I just got an email asking for which bacteria are involved with Light Sensitivity. This post is just presenting the tables derived from the methodology described in this technical post: Odds Ratios and the Microbiome. 

Here are some odds ratios using BiomeSight data. Odds Low means when the reading is below the Median and Odds High above the Median (of those with this symptom). We use the symptom median to get balanced (same approximate size) categories. Using an average results in poorer results.

A 1.2 in Odds Low, means that having less then typical/median increases your odds, i.e. you want to increase the amount.

Neurological-Vision: photophobia (Light Sensitivity)

At first look for probiotics (i.e. Odds Low over 1, too low), we see:

• Bifidobacterium longum
• Bifidobacterium breve
• Bifidobacterium adolescentis

Tax_Name	tax_Rank	Odds Low	Odd High
Desulfovibrio fairfieldensis	species	0.70	1.75
Luteolibacter	genus	0.73	1.72
Finegoldia magna	species	0.71	1.71
Luteolibacter algae	species	0.73	1.71
Finegoldia	genus	0.71	1.71
Anaerotruncus colihominis	species	0.72	1.68
Anaerotruncus	genus	0.72	1.67
Oscillatoriales	order	0.75	1.66
Anaerococcus	genus	0.73	1.66
Desulfitobacteriaceae	family	1.63	0.66
Bifidobacterium indicum	species	1.60	0.67
Geobacillus	genus	0.74	1.58
Rubritalea	genus	0.75	1.58
Rubritaleaceae	family	0.75	1.58
Desulfosporosinus	genus	1.55	0.66
Eggerthella sinensis	species	0.77	1.53
Prevotella bivia	species	0.75	1.52
Peptoniphilus asaccharolyticus	species	0.75	1.51
Aerococcaceae	family	0.78	1.51
Streptococcus anginosus group	species group	0.76	1.47
Bifidobacterium longum	species	1.47	0.75
Bacteroides salyersiae	species	1.45	0.76
Ethanoligenens	genus	0.78	1.44
Coprococcus	genus	1.43	0.77
Oscillatoriaceae	family	0.78	1.43
Veillonella atypica	species	1.42	0.71
Catenibacterium	genus	1.42	0.64
Mogibacterium	genus	0.78	1.42
Eubacteriales Family XIII. Incertae Sedis	family	0.78	1.42
Thermoanaerobacter	genus	1.41	0.75
Prevotella aurantiaca	species	0.79	1.40
Bifidobacterium	genus	1.40	0.78
Bifidobacterium gallicum	species	1.39	0.77
Lachnobacterium	genus	1.38	0.78
Bifidobacteriaceae	family	1.38	0.78
Bifidobacteriales	order	1.38	0.78
Moorellaceae	family	1.38	0.74
Moorella	genus	1.38	0.74
Moorellales	order	1.38	0.74
Bifidobacterium subtile	species	1.38	0.72
Ectothiorhodospiraceae	family	0.79	1.38
Filifactor	genus	0.79	1.37
Pectinatus cerevisiiphilus	species	1.35	0.77
Chloroflexota	phylum	1.34	0.79
Sarcina maxima	species	1.33	0.79
Oribacterium	genus	1.32	0.80
Alkalithermobacter thermoalcaliphilus	species	1.31	0.73
Clostridium cadaveris	species	1.31	0.79
Oribacterium sinus	species	1.31	0.81
Enterobacter	genus	1.31	0.81
Bifidobacterium choerinum	species	1.31	0.81
Veillonella parvula	species	1.31	0.77
Bifidobacterium breve	species	1.30	0.78
Natronincola	genus	1.30	0.81
Ruminococcus albus	species	1.30	0.81
Eukaryota	superkingdom	1.29	0.71
Faecalibacterium	genus	1.29	0.81
Faecalibacterium prausnitzii	species	1.29	0.82
Thermoclostridium	genus	1.29	0.81
Thermosediminibacterales	order	1.29	0.79
Rivulariaceae	family	1.27	0.82
Devosia	genus	1.26	0.62
Devosiaceae	family	1.26	0.62
Desulfuromonadia	class	1.26	0.83
Desulfuromonadales	order	1.26	0.83
Thermoclostridium caenicola	species	1.26	0.83
Negativicoccus succinicivorans	species	1.26	0.81
Ruminococcus callidus	species	1.25	0.81
Desulfuromonadaceae	family	1.24	0.83
Actinomycetota	phylum	1.24	0.84
Anaerostipes	genus	1.24	0.84
Coprococcus eutactus	species	1.23	0.84
Peptostreptococcaceae incertae sedis	no rank	1.23	0.81
Caloramator indicus	species	1.23	0.83
Pectinatus	genus	1.23	0.83
Mycoplasmopsis edwardii	species	1.23	0.76
Holdemanella biformis	species	1.23	0.82
Holdemanella	genus	1.23	0.82
Opisthokonta	clade	1.23	0.69
Eumetazoa	clade	1.23	0.69
Metazoa	kingdom	1.23	0.69
Lachnospira	genus	1.23	0.84
Streptococcus milleri	species	1.23	0.77
Tepidanaerobacter	genus	1.23	0.83
Tepidanaerobacter syntrophicus	species	1.23	0.83
Tepidanaerobacteraceae	family	1.23	0.83
Calothrix	genus	1.22	0.76
Calotrichaceae	family	1.22	0.76
Natranaerobiales	order	1.22	0.85
Bifidobacterium adolescentis	species	1.22	0.85
Leuconostocaceae	family	1.22	0.83
Heliorestis	genus	1.22	0.84
Pasteurellaceae	family	1.22	0.84
Pasteurellales	order	1.22	0.84
Dyadobacter	genus	1.22	0.70
Paenibacillus	genus	1.22	0.72
Bilateria	clade	1.22	0.69
Anaerolineae	class	1.22	0.84
Acidaminococcus fermentans	species	1.22	0.84
Proteinivoraceae	family	1.22	0.84
Anaerobranca	genus	1.22	0.84
Anaerobranca zavarzinii	species	1.22	0.84
Protostomia	clade	1.22	0.70
Syntrophomonadaceae	family	1.21	0.84
Coprobacillus cateniformis	species	1.21	0.85
Mesoplasma entomophilum	species	1.21	0.85
Moorella group	norank	1.21	0.85
Aeromonadales	order	1.21	0.84
Streptococcus parasanguinis	species	1.20	0.82
Mollicutes	class	1.20	0.85
Mycoplasmatota	phylum	1.20	0.85
Devosia	genus	1.20	0.71
Devosiaceae	family	1.20	0.71
Salisaeta longa	species	1.20	0.66
Ectothiorhodospira	genus	1.20	0.62
Paraburkholderia phenoliruptrix	species	1.20	0.80
Deferribacter autotrophicus	species	1.20	0.38
Candidatus Phytoplasma	genus	1.20	0.84

