Foreword – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships.

Back story 

I’ve had ME/CFS 14 years (symptoms came on stronger after breast augmentation 2008) but the last 9 yrs I’ve been mostly housebound & bed bound 21 hours per day. I’d say I’m moderate/severe. (I live in the Uk) 

My diet:- 

• Brekkie :- muesli (take raisins out) with coconut milk or almond milk  Or poached egg on 1 seeded brown bread Or scrambled egg with cumin, coconut milk, salt & black pepper on 1 seeded brown bread Or porridge with coconut milk, frozen blueberries or dried goji berries 
• Lunch:-A banana, nuts (walnuts, pecans, almonds) & mixed seeds 
• Dinner:-Salad (bistro salad leaves with a little shredded beetroot) cucumber, celery, grated carrot, with jacket potato (or sweet potato) & vegan cheese on top.. I’ve just started to add a sprinkle of organic olive oil & black pepper (tasty)  Or Steamed veg – carrots, green beans, broccoli, stringless beans & sugar snap peas (or mangetout) with sweet potato & usually something out the freezer I pop in oven… which I know I need to stop as it’s processed. I will begin to change that for chicken or salmon (it’s just been easier) 

More information on diet and supplements was also sent.

Analysis

Looking at Bacteria Deemed Unhealthy, the sole item that stands out was moderately high Streptococcus oralis. Dr. Jason Hawrelak Recommendations came out to 90%ile — so better than most people.

For this person, we have a shift towards rarer bacteria with those seen in only 30-50% of samples being over represented.

Percentile	Genus	Species
0 – 9	2	2
10 – 19	8	5
20 – 29	11	9
30 – 39	10	20
40 – 49	11	19
50 – 59	9	13
60 – 69	9	9
70 – 79	5	9
80 – 89	4	6
90 – 99	5	6

Since ME/CFS is the condition, I checked the list of antibiotics often prescribed with the following being the top of the list. It is interesting to note that the literature finds that they do improve some ME/CFS patients

1. gentamicine sulfate (antibiotic)   (1) [See 2021] [2017]
2. rifaximin (antibiotic)s   (0.949) [Health Rising] [2011] and many more
3. amikacin hydrate (antibiotic)   (0.845) – no significant literature
4. gentamicin (antibiotic)s   (0.745) [2017]
5. metronidazole (antibiotic)s   (0.727) “Metronidazole/Flagyl is reported to have 75% of CFS patients improving ” [Src] also [BMJ]

On the avoid list are some antibiotics that are also prescribed for ME/CFS

1. rifampicin (antibiotic)s   ( – 0.423 )
2. tetracycline (antibiotic)s   ( – 0.291 )
3. azithromycin,(antibiotic)s   ( – 0.289 )
4. rifampicin (antibiotic)   ( – 0.289 )
5. doxycycline (antibiotic)s   ( – 0.191 )

She provided some of the items that she is taking so I looked at the estimated impact on her microbiome

• sertraline,(prescription) which she is reducing. This is likely a good course of action
  • Take Estimate:  20.4, Avoid Estimate:  24.7
• dopamine (prescription) – this is a bit of a concern to me because it is likely to contribute to microbiome dysfunction
  • Take Estimate:  13.2, Avoid Estimate:  23.1
• Vitamin C, — keep taking
  • Take Estimate:  22.3, Avoid Estimate:  13.9
• Cetirizine:
  • Take Estimate:  20.4, void Estimate:  29.1

Note: the above are estimates on whether they will improve or contribute to the microbiome dysfunction. Medical concerns should always dominate.

Suggestions

Doing my usual pick the bacteria to change using different criteria we have:

•  Use JasonH (15 Criteria) – 8
•  Standard Lab Ranges (+/- 2 Std Dev) – 3
•  Box Plot Whisker – 19
•  Kaltoft-Moltrup Normal Ranges – 34
•  Percentile in top or bottom % – 27

The number of bacteria selected for each of the above was lower than I often seen.

Going to the Consensus

The following suggestions stand out:

• whole-grain barley (she does report porridge, she may wish to make sure that it includes barley)
• Vitamins: Note ME/CFS usually benefit for B-Vitamins [1999] [2019]
  • thiamine hydrochloride (vitamin B1) –
  • vitamin b3 (niacin)
  • vitamin b7 biotin (supplement) (vitamin B7)
  • Cyanocobalamin (Vitamin B-12)
  • Vitamin C (ascorbic acid)
• Conjugated Linoleic Acid
• quercetin,resveratrol
• melatonin supplement
• N-Acetyl Cysteine (NAC),
• Cacao
• lauric acid(fatty acid in coconut oil,in palm kernel oil,) – She does use coconut milk, this is good. She may wish to increase.

