ME/CFS bacteria shifts for BiomeSight 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 Ombre/Thryve bacteria see this post.

Note: These results are lab-specific, using the data from BiomeSight.

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
61	1095	biomesight	Official Diagnosis: Chronic Fatigue Syndrome (CFS/ME)

The data available

Bacteria that appear more or less often with statistical significance

Bacteria	tax_rank	No Symptom Count	Symptom Count	No Symptom Frequency %	Symptom Frequency %
Syntrophobacterales	order	571	39	52.1	63.9
Chitinophagales	order	507	39	46.3	63.9
Anaerococcus	genus	476	36	43.5	59
Porphyromonas bennonis	species	308	25	28.1	41
Rhodovibrio sodomensis	species	231	19	21.1	31.1
Novispirillum	genus	653	43	59.6	70.5
Thiobacillus	genus	159	16	14.5	26.2
Insolitispirillum peregrinum	species	651	43	59.5	70.5
Thiobacillus thiophilus	species	123	13	11.2	21.3
Amedibacillus dolichus	species	684	46	62.5	75.4
Adlercreutzia equolifaciens	species	682	46	62.3	75.4
Hymenobacteraceae	family	737	48	67.3	78.7
Streptococcus phocae	species	91	12	8.3	19.7
Finegoldia magna	species	451	35	41.2	57.4
Anaerococcus tetradius	species	123	13	11.2	21.3
Leuconostoc	genus	483	35	44.1	57.4
Porphyromonas somerae	species	203	19	18.5	31.1
Vagococcus	genus	296	23	27	37.7
Carboxydocella	genus	591	40	54	65.6
Clostridium cadaveris	species	381	28	34.8	45.9
Bacteroides acidifaciens	species	839	54	76.6	88.5
Thiomicrospira sibirica	species	77	11	7	18
Desulfofrigus	genus	107	13	9.8	21.3
Chitinophagaceae	family	510	39	46.6	63.9
Eggerthella	genus	787	50	71.9	82
Corynebacterium jeikeium	species	80	11	7.3	18
Corynebacteriales	order	643	42	58.7	68.9
Corynebacterium aurimucosum	species	121	15	11.1	24.6
Blautia hydrogenotrophica	species	749	51	68.4	83.6
Bacteroides heparinolyticus	species	319	25	29.1	41
Rickettsia marmionii Stenos et al. 2005	species	84	13	7.7	21.3
Niabella aurantiaca	species	158	15	14.4	24.6
Carboxydocella ferrireducens	species	577	39	52.7	63.9
Bacteroides caccae	species	832	53	76	86.9
Desulfobacteraceae	family	247	20	22.6	32.8
Finegoldia	genus	537	39	49	63.9
Phascolarctobacterium faecium	species	653	43	59.6	70.5
Odoribacter denticanis	species	656	43	59.9	70.5
Corynebacterium amycolatum	species	83	11	7.6	18
Pelotomaculum	genus	387	28	35.3	45.9
Peptoniphilus asaccharolyticus	species	418	31	38.2	50.8
Corynebacterium	genus	523	37	47.8	60.7
Corynebacteriaceae	family	523	37	47.8	60.7
Pelotomaculum isophthalicicum	species	387	28	35.3	45.9
Thiobacillaceae	family	159	16	14.5	26.2
Rhodovibrionaceae	family	230	19	21	31.1
Bacteroides fluxus	species	825	55	75.3	90.2
Symbiobacteriaceae	family	641	42	58.5	68.9
Limnobacter litoralis	species	770	50	70.3	82
Clostridium akagii	species	529	36	48.3	59
Lactobacillus acidophilus	species	76	11	6.9	18
Desulfofrigus oceanense	species	106	13	9.7	21.3
Piscirickettsiaceae	family	137	14	12.5	23
Marinospirillum	genus	221	20	20.2	32.8
Moryella indoligenes	species	78	11	7.1	18
Roseospira	genus	183	21	16.7	34.4
Halanaerobiaceae	family	202	18	18.4	29.5
Rhodovibrio	genus	231	19	21.1	31.1
Limnobacter	genus	773	50	70.6	82
Schaalia	genus	531	37	48.5	60.7
Chitinophagia	class	507	39	46.3	63.9
Clostridiales Family XVI. Incertae Sedis	family	591	40	54	65.6
Symbiobacterium toebii	species	641	42	58.5	68.9
Anaerococcus hydrogenalis	species	162	16	14.8	26.2
Pediococcus	genus	644	42	58.8	68.9
Symbiobacterium	genus	641	42	58.5	68.9
Adlercreutzia	genus	786	50	71.8	82
Actinomyces	genus	797	52	72.8	85.2
Porphyromonas asaccharolytica	species	259	23	23.7	37.7
Butyricimonas synergistica	species	397	29	36.3	47.5
Bifidobacterium longum	species	795	52	72.6	85.2
spotted fever group	species group	139	17	12.7	27.9
Actinomycetaceae	family	866	55	79.1	90.2
Phascolarctobacterium succinatutens	species	786	50	71.8	82
Contubernalis	genus	143	16	13.1	26.2
Streptococcus oralis subsp. tigurinus	subspecies	440	31	40.2	50.8
Halanaerobium	genus	202	18	18.4	29.5
Shewanella upenei	species	263	21	24	34.4
Candidatus Contubernalis alkalaceticum	species	143	16	13.1	26.2
Oceanospirillaceae	family	261	22	23.8	36.1
Thiomicrospira	genus	110	13	10	21.3
Roseospira mediosalina	species	60	11	5.5	18
Amedibacillus	genus	684	46	62.5	75.4
Insolitispirillum	genus	651	43	59.5	70.5
Psychrobacter glacialis	species	190	19	17.4	31.1
Ethanoligenens	genus	518	35	47.3	57.4