DePaul Fatigue Questionnaire : Abnormal sensitivity to light

At first look for probiotics (i.e. Odds Low over 1, too low), we see:

• Bifidobacterium longum
• Bifidobacterium adolescentis

Tax_Name	tax_Rank	Odds Low	Odd High
Anaerotruncus colihominis	species	0.69	1.79
Erysipelothrix	genus	0.72	1.68
Erysipelothrix muris	species	0.72	1.67
Anaerotruncus	genus	0.72	1.67
Bifidobacteriales	order	1.66	0.71
Bifidobacteriaceae	family	1.66	0.71
Bifidobacterium longum	species	1.65	0.71
Prevotella bivia	species	0.72	1.63
Bifidobacterium	genus	1.62	0.72
Bifidobacterium adolescentis JCM 15918	strain	1.62	0.70
Desulfonatronum thiosulfatophilum	species	0.73	1.59
Desulfonatronaceae	family	0.73	1.59
Desulfonatronum	genus	0.73	1.59
Prevotella disiens	species	0.74	1.58
Desulfitobacteriaceae	family	1.56	0.70
Bifidobacterium choerinum	species	1.54	0.71
Bifidobacterium adolescentis	species	1.54	0.73
Heliorestis	genus	1.52	0.74
Bacteroides salyersiae	species	1.52	0.73
Holdemania	genus	0.75	1.49
Eubacteriales Family XIII. Incertae Sedis	family	0.75	1.49
Mogibacterium	genus	0.75	1.49
Bifidobacterium subtile	species	1.49	0.64
Rubritalea	genus	0.79	1.48
Rubritaleaceae	family	0.79	1.48
Bifidobacterium indicum	species	1.47	0.74
Erwiniaceae	family	0.78	1.47
Erwinia	genus	0.78	1.47
Bacteroides eggerthii	species	1.44	0.69
Phocaeicola coprophilus	species	1.43	0.65
Desulfosporosinus	genus	1.43	0.73
Oscillatoriales	order	0.79	1.43
Catenibacterium	genus	1.42	0.64
Peptoniphilus asaccharolyticus	species	0.78	1.42
Chloroflexota	phylum	1.42	0.75
Lachnobacterium	genus	1.41	0.76
Dyadobacter	genus	1.41	0.44
Bifidobacterium gallicum	species	1.41	0.76
Bilophila	genus	0.78	1.40
Actinomycetes	class	1.39	0.78
Luteolibacter algae	species	0.79	1.39
Veillonella parvula	species	1.39	0.72
Amedibacillus dolichus	species	0.79	1.39
Amedibacillus	genus	0.79	1.38
Hymenobacter xinjiangensis	species	0.80	1.38
Actinomycetota	phylum	1.37	0.78
Butyricimonas	genus	0.79	1.36
Oxalobacter formigenes	species	0.80	1.36
Anaerofilum	genus	0.80	1.34
Salinicoccus luteus	species	1.34	0.74
Devosia	genus	1.33	0.52
Devosiaceae	family	1.33	0.52
Natronincola	genus	1.32	0.80
Heliobacteriaceae	family	1.31	0.81
Lactococcus	genus	1.29	0.81
Alkalithermobacter thermoalcaliphilus	species	1.29	0.75
Oribacterium	genus	1.29	0.81
Coprococcus eutactus	species	1.29	0.80
Phocaeicola massiliensis	species	1.28	0.82
Streptococcus fryi	species	1.28	0.75
Aeromonadales	order	1.28	0.78
Insolitispirillum	genus	1.27	0.82
Insolitispirillum peregrinum	species	1.27	0.82
Aedoeadaptatus coxii	species	1.27	0.82
Hyphomicrobiaceae	family	1.27	0.79
Salinicoccus	genus	1.26	0.80
Oribacterium sinus	species	1.26	0.82
Clostridium cadaveris	species	1.26	0.82
Streptococcus anginosus group	species group	1.26	0.82
Novispirillum	genus	1.26	0.83
Caloramator indicus	species	1.26	0.82
Clostridium malenominatum	species	1.25	0.70
Ruminococcus callidus	species	1.25	0.81
Moorellaceae	family	1.25	0.83
Moorella	genus	1.25	0.83
Moorellales	order	1.25	0.83
Clostridium frigoris	species	1.24	0.83
Collinsella	genus	1.24	0.83
Pasteurellaceae	family	1.24	0.84
Pasteurellales	order	1.24	0.84
Ruminiclostridium cellulolyticum	species	1.24	0.82
Veillonella atypica	species	1.24	0.79
Anaerolineae	class	1.23	0.83
Collinsella aerofaciens	species	1.23	0.84
Legionellaceae	family	1.23	0.83
Legionella	genus	1.23	0.84
Rhodanobacteraceae	family	1.23	0.83
Sutterella stercoricanis	species	1.23	0.84
Atopobium	genus	1.23	0.81
Legionellales	order	1.22	0.85
Metazoa	kingdom	1.22	0.70
Eumetazoa	clade	1.22	0.70
Opisthokonta	clade	1.22	0.70
Bacteroides heparinolyticus	species	1.21	0.79
Desulfovibrio	genus	1.21	0.84
Segatella	genus	1.21	0.84
Bilateria	clade	1.21	0.71
Pediococcus	genus	1.21	0.81
Protostomia	clade	1.20	0.71
Eukaryota	superkingdom	1.20	0.80
Streptococcus infantis	species	1.20	0.80
Faecalibacterium prausnitzii	species	1.20	0.86
Bacteroidota	phylum	1.20	0.86

