What is the best diet in your opinion?

This is a repost with expansion of “What is the best diet in your opinion?” on my CFS Remission blog back in 2018. It consists of the following

  • Basic Logic for this diet
  • How diets have changed in recent years — today’s “normal diet” is radically different than your recent ancestors
  • The manifestation of “keeping up with the Jones” eating habits
  • Finding Your Historic Diet – my own exploration

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, see “mutts” below). It is based on actual science and not idealogy.

The Diet…. it’s Logic

Very simple — the type of diet that your ancestors ate 300+ years ago! Diet changes gene expression, i.e. microbiome AND DNA adapts.

Last year, researchers discovered that these kinds of environmental genetic changes can be passed down for a whopping 14 generations in an animal – the largest span ever observed in a creature, in this case being a dynasty of C. elegans nematodes (roundworms)…. Usually, environmental changes to genetic expression only last a few generations.
…  studies have shown that both the children and grandchildren of women who survived the Dutch famine of 1944-45 were found to have increased glucose intolerance in adulthood.Scientists Have Observed Epigenetic Memories Being Passed Down For 14 Generations

What is 14 human generations? 300 to 420 years.

Maternal undernutrition during pregnancy (F(0)) programs reduced birth weight, IGT, and obesity in both first- and second-generation offspring. Sex-specific transmission of phenotypes implicates complex mechanisms including alterations in the maternal metabolic environment (transmaternal inheritance of obesity), gene expression mediated by developmental and epigenetic pathways (transpaternal inheritance of LBW), or both (IGT)

Intergenerational transmission of glucose intolerance and obesity by in utero undernutrition in mice [2009]

” Thus, it is possible to construct a chain of events, based on experimentally verified biochemical mechanisms, through which an environmentally induced change in the activity of chromatin-modifying enzymes can lead to a change in DNA sequence.”

Epigenetic responses to environmental change and their evolutionary implications [2009]

A diet based on typical diet of your ancestors 400 – 1400 years ago is likely a better choice than any healthy diet pitched by most people. Your gut bacteria is likely closer to the optimized bacteria your ancestors evolved from eating the same food for a thousand years.

Risk of introducing atypical foods

A new atypical food will have some bacteria/body tolerate it. For others, it may throw the body’s balance off; leading to autoimmune disease, diabetes, gluten sensitivity, autism, ADSD and a host of other conditions that appear to be increasing in western population ‘for no apparent cause’ (… cough, cough, cough). It’s a gamble for you and for your children. Yes, people will adapt and survive — but your offspring may not.

You should avoid the newly introduced foods (for your regions) that were not in use a couple of hundred years ago, for example, potatoes, peanuts (1920’s), and banana (which has been reduced to a single species, Cavendish – because it was the most profitable)The charts below show some of the abnormalities of diet seen recently. You also avoid process foods and modern additives (especially emulsifiers and new preservatives).

Some Drastic Changes seen in Diet

BBC: Which countries eat the most meat?

We can see that Americans have DOUBLED their meat consumption with almost a 10 fold increase of “healthy” chicken.

  • ” In conclusion, consumption of lean red meat (lamb) or lean white meat (chicken) as part of the usual diet is associated with a similar lipid response.” [2011]
  • “Consumption of lean red meat (Pirenaica breed) or lean white meat (chicken) as part of the usual diet is associated with a similar response. ” [2022]
  • “There was no difference in BMI or any other marker of adiposity between consumption of pork, beef and chicken diets. ” [2014]
Drivers of U.S. Per Capita Meat Consumption over the Last Century

There are implication that this increase of meat may be a factor in increasing ADHD, Autism rates and autoimmune conditions:

Sugar Consumption in the US Diet between 1822 and 2005

Sugar is added to almost all prepared foods. The reason is simple, it encourages consumption and thus more sales.

And we are eliminating other very tradition foods from our diet, for example legumes and dry beans.

legume consumption remained low in US adults and declined from 2011 to 2014 (mature legumes: 12.8 to 8.3%; dry beans: 10.0 to 6.5%).

Legume Consumption Patterns in US Adults: National Health and Nutrition Examination Survey (NHANES) 2011–2014 and Beans, Lentils, Peas (BLP) 2017 Survey [2020]

Keeping up with the Jones [Health Issues]!

My daughter has seen this in Vancouver, Canada – where almost 50% of the people were born outside of Canada.

Having grown up around such a large amount of immigration, the changes have been really apparent. Interestingly enough, those from India and area tend to keep the traditions at home for eating, so they don’t have such a big impact on their bodies. But those from Asia, they all essentially know that when they come to North America, they are going to gain a lot of weight. Whether it’s food culture or additives in food, it’s a big struggle. They tend to also have problems with both dairy and alcohol. 


Keeping up with the Jones often include eating upscale for your own culture group or the population that you are residing in. A food that was once a special occasion food becomes a regular food as a statement of prosperity (and possibly stupidity!)

Evidence of significant impact

  • “Adherence to the ‘ethnic breads, legumes and nuts’ and ‘whole grains, fruit and dairy’ patterns was associated with a lower predicted cardiovascular diseases risk, and an inverse association for the ‘processed food and sugar-sweetened beverages’ pattern in an Asian population. ” [2022]
  • “participants in the highest quintile of the refined-foods pattern had a greater risk of elevated 10-y cardiovascular diseases risk” [2016]
  • “Patterns emphasizing higher consumption of vegetables, legumes, fruit, nuts, whole grains, fish, lean meat or poultry, … were generally associated with decreased risk of all-cause mortality. “
  • Consumption of added sugars has been associated with increased risk of obesity [23,24,25] as well as increased risk factors for cardiovascular disease (CVD) [26], including dyslipidemia [27,28], elevated blood pressure [20,29,30], diabetes [21,31,32], non-alcoholic fatty liver disease [33,34], and even cognitive decline [35] and cancer [36,37].” [2016]
  • “An estimated increase of 10 g/day in total sugar intake (about 2.4 teaspoons) was associated with an increased Alzheimer’s disease  risk  [2022]

Finding Your Historic Diet – my own exploration

From a post that I did seven years ago [2015], I am using myself as an example — you will likely need to do your own research. Beware of revisionist view of traditional diets — research!

