FMTs have been tried for Chronic Fatigue Syndrome/ME with mixed success. The why of failures has been an ongoing interest of mine. We may now have a significant factor that has been ignored in these attempts.
Fecal microbiota transplantation (FMT) as a special organ transplant therapy, which can rebuild the intestinal flora, has raised the clinical concerns. It has been used in the refractory Clostridium difficile, inflammatory bowel disease, irritable bowel syndrome, chronic fatigue syndrome, and some non-intestinal diseases related to the metabolic disorders. But this method of treatment has not become a normal treatment, and many clinicians and patients can not accept it.
In addition to this, there was a podcast reporting success with FMT was associated with higher Phage Diversity in the donor. Phages are the police of the microbiome.
In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.
This implies that for a greater chance of success and less risk, than DYI fecal transfer, that a lab that tests for possible infections AND for phage state may yield the best results.
David Morrison requested this feature. The FastQ file is produced by the physical lab machine. This file is then pushed thru software to produce a list of taxonomies. Different 16s retail providers use different software and as a result – different reports. For back ground see this “Taxonomy Nightmare before Christmas” post.
Most of the Post-Covid19 Syndrome symptoms has a strong match to the symptoms seen with Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). This condition has no conventional medical treatment known. Treatments attempt to mitigate symptoms.
There is evidence that some people develop a long-term fatigue syndrome from coronavirus infections, Dr. Anthony Fauci said Thursday.
“There may well be a post-viral syndrome associated with Covid-19,” Fauci told a news conference organized by the International AIDS Society. The group is holding a Covid-19 conference as an add-on to its every-other-year AIDS meeting.
Fauci said the symptoms resemble those seen in patients with myalgic encephalomyelitis, or ME, once known as chronic fatigue syndrome.
“If you look anecdotally, there is no question that there are a considerable number of individuals who have a post-viral syndrome that in many respects incapacitates them for weeks and weeks following so-called recovery,” Fauci said.CNN
I am very familiar with ME/CFS as anyone who knows my story can attest. And I believe that while the model of why these symptoms are there is simple, the treatment is complex, not cookbook and must be individualized for each person.
COVID19 sends out chemical signals to the body to produce chemicals (metabolites) that its need OR which create a friendlier environment for it. The signals alters the microbiome (gut bacteria) to be a factory for its needs (Viralforming the gut). Once COVID is eliminated, the alterations should return to the prior state overtime— unfortunately a percentage that take a long time or never return. The best documented example is the Bergen’s Giardia Infection.
The microbiome consists of many co-operations between bacteria. Often there are over 2000 bacteria involved in various dialogs. Identifying the bacteria that are at abnormal (too high or low) is the start. The next step is modifying the bacteria by drugs, diet, supplements. At this point, we need to point out that there may be 100 or more abnormal bacteria that needs to be adjusted. Naive adjustments may make more bacteria abnormal.
My Proposed Process
This is the process that I have done with ME/CFS and it is likely that it may also work for many people with post-covid syndrome:
Look at the suggestions for correcting and make appropriate changes
Two+ weeks after making changes, repeat the 16s analysis and make the next set of changes.
This is an iterative process. Often the suggestions will cause one symptom to lessen or disappear while leaving others untouched. This is to be expected.
For more information, see
A series of videos on manipulating the microbiome using 16s results for guidance
Rose Walbrugh and I are proud to announce one click sending of data from BiomeSight.com based in the UK to MicrobiomePrescription.com. After you get your BiomeSight data processed, you can send the data across without needing to download and upload. You will be sent an email with an automatic login link (no more making up and remembering passwords!).