Dropping down to the avoid list, we see

• saccharin
• stevia
• nuts (including walnuts, almonds/ almond skins ) – she currently use these as snacks. banana and plantain bananas are fine to use as snacks
• peppermint (spice, oil) – she may wish to change to use ginger and especially Echinacea tea instead

The full list is attached.

Trying out an Experimental feature

I have used this feature of the several recent blogs on autism (Bacteria to Hand-Pick for Autism with Ombre/Thryve samples, Bacteria to Hand-Pick for Autism with Biomesight samples). I have posted the bacteria identified here. Unfortunately sample size are small (1/3 of the Long COVID samples)

• ME/CFS bacteria shifts for Ombre/Thryve tests
• ME/CFS bacteria shifts for BiomeSight tests

Using the 61 samples annotated with CFS and processed thru the same lab (Biomesight.com). We found 11 bacteria identified as statistically associated with CFS. Three were too high and 8 were too low.

Rank	Name	Your value	Percentile
family	Actinomycetaceae	80	25.7
genus	Actinomyces	40	20.2
genus	Adlercreutzia	70	14.4
species	Adlercreutzia equolifaciens	70	21.3
species	Anaerotruncus colihominis	1560	79.7
species	Bacteroides acidifaciens	70	27.7
species	Bacteroides rodentium	1850	73.6
species	Bacteroides uniformis	21160	61.8
species	Bifidobacterium longum	300	32.8
species	Finegoldia magna	40	28.4
species	Prevotella copri	70	8.9

The results from this custom picked set are shown below.

Modifier – Suggestion to take	Confidence
Human milk oligosaccharides (prebiotic, Holigos, Stachyose)	1  📏
whole grain diet	0.576
inulin (prebiotic)	0.541
blueberry	0.4
vitamin k2	0.4  📏
bacillus subtilis,lactobacillus acidophilus (probiotics)	0.38
lactobacillus fermentum (probiotics)	0.38  📏
lactobacillus gasseri (probiotics)	0.38  📏
lactobacillus reuteri (probiotics)	0.38  📏
maltitol	0.38
oats	0.38
navy bean	0.379
ketogenic diet	0.379
vitamin a	0.345
arabinoxylan oligosaccharides (prebiotic)	0.328
chondrus crispus (red sea weed)	0.328
green tea	0.328

Modifier to avoid	Confidence
saccharin	0.533
Slippery Elm	0.382
triphala	0.382
glycyrrhizic acid (licorice)	0.382
sugar	0.38
Cacao	0.245
refined wheat breads	0.214

Probiotics that are best to take Name	Impact
Bromatech (IT) / Rotanelle plus	7.9
probiotic pur (de) / realdose nutrition	6.18
Realdose	6.18
Jetson (US) / Immunity Probiotics	6.09
douglas laboratories / multi probiotic 40 billion	6.09
Thryve L.PCasei Th1, L.PCasei Th2,L.Ferm IBF1, L.acidoph	6.09

Flavonoid Foods Flaxseed, meal Nuts, almonds Almond

Flavonoid / Supplements   Vitamin K (phylloquinone)  Resveratrol   Magnesium, Mg

We have some contradictions between these suggestions and the ones above. Why? The data we are using is very very incomplete. It is the best that is available. In keeping with my principle of less risk, when suggestions are in disagreement (for example Nuts and almonds – recommended here but to avoid above), then omit them. There are a lot of possible items, keeping to positive items where there are no disagreement is the best path.

Because this person suffers from brain fog, they may wish to sit down with a nutritionist to go thru the download list above to craft a diet plan. The suggestions are in no way a balanced nor complete diet. For example increase food rich in magnesium on the take suggestions, or using supplements.

As always, this information is computed from the best available data and is not based on clinical experience. Always review with your medical professional for appropriateness of suggestions before starting.

Bottom Line

I check with this person and the breast augmentation has not been undone. In other words, there is a reasonable chance that it is a significant contributor to the ongoing symptoms. I expect some progress from microbiome manipulation, but I suspect the side effects from augmentation will limit it. The literature seems to confirm it.