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 ideological based than actual (scientific-evidence) 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.

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) —Note this is in Northern Europe. 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..)
  • Often goat milk and goat cheese (Gjetost) were the norm and not cow milk.
  • 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)

Dropping back earlier in my ancestry, the Vikings. We have an excellent summary here “Viking Diet: Why you should eat like the Vikings did!” which cites historic text describing the food with archeological findings.
“Vikings farmed cold-hardy vegetables like cabbage, carrots, leeks, turnips, parsnips, garlic, onions, and other root vegetables to add vitamins and variety to their diets. They ate peas, beans, and other legumes. They were fond of apples and cherries from wild or cultivated trees and collected berries and nuts when they were in season.

There is an excellent interview with a specialist: Nordic food culture – A historical perspective by Henry Notake. He cites “the practice of soaking fish in lye is not an original Norwegian tradition, even though the actual raw material of dry fish is. I have found recipes for lutefisk in German cookbooks, Swedish documents from the 16th century, and Spanish and Polish cookbooks from the 17th century. ” He is also the author of Printed Cookbooks in Europe, 1470-1700

Frumenty for Breakfast?

Some foods that are common now were not the case in the past and vice versa.

A Dollop of History, describes this and how to make it. It used  Furmente wt Porpays (Frumenty with Porpoise) from the 14th century English manuscript, The Forme of Cury. This food and similar recipes dates back to Roman Times. It uses saffron. If you can’t get porpoise, oogruk (bearded seal) is a good substitute (a unique taste according to my wife from her own experience). For other recipes see: Medieval Recipes and Ancient Recipes on the same site.

One item to keep in mind, often surviving recipe books were written to the upper class and not your ancestors! Many recipes on the internet are modern adaptions of old recipes to suit contemporary tastes — so be warned!

Project Gutenberg does have some historic cook books available (besides The Forme of Cury cited above)

A list of 13-16th century cook books is on Old Cook with a list of recipes in English. Compare to this, a modern omelet is rather plain!

Ingredients (1 tsp = 1 teaspoon)
6 leaves of tansy
1 rue leaf
4 leaves of Apium (wild celery)
4 mint leaves
4 sage leaves
6 leaves of marjoram or oregano
handful of fennel (aromatic foliage)
large handful of parsley
2 handfuls of the mixture: violet leaves, spinach, lettuce, green chard
16 eggs
1tsp of ginger

Omelette with herbs, from Arboulaste , Ménagier de Paris, 1393.

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 regional medieval-food diet (partially modified for modern nutritional needs). No prepared foods (talk about being extremely unnatural!), so food prepared from scratch — ideally organic with heritage seeds. Orange carrots are unnatural! Carrots should be white! The food should also be seasonal! The rotation of food with the seasons is a significant factor. Having fresh strawberries at Christmas is so very wrong.

Are you a Mutt?

The term mutt or “Heinz 57″means mixed ancestry – for example, Asian with African, Icelander with Italian. If you are not sure, a DNA test is suggested.

If you are a mutt, look for commonality of historic foods from the dominant ancestors.

Are what you have been told is healthy wrong?

Chances are that it is corrected relative to the typical common western diet. That is the base line that most studies are done against. If you change the base line, the answer may change…

Note the “compared with other high carb foods

One other factor?

There is evidence that a combination of blood type and being a secretor  or non-secretor impacts the body and the microbiome. There is a nice blood type table by country listed here. Iceland and Ireland are very similar (partially because both had major Viking settlements 1200 years ago). One could propose a model that traditional regional diet influenced the survival rate of different blood type which would be reflected in their blood type distribution. Compare the Scandinavian (meat eaters) to India/Sri Lanka (Vegetarians) below for aNeg,bPos and oNeg.

Sri Lanka43.422125.785.1321.041.250.26
United Kingdom4428829621
United States37.435.78.53.466.31.50.6

Bottom Line

Showing off prosperity by what you eat, trying to assimilate into local or trendy eating habits and convenient “get-healthy” diets are excellent ways to cripple your microbiome (and likely future generations). One simple example is going gluten-free. For some medical conditions it is necessary — but for a person without those conditions, available studies suggests that it is a poor choice advocated by naïve people

Food taste is acquired — cutting sugar and salt from the diet can be hard for many people. Eating turnips and rutabaga may be unfamiliar tastes. Eating 100% rye bread with goat cheese is definitely a different taste. It will take time and may present extra challenges if you have kids or other in the family that want to stick to contemporary eating habits.

My daughter states “There’s a reason why old recipes don’t always work, because ingredients are either no longer available, or they have changed over the years, or techniques have changed (see this post)”

So that is my logic and my reasoning and my evidence…

Comments from Social Media

Possible help for the root of all evil in the microbiome?

Using my last post, The root of all evil in the Microbiome?, I tried identifying items that address many of the evils. The process is simple, I use Microbiome Prescription existing database with 2,099.126 interactions between gut modifiers and bacteria. I then select items that only increase the top N items. Starting with 2 items and then working up.

