint pain and joint cracking, food intolerances and food malabsorption, yellow mushy stools, and some more alarming sensations: like feeling that my body was heavy, like it was made of concrete, a sensation of electric shocks in my arms, and tingling in my feet that moved to my hands a couple of times.

Since then, some symptoms have disappeared, but others remain and new ones pop up. Right now, the symptoms I still have are joint pain and joint cracking, fasciculations, malabsorption and yellow stools, what I think is Raynaud’s phenomenon (my hands are red most of the time), and, at the moment I’m writing this message, heavy drowsiness and a general feeling of malaise, which is discouraging, since I felt better earlier this month and thought I was finally getting out of this nightmare.

A reader on CFS Remission

Overview

This is a two-sided discussion exploring the interaction between vaccinations and the microbiome from both perspectives:

  1. How vaccinations may alter the microbiome
  2. How the existing state of the microbiome may influence the effectiveness of a vaccination

To be transparent, I want to share that I personally experienced an adverse side effect following a series of vaccinations. The side effect involved severe gingival (gum) recession, causing the roots of my teeth to become fully exposed. Unfortunately, the condition progressed to the point where dentures became necessary due to the extent of gum loss.

At a high level, interactions in both directions are not only possible but expected. Vaccinations stimulate the immune system, similar to a natural infection — and any shift in immune function can, in turn, affect the microbiome. Conversely, the microbiome plays a key role in shaping immune responses, meaning it can directly influence how the body responds to vaccines.

It’s important to remember that the primary goal of any vaccination is to safely prompt the immune system to build protection against a specific infection. However, because the microbiome and immune system are deeply interconnected, this process can be more complex than it first appears.

Vaccination to Microbiome

A few studies of interest:

Growing evidence shows that the composition of the intestinal microbiota, which is known to play an important role in the development and regulation of immune responses7, influences responses to vaccination8,9,10. Studies which have investigated this have shown that a higher relative abundance of the phylum Actinobacteria is consistently associated with higher vaccine responses and a higher relative abundance of Bacteroides with lower responses, while the association between the relative abundance of the phyla Firmicutes and Proteobacteria and vaccine responses varies for different genera and species11,12,13,14,15,16,17,18.

The immunological interplay between vaccination and the intestinal microbiota [2023]

A recent study using metagenomic sequencing, reported that the intramuscular administration of an inactivated and an mRNA SARS-CoV-2 vaccine was associated with lower bacterial diversity, an increase in the relative abundance of Bacteroides caccae and a decrease in the relative abundance of Clostridiales (Coprococcus comes, Dorea longicatena and Ruminococcus obeum) in the intestinal microbiota one month after vaccination

… a total of 15 bacterial species in the baseline gut microbiome were identified, of which Bifidobacterium adolescentis was enriched in high-responders while Bacteroides vulgatus, Bacteroides thetaiotaomicron and Ruminococcus gnavus were more abundant in low-responders

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events [2021]

Microbiome to Vaccination Effectiveness

Not only do pathogens exert immunomodulatory effects, but the microbes that populate a healthy human host, known as the microbiome, can also influence the immune response.4,11

Influence of the microbiome on response to vaccination [2015]

When facing respiratory syncytial virus (RSV), mice supplemented with Lactobacillus showed an enhanced immune response 

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation. [2017]

One of these factors seems to be the microbiome differences among individuals (101, 102). A growing number of studies suggest that the microbiome can modulate immune responses induced by vaccines (103, 104). Huda et al. (105) studied infants’ microbiomes to evaluate how their microbiome composition influenced the response to oral PV and hepatitis B virus vaccines. They found that Actinobacteria species prevalence may increase the vaccine response, while Enterobacteriales, Pseudomonadales, and Clostridiales were associated with lower response to the aforementioned vaccines. Hagan et al. (106) showed that differences in the microbiome can alter the responses of humans vaccinated against IAV.

The Interplay between the Host Microbiome and Pathogenic Viral Infections [2021]

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events

Analysis

My model is that ME/CFS is a microbiome dysbiosis. A vaccination is a microbiome disruptor — for most people, they recover. If you start with dysbiosis, then recovery may be a bit less likely.

