Overview of this Blog and the Microbiome

My ideas on this blog have evolved, as more and more information becomes available. This post is an attempt to bring readers up to date with my current thinking. I am striving to be transparent in my logic — showing the evidence I am working from, and my thought processes.

Notes to Treating Physicians     Quick Self Start on treating CFS

Analysis of Microbiome/stool with recommendations

Site: has moved to http://microbiomeprescription.azurewebsites.net

The data is available in an online collaborative python workbook for analysis. See this post.

Microbiome Definition of CFS/FM/IBS

A coarse condition that results from:

  • Low or no Lactobacillus, AND/OR
  • Low or no Bifidobacteria , AND/OR
  • Low or no E.Coli , AND/OR
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/suppress Lactobacillus, Bifidobacteria, E.Coli
    • Several are two or more times higher than normally seen
    • The number of bacteria genus goes very high (using uBiome results), but most of them are low amounts.
      (“Death by a thousand microbiome cuts” and not “Death by a single bacteria blow”)
  • The appearance of rarely seen bacteria genus in uBiome Samples.

A finer definition would be a condition with a significant number of abnormalities in the ‘Autoimmune profiles see this page for the current criteria (i.e. over 25%).

The specific genus and their interactions determine the symptoms seen — likely due to the over- or under-production of metabolites (chemicals). Other autoimmune conditions may share these core shifts. The specific high and low bacteria determine the symptoms if the person was the DNA/SNP associated with the symptoms.

Replace the metabolites produced by the missing bacteria

Replacing the metabolites should result in the reduction of symptoms associated with a deficiency of these metabolites.

See this post for the study references. These items should/could be done continuously.

Other Supplements Reported to Help

Bootstrapping Bifidobacterium and Lactobacillus

The items below were found in studies to increase bifidobacterium and lactobacillus:

Unless the bifidobacterium and lactobacillus (B&L) are human sourcedthere is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established. In fact, there are grounds to believe that most commercial probiotics actually reduce your  native B&L. You want to encourage your native B&L. See this post for citations.

Bootstrapping E.Coli

The E.Coli probiotics below are human sourced and known to take up residency in the human gut.

  • Core: D-Ribose a preferred food that it uses
  • Mutaflor probiotics — E.Coli Nissle 1917
  • Symbioflor 2 — multiple strains

Dealing with the other microbiome shifts

The other microbiome shifts appear to be in different clusters of microbiome shifts. This 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in its title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”.

The best way at present to proceed is to order an analysis from uBiome. (Disclosure: I have no financial interest in this company.) When your get your results back, log in, click on the “Compare” tab, then go to “Genus,” and click on “ratio” twice, so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk provides a nice summary of what we know about these. See, for example, Alistipes:

At this point, we run into a logistical challenge.  You want to avoid items that are “Enhanced By” (which is in common across all of the high items) and take the items that are “Inhibited By” (which are not on any of the “Enhanced By” lists).  You may also wish to reduce foods that are high in items listed in “Nutrients/Substrates.”  It becomes a jig-saw puzzle! I have done this exercise for many readers’ uBiome results:

I have discovered that DataPunk is not absolutely current, and have started creating posts based on its data, and then added studies from 2016 and 2017 to the page. Past pages are below, for current list MicrobiomePrescription site.


Src: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/

General Suggestions (no uBiome results)

Some of these items are contraindicated with a few uBiomes that I have reviewed. This likely is why person B reports no results while person A reports improvement. Example: Magnesium is usually very helpful — but there are a few cases where it encourages overgrowth of undesired  bacteria.


Most probiotics do not take up residency. They are “here today, gone tomorrow”. Their primary role in my model is producing natural antibiotics against other bacteria. For example:

Probiotics should be rotated: 2 weeks on a specific one, then several weeks off. As a general rule, you want about  6-12 B CFU taken three times a day (or 2-3 times the recommended dosage) — but work up slowly because you may get be a major herx! In general, do not take Lactobacillus with Bifidobacteria or with E.Coli etc. Keep to one family per cycle. You do not want them to kill off one another!

Why 3x per day? Because almost none of them are detected after 12-24 hrs. So to keep them — and the production of natural antibiotics — going, you need to keep taking them during the day. See this post for citations.