Two Items: Prevotella, Veillonella

Produced following items

  • Amino Acid and similar
    • acetic acid
    • l-citrulline
      • propionate
  • Antibiotics, Antivirals etc
    • rifaximin (antibiotic)s
  • Diet Style
    • ketogenic diet
  • Food (excluding seasonings)
    • blackcurrant
    • cranberry bean flour
    • Far infrared Sauna
    • fasting
    • lupin seeds (anaphylaxis risk, toxic if not prepared properly)
    • Miso
    • pea (fiber, protein)
    • Pulses
    • red wine
    • wheat bran
  • Herb or Spice
    • Bofutsushosan
    • chinensis (Chinese goldthread)
    • isobutyric acid
    • isovaleric acid(fatty acid)
    • smoking
  • Prebiotics and similar
    • arabinoxylan oligosaccharides (prebiotic)
    • galacto-oligosaccharides (prebiotic)
    • xylan (prebiotic)
  • Probiotics
    • Lentilactobacillus buchneri
  • Sugar and similar
    • non-starch polysaccharides
    • saccharin
  • Vitamins, Minerals and similar
    • vitamin d

Three Items: Prevotella, Veillonella, Clostridium

We are done to just one item: Amino Acid and similar l-citrulline

This is not unexpected, in building the suggestions algorithms, I often encountering items that helps one and hurts another; also a lack of studies.

Alternative Approach

I am going to pick the top dozen (12) genus, and then select the items by the number of genus positively impacted. As you see, the best that we get is impacting 50% of the genus picked.

Remember: we are doing items with absolutely positive impact only. We exclude all items that has a negative impact on any of the genus reported in any study. For clarity, if a substance increases a genus in some studies and decreases in other studies, it is excluded. This is the most conservative approach.

Caution: this assumes undergrowth for all 12 genus. It may make an overgrowth worse.

Prescription – Otherproton-pump inhibitors (prescription)6
Sugar and similarnon-starch polysaccharides5
Amino Acid and similaracetic acid3
Amino Acid and similarConjugated Linoleic Acid3
Amino Acid and similarl-citrulline3
Amino Acid and similarproline (amino acid)3
Diet Styleanimal-based diet3
Food (excluding seasonings)blackcurrant3
Food (excluding seasonings)fasting3
Food (excluding seasonings)lupin seeds (anaphylaxis risk, toxic if not prepared properly)3
Food (excluding seasonings)Pulses3
Food (excluding seasonings)safflower oil3
Food (excluding seasonings)wheat bran3
Miscellaneous, food additives, and other odd itemsisobutyric acid3
Miscellaneous, food additives, and other odd itemsisovaleric acid(fatty acid)3
Prebiotics and similararabinoxylan oligosaccharides (prebiotic)3
Sugar and similarsaccharin3
Amino Acid and similarpropionate2
Diet Stylefibre-rich macrobiotic ma-pi 2 diet2
Food (excluding seasonings)barley,oat2
Food (excluding seasonings)cranberry bean flour2
Food (excluding seasonings)Miso2
Food (excluding seasonings)navy bean2
Food (excluding seasonings)pectin2
Food (excluding seasonings)red alga Laurencia tristicha2
Herb or SpiceBofutsushosan2
Herb or Spicecoptis chinensis (Chinese goldthread)2
Herb or Spiceplantago asiatica l.2
Herb or Spiceschisandra chinensis(magnolia berry or five-flavor-fruit)2
Miscellaneous, food additives, and other odd itemsTributyrin2
Prebiotics and similarcarboxymethyl cellulose (prebiotic)2
Prebiotics and similaroligofructose (prebiotic)2
Prebiotics and similarresistant maltodextrin2
Prescription – Otherepicor2
Probioticsbacillus subtilis natto (probiotics)2
Probioticssaccharomyces boulardii (probiotics)2
Sugar and similarglucose (sugar)2
Sugar and similarlevan2
Vitamins, Minerals and similarFerric citrate2

Bottom Line

The above is a generic list that should “do no harm” for most people and will likely help. Better results are likely to occur using a 16s microbiome report (OmbreLabs [US only] and Biomesight [World wide] are the most used) and using the Artificial Intelligence on Microbiome Prescription that factors in the 2 million facts that it has available (see this example). That would produce a targeted list for your needs.

The root of all evil in the Microbiome?

From Special Studies, I extracted the genus who are associated with various symptoms/conditions and then aggregated into a single table below. See Special Studies Updated and A new specialized selection of suggestions links for background.
UPDATE: Just added Possible help for the root of all evil in the microbiome?

Conceptually, these are the ones that will lead to a variety of symptoms and conditions. Two of the more significant ones are available as probiotics:

  • Clostridium (i.e. miyarisan (jp) / miyarisan)
  • Bifidobacterium (many brands, I tend to favor Custom Probiotics offerings with HMO)
  • Prevotella may be available as a retail probiotic soon (see Prevotella copri as Next Generation Probiotics). There is also a US Patent for  Prevotella histocola which implies work on producing it.
  • Veillonella probiotics appear to be available in a mixture (ULTRA-VEILLONELLA) however, I have reservations about the seller (site is new – 2022, no species information, no safety or other studies (legally required in the USA), no information about the company, etc. in other words has an unpleasant smell)
  • Note that Lactobacillus is far down this list.


Bacteria RankShiftedConditionsSum Of Conditions
The Genus associated most with health issues

Special Studies Updated

With this being the Thanksgiving Weekend, I had time to work on my backlog. One of the items was special studies. I have done the following changes:

  • Executed the analysis for both uBiome and Thryve/Ombre samples. So more samples will have the option of using special studies.
  • Implemented Consensus/Monte Carlo between the bacteria, casting the species (which are not reported consistently between labs) to their genus. These are shown on the [Key Bacteria] link below.

Last, I have added per  Peripheral neuropathy to the symptom list.


This is what Special Studies use.

Common Bacteria across labs is now available for each.

