After a good night sleep after doing the video below, I realized the next step in this journey. With hundreds of bacteria in the microbiome the question arises which ones to focus on if the condition is not a known single bacteria condition. I.e. Crohn’s, Asthma vs Tuberculosis, Ulcers.

Recently I had major success is identifying bacteria associated to hundreds of symptoms. This was done by using the percentile ranking of each microbiome sample over the population and then examining the counts of the top and bottom 15%ile (simplified version). These should be equal if there is no relationship of the bacteria to the symptom. The difference allows a Chi2 value and probability to be computed for significance. Comparing the averages perform very poorly for finding equivalent statistical significance.

The result was a list of bacteria where the high in these end 15%ile was associated with symptoms / diagnosis. This allows us to filter out the noise from the significance in a sample. The question arises, should all of these be used or is there a critical limit? The current count is 1,960 taxa-shifts with one or more

To address this issue, I decided to plot the counts.

Applying a log function found a region became a straight line. Two apparent inflection points are suggested. Applying different function kept showing the same inflection points.

Bacteria with high and low associated to Symptoms

There are two species in this list. Both are reported in published clinical studies often.

Bacteria	Rank
Faecalibacterium prausnitzii	species
Dorea formicigenerans	species
Weissella	genus
Faecalibacterium	genus
Acidaminococcaceae	family
Acidaminococcales	order

The Short List of Bacteria

We see many bacteria not usually associated plus two familiar ones. Increases means more are in the 85-100%ile, decrease means more are in the 0-15%ile

Bacteria	Rank	Direction	Count of Associations
Thermodesulfobacteriota	phylum	increases	460
Rhodothermota	phylum	increases	247
Rhodothermia	class	increases	247
Rhodothermales	order	increases	247
Actinomycetota	phylum	decrease	146
Holdemania	genus	increases	135
Faecalibacterium	genus	decrease	133
Coriobacteriaceae	family	decrease	125
Coriobacteriales	order	decrease	120
[Clostridium] thermoalcaliphilum	species	increases	116
Coriobacteriia	class	decrease	115
Lactobacillaceae	family	decrease	114
Bifidobacterium	genus	decrease	113
Sphingobacteriaceae	family	increases	113