The following probiotics commonly seem to help people with CFS/Lyme/Fibro:

Some probiotics, however, may make your symptoms worse! And, unfortunately, most commercial probiotics contains some of these. At the moment Bifidobacterium animalis, Saccharomyces boulardii and Lactobacillus acidophilus are on my best to totally avoid list.

  • “. The findings show that the six species of Bifidobacterium differed in their ability to relieve constipation. B. longum, B. infantis and B. bifidum were the most effective in relieving constipation, B. adolescentis and B. breve were partially effective and B. animalis was not effective. Furthermore, edible Bifidobacterium treated constipation by increasing the abundance of Lactobacillus and decreasing the abundance of Alistipes, Odoribacter and Clostridium. .” [2017]

On my neutral list (no clear benefit) is Lactobacillus Plantarum.


Some teas can also be antibiotics (among other roles). There are two teas that seem to produce significant results quickly:

Again, rotate and, if practical, change brands too. Their antibiotic compounds are different from different sources.

Herbs and Spices

The best choice needs examination of your microbiome (i.e. uBiome results) and doing the work cited above.  Survey results found:

  1. Neem and Oregano with 80% improving
  2. Olive Leaf and Licorice with 56% improving
  3. Thyme with 50% improving
  4. Wormwood and Tulsi with 33% improving

Other things

If you do not know your microbiome, then see https://cfsremission.com/reader-surveys-of-probiotics-herbs-etc/  for suggestions. Your results will vary because your microbiome vary.

Thick blood is an issue also — but here things gets more complicated and not suitable for this recap.

Antibiotics can have a role — but getting prescriptions for the right ones can be a major challenge.

Metabolism Shifts

From volunteered data, we can identify some distinctive shifts, see Metabolism Explorer Summary

Bottom Line

Working with the microbiome and autoimmune is like working with fragments of the dead sea scrolls. For many bacteria we can identify it — what inhibits or encourages it is not known to modern medical science.  We have extremely thin slices of knowledge –Almonds enhances Bifidobacterium, Lactobacillus (B&L)  as do sesame seeds. What about sunflower seeds? Peanuts? Cashews? We find that Walnuts help the bacteria that inhibits B&L — so we cannot safely generalize to “all seeds/nuts are helpful”.

In many cases, we find that healthy diet or supplements demonstrated to work for normal people have the opposite effect on CFS and other altered microbiome conditions. This is made even worst because most of the studies were done on males and most people with CFS are females. We end up having to swim up-stream thru good and valid suggestions — that are just wrong for us.

My model is simple to understand and allows us to filter many suggestions and candidates. With the availability of uBiome testing (without needing a prescription!) we have entered the age of explicit treatment based on your unique microbiome. We do not know the role of many bacteria involved. We do not know what will inhibit or enhanced all of these bacteria. Frustrating little knowledge!

On the flip side, many readers have reported significant improvement, reduction of prescription medication, etc. so the model and suggestions have potential and thus hope of remission! Microbiome studies are exploding on PubMed, a lot of research is being done and we can often borrow their results.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

New Chart Style for Conditions to Bacteria Taxonomy

I have created a new set of charts showing the connection of bacteria to various conditions.  These charts allow drill down by taxonomy rank (phylum, order, class, genus, etc).


NOTE: As you move down the rank, some items may not be available to graph



By Class


By Order


by Family


By genus


Often at this level — there may be no studies.

Compensating for Prescription Drugs

A reader asked how to compensate for some prescription drugs that he takes for other conditions. In an earlier post, I had added the ability to see the Compare Impact on the microbiome of drugs, supplements, etc. for example


The result can be a long list of bacteria taxonomy impacted Changing this information into an actionable plan is a challenge — until now.

You will notice a new button Get Suggestions for reversing impact on Microbiome.


Clicking this button takes you to the classic suggestion page 

That’s it!

Bottom Line

Trying to correct a microbiome while taking various needed prescription drugs is a complex situation. I hope the above tool will assist you,

Quality Assurance:

For each of the above pages, I have them open in new windows so readers that are interested, can verify the logic being used.

