Another ME/CFS after 19 years

This is actually a referral from a person from a previous blog, Another ME/CFS person has gone to Firmicutes!. He shared his experience (see that post) “ 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!” and a friend decided to try

Back Story

I became symptomatic around 19, progressively got worse so that by the age of 23 I had fully crashed with classic CFS symptoms. Severe symptoms persisted for 5 years during which time I was unable to work due to unrelenting fatigue. Slowly got about 50% better through an extremely low stress lifestyle and dietary/food changes. I’ve tested positive for a few Lyme co infections, chronically low cortisol and pretty much anything else the chronic illness community tests for, I’ve tested and treated. I’m now 38 and my recovery seems to hang at about 40% of optimal capacity. I wake up unrefreshed and have lagging energy all day long. I have to live an extremely low stress life, if I don’t, my sympathetic system kick into high gear. I seem to have issues with histamines (though I can ingest them, I just get flushed, puffy and hot at times), and my fatigue gets profoundly worse around my cycle. I don’t have any significant digestive issues that I’m aware of.


The first thing that I should mention is that I recall a study finding that the duration of ME/CFS does not impact the probability of remission. So 19 years with ME/CFS is not a factor.

Dr. Jason Hawrelak Recommendations came in at 99.9%ile, so no pro-forma general issues. That is not unusual, most labs on ME/CFS patients report normal. Looking at the Potential Medical Conditions Detected list, nothing of concern.

Looking at specific bacteria, a few bacteria stand out:

Looking at bacteria distributions we see a good pattern except with the rare bacteria which appear under represented. An ideal microbiome would have the same count in this range. This suggests a well established microbiome, perhaps with a touch of “inbreeding”.

Diving into the species of Lactobacillus interests me. We find just one species dominates,  Lactobacillus rogosae. A 2018 review,”Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective“, states “All in all, no consistent marker for any pathology or a healthy state is simply defined by a specific proportion of Lactobacillus“. This strain being classified as a Lactobacillus has been challenged [1974] with the suggestion that they may belong to Propionibacterium, a family associated with Acne. We are back to the fuzziness of 16s lab software as well as challenge of RNA/DNA being exchanged between different bacteria.

We have irony here, because the friend was high in Firmicutes and we have 77% of the microbiome in this sample also being Firmicutes with heavy domination of several ones as shown in the Krona chart below

I am inclined to do the customary ones PLUS one just trying to reduce Lactobacillus to build the consensus.

Take Suggestions

The top items had one little surprise – Cadium! There is a source for this that is also known to be good for ME/CFS – dark chocolate! See Dark chocolate is high in cadmium and lead. Prior studies on ME/CFS found that dark chocolate/ cacao improves ME/CFS symptoms.

The full consensus and simple consensus (with some dosages) are below

Items to Reduce or Avoid

The avoid list containing many popular items claimed to help the microbiome (which it does in some cases). Some are obvious with high lactobacillus — i.e. avoid lactobacillus probiotics. lactulose is a key food for lactobacillus.

Vitamin A is omitted because one form helps and the other form hurts.


Only one probiotic had all 4 saying take: bacillus coagulans (probiotics). KEGG suggestions had #1 being Escherichia coli (Mutaflor or Symbioflor2) which was also on the take list with a variety of Bacillus probiotic on the list ( Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus subtilis, Bacillus licheniformis, Bacillus subtilis subsp. natto) with all of the same ones on the take list (but not recommended by all 4 sets of suggestions).

In short, avoid Lactobacillus and Bifidobacterium probiotics. We want to greatly reduce the Lactobacillus from the 94%ile – it is very likely that d-lactic acid from lactobacillus is responsible for many symptoms. Bifidobacterium INCREASES Lactobacillus which is the opposite of what we want to do. We want to get lactobacillus down as a first priority, later we look at increasing bifidobacterium once it is down far enough.

Questions and Answers

  • Q: Is there any reason you chose to focus on the lowering Lactobacillus, as opposed to the Bifidobacterium being low?  Is it because the “bacteria deemed unhealthy” table is a more important focus to you than the jason hawrelak recommendations?
    • A: The medical condition of ME/CFS and Lactobacillus has a long connection to each other. Both “bacteria deemed unhealthy” and Hawrelak are general criteria. Being at the top of Hawrelak’s rating (99+% of people are worst), would imply no issues — you have issues.
  • Q:  Why not focus on the Mogibacterium that’s in the 100 percentile?
    • A: We could — it was a factor included in the bacteria picked to modify. The list of items is here.
      Some people go after a single bacteria with a “all other factors be ignored”. For example, Fennel reduces Mogibacterium BUT it also increases Lactobacillus!! The AI algorithm attempts to balance the dozens or substances impact on dozens (or thousands) of bacteria. You are welcome to do it by hand for the 123 bacteria flagged and the several thousand modifiers.
  • Q: the last question is about interpreting Krona charts. The Krona chart doesn’t seem to provide standard ranges
    • A: This form of visual display will get extremely busy and confusing with ranges. If you attempt to draw a high range line it will sit over a different bacteria.
  • Q:  So is there any easy way to know when a bacteria is high or low by looking at that chart?
    • A: Use the hierarchy chart. You can pick one set of ranges at the top of the page. Items that are high (by the selected ranges) are in blue, and low in pink.
      You can also hand pick bacteria to alter.
On My Profile Tab
Checking the checkboxes, then clicking Create… allows a hand picked set of targets.