Urban Legend in some ME/CFS groups is that people with ME/CFS do not catch things. There may some truth to it — virus friendly to the typical microbiome may find the dysbiosis of the ME/CFS patient very unfriendly. Secondly, (with a little tongue in check humor) how can they tell!!!

It turns out that virii often requires specific species to infect a person.

 certain microbiome can be essential for a virus to infect its host. Jones et al. (82) showed that human norovirus needs Enterobacteria spp. to successfully infect B cells, as this bacterium aids in the attachment of the virus to the host cell. Norovirus infection in mice requires the microbiota to be persistent (83): mice with a depleted microbiome prevented persistent norovirus infection. 

The Interplay between the Host Microbiome and Pathogenic Viral Infections

Going Forward

The phrase of “Vaccine Injury” is very misleading and implies that the body is somehow injured in potentially a permanent way. I believe that “Vaccine Dysbiosis” is a better and more accurate term.

We find a mountain of literature associating a vast array of different virii to ME/CFS. A few examples are:

  1. Epstein-Barr Virus (EBV)
    EBV, which causes infectious mononucleosis, is one of the most frequently implicated viruses in ME/CFS. Studies show that 8–15% of people who develop infectious mononucleosis go on to meet ME/CFS criteria, and a subgroup of ME/CFS patients show evidence of EBV reactivation or immune response abnormalities related to EBV5 7.
  2. Human Herpesvirus 6 (HHV-6)
    Reactivation of HHV-6, another common herpesvirus, has been hypothesized to contribute to ME/CFS symptoms, particularly in combination with EBV reactivation7.
  3. Enteroviruses
    Historical and contemporary evidence links enteroviruses (a group that includes polioviruses, coxsackieviruses, and echoviruses) to ME/CFS. Outbreaks of ME/CFS have coincided with enteroviral epidemics, and some researchers consider enteroviruses a likely culprit, especially in cluster cases1.
  4. Influenza Viruses
    Influenza infection has been associated with a more than two-fold increased risk of developing ME/CFS in the years following infection17.
  5. SARS-CoV-2 (COVID-19)
    Many individuals with long COVID meet criteria for ME/CFS, and SARS-CoV-2 is recognized as a trigger for ME/CFS in some cases67.
  6. Other Herpesviruses
    Varicella zoster virus (which causes chickenpox and shingles) and other herpesviruses have also been reported as potential triggers7.
  7. Ross River Virus
    This mosquito-borne virus has been linked to ME/CFS onset, likely through immune system dysregulation3.
  8. Retroviruses (e.g., XMRV)
    Early studies suggested an association between the retrovirus XMRV and ME/CFS, but this link has been discredited by subsequent research and retraction of the original findings2.

The goal of vaccines is to trigger enough of a response to set up the body to fight the target infection. Unfortunately, it also has a risk of triggering ME/CFS in some cases. If the person has ME/CFS, it may trigger cascades like reported above.

Going Forward

Forget about trying to “repair the injury”, the ‘injury’ is dysbiosis. You want to correct the dysbiosis. He did not have a prior to vaccination test to use for reference 🙁 .

Looking at the forecasted symptoms and the symptoms he marked we see a lot of matches at a high level (> 85%)

Looking at the bacteria that the above picked, we have one that is in the literature is associated with norovirus above.

Looking at the shifts reported for COVID, we see 64 matches to reported bacteria shifts from the literature.
 