• “Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation” [2021]
• “The most common cause of surgical readmission after breast implant surgery remains infection. Six causative organisms are principally involved: Staphylococcus epidermidis and S. aureus, Escherichia, Pseudomonas, Propionibacterium, and Corynebacterium.” [2015]
• “The researchers found that the women with silicone gel-filled breast implants were significantly more likely to be diagnosed with autoimmune or rheumatic disorders, such as Sjögren syndrome, systemic sclerosis, and sarcoidosis, compared with women without breast implants of a similar age and socioeconomic status.” [2022]
• “Silicone breast implants(SBI)  are associated in a proportion of patients with complaints such as fatigue, cognitive impairment, arthralgias, myalgias, pyrexia, dry eyes and dry mouth. Silicones can migrate from the implant through the body and can induce a chronic inflammatory process. Explantation[Removal] of SBI results in the majority of patients in an amelioration of the symptoms.” [2017]

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)

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

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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

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)

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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

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

Overview

Short bio: 35yr Male have had ME/CFS for about 7 years, see A review of a ME/CFS Microbiome for prior review plus backstory. This was my review for “A – Thryve:2021-11-21 self” below.

This person has had done three samples, so we will both look at the latest sample and across samples.

• A – Thryve:2021-11-21 self
• B – Thryve:2022-03-15 self (he used the microbiome prescription site himself to get next course adjustment)
• C – Thryve:2022-05-16 self (this review)

The key questions focus on objective improvement and subjective improvement.

General Health Issues

The evenness of Genus and Species across percentile is shown below

	A	A	B	B	C	C
Percentile	Genus	Species	Genus	Species	Genus	Species
0 – 9	11	16	6	9	11	15
19-Oct	12	30	15	30	19	27
20 – 29	19	31	20	24	12	31
30 – 39	18	35	23	45	16	33
40 – 49	16	24	20	37	18	30
50 – 59	21	31	25	45	21	33
60 – 69	18	20	17	30	14	22
70 – 79	16	23	11	28	16	23
80 – 89	5	14	16	24	13	21
90 – 99	3	14	13	20	5	14
Total	139	238	166	292	145	249
Std.Dev.	6.05	7.71	5.72	11.10	4.60	7.02

My reading is that at the Genus level, the microbiome is stablizing. An ideal microbiome would have a Standard Deviation of 0.0 (i.e. the appropriate percentage is in each class). We see for Genus move from 6.0 -> 5.7 -> 4.6. Species have a far greater degree of randomness because may species are not identified, most genus are identified.

Potential Medical Conditions Detected

The count has been similar: A:3 B:6 C:2 with the one items in common being Allergies.

Unhealth Bacteria

The counts were similar between all samples: A:18, B:20, C:21

Dr. Jason Hawrelak Recommendations

We had significant improvement between the first two samples and a slight loss going to the third: A: 56.5%(5) B:95.5% (8) C: 89% (7)

AI Computed Probiotics

AI Suggested Supplements

Using the default 10% level, we found samples A and B only suggested one supplement. C suggested 2 (L-Histidine and manganese). I looked up the item from A and B and saw that it had continued to improve. 

Supplements	A	B	C
beta-alanine	7.3	9.2	17.3

Has there been positive change?

My reading of the above objective numbers is yes in several vectors. There was nothing show a clear negative change. Somethings stayed put — that is fine, it is small steps. As the picture below illustrates, it is not a direct line/tunnel through the mountain ranges of dysbiosis, we have to work our way across passes and valleys.

The “I don’t feel better” quicksand

I have too often seen — especially with people suffering from Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) — patients giving up on a course of action because they reached a point where they may state “I don’t feel better from doing this, so I am changing…”. For these people, this is often caused by several factors:

• They do not remember how they were actually 2 weeks or 2 months ago…
• Their MD have no objective tests to show progress
• They expect significant constant change constantly (they are frustrated waiting for improvement)

Using the microbiome and repeated testing, they can get objective measurement of changes instead of relying on subjective measurement being done under the influence of brain fog with memory problems.

In this person case, we do see objective improvement of the dysbiosis. What about subjective?