How to Do It and get Expert System Suggestion
Log in to Biomesight then on left Menu:
Click Third Part App
Click Microbiome Prescription
Find the sample that you wish to send:
If you need to RESEND sample, see the bottom — there is an alternative way. A rotating circle will appear
When Complete, you will see this shown
Check your email. You should get one like below (it is sent to the email used by biomesight)
Click Link. You should see a page like below
Updated to 2025 Changes
This will land you on the SIMPLE UI ANALYSIS page. This is an extract of the older tools that are still accessible if you click [Old UI]
The recommended approach is to click on [Beginner-Symptoms] which will update the page like shown below.
On the left is a scrolling list of predicted symptoms based on your sample using some 4000 other samples uploaded. Check the items that apply to you.
Why Checking Helps?
Depending on your test, you may have between 300 and 3000 bacteria. We want to identify the bacteria that are statistically associated to your symptoms. That is the bacteria causing the symptoms and not bacteria that may be out of range and likely just “noise”. The default [Novice] uses all bacteria out of range and typically give less targeted suggestion. You want to correct the bacteria that matters.
Check the types of suggestions you want made. If you are taking any prescription drugs, you likely want to include those. Some drugs will cause shifts in bacteria and the computation will indicate if they help or hurt you.
Then click Get Suggestions. After a few minutes of calculation (over 8 million pieces of information is evaluated), a page like this will appear with with short lists of key items to take or avoid.
Click on my Profile and then click “Just give me suggestion”
You will get a list of symptoms that are being used and the bacteria identified as being significant. Suggestions will only use these.
Using Novice will list all out of range, 46 target bacteria instead of 3.
Compact Suggestions
The number of items shown depends on the number that you requested. Weight is NOT how well things work (we do not have data to compare items), but the confidence it will cause a desired change (based on the number of studies showing the desired changes).
Digging Deeper
No one really knows how to correct dysbiosis. There is too much data (huge volumes) and sparse data (many things we have no data on). The safest approach is to do what every report says to take and avoid as much as possible on items to avoid.
At the top of this report are three links:
Further down the page is an option to ask some of the free AI sites what they would suggest. They is also a link to just get probiotics.
Consensus Suggestions
The above computations uses several different models of the microbiome. You can see what they agree about or disagree about on this page.
If you click the “books” on the right, you will see the precise logic used with links to clinical studies.
Food Menu Planner
This takes you to a sister site. All of the nutrients are transferred there and it uses a massive database of nutrients in different foods from around the world.
Clicking on Nutrients will show you the nutrients identified. Studies often use extracts and not foods. Most people have no idea of what foods contains what. Look at the list below!
Clicking on Takeswill translate these into foods — balancing the to take and to avoid nutrients
Clicking on Avoidswill translate these into foods — balancing the to take and to avoid nutrients. You will not find any studies on the microbiome impact of KIT-KAT….
Using AI Models
Just clicking the link sends the question to the AI (the question is also shown, so you can copy and paste the text into other AIs). Examples below.
R2 Probiotics
This is a new novel approach. Just click will send the data to another sister site that will attempt to compute the best probiotics — not based on studies, but based on what was seen with a healthy population of 1000 individuals.
This resource is atypical because it will identify probiotics that may be counter indicated on other suggestions. Remember the key concept: Take what everyone agrees upon! It is the safest option in the face of uncertain limited data.
DISCOUNT CODE
As part of this celebration, a discount code “MICRO” is offered on BiomeSight services. This results in £60 off, which brings the price down to £89 per kit ($110). Local USA fulfillment is now setup. Expedited 2 day delivery at £4.95.
Resend Sample
From Biomesight Support:
To be clear, there’s 2 ways to send it – on the row itself, the button will not be available it was sent already. But you can also do it by selecting the rows and using an alternative button that will send it again regardless. The screenshot below shows both.
New Feature
After transferring the data you will get two emails. One to log into the site. The second is a PDF analysis with suggestions and literature supporting the suggestions.
Bottom Line
Microbiome Prescription is dedicated to working with labs to enrich user experience and knowledge. BiomeSight has stepped up to the plate for cooperation and win-win attitude.
