Evidence of ME/CFS improving using Microbiome Data

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

0 – 91116691115
20 – 29193120241231
30 – 39183523451633
40 – 49162420371830
50 – 59213125452133
60 – 69182017301422
70 – 79162311281623
80 – 8951416241321
90 – 993141320514

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

Sample A
Sample B
Sample C — NOTHING!!!

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. 🙂


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:

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):

The new layout of the consensus page is shown below

Remember these are blindfolded suggestions, items like polysorbate 80 as a supplement is not recommended by any MD, it is in many supplements. [src]

My suggestion for 3 probiotics to rotate thru are:

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)

RankNameYour valuePercentile
class Flavobacteriia217
order Chromatiales219.4
order Flavobacteriales217
order Marinilabiliales2113.5
phylum Tenericutes429.5
species Bifidobacterium bohemicum2111.8
species Eubacterium ramulus872095.5
species Prevotella disiens94684.1

With the top suggestions for this small subset being:

  chicory (prebiotic)0.955
  inulin (prebiotic)0.955
  jerusalem artichoke (prebiotic)0.955  📏
  resveratrol (grape seed/polyphenols/red wine)0.955  📏
  glycyrrhizic acid (licorice)0.509  📏
All of the prebiotics listed are similar, any one would do.

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.


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