“You’re welcome to mention I have noticed improved sleep and lower anxiety despite my good and bad bacteria shifting around “

From the reader

Moving Forward

As reviewed above, we have no KEGG suggested probiotics, but do have these supplements suggested:

• L-Histidine – Percentile: 2.7
• manganese – Percentile: 3.7
• NADH – Percentile: 15.6 (this has been studied for ME/CFS
  • Effect of Dietary Coenzyme Q10 Plus NADH Supplementation on Fatigue Perception and Health-Related Quality of Life in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial, 2021
  • Effect of coenzyme Q10 plus nicotinamide adenine dinucleotide supplementation on maximum heart rate after exercise testing in chronic fatigue syndrome – A randomized, controlled, double-blind trial 2015
  • Does oral coenzyme Q10 plus NADH supplementation improve fatigue and biochemical parameters in chronic fatigue syndrome? [2014]
  • Comparison of oral nicotinamide adenine dinucleotide (NADH) versus conventional therapy for chronic fatigue syndrome [2004]
  • Is NADH effective in the treatment of chronic fatigue syndrome? [2000]
  • [Nicotinamide adenine dinucleotide (NADH) in patients with chronic fatigue syndrome] [2010]
  • Therapeutic effects of oral NADH on the symptoms of patients with chronic fatigue syndrome [1999]
  • Chronic lactic acidosis in an adult. A new syndrome associated with an altered redox state of certain NAD-NADH coupled reactions [1970] – this paper was pre ME/CFS existing, but lactic acidosis has been establish as frequently happening with ME/CFS subsequently.

On a personal note, I used NADH during my 1999-2000 relapse (1st time diagnosis). I eventually switched to 400 mg of flushing niacin twice a day (after MD checked my liver function see facts) and have continue to do so (with liver being tested every year).

Getting suggestions based on US National Library of Medicine Studies

As is my pro forma approach, I did each of the following (with number of bacteria picked after):

•  Use JasonH (15 Criteria) – 8
•  Use Medivere (54 Criteria) – 8
•  Use Metagenomics (59 Criteria) – 8
•  Use Nirvana/CosmosId (36 Criteria) – 8
•  Use XenoGene (22 Criteria) – 8
•  Standard Lab Ranges (+/- 2 Std Dev) – 2 (Too High:   Bacteroides clarus, Roseburia hominis)
•  Box Plot Whisker – 39
•  Kaltoft-Moltrup Normal Ranges – 85
•  Percentile in top or bottom 10% 69

The new layout of the consensus page is shown below

My suggestion for 3 probiotics to rotate thru are:

• bifidobacterium animalis lactis (probiotics) – the cheapest source (per BCFU) is Custom Probiotics
• Akkermansia muciniphila (probiotic) – the only source is Pendulum
• Any bacillus only probiotic containing bacillus coagulans (probiotics) and Bacillus clausii (Probiotics)
  • Many possible products, search this page

For more information on probiotics see the bottom section of this recent review.

For supplements, there are only 3 easily accessed items that are positive, everything else is negative impact!!: Ferric citrate (iron supplement), magnesium (commonly used for ME/CFS) and vitamin k2

For other things, see the video or the suggestions on your microbiome.

Bottom Line

You are making objective progress. A word of caution, if some of the items that you are currently taking on the avoid list, slowly remove them by reducing amount and watching for potential adverse effect. Some of the positive objective changes may be due to them (there is a risk of a feedback loop: if you are taking them, they are not needed BUT it you stop taking them, your microbiome may devolve to a state needing them).

Last – Using Symptoms

This is EXPERIMENTAL. It is a thought experiment and I am still learning it’s behavior. For some symptoms it may reduce awesome results, for others it may improve one set of symptoms at a cost of other symptoms getting worst. I picked two of the more unusual symptoms that he had:

• Comorbid: Methylation issues (MTHFR)
• Immune: Chronic Sinusitis

This resulted in this list being selected with a very strong Filter (first time I have seen this)

Rank	Name	Your value	Percentile
class	Flavobacteriia	21	7
order	Chromatiales	21	9.4
order	Flavobacteriales	21	7
order	Marinilabiliales	21	13.5
phylum	Tenericutes	42	9.5
species	Bifidobacterium bohemicum	21	11.8
species	Eubacterium ramulus	8720	95.5
species	Prevotella disiens	946	84.1

I would suggest using it to increase the priority of some items that are positive suggestions in the consensus list, I would not go with using this set of suggestions alone.