I am currently working with BiomeSight.com to add Taxon numbers to their downloadable reports.
At first sight, this should be easy, the sample of their complete taxonomy looks like this:
The problem is that their software have forced items into an unnatural structure to make presentation easy. An item that is under Class — when you go to NCBI Taxonomy Browser may be listed as:
Sub-Class
Super-Class
Order
Sub Order
Family
The result is that many many items have to be resolve by manual inspection of NCBI to find the apparent match and individually assigned. Example below, notice the “Group II” item which required working from existing matches for a line to identify probable candidates.
Update [MicrobiomeSight] Set OID=2731342 Where [Order]='Group II'
Update [MicrobiomeSight] Set OID=1643688 Where [Order]='Leptospirae'
Other issues concern differences of spelling and renaming, i.e. Cerasicoccales vs Cerasicoccus that was found….
While NCBI shows
We have a possible old/atypical name being used which obtuficates reports. This is one of the key reasons that I am pushing for taxon numbers in all uploads because without them, we would have massive inconsistencies.
After getting all of the Genus and Above resolved, I hit an issue with the species.. namely the list shown below remain unresolved. A few I did a google for and found no hits. Many had incomplete names.
Example:
Bacillus polyfermenticus in NCBI is Bacillus velezensis variant polyfermenticus
Acholeplasma ales
Burkholderia eae
Candidatus Methylacidiphilum infernorum
Cryocola poae
Dechloromonas fungiphilus
Desulfovibrio aceae
Enterobacter aceae
Enterobacter rottae
Erwinia dispersa
Haererehalobacter salaria
Haloterrigena gari
Herpetosiphon agaradhaerens
Megasphaera geminatus
Mycobacterium indicus
Oscillospira eae
Tessaracoccus terricola
Pasteurella eae
Stenotrophomonas retroflexus
Stenotrophomonas griseosporeus
Trabulsiella farmeri
Vibrio bacterium
Bottom Line
All Phylum, Orders, Classes, Families and Genus had matching taxon assigned. At the Species level, 6445 were identified and 21 were not. This means 99.7% of species were given taxon numbers. I expect BiomeSight.com to offer uploadable formats soon, ideally with automatic transfer from their web site.
I just got out of the hospital for cellulitis where I was treated with IV antibiotics. My discharges notes said “take antibiotics to prevent diarrhea”. I asked which ones… blank faces. No one seem to have a concrete idea. So this is a review of the literature:
“Antibiotic-associated diarrhea (AAD) occurs in approximately 25% of patients receiving antibiotics.” [2008]
” analyzing 25 randomized controlled trials of probiotics for the prevention of AAD … more than half of the trials demonstrated efficacy of the probiotic. ” So a random probiotic may have just a 50% chance of being effective. [2008]
“We identified no evidence that a multistrain preparation of lactobacilli and bifidobacteria was effective in prevention of AAD or CDD. ” [2013]
A reader asked about this, which I have no covered yet. Increased allergies and mast cell issues often occur with microbiome dysfunction and chronic fatigue syndrome.
Pycnogenol® (Extract of French Maritime Pine Bark) for the Treatment of Chronic Disorders [2012] “Due to small sample size, limited numbers of trials per condition, variation in outcomes evaluated and outcome measures used, as well as the risk of bias in the included studies, no definitive conclusions regarding the efficacy or safety of Pycnogenol(®) are possible.” Note dates of later studies below….
Effect of Pycnogenol® on an Experimental Rat Model of Allergic Conjunctivitis[AC] 2018 “The animal model of AC was successfully developed by using aforementioned way. PYC is a safe herbal product and it has alleviated the findings of ovalbumin-induced AC-similar to dexamethasone-histologically in this experimental model.”