Items deem significant based on Bernoulli distribution

Bacteria where the difference in counts is significant

tax_name	tax_rank	No Symptom Mean	Symptom Mean	No Symptom StdDev	Symptom Std Dev	Symptom Obs	No Symptom Obs
Novispirillum	genus	8305	16138	15057.3	30286.7	43	653
Insolitispirillum peregrinum	species	8327	16133	15072.1	30272.3	43	651
Streptococcus australis	species	196	753	434.5	3495.9	40	739
Anaerovibrio	genus	1217	2540	2719	10547.7	56	968
Anaerotruncus colihominis	species	1749	2433	1677.8	2418.4	61	1054
Prevotella copri	species	65082	5361	148361.2	23886.1	57	1000
Rhodospirillaceae	family	12814	27057	25272.7	53923.2	51	896
Bacteroides rodentium	species	2967	6227	4910.2	10044.9	61	1067
Anaerovibrio lipolyticus	species	1201	2537	2700.6	10546.9	56	963
Bacteroides fluxus	species	223	1213	1400.4	5587.4	55	825
Bacteroides uniformis	species	25980	40747	37165.5	40517.7	60	1075
Streptococcus parasanguinis	species	192	633	387.9	2639.1	38	685
Alphaproteobacteria	class	11939	23394	26761.1	50681.6	60	1062
Streptococcus	genus	3048	6152	7181.5	26974	61	1082
Burkholderiaceae	family	324	578	559.3	817.5	56	970
Rhodospirillales	order	12779	26131	26212.8	53158.4	53	933
Blautia obeum	species	5857	10753	10528.1	22306.7	60	1043
Streptococcus thermophilus	species	863	2106	2185.9	8681.6	54	905
Insolitispirillum	genus	8327	16133	15072.1	30272.3	43	651

Items deemed significant based on mean and standard deviation

CFS Remission

Striving for true remission of CFS, chronic Lyme, FM, IBS etc

ME/CFS bacteria shifts for BiomeSight tests

Bacteria that appear more or less often with statistical significance

Bacteria where the difference in counts is significant

Bacteria that appear more or less often with statistical significance

Bacteria where the difference in counts is significant

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