A reader asked me what is the impact on the microbiome of prunes. My response was simple — I know of no studies reporting the impact on the microbiome. Having a study is first class evidence.
I then pointed out to him that I have prunes on my web site under Foods with Flavonids,
With several listed
Clicking on it shows the contents, data is coming from these open sources:
I suggested that he looks up the main items that have studies and estimate.
Over the weekend, I reflected and realized that it would be more friendly for me to do this mathematically using some simplifying assumptions (i.e. the impact is linearly related to the component for all bacteria). The result is now added to the existing list of modifiers
These are second, perhaps even third class suggestions. We are running off inference.
You can get suggestions using these by selecting this
WARNING
I am refreshing source data from US Dept of Agriculture and the EU equivalent and then need to redo the mapping of the components to appropriate proxies. This is not expected to be done before 2023. Feel free to play around with it — but the results are suspect until the data is updated and re-mapped.
People may transcribe data from the tests below to microbiome prescription for suggestions. I just added statistics for how many transcriptions that has been done for each, and I also provided statistics for what they report by bacteria. These latter statistics are very interesting, one lab reports 50% of people have too low lactobacillus, another lab reports 8% only.
From https://www.microbiomeprescription.com/labs/stats
In the video below, I show how you can verified that the ranges they are using are correct, or if the ranges are incorrect — perhaps based on some ideological theory about what makes a healthy microbiome.
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)
” 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.”
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).
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]
“Maternal obesity, metabolic conditions, and high fat diet consumption increase maternal leptin, insulin, glucose, triglycerides, and inflammatory cytokines. This leads to increased risk of placental dysfunction, and altered fetal neuroendocrine development. Changes in brain development that likely contribute to the increased risk of behavioral and mental health disorders include increased inflammation in the brain, as well as alterations in the serotonergic system, dopaminergic system and hypothalamic-pituitary-adrenal (HPA) axis.” [2015]
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.
Daughter
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!)
“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:
“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.
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 salt.
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.
country
oPos
aPos
bPos
abPos
oNeg
aNeg
bNeg
abNeg
Denmark
35
37
8
4
6
7
2
1
Norway
33.2
41.6
6.8
3.4
5
7.4
1.2
0.6
Sweden
32
37
10
5
6
7
2
1
Iceland
46.8
27.2
9
2
8
4.8
1.6
0.4
Sri Lanka
43.42
21
25.78
5.13
2
1.04
1.25
0.26
India
32.53
21.8
32.1
7.7
2
1.36
2
0.48
United Kingdom
44
28
8
2
9
6
2
1
United States
37.4
35.7
8.5
3.4
6
6.3
1.5
0.6
Ireland
47
26
9
2
8
5
2
1
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…
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.
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.
ModifierType
Modifier2
Cnt
Prescription – Other
proton-pump inhibitors (prescription)
6
Sugar and similar
non-starch polysaccharides
5
Amino Acid and similar
acetic acid
3
Amino Acid and similar
Conjugated Linoleic Acid
3
Amino Acid and similar
l-citrulline
3
Amino Acid and similar
proline (amino acid)
3
Diet Style
animal-based diet
3
Food (excluding seasonings)
blackcurrant
3
Food (excluding seasonings)
fasting
3
Food (excluding seasonings)
lupin seeds (anaphylaxis risk, toxic if not prepared properly)
3
Food (excluding seasonings)
Pulses
3
Food (excluding seasonings)
safflower oil
3
Food (excluding seasonings)
wheat bran
3
Miscellaneous, food additives, and other odd items
isobutyric acid
3
Miscellaneous, food additives, and other odd items
isovaleric acid(fatty acid)
3
Prebiotics and similar
arabinoxylan oligosaccharides (prebiotic)
3
Sugar and similar
saccharin
3
Amino Acid and similar
propionate
2
Diet Style
fibre-rich macrobiotic ma-pi 2 diet
2
Food (excluding seasonings)
barley,oat
2
Food (excluding seasonings)
cranberry bean flour
2
Food (excluding seasonings)
Miso
2
Food (excluding seasonings)
navy bean
2
Food (excluding seasonings)
pectin
2
Food (excluding seasonings)
red alga Laurencia tristicha
2
Herb or Spice
Bofutsushosan
2
Herb or Spice
coptis chinensis (Chinese goldthread)
2
Herb or Spice
plantago asiatica l.