Looking next at the suggestions:

Clicking on one of the items, Fish Oil, we see that it increases http://localhost:42446/Library/Modifier?mid2=142

Verification can be complex between of multiple impacts of modifiers against multiple items. If you set the filters as shown below:

Then just clicking thru items until you find the above (or another taxonomy). For example, http://localhost:42446/Library/Modifier?mid2=1768

Microbiome impact for Seniors and Low diversity

Recently I have seen a number of articles looking at how the diet needs of the seniors (over 60 y.o.) are very different from younger people. One characteristics of many seniors is a decrease of microbiome diversity — the same situation that happens with some medical conditions. 

Changes with Age

“Beyond descriptive connections between microbial composition and host health status, very few studies to date have dissected the causal role of the gut microbiota during ageing. ” [2018]

“Besides microbiota diversity, reduced microbiota-related metabolic capacity, such as lower short-chain fatty acids (SCFAs) levels, in old age may also be associated with aging-related maladies such as irregular bowel transit, reduced appetite, frailty, weight loss, cognitive decline, hypertension, vitamin D deficiency, diabetes, arthritis, sarcopenia, etc. [47–50].”

  • “As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians.” [2010]
  • “In centenarians, we observed a reduction in the quantity of enterobacteriaceae, bifidobacteria, and bacteroides and an increase in clostridia sensu stricto.  The presence of Bifidobacterium longum in the gut seems to be a particular feature in centenarians. It is interesting to note that only 1 strain of B. longum was isolated from each centenarian subject.” [2012]

Diet Changes Suggested in the literature

Back to my primary topic of this blog

Old muscle in young body: an aphorism describing the Chronic Fatigue Syndrome [2018]. 

  • “The data support the hypothesis that patients with CFS are subjected to some of the problems typical for muscle aging, which is probably related to disorders of muscle protein synthesis and biogenesis of mitochondria.

Bottom Line

There is a lot of literature recently published stating the same things:

  • Higher protein content than a younger person “The optimum amount for elderly adults (0.24 g/kg/meal) is approximately 70% greater than that for young adults (0.8 g/kg/day) [19], indicating an age-associated anabolic resistance to dietary protein.”
  • Leucine content is very important. See this page for the suggested foods and this page also.
    • 2.5 g is 1 serving of Greek Yogurt = 5 eggs, but half the calories
    • Study with an addition of ( 3.2 g L-leucine, 0.9 g L-valine, 0.9 g L-isoleucine) [2018]

Some 15 years ago, I recall many people with CFS/ME had significant improvement with non-denatured whey — an excellent source of protein.

Translation to American

0.24 g/kg/meal – means for a 200 lb person we are talking ~ 3 oz/day of good quality protein that is high in Leucine.

Some more enhancements for condition analysis

Condition Citations

I have made viewing the citations (sources of information) easier. At present, there is at least one academic research using my site to find the articles of interest and validating my encoding of the information into the database.

This is located here , http://microbiomeprescription.azurewebsites.net/Library/ConditonAdjustments

Where to find the citations

When you click on one of these, you will be shown the citations:

Easier viewing of Taxonomy Layers to Conditions 

I have enabled changing the condition by just selecting a condition and clicking a button.

What is the best diet in your opinion?

I have been asked this often. My answer is extremely logical but not what you will get from most health experts (and unfortunately, may not be easy to determine for some).

The Diet….

Very simple — the type of diet that your ancestors ate 300+ years ago! 

From a post that I did three years ago:

Some nuggets that I found in a Christmas Present…

My wife gave me “Danish Cookbooks” by Carol Gold. This is NOT a cook book, but rather an academic study of cookbooks published in Denmark.  I’m 100% Danish and very interested in history.

I have always been inclined towards going for ancestral diet patterns, and did Paleo for a while. My problem with Paleo is that it is more idealogical based than actual (scientific) archeologically based. It is also trying to jump the diet back thousands of years which effectively ignores how our bacteria evolved to meet our changes of diet.

A diet based on typical diet of your ancestors 400 – 1400 years ago is likely a better choice. You avoid the newly introduced foods, for example, potatoes. You also avoid process foods and modern additives. On the plus side, your gut bacteria is likely closer to the optimized bacteria your ancestors evolved from eating the same food for a thousand years.