Example: for Chronic Fatigue Syndrome

The page below shows a distinct pattern for ME/CFS with Bifidobacterium being the greatest significance. For this bacteria, my first suggestion is simple:  Human milk oligosaccharides (HMOs) and Bifidobacerium infantis probiotics.


It is interesting to note that Lactobacillus does not appear as significant.

Bottom Line

Special Studies are still a “work-in-progress”. Using them “as is” have not produced superior results to those from the standard triplet (Outside Lab Range, Box-Plot-WhiskersKaltoft-Moldrup) — see this post for an example. How do I determine which is better? For ME/CFS, we should have the top suggested items being cross validated with clinical studies. Feel free to explore the results.

I will continue working on getting superior results from special studies — stay tune!

An ME/CFS Journey using their Microbiome

Back Story

I go this email from someone who just moved to Spain from the U.S. She has being using Microbiome Prescription to try improving her ME/CFS. She had the testing done by Ombre Labs, and then transfer the data to BiomeSight. This allows her to keep consistent analysis on her journey of recovery.

I’m doing pretty well with bacillus coagulans and pretty bad with some other recommendations so I’m looking for some extra clarity. When I hit a great herbal antibiotic and a great probiotic life gets so much better, but oftentimes it’s harder than that. Sometimes I don’t get enough  herbal antibiotic recommendations. Some of the probiotics I may need, like e-coli or bifidus, cannot sustain me the way coagulans does -keeping my local infections at bay. So I try to combine them  or if it’s not clear if they are compatible, I tend to not take them, which is a shame. So I’m considering prescription medicine to see if I can get a bit more help.

I’m also figuring out where to buy supplements etc. Life is really an adventure!

Comparison Between Samples And Lab Interpretations

For those not familiar with the issue of Lab Interpretation of the identical data see The taxonomy nightmare before Christmas…[2019]. Ombre typically reports on 25-30% more bacteria types than BiomeSight. The quality improved, but the number of bacteria identified are very similar. I give observations below:

OmbreLabResultsBiomeSight LabResults
Lab Read Quality2.
Bacteria Reported By Lab365628625280497490
Bacteria Over 99%ile560271
Bacteria Over 95%ile27241193111
Bacteria Over 90%ile49511375824
Bacteria Under 10%ile18604854562224
Bacteria Under 5%ile10284112830175
Bacteria Under 1%ile17317113135
Lab: Thryve
Rarely Seen 1%091042
Rarely Seen 5%8402741817
Outside Range from Medivere16165444
Outside Range from Metagenomics7719171716
Outside Range from MyBioma14148777
Outside Range from Nirvana/CosmosId23238997
Outside Range from XenoGene333325222219
Outside Lab Range (+/- 1.96SD)101442282822
Outside Box-Plot-Whiskers6461126137
Outside Kaltoft-Moldrup11218231708464
Condition Est. Over 99%ile0054270113175
Condition Est. Over 95%ile000010
Condition Est. Over 90%ile2210040
Enzymes Over 99%ile131517060
Enzymes Over 95%ile698200100
Enzymes Over 90%ile155411022320
Enzymes Under 10%ile551382455121
Enzymes Under 5%ile22671593308219212
Enzymes Under 1%ile521320187132146
Compounds Over 99%ile104126641124767
Compounds Over 95%ile385397430719
Compounds Over 90%ile5335486011276138
Compounds Under 10%ile183248103342313323
Compounds Under 5%ile109127359180125224
Compounds Under 1%ile1617303376473
Compounds Under 1%ile1721224172140
Comparison Table

The following are apparent, between the last two samples, the reader was trying to follow the suggestions.

  • The number of high bacteria (> 90%ile, > 95%ile, > 99%ile) show significant decline
  • Rarely Seen bacteria show significant decline
  • The number of low bacteria (< 10%ile, < 5%ile, < 1%ile) show significant increases – suggesting more diversity
  • The Outside Range is a little mixed, with either both labs showing a decline, OR one showing a decline and one an increase. None showed increase on both.
  • High Enzymes show decline. Low Enzymes had inconsistent results.
  • Compounds and Conditions had inconsistent results

Enzymes, Compounds and Conditions are best effort estimates (and experimental) and be taken with a grain of salt (50 mg). By conventional thinking, the microbiome has improved (less extreme high levels), less pathogenic bacteria types.

Going Forward

Consensus approach (also known as Monte Carlo Simulation) remains the safest choice. To simplify the analysis, I will use the standard triplet (Outside Lab Range, Box-Plot-Whiskers, Kaltoft-Moldrup) on both latest samples processed through Ombre and Biomesight data processing. Given the report that some did not work subjectively, I decided to proceed down the most restrictive approach. I used the new quick suggestions (best choice for someone with brain fog).


The #1 and #2 choices are lactobacillus paracasei and bacillus subtilis. Kegg choices are Escherichia coli, Bacillus subtilis (with Biomesight numbers being much less than Ombres).

Microbiome ModifierSuggestionsClinical DosageEst ConfidenceSuggestionsEst Confidence
bacillus subtilisTake10 BCFU/day340.4Take223.6
bacillus lichenformisTake279.1Take20.9
enterococcus faeciumTake1 BCFU/day13.2Take8
bifidobacterium longumTake10 BCFU/day516.2Take182.5
lactobacillus paracaseiTake40 BCFU/day58.7Take397.5
pediococcus acidilacticiTake157.7Take215.4
Items with Agreement

For other items, there were a surprisingly few in agreement.