Adlercreutzia – genus : Low 21
Adlercreutzia equolifaciens – species : Low 14
Aeromonadaceae – family : Low 2
Akkermansia – genus : Low 12 15 16 22 24
Akkermansia muciniphila – species : Low 10 13
Anaerococcus – genus : Low 13
Bacillota – phylum : Low 14
Bacteroides – genus : High 1 4 11 13 14 24 25
Bacteroides stercoris – species : High 13 14
Bacteroides uniformis – species : Low 13 14
Bacteroidia – class : High 9
Bacteroidota – phylum : High 9 14
Blautia – genus : Low 5 6 12 13 16
Blautia obeum – species : Low 8 13
Clostridia – class : Low 23
Clostridiaceae – family : Low 14
Collinsella aerofaciens – species : High 7 14
Coprococcus – genus : Low 12 13 14
Coprococcus catus – species : Low 14a
Dorea formicigenerans – species : Low 8 13
Enterobacterales – order : High 18
Enterobacteriaceae – family : High 2 13 14 16 17 19 20
Escherichia – genus : High 3 14 17
Escherichia coli – species : High 14
Eubacterium – genus : Low 11 13 21
Faecalibacterium – genus : High 1 4 12
Finegoldia – genus : Low 13
Flavobacteriaceae – family : High 14
Gammaproteobacteria – class : High 14
Haemophilus – genus : High 16
Lachnospiraceae – family : Low 3 11 14 21
Moraxellaceae – family : Low 2
Oscillospira – genus : Low 24
Ruminococcus – genus : Low 6 12 13 16 24
Ruminococcus bromii – species : Low 13
Spirochaetia – class : Low 14
Spirochaetota – phylum : Low 14
Verrucomicrobiota – phylum : Low 22

The top results are very typical for ME/CFS: specific antibiotics used with the Jadin Protocol for ME/CFS. I know that both getting specific antibiotics off-label and often human reluctance to do them(valid from many horror stories of them being arbitrarily selected by MDs and making people worse) — makes that a path rarely travelled.

Looking at the R2 model for making probiotics do the work, the top ones (that are commercially available)

  1. In Research — not for sale
    • Anaerobutyricum hallii – rank: 998
    • Christensenella minuta – rank: 888
    • Roseburia intestinalis – rank: 882
    • Blautia wexlerae – rank: 823
    • Blautia hansenii – rank: 748
    • Faecalibacterium prausnitzii – rank: 697
  2. Top Recommendations
    • Enterococcus faecium – rank: 687
    • Lactococcus cremoris – rank: 558
    • Akkermansia muciniphila – rank: 547
    • Lactococcus lactis – rank: 331
    • Leuconostoc mesenteroides – rank: 282
    • Levilactobacillus brevis – rank: 236
  3. Fall backs – very small impact.
    • Segatella copri – rank: 189
    • Bacteroides uniformis – rank: 137
    • Parabacteroides goldsteinii – rank: 136
    • Ligilactobacillus salivarius – rank: 127
    • Latilactobacillus sakei – rank: 111
    • Bacteroides thetaiotaomicron – rank: 106
    • Streptococcus thermophilus – rank: 89
    • Lactiplantibacillus plantarum – rank: 88
    • Bifidobacterium adolescentis – rank: 67

All of the items listed in 2 above are available from one or more of my usual sources except for Akkermansia which does have several providers today:

The next item are other suggestions which are listed below and high in herbs. As a FYI, Enterococcus faecium is actually the top probiotic using PubMed literature (and not R2 infererence) – I do like that type of convergence of different paths.

Suggested Methodology

  • Get the probiotics in 2 above.
    • Start the first and keep taking for 4 weeks (then 2 week break)
    • Every week, add in one more probiotic for 4 weeks followed by 2 week break
  • Do a lot of teas with different ones of the above herbs — if it is liquid, it should be a tea!
  • Wheat bread are all avoids, so do 100% Rye bread which is on the above list (not wheat-rye mixtures)

Go through the consensus list for more information. Do a retest about 2-3 months after starting the above. The retest will show the next course correction (often there are many).