I just got an email asking for which bacteria are involved with Mast Cells and Histamine issues. This post is just presenting the tables derived from the methodology described in this technical post: Odds Ratios and the Microbiome. We do not have sufficient data for Mast Cell Activation Syndrome (MCAS)

Here are some odds ratios using BiomeSight data. Odds Low means when the reading is below the Median and Odds High above the Median (of those with this symptom). We use the symptom median to get balanced (same approximate size) categories. Using an average results in poorer results.

A 1.2 in Odds Low, means that having less then typical/median increases your odds, i.e. you want to increase the amount.

Official Diagnosis: Mast Cell Dysfunction

At first look for probiotics (i.e. Odds Low over 1, too low), we see:

• Akkermansia muciniphila
• Lactococcus

Tax_Name	tax_Rank	Odds Low	Odd High
Sharpea	genus	0.73	1.67
Sharpea azabuensis	species	0.73	1.66
Haemophilus	genus	1.58	0.69
Haemophilus parainfluenzae	species	1.57	0.70
Pasteurellales	order	1.54	0.74
Pasteurellaceae	family	1.54	0.74
Veillonella atypica	species	1.53	0.63
[Ruminococcus] torques	species	0.75	1.49
Erysipelothrix muris	species	0.76	1.49
Amedibacillus dolichus	species	0.76	1.48
Amedibacillus	genus	0.76	1.48
Lactococcus	genus	1.48	0.70
Erysipelothrix	genus	0.77	1.48
Syntrophobacterales	order	0.77	1.45
Syntrophobacteria	class	0.77	1.45
Holdemania	genus	0.77	1.43
Turicibacter	genus	1.42	0.77
Turicibacteraceae	family	1.42	0.77
Alkaliphilus crotonatoxidans	species	1.41	0.77
Chloroflexota	phylum	1.41	0.75
Slackia	genus	1.40	0.77
Serratia entomophila	species	0.78	1.40
Yersiniaceae	family	0.79	1.38
Limnobacter	genus	0.79	1.38
Limnobacter litoralis	species	0.79	1.38
Holdemanella	genus	1.37	0.77
Holdemanella biformis	species	1.37	0.77
Thermodesulfobacteriota	phylum	1.36	0.79
Ruminiclostridium cellobioparum subsp. termitidis	subspecies	1.36	0.79
Ruminiclostridium cellobioparum	species	1.36	0.79
Alkaliphilus	genus	1.36	0.78
Sutterella sanguinus	species	1.35	0.78
Akkermansiaceae	family	1.35	0.78
Ruminococcus albus	species	1.35	0.79
Akkermansia	genus	1.35	0.78
Akkermansia muciniphila	species	1.35	0.78
Anaerolineae	class	1.34	0.75
Desulfuromonadia	class	1.34	0.78
Desulfuromonadales	order	1.34	0.78
Parabacteroides merdae	species	1.33	0.80
PVC group	clade	1.33	0.80
Rhodanobacteraceae	family	1.33	0.79
Verrucomicrobiota	phylum	1.33	0.80
Sphingobacterium	genus	1.31	0.81
Oribacterium	genus	1.30	0.81
Veillonella dispar	species	1.30	0.77
Ruminiclostridium	genus	1.30	0.80
Oribacterium sinus	species	1.29	0.82
Odoribacter	genus	1.28	0.82
Verrucomicrobiaceae	family	1.28	0.82
Verrucomicrobiia	class	1.28	0.82
Desulfuromonadaceae	family	1.28	0.81
Verrucomicrobiales	order	1.27	0.82
Streptococcaceae	family	1.27	0.82
Clostridium taeniosporum	species	1.26	0.79
Flavobacteriia	class	1.26	0.82
Flavobacteriaceae	family	1.26	0.82
Flavobacteriales	order	1.26	0.82
Sutterella wadsworthensis	species	1.26	0.81
delta/epsilon subdivisions	clade	1.25	0.83
Lysobacterales	order	1.25	0.83
Heliobacteriaceae	family	1.25	0.77
Streptococcus thermophilus	species	1.24	0.82
Deltaproteobacteria	class	1.24	0.83
Gillisia	genus	1.24	0.83
Actinomycetota	phylum	1.24	0.84
Actinobacillus	genus	1.24	0.84
Sutterella stercoricanis	species	1.24	0.83
Gillisia limnaea	species	1.23	0.84
Phocaeicola plebeius	species	1.23	0.75
Bacteroides stercoris	species	1.22	0.85
Streptococcus	genus	1.22	0.84
Alcaligenaceae	family	1.21	0.85
Desulfovibrionia	class	1.21	0.85
Desulfovibrionales	order	1.21	0.85
Sutterella	genus	1.21	0.85
Sutterellaceae	family	1.21	0.85
Mitsuokella	genus	1.21	0.77
Actinomycetales	order	1.21	0.83
Betaproteobacteria	class	1.20	0.85
Rhodothermaceae	family	1.20	0.84
Anaerobranca zavarzinii	species	1.20	0.85
Anaerobranca	genus	1.20	0.85
Proteinivoraceae	family	1.20	0.85

