Most of the content was originally posted on https://cfsremission.com/ with the pages on the left being a restructuring of selected posts from over a thousand posts on that site.
Recommended Site For Testing
If you have ME/CFS or other financially disastrous condition, there is always a nasty cost factor for testing. My usual recommendation is for the cheapest, high quality provider that provides information for upload to my analysis site. Some sites provide a mountain more of information — but the benefit from that extra information is almost nothing (and it adds $$$$ and complexity).
uBiome.com is shutting down. This had been my personal usual site because using a variety of techniques, the cost was $25/sample. Don’t order from there.
BiomeSight.com (EU based) is an excellent buy using our discount code [MICRO]. They have also automated data transfer to our analysis site.
Thryve is what I am starting to use. Their reports may be processed here for independent suggestions. I would also recommend
This is a part of an ongoing series of posts that are intended for microbiome testing labs, or those interested in starting one. I am downstream from all of the microbiome labs and will gladly work with any of them — my main concern is making people better — not the financial bottom line.
This post looks at issues involved with selecting studies to use for giving suggestions to consumers of microbiome result. These are questions that I have looked at and have made my own choices (a.k.a. technically trade secrets).
Method of microbiome detection used
There are three main types, listed below. Do you restrict to only one? Do you give a weight to different methods, for example the values suggested after each below?
Different studies report things differently. For example some may report the % change of a bacteria average, others may provide the actual distribution, others may just report that the control or the cohort average was higher with (P < 0.5). It is like trying to buy gas – one person is offering it by the gallon in US$, another in litres in Euro, a third “sufficient fuel to drive 200 miles in a 1958 Land Rover” for 3 oz of silver.
I have my own magic in combining a multitude of studies and resolving the many many issues cited above. I encourage labs to do their own resolutions and then let people compare results (if they are in agreement, everyone should be happy). The real test is whether the suggestions work. So far, for my own experience and for a reasonable number of people that have provided feedback – they have. The suggestions may not be perfect, but my goal is to give suggestions that are more likely to help.
My short form would be to use Symbioflor-1 (to address sinus issues) and make sure that you rotate through different active ingredients in mouthwashes (and I would include my dad’s favorite: rinse your mouth with Scotch Whisky [or similar] – I will leave it to you if you spit out or not 🙂 ). I would suggest reading some of the above earlier posts.
A while back I built a bacteria to bacteria interaction model with rich results. With the addition of the anti-modifier page for professionals, my mind went over to finding probiotic interactions. This is based on the 2000+ microbiome samples uploaded. I have the basic results below
The more positive, the Impact number the more it helps the other species. A negative number indicates that it will reduce the other. Thus, you should not take Clostridium butyricum and Akkermansia muciniphila together. If you are trying to increase Bifidobacterium bifidum then take Arthrobacter (in Prescript-Assist®/SBO Probiotic) and/or Lactobacillus paracasei.
This is a personal observation post and not my traditional aggregation of studies. Your experience may differ.
This is available exclusively as Pendulum Akkermansia. We signed up for the subscription plan when it was first announced, and they have kept shipping at their low introductory price every month. Within I week of getting the first shipment, I read a few posts that “it did not persist”. Excuse me, the typical turnaround time for a microbiome test is 3-4 weeks. I suspect that someone is gas-lighting. Or, they may have been taking a hostile probiotic at the same time.
We subscribed to only one bottle and we decided that the wife would take it for the first two months (we rotate probiotics). The results were her Akkermansia muciniphila went from 4,530 to 64,920 (91%ile) — so, it appears to have persisted (or helped the native ones to prosper by creating a friendlier environment). I should point out that that the fact that she has some to start with may be a significant factor for this awesome increase (that is, the environment was not totally hostile).
She noticed some significant changes, to her the most significant one was a major improvement in sleep.
Kampo (Japanese Name)
This is also known as fang feng tong sheng san (Chinese) or Bofu-tsusho-san. A professional user of Microbiome Prescription reported a major increase of Akkermansia with his patients using this and forwarded two studies that illustrated this.
Bofutsushosan improves gut barrier function with a bloom of Akkermansia muciniphila and improves glucose metabolism in mice with diet-induced obesity. 
Increase of Akkermansia muciniphila by a Diet Containing Japanese Traditional Medicine Bofutsushosan in a Mouse Model of Non-Alcoholic Fatty Liver Disease 
As mentioned above, we rotate probiotics as a standard practice in our household. I am starting both the Akkermansia and Kampo and plan to do a new microbiome report in a month (so 2 months until this post gets updated). I expect a significant jump in my Akkermansia. At last test, it was 12,160 or 1.2% (via Biomesight), at the lower end of Dr. Jason Hawrelak Recommended ranges.
A user of my site that is active consulting on autism microbiome manipulation obtained permissions for me to do an analysis of one of his patients going through FMT. All of the microbiome testing was done via Biomesight (including the donor). This is specific type of data that I have been pleading to see if we can make predictive models of what could occur with FMT.