In this book, I found two gems from the historical records:

  • We have decreased the use of spice considerably — in 1600, the common spices were:
    • cumin, anise, coriander, dill, fennel, lavender, sage, rosemary, mint, bay leaves, cloves, pepper, saffron, thyme, marjoram, nutmeg, cardamon, ginger, cinnamon, hyssop, wormwood, lemon balm, angelica-root.
    • “The issue here is … the use of seasonings in general slackens” p.47
    • Many of these spices (like wormwood and ginger) have strong antibacterial characteristics which would have kept some gut bacteria families in control well.
  • “Their most common food was meat” p. 122
  • White (wheat) bread was very uncommon, expensive, and typically seen only in upper class homes on special occasions(not as part of the regular menus). It appears that most of the carbohydrates came from Rye Bread.

I am sure that some readers who favor a diet that is vegan or vegetarian on ideological grounds would object to these suggestions.  My response is simple, if your ancestors were vegetarians for centuries or millenniums (as some friends who were born in India can validly claim), then that is the right diet without any doubts.

Evidence shows that gut bacteria is inherited through generations — hence it is good to know what your ancestors ate because your gut bacteria have likely adapted to that diet. Given my heritage (which likely applies to people from the UK, Poland, northern France and Germany etc), this boils down to:

  • Rye Bread without any wheat flour
  • Meat and Fish (especially since the family seemed to always been within 5 miles of the coast back to 1500..)
  • Vegetables:

No potatoes — they really did not enter my ancestor dies until the early 1800’s – after one of my great-grandfathers was born. Little or no sugar (“Worldwide through the end of the medieval period, sugar was very expensive[1] and was considered a “fine spice“,[2] but from about the year 1500, technological improvements and New World sources began turning it into a much cheaper bulk commodity.” – Wikipedia)

This Wikipedia article may be a helpful start for many.

The last item needs to be taken with a touch of salt and sung: “A spoonful of soil helps the microbiome recover!” We have become hyper-hygienic. See the Hygiene hypothesis. This comes from a post in 2016:

“The Amish and Hutterites are U.S. agricultural populations whose lifestyles are remarkably similar in many respects but whose farming practices, in particular, are distinct; the former follow traditional farming practices whereas the latter use industrialized farming practices….Despite the similar genetic ancestries and lifestyles of Amish and Hutterite children, the prevalence of asthma and allergic sensitization was 4 and 6 times as low in the Amish” – i.e. industrialized farming practices resulted in six times (600%) the rate of asthma and allergies. See Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children(2016). This is also echoed in their farm products!!! Amish and Hutterite Environmental Farm Products Have Opposite Effects on Experimental Models of Asthma [2016]. Given a choice of buying groceries from a Hutterite farm or a Amish farm, buy the Amish (non industrialized) groceries!!!!

So I advocate not a Paleo diet, but a medieval-food diet (modified for modern nutritional needs). No prepared foods (talk about being extremely unnatural!), so food prepared from scratch — ideally organic with heritage seeds.

More Conditions added and Sweet Charts of them

A reader asked me to add some more conditions (and nicely supplied some links to pubmed articles for those conditions reporting the microbiome shifts). So if you want additional ones, just do the same — send me the conditions and pubmed articles for those conditions reporting the microbiome shifts

Available Conditions

These are from this page, http://microbiomeprescription.azurewebsites.net/Library/ConditonAdjustments

New Chart types

Above you see “View Taxonomy Layers” which I spent most of today coding and testing. Some examples below. The reason is simple, some data is by species, other by genus, other by family — these charts connect the data better in a visual fashion. (Click on image below to see it better)

Modifying Microbiome based on multiple conditions

Earlier I had created a page for suggestions based on microbiome shifts reported in the literature. A chart of these relationship is shown here.

Today, I have updated the page to allow multiple conditions to be picked and see what the net results are. For example, suppose someone has:

  • Allergies
  • Asthma
  • Depression
  • IBS

Then just click the Suggestions button and the usual suggestions screen appears:

Items like L. Reuteri, L.Rhamnosus gg, L.Kefiri and mastic gum are strong recommendations, while L. Gasseri and E.Coli probiotics are to be avoided.

Bottom Line

This enhancement should reduce the complexity of trying to use this page when you have multiple conditions. 

I review the literature about once a month and add new information regularly — so your results may change each month.