Comorbid: Histamine or Mast Cell issues

This is a little more fuzzy for the criteria. With too low levels being very common but not as common as seen with Odds Ratios for Neurological-Audio: hypersensitivity to noise

At first look for probiotics (i.e. Odds Low over 1, too low), we see:

• Bifidobacterium adolescentis
• Lactococcus
• Bifidobacterium longum
• Ligilactobacillus, i.e. Ligilactobacillus salivarius (L. Salivarius)

Tax_Name	tax_Rank	Odds Low	Odd High
Bifidobacterium angulatum	species	1.96	0.58
Sphingobium	genus	1.73	0.63
Vagococcus teuberi	species	1.69	0.70
Catenibacterium mitsuokai	species	1.65	0.52
Polyangia	subclass	1.58	0.65
Segatella paludivivens	species	1.56	0.73
Hoylesella loescheii	species	1.54	0.64
Filifactor villosus	species	0.78	1.54
Myxococcota	phylum	1.54	0.59
Myxococcales	order	1.54	0.59
Myxococcia	class	1.54	0.59
Aggregatibacter	genus	1.48	0.76
Luteolibacter	genus	0.77	1.42
Azospirillum	genus	1.42	0.64
Luteolibacter algae	species	0.78	1.41
Bilophila	genus	0.78	1.41
Actinobacillus pleuropneumoniae	species	1.39	0.69
Acetobacteraceae	family	1.38	0.72
Catenibacterium	genus	1.38	0.68
Caldilineae	class	1.37	0.76
Caldilineaceae	family	1.37	0.76
Caldilinea tarbellica	species	1.37	0.76
Caldilineales	order	1.37	0.76
Caldilinea	genus	1.37	0.76
Bilophila wadsworthia	species	0.79	1.36
Sutterella stercoricanis	species	1.35	0.76
Actinomycetota	phylum	1.34	0.80
Bifidobacterium dentium	species	1.33	0.80
Bacteroides salyersiae	species	1.33	0.80
Ruminococcus callidus	species	1.32	0.80
Schaalia	genus	1.32	0.78
Prevotella dentasini	species	1.31	0.80
Actinomycetes	class	1.31	0.81
Schaalia naturae	species	1.31	0.63
Brachybacterium	genus	1.31	0.41
Anaerolineae	class	1.30	0.79
Bifidobacteriaceae	family	1.30	0.81
Bifidobacteriales	order	1.30	0.81
Desulfovibrio simplex	species	1.30	0.81
Thermosediminibacterales	order	1.29	0.79
Bifidobacterium	genus	1.29	0.82
Oribacterium	genus	1.29	0.82
Turicibacteraceae	family	1.28	0.82
Turicibacter	genus	1.28	0.82
Tepidibacter	genus	1.28	0.75
Alishewanella	genus	1.28	0.55
Candidatus Tammella caduceiae	species	1.27	0.72
Candidatus Tammella	genus	1.27	0.72
Oribacterium sinus	species	1.27	0.82
Mannheimia	genus	1.27	0.82
Mesoplasma entomophilum	species	1.27	0.81
Coprococcus eutactus	species	1.26	0.83
Heliorestis	genus	1.25	0.82
Chloroflexota	phylum	1.25	0.77
Luteibacter anthropi	species	1.25	0.83
Streptococcus sanguinis	species	1.25	0.74
Neisseriales	order	1.25	0.78
Tepidanaerobacteraceae	family	1.25	0.82
Tepidanaerobacter syntrophicus	species	1.25	0.82
Tepidanaerobacter	genus	1.25	0.82
Mannheimia caviae	species	1.24	0.82
Luteibacter	genus	1.24	0.84
Holdemanella biformis	species	1.24	0.81
Holdemanella	genus	1.24	0.81
Entomoplasmataceae	family	1.24	0.83
Entomoplasmatales	order	1.24	0.83
Mesoplasma	genus	1.24	0.83
Anaeroplasma	genus	1.24	0.82
Anaeroplasmatales	order	1.24	0.82
Anaeroplasmataceae	family	1.24	0.82
Succinivibrionaceae	family	1.24	0.80
Natranaerobiales	order	1.24	0.84
Coraliomargarita akajimensis	species	1.24	0.62
Coraliomargaritaceae	family	1.24	0.62
Coraliomargarita	genus	1.24	0.62
Schaalia odontolytica	species	1.24	0.76
Chroococcus minutus	species	1.24	0.80
Chroococcus	genus	1.24	0.80
Chroococcaceae	family	1.24	0.80
Morganellaceae	family	1.24	0.74
Ligilactobacillus	genus	1.24	0.76
Sphingomonas	genus	1.23	0.58
Anaerobranca	genus	1.23	0.83
Anaerobranca zavarzinii	species	1.23	0.83
Proteinivoraceae	family	1.23	0.83
Helicobacteraceae	family	1.23	0.65
Dermabacteraceae	family	1.23	0.63
Syntrophomonadaceae	family	1.23	0.84
Helicobacter	genus	1.23	0.65
Lactococcus lactis	species	1.23	0.84
Slackia	genus	1.23	0.84
Sutterella sanguinus	species	1.23	0.84
Streptococcus infantis	species	1.22	0.79
Sporotomaculum	genus	1.22	0.81
Desulfallaceae	family	1.22	0.81
Streptococcus oralis	species	1.22	0.78
Bifidobacterium longum	species	1.22	0.85
Lactococcus	genus	1.22	0.84
Bifidobacterium asteroides	species	1.21	0.79
Succinivibrio	genus	1.21	0.83
Coprococcus	genus	1.21	0.85
Bifidobacterium adolescentis	species	1.21	0.84
Segatella albensis	species	1.21	0.83
Geobacillus	genus	1.21	0.77
Lachnobacterium	genus	1.21	0.85
Deferribacter	genus	1.21	0.37
Salisaeta	genus	1.21	0.66
Salisaetaceae	family	1.21	0.66
Atopobium fossor	species	1.20	0.72
Mollicutes	class	1.20	0.85
Mycoplasmatota	phylum	1.20	0.85
Devosia	genus	1.20	0.71
Devosiaceae	family	1.20	0.71
Salisaeta longa	species	1.20	0.66
Ectothiorhodospira	genus	1.20	0.62
Paraburkholderia phenoliruptrix	species	1.20	0.80
Deferribacter autotrophicus	species	1.20	0.38
Candidatus Phytoplasma	genus	1.20	0.84