I did analysis at the Species, Genus, Family, Order and Class level trying many many approaches. This summarize my key findings.
The second sample was done one month after the FMT. Patient was very good for a couple of days, then “the war started”. New more severe autism symptoms appeared.
Do NOT expect it to reduce overgrowths!
Looking at the lowest numbers of the recipient prior and the donor, we found that the post-FMT numbers had a clear pattern.
At the Class level, 97% was higher than the lowest of the two, 58% was higher than the highest
At the Order level, 96% was higher than the lowest of the two, 56% was higher than the highest
At the Family level, 95% was higher than the lowest of the two, 61% was higher than the highest
At the Genus level, 91% was higher than the lowest of the two, 51% was higher than the highest
At the Species level, 94% was higher than the lowest of the two, 47% was higher than the highest
This was shocking — 50% of the bacteria will be higher than either the donor’s or recipient’s levels. Many people will assume that the levels will magically average the two levels. The reality seen here is that only 50% of the time will the new level be between these two levels and 50%of the time it will be higher than either. This is unlikely to be a preferred outcome.
There were several items where both the recipient and the donor had bacteria, they were gone in the post-FMT sample! This was not expected, of special interest is that Lactobacillus was wiped out.
Family: Clostridiales Family XVI. Incertae Sedis
Species: Streptococcus oralis
Species: Veillonella parvula
Species: Streptococcus pseudopneumoniae
Species: Carboxydocella ferrireducens
Species: Sutterella wadsworthensis
Species: Catonella morbi
Many New Kids showed up!
These are bacteria not seen in the recipient prior nor the donor sample
Class Level: Acidobacteria, Calditrichae,Chitinophagia,Flavobacteriia,Ktedonobacteria,
Bottom line is that the microbiome has become much more diverse
Recent FMT aspects
FMT destabilizes the microbiome, there are “strain riots” in the guts. We can see this with all of the “New Kids” showing up because the existing occupants are busy dealing with each other. This can be seen by the post microbiome having a lot more taxonomical items (550 vs 374 before – a 47% increase), The microbiome, over time, will downsize and stabilize with a new normal. During this period, you want to entrench your desired items by feeding it the right things and avoiding the wrong thing.
Personally, I would suggest a new sample every 6 weeks to monitor the stabilization.
Is FMT Worth the Risk?
FMT is effectively an organ transplant. Like organ transplants, there are significant risks of rejection and no way to undo it once it happens. From correspondence with many people who have tried it for ME/CFS, my feelings are that it is not a magic bullet. It is closer to playing Russian roulette, but with 5 of the 6 bullet chambers having bullets in the chambers.
I just spent 90 minutes zooming to the consultant involved with this autistic child. We both agreed that FMT for autistic children is not a wise course. The consultant is scratching their head on what to help this child recover from this situation.
If you are dehydrated you will typically see a change of stools. Seeing hard pebbles and dry stools is a logical consequence of the body rationing water. Recently, we got a new smart scale ($30 on Amazon) that comes with a smart phone app and does multiple measures, including hydration. I have been running below the desired range, so I am busy hydrating with Gerolsteiner Mineral Water (from Traders Joe) etc.
Conceptually, the availability of water should impact the microbiome. So tonight I started to search out studies to confirm my speculation.
There were five out of the 108 types of intestinal bacterium at the genus level that showed significant differences within and between groups due to water supplementation, and 17 out of 564 species identified by the homology search of OTU representative sequences in the DDBJ 16S database showed the same behavior… Of these, a slight correlation was seen in the intervention group between changes in blood pressure and changes in the Psudoflavonifractor capillosus bacterial count (R = 0.42) Kineothrix sp. (R = 0.36), Feacalibacterium prausnitzii (R = 0.38), and Ruminococcaceae (R = 0.34) showed weak correlations between changes in body temperature and changes in bacterial count
Some related studies that implies impact on the microbiome but failed to do microbiome analysis with the study
Hydration is an often overlooked aspect of improving the microbiome. It has impacts on blood pressure, body temperature, mood and cognitive ability. While we have few studies on it’s microbiome impact, we can likely assume safely that improved hydration will improve the microbiome. It should not be left to a “I drink enough water, I do not feel dehydrated”, but with actual measurements. Improving it is actually a slow process — my goal is to shift from my current level below, to at least 55%.
I just pushed an update that included features requested by a reader. The main items are:
Ability to enter symptoms when you do a test (“Pending Sample”)
Ability to copy symptoms from one sample to another
Ability to delete all symptoms for a sample with one click
Generation of a short list of possible symptoms from your bacteria
All of these options are shown for each sample via the dropdown:
This has had one minor change, a new choice appears, “Pending Sample”. It allows you to enter symptoms when you do the sample (instead of trying to remember them 4 weeks later). Also two buttons are added to make status easier. Remember to use the Search box to filter
Quick Symptoms Additions
This takes your forecast symptoms with sufficient significance, removes any symptoms already entered, then show symptoms to consider.