Longer List of Bacteria

Bacteria	Rank	Shift	Count
Oscillospiraceae	family	decrease	108
Anaerotruncus colihominis	species	increases	107
Actinomycetes	class	decrease	106
Bacteroides	genus	increases	106
Hathewaya	genus	increases	105
Sharpea azabuensis	species	increases	105
Bacillota	phylum	decrease	105
Sharpea	genus	increases	105
Anaerotruncus	genus	increases	104
Sphingobacteriia	class	increases	104
Sphingobacteriales	order	increases	104
Lactobacillales	order	decrease	101
Ruminococcaceae	family	decrease	101
Erysipelothrix muris	species	increases	100
Erysipelothrix	genus	increases	96
Veillonellaceae	family	increases	94
Bacteroides caccae	species	increases	92
Clostridia	class	decrease	90
Bacteroides fluxus	species	increases	89
Eubacteriales	order	decrease	89
Ethanoligenens	genus	increases	89
Finegoldia	genus	increases	88
Hathewaya histolytica	species	increases	87
Hymenobacter xinjiangensis	species	increases	87
Roseburia faecis	species	decrease	85
Blautia obeum	species	decrease	84
[Clostridium] leptum	species	increases	83
Hymenobacter	genus	increases	82
Negativicutes	class	increases	80
Terrabacteria group	clade	decrease	79
Bifidobacteriaceae	family	decrease	79
Bacilli	class	decrease	78
Bifidobacterium adolescentis	species	decrease	78
Marvinbryantia	genus	increases	77
Phocaeicola vulgatus	species	increases	77
FCB group	clade	increases	76
Odoribacter denticanis	species	increases	75
Mediterraneibacter	genus	increases	74
Faecalibacterium prausnitzii	species	decrease	73
Eggerthella	genus	increases	72
Bifidobacteriales	order	decrease	72
Lachnoclostridium	genus	increases	70
Acidaminococcales	order	increases	70
Odoribacter	genus	increases	70
Acidaminococcaceae	family	increases	70
Blautia schinkii	species	increases	69
Dorea formicigenerans	species	increases	69
Collinsella	genus	decrease	69
Bacteroides stercoris	species	decrease	69
Lactobacillus	genus	decrease	68
Pseudomonadota	phylum	increases	67
Odoribacteraceae	family	increases	67
Peptoniphilaceae	family	increases	67
Fusobacteriaceae	family	decrease	66
Dorea formicigenerans	species	decrease	66
Amedibacillus dolichus	species	increases	65
Amedibacillus	genus	increases	65
Candidatus Glomeribacter	genus	increases	64
Eggerthella lenta	species	increases	63
Finegoldia magna	species	increases	63
Oscillatoria corallinae	species	increases	62
Ruminiclostridium cellobioparum subsp. termitidis	subspecies	decrease	62
Oscillatoria	genus	increases	62
Tissierellales	order	increases	62
Ruminiclostridium cellobioparum	species	decrease	62
Hymenobacteraceae	family	increases	62
Pseudoflavonifractor	genus	increases	61
Mycobacteriales	order	increases	61
Tissierellia	class	increases	60
Lachnoanaerobaculum	genus	decrease	60
Coprococcus	genus	decrease	59
Blautia	genus	increases	59
Collinsella aerofaciens	species	decrease	59
Verrucomicrobiota	phylum	increases	59
Veillonellales	order	increases	58
[Ruminococcus] gnavus	species	increases	58
Selenomonas infelix	species	increases	58
Eubacterium ventriosum	species	decrease	58
Lactonifactor	genus	increases	57
Bacteroides cellulosilyticus	species	increases	57
Enterococcaceae	family	decrease	57
Fusobacterium	genus	decrease	57
Alistipes putredinis	species	increases	57
Sutterella	genus	decrease	56
Anaerotignum lactatifermentans	species	increases	56
Anaerotignum	genus	increases	56
Clostridium akagii	species	increases	56
Burkholderiaceae	family	increases	55
Akkermansiaceae	family	increases	55
Turicibacter	genus	decrease	55
Butyricimonas	genus	increases	55
Segatella copri	species	decrease	55
Mycoplasmoidales	order	increases	55
Turicibacteraceae	family	decrease	55
Turicibacter sanguinis	species	decrease	55
Akkermansia muciniphila	species	increases	54
Sporomusaceae	family	increases	54
Limnobacter	genus	increases	54
Limnobacter litoralis	species	increases	54
Lactobacillus rogosae	species	decrease	54
PVC group	clade	increases	54
Thiocapsa	genus	increases	53
Sphingobacterium bambusae	species	increases	53
Enterobacteriaceae	family	increases	53
Pseudoflavonifractor capillosus	species	increases	53
Blautia hansenii	species	increases	53
Akkermansia	genus	increases	53
Marvinbryantia formatexigens	species	increases	52
Enterococcus	genus	decrease	52
Corynebacteriaceae	family	increases	52
Lachnospira	genus	increases	52
Lachnospira eligens	species	increases	52
Corynebacterium	genus	increases	52
Mycoplasmataceae	family	increases	52
delta/epsilon subdivisions	clade	decrease	52
Bacteroides faecis	species	increases	52
Bacteroides gallinarum	species	increases	52
Veillonella	genus	increases	51
Weissella	genus	increases	51
Dialister invisus	species	increases	51
Blautia hydrogenotrophica	species	increases	51
Lactonifactor longoviformis	species	increases	50
Dorea longicatena	species	decrease	50

Best Test/Lab?

The above is based on percentile and not the typical percentage. The results from Clinical Microbiomics A/S (a.k.a. CosmosId) provides percentile ranking again a regionalized healthy population. In the US, their tests are available retail from Thorne. They will soon be available retail from Precision Biome in the EU.

A walk thru using Microbiome Prescription