“PYC inhibited the number of total inflammatory cells and levels of interleukin (IL)-4, IL-5, IL-9, and IL-13 in bronchoalveolar lavage fluid of OVA-induced mice”
“The probiotic Symbioflor 1 is a historical concoction of 10 isolates of Enterococcus faecalis. Pulsed-field gel electrophoresis revealed two groups: one comprising eight identical clones (DSM16430, DSM16432, DSM16433, DSM16435 to DSM16439) and a further two isolates (DSM16431, DSM16434) with marginally different profile” [2016]
“A double-blind, placebo-controlled multicenter study in 157 patients with chronic recurrent sinusitis investigated the occurrence of acute relapses during treatment of patients with a bacterial immunostimulant (3 x 30 drops/day), comprised of cells and autolysate of human Enterococcus faecalis bacteria (Symbioflor 1, n = 78) in comparison to placebo (n = 79)…. the occurrence of relapses (50 incidents) was about half (56%) the number observed under placebo (90 incidents)” [2002]
“the time span until occurrence of the first relapse was clearly longer under verum[Symbioflor-1] (699 days) than under placebo (334 days) and after the end of the observation period 91% of patients under verum experienced only one relapse compared to 62% in the placebo group (p = 0.01). ” [2001]
From PubMed
“Compared with the controls, probiotic intervention significantly upregulated the level of IL-10 and TGF-β, downregulated levels of IFN-γ, and increased progesterone level that reversed the trend of being Th1 predominance state ” [2020]
“1. E. faecalis stimulates the liberation of interleukin 1 (IL-1 beta) and interleukin-6 (IL-6) in a dose-dependent manner; the E. faecalis induced liberation of IL-1 beta and IL-6 is inhibited by dexamethasone (Dm) but not by cyclosporin A (CsA).” ” 2. E. faecalis stimulates the liberation of gamma-interferon (IFN-gamma) in a dose-dependent manner, which is inhibited by both Dm and CsA.” “3. Phytohemagglutinin (PHA)-induced liberation of gamma-IFN and interleukin-2 (IL-2) is inhibited by E. faecalis in a dose-dependent manner. ” [1994]
“For instance, Escherichia coli Nissle 1917 was a poor inducer of iNOS gene expression compared to the other E. coli strains, while Enterococcus faecalis Symbioflor-1 was more potent in this respect compared to all the eleven Gram-positive strains tested. ” [2014]
Personal Experience
I have used this for sinus issues in the past and it has been effective in clearing them.
A reader forwarded this to me with the following comment..
My mother is a health 58 years old women a little bit over weight she started to have after 2 weeks of use: headaches and feeling very fatigued so I think she has die-off, The interesting thing that happen she has swollen lymph nodes under her arm pits for about 25 plus years, the lumps started to regress, I cannot find the microbiome condition associated with this and this strain of probiotic she started to use.
Entero Satys
This is available from France. Link here. International availability is unknown. “Hafnia alvei is a psychrotrophic bacterium, it originates in raw milk and continues to grow in cheeses such as Camembert. abundant levels of Hafnia alvei can be found in raw milk cheese ” [Wikipedia]
“In conclusion, the present study showed that a daily provision of the H. alvei HA4597™ strain in genetically obese and hyperphagic ob/ob mice with HFD-exacerbated obesity decreased body weight gain, improved body composition, decreased food intake, and ameliorated several metabolic parameters, including plasma glucose and total cholesterol levels. “
“Finally, the low abundance of ClpB gene expressing Enterobacterales species found in the microbiota of obese subjects in the present in silico analysis may indicate insufficient anorexigenic signaling from the gut microbiota to the host, further providing the rationale for supplementation of commensal bacteria expressing the ClpB protein with an α-MSH-like motif. “
There was no detail microbiome information cited in studies above. The mechanism of operation was increase production of a metabolite from this bacteria that alters the number of meals.
The daily dosage is 50 million CFU ** / 100 billion cells, i.e. 5 x 10^7. Some (made in France) Camembert are reported to exceed this level in 1 gram (especially the surface).
Recent Comments