I have been working on better statistical detection of the bacteria associated with symptoms and conditions. The technical details are described

• An Odds-Ratio Framework for Interpreting Microbiome Detection Profiles: An Exploratory Case-Control Analysis An Odds-Ratio Framework for Interpreting Microbiome Detection Profiles: An Exploratory Case-Control Analysis
• Coming soon a Ranged Odds-Ratio Framework

The data being used is from samples processed by Biomesight (Discount Code of MICRO is available). The results are unlikely to apply to other labs (Why? See The taxonomy nightmare before Christmas…)

Performance for Using Odds Ration

Performance is good, using a value of 1 (Log(1) = ZERO) We have

• People with Autism correctly predict 87.2% of the time
• People without Autism correctly predict 73.2% of the time

The following is done with a statistical significance of P < 0.001 (Chi Square >=10.83)

Presence of Bacteris Associated With Increased Odds of Autism

Top items only.

Odds	tax_name
6.5	Streptococcus macedonicus
3.8	Schaalia georgiae
3.6	Thiomonas perometabolis
3.5	Bifidobacterium pseudocatenulatum
3.4	Streptococcus alactolyticus
3.4	Ralstonia detusculanense
3.2	Streptomyces coriofaciens
3.2	Ligilactobacillus pobuzihii
3.1	Sarcina ventriculi
3.1	Proteus penneri
3	Bifidobacterium magnum
2.9	Prevotella veroralis
2.8	Lactococcus garvieae
2.6	Ralstonia pickettii
2.6	Pseudoalteromonas
2.6	Pseudoalteromonadaceae
2.6	Tepidimicrobium ferriphilum
2.6	Pediococcus cellicola
2.6	Staphylococcus pseudolugdunensis
2.5	Bifidobacterium catenulatum subsp. kashiwanohense
2.4	Hungateiclostridiaceae
2.4	Hungateiclostridium
2.4	Candidatus Blochmanniella vafra
2.4	Bifidobacterium pullorum subsp. saeculare
2.4	Bifidobacterium pullorum
2.4	Bradyrhizobium
2.4	Lactococcus raffinolactis
2.4	Bifidobacterium angulatum
2.3	Clostridium cellulovorans
2.3	Enterococcus hawaiiensis
2.3	Bifidobacterium tsurumiense
2.3	Absiella
2.2	Bifidobacterium thermacidophilum
2.2	Ralstonia insidiosa
2.2	Bifidobacterium merycicum
2.2	Candidatus Blochmanniella camponoti
2.2	Streptococcus gallinaceus
2.2	Proteus
2.1	Aggregatibacter segnis
2.1	Herminiimonas
2	Prevotella micans
2	unclassified Burkholderiales
2	Gemella sanguinis
2	Chromobacterium group
2	Abiotrophia defectiva
2	Halochromatium salexigens
2	Chelonobacter

Presence of Bacteris Associated With Decreased Odds of Autism

Top items only.

Odds	tax_name
0.4	Mogibacterium timidum
0.4	Acetivibrio clariflavus
0.5	Thermodesulfatator
0.5	Olivibacter soli
0.5	Streptococcus phocae
0.5	Filifactor alocis
0.5	Sedimentibacter hongkongensis
0.5	Thermodesulfobacteriales
0.5	Thermodesulfobacteriaceae
0.5	Porphyromonas catoniae
0.5	Bacteroides zoogleoformans
0.5	Thermodesulfobacteria
0.5	Ochrobactrum
0.5	Peptostreptococcus anaerobius
0.5	Moryella
0.5	Segetibacter
0.5	Thermodesulfatator atlanticus
0.5	Segetibacter aerophilus
0.5	Bifidobacterium adolescentis JCM 15918
0.5	Brucella/Ochrobactrum group
0.5	Thermodesulfatatoraceae

Ranges of Bacteris Associated With Increased Odds of Autism

Top Items Only. Range is in PERCENTILE RANKING and not percentage.