If you check a few and click [Add]
These items will disappear from this list.
This allows you to copy symptoms between samples (for example, the same sample may be processed by multiple labs). Just select the sample you wish to copy from and click [Copy]
If you realized that you made a mistake, you do not have to uncheck item by item. you can single click all of the items.
The algorithm for predicting symptoms has been revised (hopefully improved). There may be a further change, have some complex modelling to add. Also the ability to change from sample to sample has been added
A reader mentioned getting scheduled for one. Coincidentally, a week ago, I had a natural clearing out of the bowels (source unknown). I suspect that both scenario may produce the same opportunity to do some restructuring.
The first item to be aware of, gravity, bacteria further up the flow will repopulate (for better or worst). For myself, once it became clear that the bowels were being deeply emptied, I loaded up on herbs that impact many of the bad bacteria for a day (several capsules of each, several times a day).
The rationale was to thin out the bacteria that are up-channel.
I then started to repopulate, the first item, an E.Coli probiotic, symbioflor 2 e.coli probiotics, stopped the natural clearing within 2 hrs (not surprising given what made Mutaflor, the alternative E.Coli probiotic, famous back in 1918). I then proceeded to load up on only probiotics that are known to persist (see thus post, Studies on Probiotic Persistence). For myself, I noticed some improvements (but really I do not have much wrong to improve).
These are often asked for with people often running off old research. Often the research is based on seeing an increase of one of these when a specific bacteria increase… hence. this bacteria must be producing it! This was the best that we could do from old, last millennium technology and lab tests. We have enter a new world that is summarized on Kyoto Encyclopedia of Genes and Genomes. Instead of measuring substances (never with a pure culture of a specific bacteria), we can look at the gene in each bacteria and what they produce. In other words, we can get more accurate information that is truly bacteria specific.
These pages list the enzymes that produces it, for example 18.104.22.168.1.1.8 2.3.1.- 22.214.171.124 126.96.36.199. We can then look to see if the enzyme consumes (substrate) or produces it.
Then it is just a matter of looking up which bacteria has these enzymes!
Unfortunately, no lab detects all of these strains and often report “unknown Species in Some Genus“. I have seen that being as high as 45% not being identified in some samples. A work around is to look at the genus numbers — which are usually pretty complete for most labs. This is a two sided coin, because some members of a genus may be a producer and some may not be. We do not know the ratio for a genus between these two. This approach will identify potential candidates, but not definite candidates… more fuzzy logic.
All of this information is freely available on Kyoto Encyclopedia of Genes and Genomes, it just take diligence to extract and assemble it. If you see items on a labs reporting that is NOT on these lists, challenge the lab to produce evidence. I suspect most labs will produce studies with circumstantial evidence only, “because crime goes up when this ethnic group moves in — it must be that ethnic group” — ignoring that a different ethnic group may be behind it. An example of a drug problem in one city at one time. Most of the drug dealers were African-Americans, but the importers were Vietnamese. With KEGG, we are looking for the fingerprints on the gun or drug packages intercepted,
Back story-long history of gut issues/IBS.Terrible time post partum 22 years ago with sleep issues and mental health. I’ve been down the hell hole of modern medicine on all kinds of meds for years. Finally diagnosed with SIBO in 2019 and then no luck with treatment. More recently had bad reaction to high doses of Vitamin D-gut issues worse- total body pain, inflammation, food intolerances, terrible insomnia. I will add-horrific constipation not resolved unless I take herbal formulas [Microbe Formulas Bowel Mover and Dr. Christophers Lower Bowel Formula. I try to rotate. No specific order. I do think the garlic in the Microbe formulas does help.]
Our third pass, is using US National Library of Medicine studies that identify certain bacteria associated with IBS. We will use IBS but widen the criteria used to extreme 6%. Some of the bacteria are cited above, and some are new.
As always, this is produced from a computer AI model and not clinical experience. Before any change is done, it should be discussed with your medical professional. Some items, like 1000 mg of niacin per day may require testing (see this summary on niacin from the National Institute of Health)
Mold and Lyme Markers
Lyme is always a fuzzy area –if the person had ever had EBV and their microbiome is off, then false positives are well reported in the literature.
The suggestions are shown below, there are a few matches with the above
I did a side by side comparison and found that there was a lot of disagreement between the sets of suggestions. That is not unexpected, because the bacteria selected determines the suggestions.
My gut feeling is that the IBS/SIBO is the preferred one — the citizen science did not have a single item auto checked, I had to go with the secondary items 💡 to get suggestions. This implies a weak match. Second, the IBS/SIBO included the gold standard bacteria identified from formal clinical studies. In short, likely better quality of information.
For those that are interested in how I created the above comparison, see this video — just change the URL to Source and enter a name in the column before pasting between sheets.