I just got an email asking for which bacteria are involved with hypersensitivity to noise. This post is just presenting the tables derived from the methodology described in this technical post: Odds Ratios and the Microbiome. 

Here are some odds ratios using BiomeSight data. Odds Low means when the reading is below the Median and Odds High above the Median (of those with this symptom). We use the symptom median to get balanced (same approximate size) categories. Using an average results in poorer results.

A 1.2 in Odds Low, means that having less then typical/median increases your odds, i.e. you want to increase the amount.

At first look for probiotics, we see:

• Bifidobacterium adolescentis
• Bifidobacterium longum
• Lactococcus

I also note that Odds Low really dominant, i.e. too little of a lot of different bacteria. This hints at Prescript-Assist®/SBO Probiotic with 22 different unusual probiotics as being a possible candidate as well as General Biotics/Equilibrium.

Tax_Name	tax_Rank	Odds Low	Odd High
Collinsella tanakaei	species	0.74	1.67
Segatella paludivivens	species	1.56	0.73
Viridiplantae	kingdom	1.51	0.65
Peptostreptococcus stomatis	species	1.47	0.69
Bacteroides salyersiae	species	1.42	0.74
Neisseriales	order	1.42	0.63
Bifidobacterium	genus	1.42	0.77
Bifidobacterium adolescentis	species	1.41	0.76
Bifidobacteriales	order	1.41	0.77
Bifidobacteriaceae	family	1.41	0.77
genistoids sensu lato	clade	1.40	0.72
rosids	clade	1.40	0.72
Rothia	genus	1.40	0.72
core genistoids	clade	1.40	0.72
Crotalarieae	tribe	1.40	0.72
Fabaceae	family	1.40	0.72
Papilionoideae	subfamily	1.40	0.72
50 kb inversion clade	clade	1.40	0.72
Fabales	order	1.40	0.72
fabids	clade	1.40	0.72
Desulfosporosinus	genus	1.39	0.76
Gunneridae	clade	1.39	0.73
Streptophytina	subphylum	1.39	0.73
Tracheophyta	clade	1.39	0.73
Embryophyta	clade	1.39	0.73
eudicotyledons	clade	1.39	0.73
Spermatophyta	clade	1.39	0.73
Magnoliopsida	class	1.39	0.73
Mesangiospermae	clade	1.39	0.73
Euphyllophyta	clade	1.39	0.73
Streptophyta	phylum	1.39	0.73
Pentapetalae	clade	1.39	0.73
Bifidobacterium choerinum	species	1.38	0.77
Neisseria	genus	1.38	0.67
Bifidobacterium adolescentis JCM 15918	strain	1.37	0.79
Lysobacter	genus	0.79	1.37
Neisseriaceae	family	1.37	0.65
Rothia	genus	1.36	0.75
Actinomycetota	phylum	1.36	0.79
Bifidobacterium gallicum	species	1.35	0.75
Catenibacterium mitsuokai	species	1.35	0.72
Planococcus	genus	1.34	0.57
Bifidobacterium indicum	species	1.34	0.75
Planococcus columbae	species	1.34	0.58
Enterobacter	genus	1.34	0.80
Morganellaceae	family	1.33	0.64
Clostridium chartatabidum	species	1.33	0.78
Sutterella stercoricanis	species	1.32	0.78
Aeromonadales	order	1.32	0.75
Mesoplasma entomophilum	species	1.31	0.78
Rothia mucilaginosa	species	1.30	0.78
Entomoplasmataceae	family	1.30	0.79
Entomoplasmatales	order	1.30	0.79
Eukaryota	superkingdom	1.30	0.71
Mesoplasma	genus	1.30	0.79
Succinivibrio	genus	1.30	0.76
Bifidobacterium longum	species	1.29	0.81
Succinivibrionaceae	family	1.29	0.81
Ruminococcus callidus	species	1.29	0.78
Streptococcus cristatus	species	1.28	0.58
Tepidibacter	genus	1.28	0.82
Catenibacterium	genus	1.28	0.76
Atopobium fossor	species	1.28	0.62
Rivulariaceae	family	1.27	0.82
Dyadobacter	genus	1.27	0.63
Actinomycetes	class	1.27	0.82
Oribacterium	genus	1.27	0.82
Clostridium cadaveris	species	1.26	0.83
Micrococcaceae	family	1.26	0.72
Micromonosporaceae	family	1.26	0.65
Micromonosporales	order	1.26	0.65
Streptococcus sanguinis	species	1.25	0.73
Citrobacter	genus	1.25	0.83
Oribacterium sinus	species	1.25	0.83
Acinetobacter	genus	1.25	0.75
Salisaetaceae	family	1.25	0.59
Salisaeta	genus	1.25	0.59
Salisaeta longa	species	1.24	0.59
Thermosediminibacterales	order	1.23	0.83
Candidatus Tammella caduceiae	species	1.23	0.76
Lachnobacterium	genus	1.23	0.84
Alishewanella	genus	1.23	0.62
Heliorestis	genus	1.23	0.84
Actinocatenispora	genus	1.22	0.65
Azospirillum	genus	1.22	0.80
Candidatus Tammella	genus	1.22	0.77
Bifidobacterium catenulatum PV20-2	strain	1.22	0.84
Lactococcus	genus	1.22	0.83
Bifidobacterium subtile	species	1.22	0.84
