Another ME/CFS person has gone to Firmicutes!

Report Back

As an update, I’m nearly 5 weeks in and am beginning to feel better.  My energy levels are perhaps the best they’ve been in the last 5 years.  I’ve still got a very long way to go but the results thus far are promising!

I’m taking 5-7 foods/ supplements, 2-3X a day.  And every 2 weeks I’m rotating all of it to prevent antibiotic resistance.  In another month I plan to retest myself and make the necessary adjustments to my protocol.  

This person sent a request just after this post went out: My gut has gone to Firmicutes!

Reader’s Backstory

I am a 39 year old male from the US whose symptoms appeared at or around the time of puberty.  My case is not particularly severe – in fact it took me until the age of 23 to acknowledge to myself that I had a problem. While I fit the diagnostic criteria for ME/CFS, I specifically suffer from brain fog, low mental and physical energy, food sensitivities, 3 trips to the bathroom each morning, mild joint pain, and unrefreshing sleep. My symptoms have gradually worsened as I’ve aged. Certain vitamins, herbs, and foods have helped me to feel better but these solutions do not last more than a few days max. Nobody else in my family shares my symptoms, and I’m told I didn’t take antibiotics as a child.  My BMI is 22.

Proforma Review

Well you can see the process in this My gut has gone to Firmicutes! post, I thought that I should do a step by step walk thru of the process that I use.

After logging in, I go to [My Profile] and then on the [Overview] panel, click Health Analysis.

Under Potential Medical Conditions Detected, there were no red flags (see 📹 Explaining these measurements).

Similarly, [Bacteria deemed Unhealthy] had no red flags but does have a few bacteria that are not healthy predictors (Eggerthella lenta, Blautia producta, [Clostridium] symbiosum) and Collinsella (90%ile) which is viewed as proinflammatory – not unexpected with ME/CFS. Dr. Jason Hawrelak Recommendations came in at 98.8 percentile, so generally healthy. Blautia is of interest, it is at 36% of the microbiome versus Dr. Harelak preferred 5-10% and one of the highest levels in over 3,000 samples. This seems to be a possible smoking gun. The person is at the 70%iles using PubMed studies for ME/CFS without IBS.

Using the Krona Chart panel we see that the dominant species is Blautia obeum (which lacks any clear condition associations).

The next step is to look under [Visualizations] – Microbiome Tree, to visually scan for unusual disturbances. What I usually look for on the first pass are HIGH Percentiles with a high % of the microbiome. 💥BOOM we had some major ones. The 100%ile means that the value was higher than any of the 3000+ samples

Taxa / BacteriaPercentilePercentage
Firmicutes phylum96%ile97.7%
Collinsella aerofaciens91%ile1.3%
Blautia obeum100%ile21.3%
Dorea longicatena100%ile6.5%
Agathobaculum desmolans99%ile3.1%

At this point, we have a ton of items that are overgrowth. This is a very atypical sample with a bunch of unusually high shifts. So we will move on to getting suggestions.

Bacteroidetes is 0.43% of the microbiome so we are talking a Firmicutes/Bacteroidetes ratio of 228:1. The normal ration is around 1.5 (The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age, 2009), There is also considerable variation across the world.

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? [2020]

If there was not so many extreme high values, then our suggestion process usually work with both high and low values.

Getting Suggestions

My usual process is doing three methods and looking at the consensus report. The methods are:

Because of the extreme values, I am also doing Percentile in top or bottom 5% [28 taxa picked], For all four of these, I am restricting the suggestions to High Items. We need to reduce bacteria to make room!

The list was interesting — and also typical for ME/CFS patients:

The high-protein/meat diet would also provide B-vitamins listed above. Hesperidin’s best natural source is lemons — which also will provide Vitamin C. The best source for Arbutin is likely Lingonberry (available at IKEA) – for other see Arbutin – Microbiome Prescription Food And Nutrients. For the top items, use Nutrients with Number of Foods – Microbiome Prescription Food And Nutrients to see what foods contains it if you wish natural sources (or as supplements is not available).

There is one interesting diet to consider: Eating traditional Indian (based on chart above) – i.e. meatless high spice diet consisting of a lot of Dal and other foods from Taste of India or Kitchens Of India. Alternatively, spend 6 months at a traditional Ashram in India. This diet appears to result in the lowest Firmicutes/Bacteroidetes ratio.


While there were a few suggestions, the computed impact were relatively low compare to those with negative impact. I would skip probiotics.

Questions from Reader

Q: Does the Consensus View only show me what to increase, or does it also show me what to avoid? 
A: Yes, Just click on the column titles to reverse the order. If you hold the shift key, you can do sorting by multiple columns.

Q: This may seem like a silly comment, but it’s difficult for me to envision a vitamin (such as B1) or a supplement (such as melatonin) significantly influencing the microbiome. I picture large foods filled with bacteria like sauerkraut, or sugary foods like cookies, as the items that would have the biggest impact.  I clearly have a lot to learn.

A: Bacteria feed on chemicals, including vitamins. If you click on the modifier name, i.e. thiamine hydrochloride (vitamin B1), AFTER setting display level to Intermediate, you will see a column called citations:

Clicking on Source Study will show where the data is coming from, with links to the studies.
Some studies are on animals — but the bacteria is expected to respond in the same manner.

Remember: The site works off of actual peer-review studies only. Evidence, not speculation or wishful thinking.

Q: When I adjust the recommendations to include prescription items, I get a whole bunch of prescriptions that show up.  I’ll try to convince my doctor to prescribe!
A: It is not worth the effort — because this is an off-label usage and there will be resistance. Especially since half of the top items in the list are not prescription and similar predicted impact. Hesperidin is in Lemons and Buchu, no prescription needed. Try the other items first, if the next test shows improvement (expected) and a prescription item jumps out far above the others — then it will be a good time to ask.

Q: Random question:  The Probable Symptoms link under My Profile seems to be broken at the moment.  This isn’t the same as the Potential Medical Conditions Detected under the Health Indicators, right?  
A: Correct, the probable symptoms is done by pattern matching. Your numbers are so different that the A.I. was unable to make a reasonable infererence.

Q: I’d think the microbiome would be a really accurate way to predict obesity, but under Potential Medical Conditions I was surprised to see i’m in the 100th percentile for Obesity.  I weighed 120 pounds throughout high school and even now can’t break 150 lbs.  I plan on getting updated samples every couple months, so i’ll be interested to see if my next sample shows something different here.
A. Once we get things changing, we can use the National Library of Medicine Citations for Obesity to see how we want to target further shifts. We know what bacteria is associated with it, we just want to push the same bacteria in the opposite direct from that which was reported.

Course of Action

The first item of concern is simple: make sure that the dosages are adequate to effect changes. Taking a once-a-day supplements that has all of the vitamins listed above is unlikely to have any significant effect. Use the Dosages for Supplements to find the dosages. This can also be found by clicking on the Simplified Suggestions

Quick summary of dosages

After 4-8 weeks (depending on finances), repeat the microbiome test (using the same lab) and see what has changed. Recovery is like steering a sailing ship: it is a continuous set of course correction. Sometimes just a few to get to a safe harbor; other times, you may feel like you are circumnavigating the world.

Literature on ME/CFS and Firmicutes: I review studies on ME/CFS, Chronic Q-Fever, Lyme etc, and I do not find this pattern being cited. It is a very big 💥 BOOM pattern

Postscript – 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 appears to 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. All suggestions should be reviewed by your medical professional before starting.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information above should always be considered/discussed with your medical professional if possible.

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