Tax_Name	Tax_Rank	Start Range	End Range	Odds Ratio
Alishewanella fetalis	species	90	100	48
Alishewanella fetalis	species	80	100	48
Schaalia georgiae	species	70	90	45
Schaalia georgiae	species	60	90	45
Lancefieldella rimae	species	80	100	40.5
Schaalia georgiae	species	70	100	32
Schaalia georgiae	species	50	100	32
Liberibacter	genus	70	80	28
Lancefieldella	genus	80	100	25.091
16SrXXI (Pine shoot proliferation group)	species group	80	90	24.889
Candidatus Phytoplasma pini	species	80	90	24.889
Desulfacinum	genus	90	100	24.25
Desulfacinum subterraneum	species	90	100	24.25
Lactococcus garvieae	species	90	100	24
Chryseobacterium	genus	80	90	20.75
Chryseobacterium group	no rank	80	90	20.75
Bifidobacterium tsurumiense	species	70	90	19.667
Lancefieldella	genus	90	100	18.5
Pedobacter aquatilis	species	50	80	17.5
Hyphomonas	genus	60	90	16.154
Hyphomonas	genus	70	90	16.154
Lacticaseibacillus manihotivorans	species	50	75	15.632
Ligilactobacillus hayakitensis	species	90	100	13.867
Ligilactobacillus ruminis	species	80	100	13.524
Desulfacinum	genus	80	100	13.143
Desulfacinum subterraneum	species	80	100	13.143
Desulfacinum	genus	70	100	13.143
Desulfacinum subterraneum	species	70	100	13.143
Desulfacinum	genus	75	100	13.143
Desulfacinum subterraneum	species	75	100	13.143
Desulfacinum	genus	50	100	13.143
Desulfacinum subterraneum	species	50	100	13.143
Hyphomonas	genus	50	80	13.037
Hyphomonas	genus	60	80	13.037
Hyphomonas	genus	70	80	13.037
Corynebacterium aurimucosum	species	10	40	12.6
Ligilactobacillus ruminis	species	75	100	12.444
Bifidobacterium tsurumiense	species	50	100	11.714
Clostridium aestuarii	species	90	100	11.176
Ligilactobacillus ruminis	species	90	100	10.972
Bifidobacterium bombi	species	90	100	10.8
Streptococcus agalactiae	species	40	50	10.667
Ligilactobacillus ruminis	species	70	100	10.667
Bifidobacterium tsurumiense	species	70	100	9.36
Bifidobacterium tsurumiense	species	75	100	9.36
Corynebacterium aurimucosum	species	10	20	8.875
Corynebacterium aurimucosum	species	10	30	8.875
Bifidobacterium tsurumiense	species	60	90	8.571
Hyphomonadaceae	family	60	90	8.304
Hyphomonadales	order	60	90	8.304
Hyphomonadaceae	family	70	90	8.304
Hyphomonadales	order	70	90	8.304
Serratia marcescens	species	50	100	8.273
Thiobacillus thiophilus	species	80	90	8.016

Ranges of Bacteris Associated With Decreased Odds of Autism

Top Items Only. Range is in PERCENTILE RANKING and not percentage.

Tax_Name	Tax_Rank	Start Range	End Range	Odds Ratio
Shouchella	genus	0	50	0.001
Corynebacterium aurimucosum	species	50	100	0.001
Schaalia georgiae	species	0	50	0.031
Desulfacinum	genus	0	50	0.076
Desulfacinum subterraneum	species	0	50	0.076
Bifidobacterium tsurumiense	species	0	50	0.085
Serratia marcescens	species	0	50	0.121
Salinicoccus luteus	species	0	10	0.126
Nostoc	genus	0	10	0.149
Alkaliphilus peptidifermentans	species	0	50	0.177
Synechococcales	order	0	25	0.24
Thioalkalivibrio	genus	0	50	0.242
Thioalkalivibrio jannaschii	species	0	50	0.242
Blautia coccoides	species	70	90	0.244
Caloramator indicus	species	50	100	0.26
Bifidobacterium	genus	0	25	0.268
Bifidobacteriaceae	family	0	25	0.269
Bifidobacteriales	order	0	25	0.269
Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	0	50	0.284
Actinomycetota	phylum	0	25	0.298
Halomonadaceae	family	0	25	0.301
Halomonadaceae	family	0	50	0.301
Veillonella montpellierensis	species	0	25	0.301
Actinomycetes	class	0	25	0.304
Tolumonas	genus	0	50	0.304
Tolumonas auensis	species	0	50	0.305
Enterobacter	genus	0	25	0.329
Bifidobacterium adolescentis	species	0	10	0.341
Burkholderiales genera incertae sedis	no rank	0	50	0.344
Actinomycetes	class	0	50	0.346
Bacteroides rodentium	species	80	100	0.351
Leyella	genus	0	50	0.353
Leyella stercorea	species	0	50	0.353
Veillonella montpellierensis	species	0	50	0.356
Bifidobacterium	genus	0	50	0.36
Bifidobacterium angulatum	species	0	50	0.36
Bifidobacteriaceae	family	0	50	0.36
Bifidobacteriales	order	0	50	0.36
Campylobacteraceae	family	0	50	0.365
Bifidobacterium catenulatum PV20-2	strain	0	50	0.367
Aedoeadaptatus coxii	species	50	70	0.37
Bifidobacterium gallicum	species	0	50	0.371
Bifidobacterium gallicum	species	0	25	0.377
Bacteroides rodentium	species	75	100	0.389
Peptococcus niger	species	50	70	0.39

Summary

This is quick dumping of statistical results. The data used is available at the Microbiome Prescription Citizen Science site. Generating interventions to shift above taxa in a favorable direction is in development. Stay Tune