Microbiome ModifierSuggestionsClinical DosageEst ConfidenceSuggestionsClinical DosageEst Confidence
galactooligosaccharides (GOS)Take10 gm/day15Take10 gm/day139.1
CalciumTake500 mg/day129.2Take500 mg/day36.2
MagnesiumTake500 mg/day189.7Take500 mg/day119.2
D-RiboseTake10 gm/day80.6Take10 gm/day23.6
GlycineTake15 gm/day409.2Take15 gm/day258.5
Omega-3 fatty acidsTake4 gm/day166.8Take4 gm/day289.4

Using the Consensus across Multiple Samples

This gives a lot more information, but at the cost of more complexities.

The approach is similar to the above, except for suggestions we change to Every thing. I have extracted the items > 100 that are 5 or 6 Take Count with 0 or 1 Avoid Count to the table below in decreasing order

Prescription Drugs Analysis

The approach is similar to the above, except for suggestions we change to Every thing.

And then use the option on the Multiple Samples tab,

Remember to empty the old baskets.

The items that came up (as discussed above) are:

So every item at the top of the list (from over a possible choice of 3000 different prescription drugs), are cross-validated against the literature with the exception of proton-pump-inhibitor. This person can show their medical professional that the microbiome model suggests it and clinical studies confirm that they are reasonable.

I favor Dr. Cecile Jadin protocol of rotating antibiotics typically a course (7-10 days), then a break of 1-2 weeks, and then proceed to the next one.

Feedback from Reader

I love Dr. AI [Artificial Intelligence], which other doctor asks you to eat as much 100% chocolate I can??? And I tolerate it, luckily. And there are so many yummy brands in Spain, I don’t remember having that much choice when I left! 

Thanks for all the info, very helpful, very encouraging to see progress “on paper”, and to have clear things to share with my new doctor. I’m confident I’ll find a microbiome helper here in Barcelona.

The greatest challenge in treating ME/CFS is that there is no clear test to see if something is helping. Using repeated microbiome samples with systematic trials of suggestions, provides objective evidence — even when the subjective evidence is not pronounced. ME/CFS patients have a real challenge on doing subjective evaluation — they often cannot recall how they were two weeks ago!

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 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Experiment with Kefir

A reader asked to look at the data from an experiment she did.

I have provided two biomesight results from biomesight (BS) to microbiome prescription (MP). The sample consuming kefir daily was sent first (both to BS and MP). The second sample was after stopping kefir consumption between the two samples.

This was not the ideal sequence, getting a sample before doing Kefir and one after would be the typical approach. This approach should indicate what is lost by stopping. There was 3 weeks washout time before samples.


The stopped Kefir sample is higher quality, so the expectation would be for the numbers to be higher. This is not the case. Stopping resulted in more extreme ranges for bacteria(1.5x more), less types of bacteria, dramatic drop in the count of bacteria out of range (93% decrease in Outside Lab Range). There was a significant in compounds being produced by the microbiome that were more extreme (8x increase) and enzymes also (3.6x increase).

CriteriaOn KefirStopped Kefir
Lab Read Quality3.95.3
Bacteria Reported By Lab470404
Bacteria Over 99%ile110
Bacteria Over 95%ile305
Bacteria Over 90%ile4319
Bacteria Under 10%ile1074
Bacteria Under 5%ile139
Bacteria Under 1%ile07
Lab: BiomeSight
Rarely Seen 1%22
Rarely Seen 5%1214
Outside Range from JasonH44
Outside Range from Medivere1414
Outside Range from Metagenomics77
Outside Range from MyBioma55
Outside Range from Nirvana/CosmosId1919
Outside Range from XenoGene2121
Outside Lab Range (+/- 1.96SD)181
Outside Box-Plot-Whiskers7329
Outside Kaltoft-Moldrup8174
Condition Est. Over 99%ile00
Condition Est. Over 95%ile00
Condition Est. Over 90%ile11
Enzymes Over 99%ile10
Enzymes Over 95%ile32
Enzymes Over 90%ile2441
Enzymes Under 10%ile79240
Enzymes Under 5%ile26158
Enzymes Under 1%ile147
Compounds Over 99%ile02
Compounds Over 95%ile4113
Compounds Over 90%ile29453
Compounds Under 10%ile44163
Compounds Under 5%ile1861
Compounds Under 1%ile28

As often happens, there is a Yin/Yang with some indicators improving and other worst. My general impression is that this microbiome does better on Kefir.

Bacteria Specifics

I then went to compare specific bacteria shifts that had special interest or large shifts

BacteriaOn Kefir Percentile (Percentage)Stop Kefir Percentile (Percentage)
(genus) Bifidobacterium3572
(genus) Lactobacillusnone43
(genus) Blautia38 (6.5%)46 (7.2%)
(genus) Faecalibacterium34 (8.4%)62 (14.6%)
(genus) Lachnospira21 (0.6%)70 (3.5%)
(genus) Bacteroides66 (29.1%)88 (40.5%)
(genus) Phocaeicola79 (15%)93 (23%)

In terms of the literature, I could only find Bacteroides and Phocaeicola, which are both reported to increase (agrees). Different Kefirs will have different impact because each has different bacteria in it. “The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. ” [2022]

See Milk kefir: composition, microbial cultures, biological activities, and related products [2015] for various lists of bacteria in different kefir tested.

List of Possible Bacteria in Kefir

The following list illustrates why I tend not to recommend Kefir — too many possible bacteria, some good and some bad. It’s probiotic roulette! If you buy commercial Kefir, have some fun — email the producer and ask which strains are in it, and the last full shotgun lab report verifying it.