Questions from Reader

• Ferric Citrate ,  haven’t been able to find this type? Have you seen it anywhere? Also how would one figure out the dose for gut bacteria shifting?
  • I am an ex-science teacher and thus know it more common name, Iron Citrate. Swanson and others sells it.
• Bacillus- taking terraflora , think I’m up to 6 caps. I saw in a study I need to get to 20 !!
•  …I also have prescript on hand BUT that has a lot of other SBO strains. Would you stuck to TERRAflora for now?  
  • I would keep the Prescript Assist on the shelf, and keep to Terraflora, I would keep increasing the dosage every second day until the bottle was finished. I would look around for ones with similar probiotics for the next cycle, for example Youtheory, Spore Probiotic, 6 Billion CFU, 60 Vegetarian Capsules – for two reasons:
    • Cheaper per BCFU (and also higher BCFU per dosage)
    • Different strains often helps because they produce slightly different products
• Miyarisan , I thought I saw this in my results somewhere , maybe it was far down the list…would you save or finish if you had my results?
  • It is on the list, I would finish it before starting the next cycle of probiotics (REMEMBER: we want to be rotating the probiotics – not take them continuously)

• Akkermansia – I have 2 bottle of this stuff actually from pendulum . I read you and your wife has taken it. How much did you take or I know it’s a new product but if you’ve seen a study with dosing please let me know. 
  • The one existing study used 10 BCFU/day, and the bottle reads 0.4 gm. Lacking more information, I would just keep to the bottle recommended dosage.
• NADH- I have the flush stuff and cq10? Do you think that combo works or does it have to be Nadh?
  • Personally, I found flush niacin had greater impact and still look forward to my morning flush to get the mind working (it improves oxygen delivery because it’s a vascular dilator). Assuming you can tolerate the flush.

ALWAYS REVIEW WITH YOUR MEDICAL PROFESSIONAL FIRST

A reader emailed about my earlier post, RESTORE for gut health Danger Will Robison! I am a firm believer in evidence based medical treatment. Ideally the source of the information will be a study on the US National Library of Medicine (PubMed). If it is not studied, IMHO there is a significant risk of danger.

He writes:

I purchased  a bottle of RESTORE a couple years back which was manufactured by Bionic Sciences LLC which is now ION* Gut Health and the company changed its name to Intelligence of Nature  the ingredients of my RESTORE bottle says Aqueous Humid Substances ( Terrahydrate). 150mg per teaspoon and now the ingredients on the ION* bottle says Humic Extract from ancient soil 5mg per teaspoon …
Are we talking about the same product here???

I proceeded to their site to see if they have any evidence. They linked to studies, I downloaded many of them:

My first impression is that we have gas-lighting here. It has not been peer-reviewed, but most people will not registered the “pending”. It has not been published.

Another of their studies seems like a deliberate attempt to mislead, iMedPub seems to be an attempt to mimic PubMed… Going to that site I see “All Published work is licensed under a Creative Commons Attribution 4.0 International License” and who owns that site is willfully hidden (checking its registration) and it is a “we publish anything for a fee site” – “Hence, the Journals operate solely through processing charges we receive from the authors and some academic/corporate sponsors. ‘[src]

So what is in it? They appear to have obfuscate the ingredients – Dropping the list and replacing it with a non-descript “Humic Extract (from Ancient Soil)”. In other words, I can get the same thing by just going to any National park and collecting some soil!!

There are studies for other products

• Impact of humic acids on the colonic microbiome in healthy volunteers [2017] using (Activomin^®) Sample size is very small….
• The Anti inflammatory Properties of Humic Substances: A Mini Review [2015]
• Brown coal derived humate inhibits contact hypersensitivity; an efficacy, toxicity and teratogenicity study in rats [2007] “Only the leonardite humate compared favourably“
• Anti-Allergic Properties of Humic Acids Isolated from Pine-Sphagnum-Cotton Sedge Peat [2022]
• Potassium humate inhibits complement activation and the production of inflammatory cytokines in vitro [2009]

Bottom Line

The firm is my issue, not the concept. Studies have shown that results depend on the source/content of the humic acids. They have failed to provide scientific information on the content. They have failed to publish respectable studies and the studies on their site appears to be gas-lighting. Their prices is $72 for a 2 month supply… well, I can get 25 pounds of Granular Humic Acid Powder – 25lb Bag, for $20 from Walmart!

I have also commented in the past” A teaspoon of good soil will likely help many microbiome issues” (i.e. the hygiene hypothesis). Most of the bacillus probiotics are soil based bacteria.