2
Herb or Spice
schisandra chinensis(magnolia berry or five-flavor-fruit)
2
Miscellaneous, food additives, and other odd items
Tributyrin
2
Prebiotics and similar
carboxymethyl cellulose (prebiotic)
2
Prebiotics and similar
oligofructose (prebiotic)
2
Prebiotics and similar
resistant maltodextrin
2
Prescription – Other
epicor
2
Probiotics
bacillus subtilis natto (probiotics)
2
Probiotics
saccharomyces boulardii (probiotics)
2
Sugar and similar
glucose (sugar)
2
Sugar and similar
levan
2
Vitamins, Minerals and similar
Ferric citrate
2
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.
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.
CLICK ON THE BACTERIA BELOW TO SEE WHAT INCREASES OR DECREASES EACH
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.
REMEMBER TO ANNOTATED YOU SAMPLES WITH YOUR SYMPTOMS
This is what Special Studies use.
Common Bacteria across labs is now available for each. https://microbiomeprescription.com/Library/CitizenScience
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.
“The results reflect the metabolic abilities of the respective bifidobacteria. B. bifidum used secretory glycosidases to degrade HMOs, whereas B. longum subsp. infantis assimilated all HMOs by incorporating them in their intact forms.” [2011]
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-Whiskers, Kaltoft-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!
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:
Ombre
Lab
Results
BiomeSight
Lab
Results
Criteria
6-Jul
19-Aug
10-Oct
6-Jul
19-Aug
10-Oct
Lab Read Quality
2.1
5.4
7.1
2.1
5.4
7.1
Bacteria Reported By Lab
365
628
625
280
497
490
Bacteria Over 99%ile
5
6
0
2
7
1
Bacteria Over 95%ile
27
24
1
19
31
11
Bacteria Over 90%ile
49
51
1
37
58
24
Bacteria Under 10%ile
18
60
485
45
62
224
Bacteria Under 5%ile
10
28
411
28
30
175
Bacteria Under 1%ile
1
7
317
1
13
135
Lab: Thryve
Rarely Seen 1%
0
9
1
0
4
2
Rarely Seen 5%
8
40
27
4
18
17
Pathogens
19
28
25
15
26
16
Outside Range from Medivere
16
16
5
4
4
4
Outside Range from Metagenomics
7
7
19
17
17
16
Outside Range from MyBioma
14
14
8
7
7
7
Outside Range from Nirvana/CosmosId
23
23
8
9
9
7
Outside Range from XenoGene
33
33
25
22
22
19
Outside Lab Range (+/- 1.96SD)
10
14
42
28
28
22
Outside Box-Plot-Whiskers
64
61
12
6
13
7
Outside Kaltoft-Moldrup
112
182
31
70
84
64
Condition Est. Over 99%ile
0
0
542
70
113
175
Condition Est. Over 95%ile
0
0
0
0
1
0
Condition Est. Over 90%ile
2
2
10
0
4
0
Enzymes Over 99%ile
13
15
17
0
6
0
Enzymes Over 95%ile
69
82
0
0
10
0
Enzymes Over 90%ile
155
411
0
22
32
0
Enzymes Under 10%ile
55
138
2
45
51
21
Enzymes Under 5%ile
22
67
1593
308
219
212
Enzymes Under 1%ile
5
2
1320
187
132
146
Compounds Over 99%ile
104
126
641
12
47
67
Compounds Over 95%ile
385
397
4
30
7
19
Compounds Over 90%ile
533
548
60
112
76
138
Compounds Under 10%ile
183
248
103
342
313
323
Compounds Under 5%ile
109
127
359
180
125
224
Compounds Under 1%ile
16
17
303
37
64
73
Compounds Under 1%ile
17
21
224
17
21
40
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).
