ME/CFS bacteria shifts for Ombre/Thryve tests

This post is intended for researchers by pointing to bacteria whose genetics are likely significant for ME/CFS. The microbiome specific raw data is below. Preliminary z-scores indicated that they are significant (Pr < 0.01) and no filtering has occurred for False Detection Rate. Users are advised to perform their own statistics. For bacteria associated using BiomeSight tests, see this post.

Note: These results are lab-specific, using the data from OmbreLabs / formerly known as Thryve.

The raw data is available at: http://citizenscience.microbiomeprescription.com/.

NOTE: The sample size is very low (less than 1/3 of the size of current Long COVID Study)

Symptom Obs	No Symptom Obs	Lab	SymptomName
51	935	thryve	Official Diagnosis: Chronic Fatigue Syndrome (CFS/ME)

Basic Data

Bacteria	tax_rank	No Symptom Count	Symptom Count	No Symptom Frequency %	Symptom Frequency %
Burkholderiales Genera incertae sedis	norank	268	20	28.7	39.2
Anaerococcus	genus	530	37	56.7	72.5
Vibrionales	order	89	10	9.5	19.6
Porphyromonas bennonis	species	418	35	44.7	68.6
Anaeroglobus geminatus	species	474	33	50.7	64.7
Parvimonas micra	species	178	17	19	33.3
Insolitispirillum peregrinum	species	169	17	18.1	33.3
Rickettsia honei	species	91	13	9.7	25.5
Levyella massiliensis	species	327	25	35	49
Ezakiella	genus	243	25	26	49
Synergistaceae	family	343	25	36.7	49
Odoribacter splanchnicus	species	702	46	75.1	90.2
Mucinivorans	genus	50	9	5.3	17.6
Prevotella buccalis	species	470	35	50.3	68.6
Enorma massiliensis	species	80	11	8.6	21.6
Microbacter	genus	171	17	18.3	33.3
Flavobacteriales	order	499	34	53.4	66.7
Porphyromonas somerae	species	182	16	19.5	31.4
Parvimonas	genus	178	17	19	33.3
Anaeroplasmatales	order	326	28	34.9	54.9
Desulfurispora thermophila	species	507	35	54.2	68.6
Ruminococcus gauvreauii	species	285	22	30.5	43.1
Synergistetes	phylum	344	25	36.8	49
Prevotella disiens	species	237	20	25.3	39.2
Holdemania filiformis	species	641	41	68.6	80.4
Prevotella baroniae	species	346	24	37	47.1
Corynebacterium jeikeium	species	51	8	5.5	15.7
Corynebacteriales	order	585	41	62.6	80.4
Campylobacter hominis	species	177	18	18.9	35.3
Peptostreptococcaceae incertae sedis	norank	523	36	55.9	70.6
Campylobacterales	order	401	29	42.9	56.9
Clostridium frigidicarnis	species	65	9	7	17.6
Pseudomonadaceae	family	336	26	35.9	51
Dialister propionicifaciens	species	299	23	32	45.1
Absiella tortuosum	species	209	17	22.4	33.3
Epsilonproteobacteria	class	439	31	47	60.8
Ezakiella coagulans	species	235	22	25.1	43.1
Anaeroglobus	genus	475	33	50.8	64.7
Tannerella	genus	270	22	28.9	43.1
Gordonibacter pamelaeae	species	346	29	37	56.9
Bacteroides ovatus	species	812	50	86.8	98
Schaalia suimastitidis	species	199	17	21.3	33.3
Lacrimispora sphenoides	species	151	14	16.1	27.5
Propioniferax innocua	species	128	14	13.7	27.5
Rickettsia	genus	142	16	15.2	31.4
Corynebacterium	genus	529	36	56.6	70.6
Prevotella loescheii	species	202	20	21.6	39.2
Corynebacteriaceae	family	534	36	57.1	70.6
Desulfovibrio idahonensis	species	231	20	24.7	39.2
Thiomonas	genus	191	16	20.4	31.4
Peptoniphilus lacrimalis	species	223	18	23.9	35.3
Lactonifactor longoviformis	species	607	39	64.9	76.5
Synergistia	class	343	25	36.7	49
Fulvitalea	genus	49	8	5.2	15.7
Alistipes shahii	species	702	44	75.1	86.3
Anaerococcus octavius	species	125	15	13.4	29.4
Levyella	genus	332	27	35.5	52.9
unclassified Burkholderiales	family	183	16	19.6	31.4
Enorma	genus	81	11	8.7	21.6
Sphingomonas abaci	species	52	8	5.6	15.7
Anaerococcus vaginalis	species	302	24	32.3	47.1
Rickettsiales	order	214	21	22.9	41.2
Thermoanaerobacteraceae	family	262	21	28	41.2
Flavobacteriia	class	499	34	53.4	66.7
Eubacterium pyruvativorans	species	522	34	55.8	66.7
Anaeroplasmataceae	family	325	28	34.8	54.9
Peptostreptococcus anaerobius	species	89	14	9.5	27.5
Mogibacterium timidum	species	168	16	18	31.4
Alistipes obesi	species	553	36	59.1	70.6
Tissierellia incertae sedis	norank	564	40	60.3	78.4
Dielma fastidiosa	species	502	33	53.7	64.7
Clostridium chartatabidum	species	638	41	68.2	80.4
Desulfocella	genus	266	21	28.4	41.2
Mucinivorans hirudinis	species	49	9	5.2	17.6
Rickettsieae	tribe	193	20	20.6	39.2
Syntrophomonas sapovorans	species	88	10	9.4	19.6
Rickettsiaceae	family	195	20	20.9	39.2
Butyricimonas faecihominis	species	314	23	33.6	45.1
Ectothiorhodospiraceae	family	213	17	22.8	33.3
Anaeroplasma	genus	141	14	15.1	27.5
Gordonibacter	genus	497	34	53.2	66.7
Fulvitalea axinellae	species	48	8	5.1	15.7
Dehalobacter	genus	172	15	18.4	29.4
Hydrogenispora	genus	423	31	45.2	60.8
Fenollaria	genus	470	31	50.3	60.8
Anaerococcus murdochii	species	121	16	12.9	31.4
Anaerococcus senegalensis	species	112	17	12	33.3
Porphyromonas asaccharolytica	species	228	21	24.4	41.2
Mogibacterium	genus	664	42	71	82.4
Campylobacter	genus	352	25	37.6	49
Firmicutes sensu stricto incertae sedis	norank	417	31	44.6	60.8
spotted fever group	species group	110	15	11.8	29.4
Acinetobacter	genus	256	20	27.4	39.2
Synergistales	order	343	25	36.7	49
Lactonifactor	genus	613	40	65.6	78.4
Persicobacteraceae	family	59	13	6.3	25.5
Desulfurispora	genus	508	35	54.3	68.6
Holdemania	genus	779	48	83.3	94.1
Desulfocella halophila	species	263	20	28.1	39.2
Ezakiella peruensis	species	25	8	2.7	15.7
Tannerella forsythia	species	265	21	28.3	41.2
Campylobacteraceae	family	366	26	39.1	51
Absiella	genus	352	25	37.6	49
Flavobacteriaceae	family	453	30	48.4	58.8
Tepidibacter	genus	83	10	8.9	19.6
Dehalobacter restrictus	species	172	15	18.4	29.4
Peptoniphilus coxii	species	270	24	28.9	47.1
Hydrogenispora ethanolica	species	416	30	44.5	58.8
Pseudomonas	genus	327	23	35	45.1
Insolitispirillum	genus	173	17	18.5	33.3
Thermoanaerobacterales	order	390	28	41.7	54.9
Odoribacter	genus	737	46	78.8	90.2
Microbacter margulisiae	species	168	17	18	33.3
Propioniferax	genus	129	14	13.8	27.5