Negativicoccus	genus	1.22	0.82
Succinivibrio dextrinosolvens	species	1.21	0.85
Opisthokonta	clade	1.21	0.71
Eumetazoa	clade	1.21	0.71
Metazoa	kingdom	1.21	0.71
Caloramator indicus	species	1.21	0.85
Desulfurisporaceae	family	1.21	0.78
Desulfurispora	genus	1.21	0.78
Desulfurispirillum alkaliphilum	species	1.21	0.81
Streptococcus milleri	species	1.21	0.79
Coprococcus eutactus	species	1.21	0.84
Desulfurispora thermophila	species	1.21	0.78
Herbaspirillum magnetovibrio	species	1.20	0.59
Phocaeicola massiliensis	species	1.20	0.85
Prevotella dentasini	species	1.20	0.79
Collinsella intestinalis	species	1.20	0.81
Pseudomonas	genus	1.20	0.85
Coraliomargarita akajimensis	species	1.20	0.67
Coraliomargaritaceae	family	1.20	0.67
Coraliomargarita	genus	1.20	0.67
Pseudomonadaceae	family	1.20	0.85
Bilateria	clade	1.20	0.72

In working with Microbiome Prescription, I experimented with various prediction approaches before settling on a workaround that, in many cases, could successfully predict the top 10 symptoms for new microbiome samples, with individuals confirming about 80% of them as accurate reflections of their own symptoms. Though this solution was adequate for practical needs, it was admittedly less than ideal in theory. Recently, I recognized that a more robust and principled prediction algorithm is achievable. The aim of this post is to walk through that process, making it accessible for anyone interested in trying this more rigorous approach.

Accurate prediction identifies the key bacteria that should be altered with statistical justification.

An odds ratio (OR) is a measure of association that describes the odds of a disease, symptom, or event occurring in one group compared to another, often used in medical and epidemiological studies to estimate the strength of risk factors or the effectiveness of interventions.​

Understanding Odds Ratios

• The odds ratio is calculated by dividing the odds of the event in the exposed group by the odds in the non-exposed group.​
• OR > 1 indicates higher odds of disease with the exposure or risk factor; OR < 1 indicates reduced odds; OR = 1 means no difference in odds between groups.​
• Odds ratios are especially used in case-control studies, but also in cohort and cross-sectional studies, and they can approximate risk ratios when the disease or symptom is rare.​

Using Multiple Odds Ratios in Disease Analysis

When you have several odds ratios related to a disease, there are several key uses:

• Compare the magnitude of different risk factors: By looking at the odds ratios for various exposures (e.g., smoking, age group, genetic markers), you can identify which exposures are most strongly associated with the disease.​​
• Synthesize evidence: Meta-analysis allows combining odds ratios from multiple studies to produce a summary effect estimate, which helps determine overall strength of association and consistency across populations.​

Example Table of Interpreting Odds Ratios

Exposure/Risk Factor	Odds Ratio	Interpretation
Smoking	3.5 ​	Exposure increases odds
Physical Activity	0.7 ​	Exposure decreases odds
High BMI	1.2 ​	Exposure slightly increases odds
Family History	4.0 ​	Strong increased odds

These odds ratios can guide targeted interventions, identify priority risk factors, and inform clinical decision-making or public health policy.​

Each odds ratio’s confidence interval should be considered to determine statistical significance: if it includes 1, the specific association may not be statistically meaningful.​

Summary

Odds ratios quantify the likelihood of disease or symptoms given exposures and allow comparison and synthesis of risk across different factors or populations. When handling multiple odds ratios, use them to identify, adjust for, and summarize the impact of risk factors on disease occurrence.​

Applying to the Microbiome

We encounter some challenges here. Consider this constructed example:

• Bacteria Foo has OR of 1.5 when the microbiome exceeds 5%
• Bacteria Bar has OR of 2 when the microbiome exceeds 3%
• Bacteria Foo and Bar are associated.

