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

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

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

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

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

Official Diagnosis: Mast Cell Dysfunction

Biomesight

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

Ombre

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

Comorbid: Histamine or Mast Cell issues

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

Ombre

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

Biomesight

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

Bottom Line

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

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

Actual example:

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

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

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

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

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

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

Biomesight Data

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

We have some commonalities

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

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

Bottom Line

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

• Bif. Adolescentis

And all Lactobacillus and Lactococcus probiotics should be avoided.

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

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

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

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

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

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

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

Actual example:

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

Not all symptoms have many bacteria associated

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

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

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