  1. Acetobacter acetic
  2. Acetobacter fabarum
  3. Acetobacter lovaniensis
  4. Acetobacter orientalis
  5. Acetobacter rancens
  6. Acetobacter sp.
  7. Acetobacter syzygii
  8. Acinetobacter sp.
  9. Bacillus sp.
  10. Bacillus subtilis
  11. Bifidobacterium bifidum
  12. Bifidobacterium sp.
  13. Brettanomyces sp.
  14. Candida inconspicua
  15. Candida krusei
  16. Candida lambica
  17. Candida maris
  18. Candida sp.
  19. Cryptococcus sp.
  20. Dekkera anomala
  21. Dysgonomonas sp.
  22. Enterococcus durans
  23. Enterococcus faecalis
  24. Enterococcus sp.
  25. Escherichia coli
  26. Gluconobacter frateurii
  27. Gluconobacter japonicus
  28. Halococcus sp.
  29. Kazachastania khefir
  30. Kazachstania aerobia
  31. Kazachstania exigua
  32. Kazachstania unispora
  33. Kluyveromyces lactis
  34. Kluyveromyces marxianus
  35. Kluyveromyces marxianus var. lactis
  36. Lachancea meyersii
  37. Lactobacillus acidophilus
  38. Lactobacillus amylovorus
  39. Lactobacillus brevis
  40. Lactobacillus buchneri
  41. Lactobacillus casei
  42. Lactobacillus casei ssp. pseudoplantarum
  43. Lactobacillus crispatus
  44. Lactobacillus delbrueckii ssp. bulgaricus
  45. Lactobacillus helveticus
  46. Lactobacillus kefir
  47. Lactobacillus kefiranofaciens
  48. Lactobacillus kefiranofaciens ssp. kefiranofaciens
  49. Lactobacillus kefiranofaciens ssp. kefirgranum
  50. Lactobacillus kefiri
  51. Lactobacillus lactis
  52. Lactobacillus lactis ssp. lactis
  53. Lactobacillus parabuchneri
  54. Lactobacillus paracasei
  55. Lactobacillus parakefir
  56. Lactobacillus parakefiri
  57. Lactobacillus plantarum
  58. Lactobacillus satsumensis
  59. Lactobacillus sp.
  60. Lactobacillus uvarum
  61. Lactococcus cremoris
  62. Lactococcus lactis
  63. Lactococcus lactis ssp. cremoris
  64. Lactococcus lactis ssp. lactis
  65. Lactococcus lactis ssp. lactis biovar diacetylactis
  66. Lactococcus sp.
  67. Leuconostoc lactis
  68. Leuconostoc mesenteroides
  69. Leuconostoc paramesenteroides
  70. Leuconostoc pseudomesenteroides
  71. Leuconostoc sp.
  72. Naumovozyma sp.
  73. Pelomonas sp.
  74. Pichia guilliermondii
  75. Pichia kudriavzevii
  76. Pseudomonas sp.
  77. Saccharomyces cerevisiae
  78. Saccharomyces sp.
  79. Saccharomyces turicensis
  80. Saccharomyces unisporus
  81. Saccharomycodes sp.
  82. Shewanella sp.
  83. Streptococcus durans
  84. Streptococcus sp.
  85. Streptococcus thermophilus
  86. Weissella sp.
  87. Zygosaccharomyces sp.

Comments from Social Media

Border Walls in the Human

There are two border walls that can be important to health, we will used these terms:

  • increased intestinal permeability or IIP (often called Leaky Gut, but note: “Leaky gut syndrome is a hypothetical condition that’s not currently recognized as a medical diagnosis.”[src])
  • bloodbrain barrier permeability or BBBP

The first is an indicator of the availability of bacteria, fungi, chemicals, etc. to move from the intestines into the body/blood. The second is the ability of bacteria, fungi, chemicals, etc. to enter the brain. Both are important — the latter with neurological conditions (for example brain fog, autism, etc).

IIP – Increased Intestinal Permeability

This is usually associated with the Zonulin protein.

Zonulin is a protein modulator of intercellular tight junctions. It has been shown to induce a significant and reversible increase in gastroduodenal and small intestinal permeability and is involved in tolerance/immune response balance. The hybridization of wheat to dramatically increase gluten (gliadin) content and its overconsumption, multiple times a day, every day, in the typical diet, chronically disrupts this tolerance/immune response balance.

Michael T. Murray ND, John Nowicki ND, in Textbook of Natural Medicine (Fifth Edition), 2020

Zonulin is a member of the MASP (mannose‐binding lectin‐associated serine protease) family of proteins, and elevated serum zonulin levels have been reported in a number of neurological conditions such as multiple sclerosis 7 and Alzheimer’s disease. 8 

Zonulin and blood-brain barrier permeability are dissociated in humans [2022]

There is a massive number of studies, speculations, and theories on addressing this issue, especially theories on fixing leaky gut. One example:

BBBP – blood–brain barrier permeability

First, we need to be aware that they are different: Zonulin and blood-brain barrier permeability are dissociated in humans [2022]. For a general discussion, see A blood–brain barrier overview on structure, function, impairment, and biomarkers of integrity [2020]

Some studies that are of special interest:

When dealing with neurological issues when there is a choice of several different substances, I have looked up the molecular weight and advocated for the lower molecular weight choice. For illustration,

  • Acetylcysteine (N-acetylcysteine) has a weight of 163.19
  • Minocycline has a weight of 457.5
  • Azithromycin has a weight of 785
  • Amoxicillin has a weight of 365.4
  • Piracetam has a weight of 142 (this is a fast acting nootropic that clears brain fog in minutes for some people).
  • Resveratrol 228, Quercetin 302, Curcumin 368, Aspirin 180

It is an easy way to do quick evaluation— for example, I would expect Resveratrol to have a greater effect on brain function than Curcumin, with Aspirin having a still greater potential effect.

Bottom Line

The purpose of this post is frame questions that may be relevant to you — and not provide general answers.

Revisiting old data/post with latest tool set

A reader reminded me of A short ME/CFS/MCS remission with microbiome samples [2019], which used uBiome. The toolset has changed a lot since those days, so I thought it would be a good learning activity to look at the samples with the new tools.