If a sample has both, the OR is not 1.5 x 2 or 3.0. Instead, we need to know much they influence each other, i.e. the R². We can estimate this from Microbiome Taxa R² Site. Suppose that R² is 0.5, significant inference.

The Odds ratio is thus reduced to 2.66 from 3.0.

Odds Ratios and Continuous Values

Odds ratios are commonly used for binary data, such as smoker versus non-smoker or high school graduation status. Continuous data can also be categorized; for example, instead of treating smoking as simply yes/no, you might use metrics like the number of cigarettes smoked per day or packs per week. Similarly, the microbiome data can be categorized, though caution is needed to avoid over-interpreting sparse data. A rough guideline from many studies suggests a minimum of 30 cases and 30 controls are needed to calculate an odds ratio with basic reliability. For data on the lower end, it can be helpful to binarize using the median rather than the mean. This is important because bacterial abundances tend to be highly skewed—using the mean often results in about 70% of samples falling below it and 30% above, whereas the median splits the data evenly with 50% below and 50% above.

Example: Brain Fog

Here are some odds ratios using BiomeSight data. Odds Low means when the reading is below the Median and Odds High above the Median (of those with this symptom). We use the symptom median to get balanced (same approximate size) categories.

A few quick take away:

• Probiotics such as Bifidobacterium, Ligilactobacillus, Lactococcus lactis, Lactiplantibacillus
  • Bifidobacterium catenulatum subsp. kashiwanohense (OR 1.37) is the preferred one!
  • Ligilactobacillus: Ligilactobacillus salivarius is the only one available retail
  • Lactiplantibacillus: Lactiplantibacillus plantarum is the only one available retail
  • Veillonella atypica is offered as FITBIOMICS V•Nella Lactic Acid Metabolizing Probiotic …
    • Note: Brain fog is often ascribed to too much Lactic Acid.

Tax_Name	tax_Rank	Odds Low	Odd High
Cerasicoccus arenae	species	1.59	0.71
Polyangia	subclass	1.47	0.72
Lelliottia	genus	1.42	0.75
Lelliottia amnigena	species	1.42	0.75
Microcoleaceae	family	0.82	1.41
Myxococcia	class	1.38	0.71
Myxococcales	order	1.38	0.71
Myxococcota	phylum	1.38	0.71
Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	1.37	0.74
Denitratisoma	genus	0.87	1.37
Microcoleus antarcticus	species	0.81	1.36
Microcoleus	genus	0.81	1.36
Desulfosporosinus	genus	1.34	0.80
Trabulsiella	genus	1.33	0.80
Rivulariaceae	family	1.32	0.79
Segatella paludivivens	species	1.32	0.79
Prosthecobacter	genus	1.32	0.73
Ligilactobacillus	genus	1.31	0.77
Enterobacter cloacae complex	species group	1.30	0.80
Peptostreptococcus stomatis	species	1.30	0.80
Alcanivorax	genus	0.93	1.30
Alcanivoracaceae	family	0.93	1.30
Tepidanaerobacter syntrophicus	species	1.30	0.79
Tepidanaerobacter	genus	1.30	0.79
Tepidanaerobacteraceae	family	1.30	0.79
Hoylesella loescheii	species	1.29	0.81
Thermosediminibacterales	order	1.28	0.81
Enterobacter hormaechei	species	1.28	0.82
Slackia isoflavoniconvertens	species	0.84	1.27
Bifidobacterium choerinum	species	1.27	0.82
Desulfovibrio simplex	species	1.27	0.80
Chromatium	genus	0.90	1.27
Lactococcus fujiensis	species	1.27	0.67
Chromatium weissei	species	0.90	1.27
Klebsiella	genus	1.27	0.82
Klebsiella/Raoultella group	no rank	1.27	0.82
Veillonella atypica	species	1.26	0.82
Isoalcanivorax	genus	0.94	1.26
Isoalcanivorax indicus	species	0.94	1.26
Schaalia turicensis	species	1.25	0.72
Lactococcus lactis	species	1.25	0.83
Bifidobacteriaceae	family	1.24	0.84
Bifidobacteriales	order	1.24	0.84
Chloroflexota	phylum	1.24	0.79
Salidesulfovibrio brasiliensis	species	0.92	1.24
Salidesulfovibrio	genus	0.92	1.24
Enterobacter	genus	1.24	0.81
Bifidobacterium	genus	1.24	0.84
Actinomycetota	phylum	1.24	0.84
Acholeplasma hippikon	species	0.85	1.23
Mycoplasmataceae	family	1.23	0.82
Mycoplasmatales	order	1.23	0.82
Bifidobacterium angulatum	species	1.23	0.82
Clostridium nitrophenolicum	species	0.85	1.23
Bacteroides uniformis	species	0.85	1.22
Lactococcus	genus	1.22	0.83
Lactiplantibacillus	genus	1.22	0.84
Mycoplasma	genus	1.22	0.82
Filifactor villosus	species	0.88	1.22
Anaerolineae	class	1.21	0.85
Veillonella denticariosi	species	0.89	1.21
Actinomycetes	class	1.21	0.85
Acidimicrobium	genus	1.21	0.79
Cerasicoccaceae	family	1.21	0.79
Cerasicoccus	genus	1.21	0.79
Mycoplasmoidales	order	1.21	0.81
Parabacteroides gordonii	species	1.21	0.84
Thioalkalivibrio jannaschii	species	1.21	0.63
Candidatus Blochmanniella camponoti	species	1.21	0.79
Thioalkalivibrio	genus	1.21	0.63
Acidimicrobiaceae	family	1.21	0.77
Bifidobacterium adolescentis	species	1.21	0.85
Bifidobacterium longum	species	1.21	0.85