Questions and Answers

  • The vaccine I got (HPV vaccine) is documented to cause ME/CFS and is one of the vaccines with higher number of reported adverse reactions compared to others. Why would you say is this?
  • I see you highlight the family Enterobacteriacea but ignore others like Bacteroides 
    • I picked Enterobacteriacea for purpose of illustration of one virus-microbiome interaction, there is not sufficient literature on HPV vaccine. We have extremely sparse data in this area.
  • Microbiome Prescription also told me that I probably had lactic acid acidemia and biofilms but I didn’t understand it very well. Can you explain which implications have this and what bacteria may be causing it?
    • Lactic Acid Acidosis means too much lactic acid. It is very common with ME/CFS and typically associated to brain fog. This is also associated with the following symptoms:
      • Nausea and vomiting.
      • Exhaustion and fatigue.
      • Fast, deep breathing (respiratory compensation).
      • Muscle cramps and body aches.
      • Increasing weakness and drowsiness.
      • Delirium and confusion.
      • Ataxia.
      • Oliguria (low urine output).
      • Low body temperature.
      • Low blood pressure.
      • Fever.
      • Jaundice (a yellow tint to the skin and whites of the eyes).
    • Biofilms include dental plaque and often acts as “bullet proof vests” to bacteria that we want to change. See Wikipedia for more.
  • Regarding the antibiotics, I was terrorized when I saw Ciprofloxacin at the top of the recommendations as it’s infamous for injuring people and causing a ME/CFS like condition, even being sold with a black label warning in the US. It seemed ironic to me and I am frankly hesitant to try it.
    • The system does not consider these risks — that is for your medical professional to evaluate.
    • I strongly favor Cecile Jadin’s approach. One course (7-10 days) of one antibiotic, 3 weeks off, rotate to another appropriate one. the ones marked with [CFS] have been use with some success for ME/CFS. I believe the issue cited was for continuous use of this antibiotic for more than one course. See this video for her experience. She has never seen in 20+ years of using it, adverse interactions. This also details her process (to be reviewed by your medical professional).
  • The top two suggested probiotics, I haven’t heard of them in my life and haven’t seen them sold anywhere. Will they even still work? 
    • Enterococcus faecium – rank: 687 and Lactococcus cremoris – rank: 558 are likely not available at your local health food store. Enterococcus faecium Source, Lactococcus cremoris source
    • They are computed to work — and my experience using the above sources for other probiotics is they work for me. One factor may be the freshness or the probiotics.
    • Followup:  I see Lactobacillus reuteri at the top of my probiotics suggestions list and don’t see Lactococcus cremoris at all. Are we look at the same screen?
  •  I am coming out of a 14-day Rifaxamin cycle which I think caused my current neuropathy and I wonder if it altered my microbiome enough so the results of the Biomesight are no longer accurate. Is my suspicion of the neuropathy being caused by Rifaxamin accurate? It started on the very last days of the cycle and I also have neurological symptoms again after a long time without having them. 
    • Rifaximin are your current sample is listed as an avoid. Your neuropathy may have been contributed by it.
    • I suspect that the suggestions will not be dramatically altered, so I would suggest implementing the top suggestions that you are comfortable with. Also, eliminate as many of the AVOIDS as is practical.
  • I am also still taking Saccharomyces Boulardii, Lactobacillus Plantarum, Lactobacillus Gasseri and will be adding Colostridium Butyricum, Bacillus Coagulans and the mix of Bifidobacterias “Seeking Health ProBiota Bifidobacterium.” All of them suggested by ChatGPT o3 model after feeding it my Biomesight, OAT, and a wide array of conventional medical tests.
  • I find some of the recommendations given by Microbiome Prescription weird, like whole milk and camel milk. Didn’t Biomesight said that my lactose processing was low? Or walnuts. What kind of walnuts they need to be? Can they be pecans or indian walnuts? 
    • Microbiome Prescription will differ from Biomesight see Why sites suggestions disagree on the same data. In short, MP uses over 7,431,437 facts to compute decisions as of today. I do not know the number BS uses, I suspect very few. All suggestions can be traced back to studies. The names of suggestions are based on the terms used in studies.
    • I do not know how many studies they based “lactose processing was low”, I see lactose as a significant positive value in your results (400).
  • Also most of them are herbs like you said or non foods like spices and other odd things. Is this common for other microbiomes?
    • I view every microbiome as different. The suggestions that I see are similar to others with ME/CFS, see other analysis here.

Followup: As I am not doing well economically and looking for ways to save, I feed ChatGPT o3 model the Microbiome Prescription suggestions table and told it to look for probiotic mixtures with the most amount of recommended strains and the least of strains to be avoided, Seeking Health ProBiota Bifidobacterium was the result.

I was aware of the wrong strains on the mixture and asked ChatGPT about the impact they would had. It told me that even then, it was still worth the risk as the strains to avoid had relatively low impact (Bifidobacterium bifidum -132.8) compared to the recommended strains on the mix (Bifidobacterium Longum 540.3).

You see this as an accurate analysis from ChatGPT or you would still recommend to avoid them?