Items deem significant based on Bernoulli distribution

Bacteria	tax_rank	No Symptom Mean	Symptom Mean	No Symptom StdDev	Symptom Std Dev	Symptom Obs	No Symptom Obs
Alistipes onderdonkii	species	4859	11622	15348.3	23577.4	47	819
Natranaerovirga	genus	174	983	1892.4	3879.3	31	578
Rikenellaceae	family	16981	28258	24648.1	30780.6	51	920
Enterobacterales	order	3116	15635	10315.9	78732.2	46	856
Blautia glucerasea	species	1237	3446	4110.7	11731.9	40	727
Desulfobacteraceae	family	91	279	155.3	988.1	32	561
Tenericutes	phylum	1198	3169	3795.4	17659.1	46	824
Mollicutes	class	1178	3169	3773.8	17659.1	46	824
Chromatiales	order	102	491	495	2392.3	33	625
Gammaproteobacteria	class	6515	17655	16956.9	87886.1	51	933
Bacteroides intestinalis	species	1992	7432	8144.4	30306.3	43	779
Alistipes	genus	16685	27491	24264.1	30694.6	51	920
Desulfobacterales	order	94	256	155.3	933.7	36	585

Items deemed significant based on mean and standard deviation

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Cristian O. 10:23 am on June 11, 2022

Wow, high lacto and rickketsia did not expect that, I also found ricketsia in my stool sample but blood PCR and IgG IgM tests are always negative

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