That’s it for the moment

Also, see the links below for by-request tables

• Odds Ratio for Autism
• Odds Ratios for Neurological-Audio: hypersensitivity to noise
• Microbiome Odds Ratios for Mast Cells and Histamine issues
• Microbiome Odds Ratios for Light Sensitivity

The next step is seeing how these odds ratio perform against samples and against the old algorithm. Stay tune.

Special note: This is not based on using averages of healthy populations, but more on the skewness of the distribution of those with the symptom. It is a different way of thinking about the issue.

caveat emptor

The table above applies only and exclusively with Biomesight data. For an explanation of why, see The taxonomy nightmare before Christmas… If you use a different lab, you will need to get that lab to crunch their numbers in the same manner as detailed above

This morning I was trouble shooting an upload issue on Ombre CSV data — the reason was “they changed the format again!“. While triaging the issues I saw a lot of counts of “1” in the sample that I was working with. A count of 1 means that only one unit of bacteria was detected. Most microbiologists would deem that to be unreliable, the bacteria may not actually be present, i.e. a “Ghost Bacteria Identification”.

As a result, I look at the 16s tests that has been uploaded to compute the percentages of ghosts in samples.

16s Test from	Average	Lowest Rate	Highest Rate	Bacteria Reported
Biomesight	22.1%	0%	35.3%	611
Ombre	28.8%	0%	41.1%	694
Medivere	20.5%	19%	22.3%	756
BiomeSightRdp	11%	1.9%	20.0%	476
CerbaLab	13.9%	0%	24%	Over 600
SequentiaBiotech	1.4%	0%	5%	313
CosmosId	0.01%	0%	0.28%	463

The numbers above suggests that reporting on ghosts results in more bacteria reports — which is a good marketing strategy. It is a questionable service to the consumers.

For myself, for my offline research database, I will be excluding counts of “1”. I may also offer an option to remove them on the upload page in the future. This is not a significant issue with shotgun reports.

“Buyer beware,” or caveat emptor 

From Perplexity (Click to get sources):

In 16S microbiome sequencing, counts of “1” (single read assigned to a taxon in a sample) are generally not considered reliable for determining the true presence of that organism. Here’s why:

• Low-abundance signals (especially a single read) can easily result from sequencing errors, index hopping, cross-contamination, or misclassification in the bioinformatic pipeline.​
• Studies show that only OTUs (Operational Taxonomic Units) with higher counts (usually >10 reads, and especially >1% relative abundance) are consistently detected with high reliability and quantification accuracy.​
• Single-read taxa are much more likely to be false positives or background noise. They typically do not pass statistical filtering thresholds used in rigorous microbiome analysis.​
• Many pipelines recommend removing OTUs present in very low abundances (often <10 reads or <0.1–1% relative abundance) for reliable interpretation.​

Summary:

• Counts of “1” should be viewed as unreliable noise and not taken as meaningful evidence of that organism’s presence in your microbiome sample.
• Reliable detection begins at much higher read counts and relative abundances, with reproducibility improving rapidly as counts increase.​

Best practices:

• Filter out taxa with extremely low counts for clinical or quantitative interpretation.
• Use statistical and bioinformatic guidelines to set raw count and relative abundance thresholds for reporting results.

If you see a taxon with just one assigned read in your 16S data, consider it an artifact rather than true biological detection unless verified by other means.​

Lazy versus Old School

I have observed that many data scientists tend to push data into a model and report the results of the model. I am old school and was taught to always chart the data to look for abnormalities. Doing that revealed that microbiome data is highly skewed. I covered this in Microbiologist / Data Scientist Guide to Bacterium Statistics.

I subsequently came across an odds plot where we have an appearance similar to electron shell densities and not the nice linear model that is often assumed.

The result was a clear need to review a lot more data graphically. There are the main patterns:

• The condition line is clearly to the left of the reference line, i.e. transformed average is less
• The condition line is clearly to the right of the reference line, i.e. transformed average is more
• The condition line is on both sides of the reference line, i.e. a complex situation.
• The lines are on top of each other — no association to the symptom

Lower Transformed Average

Higher Transformed Average

Mixed Case

No Association

A Video Show

I generated a program to walk through some random bacteria and recorded them in the video below. Pause the video when you want to look at a specific chart in greater detail. My main conclusion is that often a bacteria is significant only when it is in a certain range.

400+ more over 20 minutes

Autism Only

Long COVID