The person had a short remission from ME/CFS after:


The table below shows about the same number of bacteria identified but with an increase in the number of bacteria at extreme values. Condition Est. had a dramatic drop which would agree with the remission. We also see a dramatic drop in extreme Enzymes and Compounds.

In my humble opinion, it suggests that reducing extremes of enzymes and compounds is a desired objective goal.

CriteriaCurrent SampleOld Sample
Lab Read Quality9.18.1
Bacteria Reported By Lab327303
Bacteria Over 99%ile85
Bacteria Over 95%ile3822
Bacteria Over 90%ile7056
Bacteria Under 10%ile3821
Bacteria Under 5%ile2411
Bacteria Under 1%ile85
Lab: uBiome
Rarely Seen 1%31
Rarely Seen 5%264
Outside Range from JasonH77
Outside Range from Medivere1616
Outside Range from Metagenomics88
Outside Range from MyBioma1111
Outside Range from Nirvana/CosmosId1616
Outside Range from XenoGene3131
Outside Lab Range (+/- 1.96SD)1617
Outside Box-Plot-Whiskers12278
Outside Kaltoft-Moldrup156102
Condition Est. Over 99%ile00
Condition Est. Over 95%ile01
Condition Est. Over 90%ile111
Enzymes Over 99%ile00
Enzymes Over 95%ile5032
Enzymes Over 90%ile14894
Enzymes Under 10%ile80246
Enzymes Under 5%ile4550
Enzymes Under 1%ile61
Compounds Over 99%ile3182
Compounds Over 95%ile16465
Compounds Over 90%ile27535
Compounds Under 10%ile81319
Compounds Under 5%ile76237
Compounds Under 1%ile7270

Spot Checking Specific Bacteria Shifts

The more extreme bacteria shifts are shown below. The drop of Faecalibacterium levels was likely due to the drop of lactic acid produced by Lactobacillus [Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria 2020]. Given that the person has a ME/CFS diagnosis, my thoughts point to the massive reduction of Lactobacillus caused by Amoxicillin and Clavulanate resulting in a drop of lactic acid (see Lactic Acidosis in ME/CFS). While the bacteria producing lactic acid may be killed, it takes time for the system to clear it. Some sources cite a half life of 18 hours in the body[src]. The VSL#3 may be incidental or may have contributed to the remission ending.

BacteriaNewest Percentile(Percentage)Older Percentile(Percentage)
(genus) Alistipes31 (0.9%)89 (5.7%)
(genus) Anaerococcus97 (1.8%)62 (0.08%)
(genus) Bifidobacterium87 (3.6%)96 (7.3%)
(genus) Erysipelatoclostridium99 (3.9%)69 (0.7%)
(genus) Faecalibacterium19 (3.9%)51 (12.1%)
(genus) Finegoldia99 (3.5%)68 (0.1%)
(genus) Intestinibacter79 (0.4%)97 (2.4%)
(genus) Klebsiella91 (1.3%)none
(genus) Kluyvera89% (1.8%)none
(genus) Lactobacillus67 (0.01%)97 (3.5%)
(genus) Megasphaera96 (2.6%)76 (0.01%)
(genus) Parabacteroides95 (7.0%)81 (3.5%)
(genus) Streptococcus99 (7.3%)13 (0.003%)

Bottom Line

Short term remission causes are often difficult to identify the cause. In this patient, the evidence appears to be for a model of Amoxicillin and Clavulanate being effective against existing lactic acid producing species (i.e. Lactobacillus). It takes time for the lactic acid to clear the body. On the flip side, the lactobacillus would start regrowing and producing lactic acid (thus ending the remission).

A compounding factor is “Antibiotic Resistance of LACTOBACILLUS Strains [2019]”

For the subset of people with ME/CFS that improves on antibiotics and then regress; it is likely because the antibiotic suppress (but does not eliminate) lactic acid bacteria which then regrows…

Missing Vitamins, Minerals suggestions


Quick question—I noticed, for my BiomeSight-via-Ombre sample, that I’m not getting Vitamins, Minerals and similar suggestions. I used to get them on this sample. This only happens when I set the “Everything” option.

Anything I might be doing wrong? I’m generating the suggestions with the KM, Box Plot whisper, and Standard Lab Ranges. Avoiding Special Studies per your recent advice.

Answer: No Reproduction

I did a video to show what I did and the results.

Long time ME/CFS

Hi I’m a 15 year CFS sufferer with severe GI / neuro problems.  I got my second Thryve results recently.  They look really quite normal to me and it says I have significant diversity.  Is there any help / analysis you could provide to help me narrow down if there’s something actionable?  I’m not sure how much capacity you have for that, but it doesn’t hurt to ask.

  And unfortunately have been sick for longer.  Got sick at age 25 with an infection (low grade fever for months), lost 30 pounds, had vision problems, headaches, fatigue and so on.  I was able to work four years in this state but eventually I had much worsening neuro and vision symptoms and was unable to work.  I developed POTS a couple years later and at times was using a walker to get to the bathroom and was bedbound.  I’ve had some episodes of vision loss that are very strokelike in that they debilitated me cognitively and visually for long afterwards (the vision loss itself resolves after some minutes or hours).

I want to emphasize the visual and cognitive impairment are totally debilitating.  I can barely read anything or reliably focus my eyes on anything, and I went from a previously extremely high functioning person to feeling drugged, barely here 24/7.  I have severe eye pain all the time.

So I’ve been sick for really my whole adult life, to varying degrees.  Primary debilitation is visual and cognitive but I have severe physical fatigue, POTS, am 30 pounds underweight, have been diagnosed with gastroparesis years back I just can’t keep the pounds on.  Also it is notable food makes me feel TERRIBLE. Right away I can feel stupid and drugged from it, but also 2-5 hours later is when I ache everywhere and get tired and non-functional.  The 2-5 hours I’m presuming is from some dysbiosis but right away is a little more puzzling.

