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)

---

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.

This is a follow up to my blog post of Dec 30, 2021. Rosacea, Circulation and mild CFS. The person has tried the suggestions, and now we will attempt to see what the consequences are and the next set of suggestions.

Remember, the suggestions are based on mathematical modelling using clinical studies on study populations, so they may work or not work for individuals.

Reminder:
I am a computer scientist and a statistician. I am not licensed to practice medicine, and where I live has strict laws about ‘appearing to practice medicine’. What I can do for readers is to write a public blog (anonymous) from your data and back story as an education post on using the software and the statistics it produces. I cannot consult. The content should be reviewed by a medical professional before implementing.

High Level Measures

• Bacteria Reported
  • Prior: 427
  • Latest: 591 (38% increase in taxonomy)
• Health Status
  • Prior: Healthy 1, Unhealthy 8
  • Latest: Healthy 1, Unhealthy 9
• Dr. Jason Hawrelak Recommendations
  • Prior: 99.7% (effectively excellent!)
  • Latest: 75.3%. What left ideal is below, nothing moved to ideal
    • Bacteroidia went up
    • Bacteroides went up
    • Methanobrevibacter went down
    • Roseburia went down
    • Faecalibacterium prausnitzii still not ideal but went up significantly
• Unhealthy Bacteria: here we had a definite improvement, less ones, lower value
  • Ruminococcus] gnavus dropped off list
  • Anaerotruncus colihominis decreased
  • Bacillus decreased
  • Blautia producta decreased
  • Clostridium decreased
  • Collinsella decreased
  • Corynebacterium dropped off list
  • Dorea decreased
  • Eggerthella lenta dropped off list
  • Legionella drop off list
  • Streptococcus australis decreased
  • Streptococcus vestibularis dropped off list
  • Veillonella atypica joined the list

Bacteria Selected using Expert Criteria

Method	Prior	Latest
Use JasonH (15 Criteria)	5	6
Use Medivere (54 Criteria)	5	6
Use Metagenomics (59 Criteria)	5	6
Use Nirvana/CosmosId (36 Criteria)	5	6
Use XenoGene (22 Criteria)	5	6
Standard Lab Ranges (+/- 2 Std Dev)	8	6
Box Plot Whisker	30	27
Kaltoft-Moltrup Normal Ranges	78	84
Percentile in top or bottom 10 %	63	99

My impression is that the microbiome has become more diverse, in one sense, unstable. The increase in the number of bacteria types reported (591) moved it just above the typical count for BiomeSight (578). My personal experience is that this is a good sign, the microbiome is changing, I experienced this spike is variety before my microbiome settled down into a new, healthier normal.

Symptoms Change

“This things has improved:

• Less bloated
• Seborrhoeic dermatitis is gone 
• Better stool
• Better libido“

Using the regression for all symptoms we had regressions for, we had 154 improved out of 209 items, or 74% had improvement in the prediction of symptoms.

Overall: Appears to be Improved

This person was a challenge originally because there was no dominate shifts or “smoking guns”. Being at the 99+% for Dr. Jason Hawrelak recommendations and the same items returned from other expert suggestions (many with more criteria) had no significant change. Supporting improvement: Increase in bacteria types closer to typical; significant decrease in number of Unhealthy Bacteria; improved symptoms; and last, prediction of symptoms had a major improvement.

Next Round of Suggestions

After the above sample, he actually started two more items:

• 10 days with doxycycline
• started to take rosemary “Feels pretty good taking it. ” 

Probiotics

There are many Ways of Choosing Probiotics, I will look at two below:

KEGG AI Computed Probiotics

The differences actually shocked me, a very very dramatic difference. On the current sample I see what is often on ME/CFS patients list appear at the top: miyarisan (jp) / miyarisan with also L. Plantarum Probiotic Powder. This suggests that he is moving towards/through a more typical ME/CFS microbiome. Given that he has issues but everything appeared normal or good, I take this as a good sign – we are exposing the issues.

Prior Sample

Current Sample

CustomProbiotics.com / L. Brevis Probiotic Powder 2 CustomProbiotics.com / L. Rhamnosus Probiotic Powder 2 digestive care 2 Metabolics / Lactobacillus Rhamnosus Powder 2 miyarisan (jp) / miyarisan 2 PureGG 2 spain (es) / bivos 2 spain (es) / kaleidon 2 spain (es) / ns florabiotic instant 2 spain (es) / suerobivos 2 reg’activ / immune & vitality 1.83 CustomProbiotics.com / L. Salivarius Probiotic Powder 1.67

miyarisan (jp) / miyarisan 907 enviromedica terraflora sbo probiotic 828.67 bio-botanical research / proflora4r restorative probiotic 730.25 perfect pass / perfect pass probiotic bacillus spore 730.25 CustomProbiotics.com / L. Plantarum Probiotic Powder 722.2 goodbelly drink 722.2 HLH BIOPHARMA(DE) / LACTOBACT ® LDL-CONTROL 722.2 jarrow formula / ideal bowel support® lp299v® 722.2 Metabolics / Lactobacillus Plantarum Powder 722.2 Prescript-Assist®/SBO Probiotic 694.5 Sun Wave Pharma/Bio Sun Instant 690.92

We also have the option of probiotics based on symptoms (adjusted for the microbiome). See Using Samples and Symptoms to Suggest Probiotics post. The data is shown below in decreasing weight order. The nice thing to see is the decrease in the weight of everyone. One totally disappeared (the sole enterococcus faecalis one). It is interesting to note that while above using only the microbiome and resulted in major shifts between samples, when the symptoms are combined the suggestions are very similar and actually reflect improvement of the microbiome.