Probiotics
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).
Thryve
Biomesight
Microbiome Modifier
Suggestions
Clinical Dosage
Est Confidence
Suggestions
Est Confidence
bacillus subtilis
Take
10 BCFU/day
340.4
Take
223.6
bacillus lichenformis
Take
279.1
Take
20.9
enterococcus faecium
Take
1 BCFU/day
13.2
Take
8
bifidobacterium longum
Take
10 BCFU/day
516.2
Take
182.5
lactobacillus paracasei
Take
40 BCFU/day
58.7
Take
397.5
pediococcus acidilactici
Take
157.7
Take
215.4
Items with Agreement
For other items, there were a surprisingly few in agreement.
Microbiome Modifier
Suggestions
Clinical Dosage
Est Confidence
Suggestions
Clinical Dosage
Est Confidence
galactooligosaccharides (GOS)
Take
10 gm/day
15
Take
10 gm/day
139.1
Calcium
Take
500 mg/day
129.2
Take
500 mg/day
36.2
Magnesium
Take
500 mg/day
189.7
Take
500 mg/day
119.2
D-Ribose
Take
10 gm/day
80.6
Take
10 gm/day
23.6
Glycine
Take
15 gm/day
409.2
Take
15 gm/day
258.5
Omega-3 fatty acids
Take
4 gm/day
166.8
Take
4 gm/day
289.4
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
Cacao (426) — not an item on the quick suggestions
“A study by Fallon et al found that some of the PTLDS patients in their trial experienced moderate short-term cognitive improvement from ceftriaxone treatment” [2008]
“Ceftriaxone has excellent penetration of the blood-brain barrier and is one of the most effective drugs for Lyme disease. Ceftriaxone is typically given once a day intravenously, typically in 45 minutes.” [Columbia-Lyme.Org]
See this 2015 post, Rifaximin and CFS , for CFS/ME that have used this
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.
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.
Analysis
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).
Criteria
On Kefir
Stopped Kefir
Lab Read Quality
3.9
5.3
Bacteria Reported By Lab
470
404
Bacteria Over 99%ile
11
0
Bacteria Over 95%ile
30
5
Bacteria Over 90%ile
43
19
Bacteria Under 10%ile
10
74
Bacteria Under 5%ile
1
39
Bacteria Under 1%ile
0
7
Lab: BiomeSight
Rarely Seen 1%
2
2
Rarely Seen 5%
12
14
Pathogens
29
22
Outside Range from JasonH
4
4
Outside Range from Medivere
14
14
Outside Range from Metagenomics
7
7
Outside Range from MyBioma
5
5
Outside Range from Nirvana/CosmosId
19
19
Outside Range from XenoGene
21
21
Outside Lab Range (+/- 1.96SD)
18
1
Outside Box-Plot-Whiskers
73
29
Outside Kaltoft-Moldrup
81
74
Condition Est. Over 99%ile
0
0
Condition Est. Over 95%ile
0
0
Condition Est. Over 90%ile
1
1
Enzymes Over 99%ile
1
0
Enzymes Over 95%ile
3
2
Enzymes Over 90%ile
24
41
Enzymes Under 10%ile
79
240
Enzymes Under 5%ile
26
158
Enzymes Under 1%ile
1
47
Compounds Over 99%ile
0
2
Compounds Over 95%ile
4
113
Compounds Over 90%ile
29
453
Compounds Under 10%ile
44
163
Compounds Under 5%ile
18
61
Compounds Under 1%ile
2
8
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
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]
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.
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])
blood–brain 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).
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.
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
The molecular weight impacts the ability to cross the barrier ” An increase of the surface area of a drug from 52 A2 (e.g., a drug with a MW of 200 Da) to 105 A2 (e.g., a drug with a MW of 450 Da) dramatically decrease its BBB permeation [Blood-brain barrier permeation: molecular parameters governing passive diffusion].”
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
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.
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.
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).
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…
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