I clearly have such bad digestion that it is not hard to imagine it is perpetuating my brain / eye / POTS symptoms.  I’ve tried everything under the sun, mainstream and holistic and nothing that is supposed to help the gut helps.  I think fasting gives me some relief but is not practical for someone so underweight.

My first thryve was on January 13, 2020.

My most recent thryve (now ombre) was October 2, 2022.

In between the two times I’ve cycled through several gut protocols, such as taking s boulardii, soil probiotics, bifidobacteria, sourkraut, and polyphenols.  Other times I tried a more killing oriented protocol with oregano oil, berberine, and once based on a stool test a prescription antifungal (sporonox).  I eat a very restricted diet and seem to react to pretty much every food, but I have cycled through different foods in the last couple years.  I’ve tried prebiotics like PHGG and lactulose recently and are finding at least in the short term I am losing weight and have worse neuro symptoms.

My digestion and overall symptoms have not really changed between the two times.  ombre says I have a quite high microbial diversity score which is surprising because I have a massive history of antibiotics.

The request

First Look at the sample

Comparing the samples, I see a much lower quality report (2.5) in 2020. It was interesting to see

  • Bacteria Over numbers drop despite more bacteria is latest sample
  • Bacteria Under numbers grew — which may be due to a better quality of sample (more bacteria)
  • Two of my usual measures showed improvement (despite more bacteria) — Outside Lab Range, Outside Box-Plot-Whiskers while the last one showed an increase which was a smaller percentage than the increase of bacteria reported.
    • My impression is that objectively he appears better than in 2020.
Lab Read Quality2.58.5
Bacteria Reported By Lab442656
Bacteria Over 99%ile102
Bacteria Over 95%ile4510
Bacteria Over 90%ile8823
Bacteria Under 10%ile54154
Bacteria Under 5%ile2194
Bacteria Under 1%ile619
Lab: Thryve
Rarely Seen 1%57
Rarely Seen 5%2837
Outside Range from JasonH66
Outside Range from Medivere1616
Outside Range from Metagenomics1010
Outside Range from MyBioma1313
Outside Range from Nirvana/CosmosId1818
Outside Range from XenoGene99
Outside Lab Range (+/- 1.96SD)275
Outside Box-Plot-Whiskers12451
Outside Kaltoft-Moldrup183239
Condition Est. Over 99%ile00
Condition Est. Over 95%ile10
Condition Est. Over 90%ile40
Enzymes Over 99%ile12190
Enzymes Over 95%ile208516
Enzymes Over 90%ile457585
Enzymes Under 10%ile59265
Enzymes Under 5%ile20154
Enzymes Under 1%ile220
Compounds Over 99%ile7324
Compounds Over 95%ile264101
Compounds Over 90%ile368172
Compounds Under 10%ile297265
Compounds Under 5%ile225223
Compounds Under 1%ile62165

In terms of bacteria distribution (not “diversity”). we see an abundance of domineering bacteria (90-99) in the earlier sample which flipped to proliferation of weak bacteria (0-9). Have tons of small amounts of bacteria at low levels should result in a good diversity. The over-representation of these nominal bacteria is a concern to me.

His attempts to change was successful. Ideally we can help more change in the desired direction.


Using PubMed data, nothing stands out and we have a very short list. This simply means that there is not a good match to the conditions reported there. In terms of Dr. Jason Hawrelak Recommendations we are at 89%ile, so generally good. The main items missing the goals by his criteria are: Faecalibacterium prausnitzii, Lactobacillus, Bifidobacerium and Akkermansia.

Given no strong pattern to match against, I will build a consensus from Lab RangeBox-Plot-Whiskers, Kaltoft-Moldrup and Dr. Jason Hawrelak Recommendations

Consensus – similar to a pattern common with ME/CFS patients

Cross validation to the literature on the above (i.e. seeing if any has been documented to help ME/CFS). Since neurological issues were called out (and I had just done another sample with this recommendation, a few more for Hesperidin)

So all of the top suggestions appear to have documented benefits for various subsets of ME/CFS. I use the term subsets because, while similar in some symptoms, there may be a lot of differences.

We also have the simplified suggestions (with dosages). This list is intended for the brain fog person.

Looking at this list, we see that he should consider using some of the probiotics he cited in his history: bacillus subtilis, bacillus clausii, bifidobacterium (animalis)lactis, bifidobacterium breve bifidobacterium infantis. We also have 3 lactobacillus which seems to often appear with ME/CFS samples: lactobacillus casei, lactobacillus gasseri and lactobacillus salivarius.

In terms of prebiotics, only chitosan was a positive. Selenium shows up as a strong recommended supplement. See the above download for more details.

Very atypically, KEGG probiotics reports very low recommendation values with E.Coli NOT being on the top of the list. I would keep to the above probiotics and ignore the KEGG list because of the low values.

Going over to the last, experimental, modelled food suggestions, Barley was the sole take. In terms of the consensus report, it’s a toss up with different variation being good to take or to avoid. Checking oats by itself, it’s a significant negative so I would exclude the last item below and suggests barley be considered.

Bottom Line

The top suggestions can all be verified in medical literature as helping ME/CFS and the suggestions are based on this individual’s microbiome — hence patient (and not study group) specific. Hopefully he will try them and in 3-4 months do another sample so we can evaluate the change (for better or worse — I want to learn, not be right).

Because of the weight issue, I would suggest trying Pendulum, the akkermansia probiotic. I noticed that it resulted in weight loss for me and recall that is also reported in the literature.

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.