Prior Sample	Latest Sample
Prescript-Assist®/SBO Probiotic (34) enviromedica terraflora sbo probiotic (4.4) symbiopharm / symbioflor 1 (3.8) (US Source, World Wide Source) klaire labs / biospora (3.7) microbiome labs/ megasporebiotic (3.6)	Prescript-Assist®/SBO Probiotic (22.6) enviromedica terraflora sbo probiotic (3.5) perfect pass / perfect pass probiotic bacillus spore (2.9) klaire labs / biospora (2.8) microbiome labs/ megasporebiotic (2.7)

Suggestions

I am going to do my current practice of relying on consensus reports because they are now quick to generate. I will be doing a consensus from:

• Standard Lab Ranges (+/- 2 Std Dev)
• Box Plot Whisker
• Kaltoft-Moltrup Normal Ranges
• Percentile in top or bottom 10 %

I will be including everything, since the reader is able to persuade his medical professional to prescribe.

Consensus Results

The following are my picks from the options presented. I provided some links to where it helped ME/CFS –i.e. the suggestions are reasonable

• On all Safest Suggestions (Take:avoid ration)
  • Cacao (21:1) — you likely want 85% chocolate or higher [2010]
  • lactobacillus casei (probiotics) (8:1) [2009]
  • polymannuronic acid (6:1) impacts restless leg syndrome
  • bacillus subtilis (probiotics) (5:1) see 2016 post
  • high fiber diet (5:1)
  • garlic (allium sativum) (5:1)
  • rosmarinus officinalis (rosemary) (3:1)
  • lauric acid(fatty acid in coconut oil,in palm kernel oil,) (7:1)
  • Only take – no negatives
    • fucoidan
    • pediococcus acidilactic (probiotic)
    • green tea
    • capsaicin (hot pepper)
    • fish oil

Items to reduce or avoid

• stevia
• xylan (prebiotic)
• high sugar diet
• sugar
• galactose (milk sugar)
• low fodmap diet
• high-saturated fat diet
• rare meat
• low fiber diet
• high processed foods diet
• vegetable/fruit juice-based diets
• nuts
• white button mushrooms
• partially hydrolysed guar gum,fructo-oligosaccharides (prebiotic)
• cranberry bean flour
• kefir
• kombucha
• Prescript Assist (Original Formula)

Remember: These are suggestions, items that improve odds.

Prescription Suggestions

This is done using advance suggestions and flipping the selections:

The top suggestions were:

• rifaximin (antibiotic)s
• piperacillin-tazobactam (antibiotic)s
• loracarbef (antibiotic)
• benzylpenicillin sodium (antibiotic)
• clindamycin (antibiotic)s
• benzathine benzylpenicillin (antibiotic)
• clarithromycin (antibiotic)s

Secondary positive suggestions are:

• lymecycline (antibiotic)
• minocycline (antibiotic)s
• doxycycline (antibiotic)s

Dangers of Filtering

The person tried using the ME/CFS filter and got very different results. This person has mild ME/CFS; the studies on the US National Library of Medicine are for ME/CFS are typically severe and matches a yard of criteria for inclusion in the study. It is often not safe to use there filters when you self-diagnosis or are mild/controlled.

Bacteria Selected using Expert Criteria

Method	Filtering By ME/CFS	Latest
Use JasonH (15 Criteria)	4	6
Use Medivere (54 Criteria)	4	6
Use Metagenomics (59 Criteria)	4	6
Use Nirvana/CosmosId (36 Criteria)	4	6
Use XenoGene (22 Criteria)	4	6
Standard Lab Ranges (+/- 2 Std Dev)	3	6
Box Plot Whisker	5	27
Kaltoft-Moltrup Normal Ranges	12	84
Percentile in top or bottom 10 %	8	99

Adding filtering dropped the bacteria consider by a large amount (up to 92%!!).

My usual criteria has been to have at least 1-2 dozen bacteria. With the new consensus report, having a large number of bacteria seems to produce clearer results.

Bottom Line

Suggestions to be discussed with their medical probiotics

• miyarisan (jp) / miyarisan
• bacillus probiotics (enviromedica terraflora sbo probiotic contains 5 different one)
• L. Plantarum Probiotic

In terms of prescription (doing rotation with breaks between):

• rifaximin (antibiotic)s see this post.
• lymecycline (antibiotic) or minocycline (antibiotic)s There is a long history of successful tetracycline (this family of antibiotics) use with ME/CFS

Supplements to try:

• Monolaurin (lauric acid(fatty acid in coconut oil,in palm kernel oil,)
• Fish Oil – if you love herring… go to it
• High Fiber Diet

We saw improvements between the sample when this reader implemented some of the suggestions. Remember, the suggestions improves the odds, they do not guarantee nor is there any requirement or protocol to follow.

New page added: Ways of Choosing Probiotics