In case that you say yes… Can I take all the probiotics I previously told at once or they antagonize each other? Is doing this risky?

ChatGPT and other Large Language Model are sophisticated Hearsay-Engines. The lack the expertise of a fuzzy logic expert system. If I was a judge, I would strike hearsay evidence from consideration. The issue of risk is a question for your medical professional. All that I can say is that it was decreased odds of helping and may have some risk of hurting.

5.- “I see lactose as a significant positive value in your results (400).”

A = I am talking about the lactose degrader shown as LOW (0.11%) under the food intolerances section on the Biomesight report.

There are some other findings here that disturb me, like butyrate producers LOW, colibactin producers HIGH, D-Lactate producers HIGH, gram negative bacteria HIGH and gram positive bacteria LOW.

Would you say that I fit on the classic ME/CFS profile? Anything else that stands out about my microbiome?

Thank you and I hope this format is easy to understand but if not, please let me know.

I avoid comment on any provider individual reports, i.e. Biomesight report, beyond what the US National Institute of Standards and Technology has stated. I will comment on methodologies, the usual comment is they “went cheap” and do not use sufficient data — MP consider 7,431,520 facts in computing suggestions.

Your sample have strong statistical associations to may symptoms of ME/CFS and Long COVID. “Fitting a profile” is question more suitable for a medical professional. I am a statistican.

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.

Also, I note that many people will make inferences (often based on influencers opinions) that are not supported by the evidence. Often people want absolute certainty and will deem things proven if they find a single case study supporting a hypothesis; this is not how science and statistics work… it is all odds.

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.

Family Convergence of Microbiome

A reader wrote me saying:

I have 5 Biomesight samples uploaded to my MP.com account, of which 3 are mine and 2 are my kids.  

When I choose a different sample from the dropdown list, the ‘Suggestions’ change as I would expect them to, however, the commercially available Probiotic recommendations do not change. So the Priobiotic ‘weighting’ is the same on all 5 samples, which I included a screenshot of.  

Any idea why this is happening and how I can get accurate commercial Probiotic suggestions for each different sample?

Thanks much,

Step #1 Reproduce the issue

First item was checking that there was not duplicate uploads – there were not. I then got suggestions from each sample and list them below: I also included the top suggestion to verify that different suggestions were made.

There were duplicate suggestions between some samples:

  • Two the same (2024-12-17, 2024-03-10)
  • Three the same ( 2023-12-15, 2024-01-08, 2023-12-15) 

One item was on all of the recommendation: L.Gasseri.

I also did Experimental Probiotics Suggestions using Taxa R2 Site. I find that I trust R2 suggestions more than the default suggestions. The differences are:

  • Default is based on available studies — most have not been duplicated and have small sample size. Small sample size means only things that really stand out are reported. Most are done with 16s testing which is much less accurate than shotgun. We have 4,625 data points.
  • R2 is based on 1000 shotgun samples and based on statistical associations ween between probiotic species and other species. There are no clinical studies showing that they work. We have 2,446,755 data points.

So the decision is trusting limited clinical studies, or trusting statistics with 529x more data points. My personal experience is that I have noticed more benefit from R2 suggestions than the default suggestions.

Sample 2025-06-29

Top amoxicillin [CFS] 1444

R2 Suggestions for Available:

Step #2 2024-12-17

Top Item: metronidazole [CFS] 1434

R2 Suggestions for Available:

Step #3 2024-03-10

Top Item: metronidazole [CFS] 584.5

R2 Suggestions for Available:

Step #4 2023-12-15

Top Ferrum {Iron Supplements} 1013

R2 Suggestions for Available:

Step #5 2024-01-08 

Top imipenemL 932

R2 Suggestions for Available:

Step #6 2023-12-15

Top Cichorium intybus {Chicory} 839

R2 Suggestions for Available:

Bottom Line

The reader did report correctly that the same suggestions were being made. The default probiotics were likely correct based on the sparse data from clinical studies available. I would suggest that this user try the top 3 probiotics suggested by the novel R2 algorithm; I suspect they will have a greater and more targeted impact.

I am not surprised that given the limited palette of probiotics from clinical studies that we have convergence because the microbiomes have convergenes.

Key findings from published studies include: