This raises all sorts of questions — which I am not interested in exploring… “For better or worse, in sickness and in health”
My wink wink suggestion for microbiome issues has been “Snog a lot of pretty young healthy things as the best probiotic” — my wife does not agree…..
Comparison between Samples
The first step that I did was to verify that all samples used the same reference sticks. This means clicking this for each sample first.
New reference tables are uploaded once a week.
This person has processed FASTQ data thru both BiomeSight and OmbreLabs. I am using OmbreLabs data below. Using reference tables uploaded in 2023.
Criteria
6/8/2022
8/4/2022
9/6/2022
10/26/2022
Lab Read Quality
2.1
3.8
3.6
8.3
Bacteria Reported By Lab
534
774
721
775
Bacteria Over 99%ile
10
3
2
6
Bacteria Over 95%ile
58
27
24
22
Bacteria Over 90%ile
99
53
44
50
Bacteria Under 10%ile
25
68
48
127
Bacteria Under 5%ile
13
28
15
77
Bacteria Under 1%ile
5
3
1
16
Lab: Thryve
Rarely Seen 1%
8
14
9
12
Rarely Seen 5%
43
80
60
73
Pathogens
21
34
33
27
Outside Range from JasonH
5
5
7
7
Outside Range from Medivere
13
13
17
17
Outside Range from Metagenomics
9
9
9
9
Outside Range from MyBioma
7
7
8
8
Outside Range from Nirvana/CosmosId
23
23
19
19
Outside Range from XenoGene
44
44
49
49
Outside Lab Range (+/- 1.96SD)
38
39
26
22
Outside Box-Plot-Whiskers
177
202
153
118
Outside Kaltoft-Moldrup
206
257
203
292
Condition Est. Over 99%ile
0
0
0
0
Condition Est. Over 95%ile
0
0
0
0
Condition Est. Over 90%ile
0
0
0
0
Enzymes Over 99%ile
14
18
5
23
Enzymes Over 95%ile
115
105
59
112
Enzymes Over 90%ile
212
192
143
320
Enzymes Under 10%ile
63
106
93
266
Enzymes Under 5%ile
29
45
27
141
Enzymes Under 1%ile
2
2
0
8
Compounds Over 99%ile
37
36
31
119
Compounds Over 95%ile
289
288
275
281
Compounds Over 90%ile
372
381
361
385
Compounds Under 10%ile
288
255
235
298
Compounds Under 5%ile
192
159
136
216
Compounds Under 1%ile
37
14
4
31
General Impression
After the first sample, the next two had improvements but the last one went the wrong way.
Too high and Too low reduce for 2 samples and then increased
Too high or too low for Enzymes were the highest for the last sample
Most of the third party ranges were constant for the first two samples and most got worst for the last two samples.
Compounds are much less indicative of issues.
Special Studies are sensitive to lab quality,
6/8/2022 4-14%, top items: ME/CFS without IBS, Poor gut motility, Cold Extremities
8/4/2022 5-17%, top items: ME/CFS without IBS, Poor gut motility
9/6/2022 4- 18%, top items: ME/CFS without IBS, Easily irritated
10/26/2022 7 -22%, top items: General: Fatigue, ME/CFS without IBS
ME/CFS without IBS is a consistent top item and we see that the percentage is increasing.
Proposed Approach
Unlike many samples, we see distinct deterioration in several 3rd party criteria. For many samples, there is no change between samples. We will include those in the consensus, namely:
JasonH
Medivere
MyBioma
Xenogene
It is interesting to note that one 3rd part criteria improved: Nirvana. To this, we do our usual:
Lab ranges
Box-Plot-Whiskers
Kaltoft-Moldrup
The net result will be more bias to those in the 3rd party criteria cited above. Another way of stating that, we will emphasis more that which everyone agrees are most concerning.
The top suggestions (easily obtained):
Grapefruit seed extract (studies suggests that the preservative used is the active ingrediant)
We mostly eat pastured meats and vegetables. No cereals and little in the way of carbs or even fruit. I used to eat linseed crackers in the USA, but here I eat buckwheat instead. Here in Spain we switched from wild Alaskan salmon, to seasonal, local, small blue fish, like mackerel, sardines, etc. Added Rabbit and can eat a lot more quality raw cured pork, if we want to. I have always enjoyed natural wine and Spain has plenty of it. Fresh made coffee and 100% cocoa. Raw goat, sheep and cow’s milk are also available and I do enjoy them with some regularity.
Remember, foods are filtered to the nutrients that are above typical levels for foods containing the same nutrients. The goal is to reduce the intake of nutrients that have been identified to shift things in the wrong direction.
For most people, if you say reduce folic acid in your diet — most people will not have a clue. The purpose of the food suggestions is to translate a precise item into common foods.
Note: If a food in your diet is not in the list then we deem it as neutral. For example: there are 24 variety of rabbit in the food database, only one shows up in the suggestions from the sample, Rabbit, meat, raw, Oryctolaguscuniculus, (Nyama ya kalulu), which suggests to keep eating rabbit. Similarly for milk, the two that shows up are Milk with Cow’s blood (from Africa) of 626 entries for milk.
The video below may help understand Food Suggestions better.
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.
The information above should always be considered/discussed with your medical professional if possible.
You seem much more switched on than some of the functional doctors I have used
He’s already on anti histamine (ketotifen) [Editor: which decreases most bacteria]. He has been on it 7 months. It initially helped with foods but now I find it makes him irritable and tired all the time. He obviously has allergies and the doctors here don’t care obviously . Well I feel it’s made him a lot more irritable. It’s helped with sleep but that’s about it. He has the erratic mood swings and he’s worse for me.
I am worry that he has PANDA.
He had 3 lots of baby vaccines I do think he got worse after each. But I’ve skipped his one year vaccines. He was given omeprazole for acid reflux [Editor: it also decreases many bacteria and only increases Actinomycetales]. I stopped it after a few months because it made him worse
Hi Ken, hope you are well. We have introduced Oats and also apple to the diet. All is going ok…. until I gave some papaya. Ever since we have had sickness and orange diarreah….. any ideas? We stopped papaya, 2 days ago. Someone suggested we try papaya ages ago as it is soothing. Obviously not for sonny, given him sickness and diarrhea.
He has very high levels of lactobacillus
He has banana and oats now and apple. We have had to pick him up from nursery because of his diarrhea. Maybe he does have a bug… [Response give him a few days to recover]
5 May 2022
I think you’ve saved my life. My little boy is so much happier
Need to find a protein to go with the oats so he doesn’t get the spike in carbs so much now
[Response: Walnuts?] We have not tried those. May try grounded walnuts .
[Response: Walnuts and Oats/Barley often show up together in suggestions.]
Other carbs? Cous cous, sweet potato, pasta? [Response: Without data from a 16s microbiome sample, IMHO, playing russian roulette.]
Nov 17,2022
Ken…. You helped me massively before. My son will be 2 next month… his gut issues are so bad it’s making his behavior / anxiety awful. He even reacted to homeopathy, he went 3 days without a poop. He’s got so much inflammation / bacteria out of whack I can’t get it under control. No official diagnosis other then dysbiosis and heavy metals I’m in the UK
His current diet:
3 x 7oz bottles of formula milk – nutramigen
Wild salmon or lamb
Broccoli
Zucchini
Green apple
Gluten free porridge oats
Parsnips
We’ve been using colostrum too. Not sure if that’s similar to hmo [Response: It is not]
Last Microbiome Report was done by Invivo. Every commensal bacteria but one was flagged as out of range. Unfortunately, this report does not reported relative amount but some proprietary scale.
I think he started off sensitive from me. Then I breast fed him whilst I had antibiotics then the doctors gave him antacids.
Analysis
The history keeps echoing the same theme, the infant microbiome has been hammered for the last two years. As a starting point, what should a 2 year old healthy child look like?
No reported Prevotella, low Faecalibacterium prausnitzii
We limited appropriate information on the microbiome (I would strongly suggest using the UK firm Biomesight for the next microbiome test), but the model is pretty simple — somehow encourage a microbiome typical for a 2 year to develop.
My first concern is raising bifidobacterium. To me, that means a Human Milk Oligosaccharides (which may be challenge to get — could not find any on Amazon.co.uk. You may wish to contact Glycom in Denmark to see if they can assist. The second part also comes from the above article, Bifidobacterium infantisprobiotics (“a prolific utilizer of human milk oligosaccharides (HMOs) that is positively associated with human health”). The suggestion on Custom Probiotics of 5 BCFU of this specific probiotic for a child is likely a good start. BEWARE of mixtures – unless it is the first ingredient then the amount may be ineffectual. Both of these may be challenges to get in the UK.
Differences in the species composition and HMO-degradation genes of the initially dominant Bifidobacterium communities are especially relevant as recent studies of these same genes suggest that their depletion in industrialized infants could have long-term negative immune consequences (Bifidobacteria-mediated immune system imprinting early in life [2021])
He has high E.Coli, given his age, my first thought go to Symbioflor-2. It is droplets (normal adult dosage is 18), so you can start with just one drop in a glass of water and slowly work up the dosage. While it is an E.Coli bacteria, it is a good E.Coli that should outcompete some of the bad E.Coli.
The last item that I would consider are some bacillus probiotics. These are often picked up from grass and fields (“the wild”). There are many listed here. Considering the allergy/histamine issues, I would avoid those that are known histamine producers.
Make one change at a time, no more than one a week.
Update with Current BiomeSight Data
Looking at Bacteria deemed Unhealthy, one item stands out: Clostridium which is at the 98%ile while only 5.5% of the sample. Dr. Jason Hawrelak Recommendations (does not include Clostridum) we see two items of special significance:
Reminder: For food suggestions, it is wise to jump up and down the list for various net-values. Most items with the same value are likely selected for the same nutrients in it.
Feedback from Reader
She expressed the opinion that the solution to the Clostridium is just taking Saccharomyces boulardii. That is may help reduce is supported by two studies:
If we look at probiotics studiedfor Clostridium, we see 112 studies; most for Clostridium difficile – especially prevention when antibiotics are taken. Florastor®(Saccharomyces boulardii CNCM I-745) is the only one studied that is available in the retail market. Other cited are Bacillus clausii,Bacillus coagulans, Bacillus mesentericus, Lactobacillus rhamnosus GG etc. Almost all of the studies are for prevention and not for treatment. In other words, it helps create an unfriendly environment for C.Diff. but appears to be in effectual fighting it.
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.
The information above should always be considered/discussed with your medical professional if possible.
In discussion with readers, interest in non-drug treatment of mast cell and histamine issues is very high. Trying to get traction with the microbiome has not been successful. On how to use Half-Life, see Half-Life: Not the game but supplements!For Arginine and Glutamine, 100mg of each every hour is suggested.
Dosages: Are the maximum deemed safe by an authority, not recommended dosage
Most of the items above are modifiers on Microbiome Prescription. An interesting experiment is to see which bacteria/taxa are modified in common with the above. Below are the taxa that occurs 6 or 7 times for the above 7 items.
Taxa Name
Rank
Impact
Times Shared
Bacteroidaceae
family
Decreases
7
Lachnospiraceae
family
Major Decrease
6
Desulfovibrionaceae
family
Major Decrease
6
Clostridiaceae
family
Decreases
6
Bacteroides
genus
Decreases
7
Faecalibacterium
genus
Increases
6
Ruminococcus
genus
Decreases
6
Desulfovibrio
genus
Decreases
6
Roseburia
genus
Decreases
6
Eubacteriales
order
Decreases
6
Bacteroides xylanisolvens
species
Decreases
7
Bacteroides caccae
species
Decreases
7
Bacteroides ovatus
species
Decreases
7
Bacteroides uniformis
species
Decreases
7
Bacteroides thetaiotaomicron
species
Decreases
7
Phocaeicola vulgatus
species
Decreases
7
Items that are marked decreases, are likely bacteria you may want to reduce if you have mast cell issues. Faecalibacterium is the one bacteria that you want to increase.
Applying to your microbiome sample
On the [Research Feature] tab. Find this section and click #2
See Video above for the rest of the steps
As always, review your plan with your knowledgeable medical professional before starting. Some substances may be inappropriate for other medical constraints.
This week I have been pinged by several people with ME/CFS who have seen drops in Saturated Oxygen Level (SO2) during the day. One model of many symptoms of ME/CFS (brain fog, easy fatigue) is that of diminished oxygen deliver and reduced products clearance (like CO2 and Lactic Acid). This reduction of oxygen can be due to many causes: Coagulation, Inflammation, Hemoglobin (iron) disruptions, etc.
People who follow me knows, know that I prefer to work from facts, models and objective measurements. Saturated Oxygen Level (SO2) gives us an objective measurement. Personally, my wife and I use a smart watch that records my (SO2) and other factors every 10 minutes. The data has been helpful to us to triage some events — it is not a Star Trek Tricorder, but better than speculation. Images at end of the data.
Importance of Half Life
What is called half-life is actually critical for dosage size and timings. MDs prescribing drugs specify one tablet a day, two tablets every 12 hours, a tablet every 8 hours; are based on half-life typically.
What is half-life? It is simply the time it takes to reduce the level in the body to half of the prior amount.
This is not always simple, it takes time to get the supplement or drug into the body as the following quote indicates:
“In healthy volunteers who have taken oral doxycycline, the maximum doxycycline plasma concentrations (Cmax) of 1.5 to 7.0 μg/ml are usually reached within 3 h, and the drug has a half-life of 14 to 24 h” [2005]
Step One — Find Half Lifes!
This is actually pretty easy, usually typing in the supplement and “half-life” will return answers from the web. For the above people, I assembled a list of possible testing supplements from prior posts on coagulation to see if we can determine the possible mechanism for the SO2 drop they saw. The purpose is to identify a probable cause which should then be discussed with your medical professionals.
See this post for the literature on these. We want to then find the half-life and the maximum safe dosage. Many of the maximum deemed safe (i.e. used in studies dosages) are listed here.
As above, there can be time to get it into the body as the following states for CoQ 10.
The T(max) is around 6 h, with an elimination half-life of about 33 h. The reference intervals for plasma CoQ10 range from 0.40 to 1.91 micromol/l in healthy adults. With CoQ10 supplements there is reasonable correlation between increase in plasma CoQ10 and ingested dose up to a certain point. Animal data show that CoQ10 in large doses is taken up by all tissues including heart and brain mitochondria.
This is a useful exercise to do for ALL OF YOUR SUPPLEMENTS. This will answer the question, should you do one mega dose a day or 4 small dosages thru the day or even 6 or 8 small dosages per day – to get the best results. You want to maintain a reasonable level in your body for the whole day.
One possible strategy
There are many possible approaches, my preference here would to start with the longest half life and work down. This leads to the following suggestions (to be discussed with your medical professional)
CoQ10: 300mg day 1, 600 mg day 2, 900 mg day 3, then 1200 mg/day for at least 2 weeks.
4 capsules per day for some products
Bromelain: : Given the half life, I would start with 1 capsule every 12 hours (typically 500mg), doubling the dosage on the second day and then keep repeating for the rest of the week
Lumbrokinase: Given the half life, I would start with 1 capsule every 12 hours, doubling the dosage for the next 4 days keep repeating for the rest of the week
etc
You want to identify the substance that hints at the source, then get your MD involved. Do not try all of them at once. Introduce one item a week and see what the response is. Personally, I did the Aspirin route which had me running up and down the walls after 7 days — that response persuaded the MD to order the Hemex Lab Coagulation Panels which identified issues. That lead to appropriate treatment.
For the short half-life items, You want to take a SO2 measurement no longer than the half-life. For Alpha Lipoic Acid, the typical capsule is around 300 mg, so I would go for one capsule every hour for 4 hours and monitor the levels for at least 6 hours. This will keep the concentration at a reasonable level. Going above the maximum dosages has significant risk. This is an example for ALA, Alpha lipoic acid intoxicatıon: An adult [2018]. As always, have your plan reviewed by your medical professional before starting.
Remember: Record in Excel or other product your base line — the daily or weekly pattern before you start. Keep up the recording of SO2 as you walk thru the substances. For me, having a smart watch that does it makes it so so easy with awesome data to show my MD.
If DAO is being taken to reduce histamine in the body – we use 18 hours. If it is being taken to quiet down the histamine release in the gut from eating something, it is 19 minutes. So, taking DAO immediately before or during a meal may have the best benefit.
The Unique Possibility of Symptom Treatment Resolving the Cause
My model of coagulation issues is simple: some group of bacteria are dumping chemical signals into the body that triggers one or another form of coagulation. Why would they be doing that? Survival! These bacteria prefers a low oxygen environment so they are taxa-forming your body for their needs. Increasing the oxygen level in the body will typically inhibit these bacteria – but may not be enough to suppress them. The use of other substances (in the personal experience that I cited above, following Cecile Jadin’s “Occult Rickettsia” protocol of rotating antibiotics) may be needed to suppress these troublesome bacteria, to “rid me of this meddlesome taxa”. Note: The virus or bacteria that trigger the illness is unlikely to be the meddlesome ones, rather, other bacteria that saw opportunity in its disruptions of the body and exploited it. I believe these bacteria are seen in stool microbiome samples.
Example of the recording on the Smart Watch of Oxygen Levels
The two videos below are intended as quick introductions to the microbiome prescription site. The site is dynamic with continuous changes of data available and being used.
This covers sites that provides comprehensive reports on your microbiome. The better reports typically report on over 500 different bacteria from a sample.
Lab/Processor
Low
Typical Count
High
Samples Uploaded
AmericanGut
73
156
213
18
BiomeSight
11
572
1305
1635
BiomeSightRdp
279
573
862
15
CosmosId
6
436
705
36
es-xenogene
5
761
5225
24
Medivere
530
721
934
7
Microba
53
126
186
21
OmbreLabs/Thryve
185
671
2238
1241
SequentiaBiotech
166
313
460
36
uBiome
6
249
589
814
Statistics at the start of January 2023
Older Labs
These are older technology and often are focused on a small number of bacteria. Often the focus was based on what was deemed significant 10 or even 20 years ago.
This feature was added because many of the suggestions were for flavonoids or other items that may or may not be available as supplements. Most people do not know what is in different foods, especially items you are wishing to avoid. The intent is to allow a more comprehensive and rich diet to be developed by users.
This is a reader with a diagnosis of Crohn’s diseases with complications (severe histamine and mast cell issues, severe multiple chemical sensitivity). She also have had ongoing hot flashes for a few decase The Crohn’s has been stabled and does not require prescription medications; it has been treated by diet and the use of E.Coli probiotics (Symbioflor-2: SOURCES: https://www.paulsmarteurope.com/ and https://www.naturitas.us/, and Mutaflor). When a flare starts, the E.Coli probiotics have been able to quiet things down quickly.
Using the new Food Suggestions (with consensus)
This is a new feature that is intended to supplement the first class suggestions from microbiome prescription. Almost 8000 different foods are evaluated. The intent is to allow people to fine tune diets for the most impact especially when flavonoids and sugar types are given by name, but not by what food contains them. Some foods may have both good and bad content, the intent is do a deep evaluation of the foods based on their reported nutrients. For more information, see this blog post.
Overview of Samples
The general impression of the samples is reasonable stableness. Some third party criteria improved (Metagnomics, Xenogeme) and other third party criteria (Medivere,MyBioma,Nirvana) got worst, and one with no change(JasonH). The same is seen with the statistical ranges.
Criteria
2022
2021
2020
Lab Read Quality
3
4.1
3.8
Bacteria Reported By Lab
524
584
721
Bacteria Over 99%ile
5
9
6
Bacteria Over 95%ile
30
44
36
Bacteria Over 90%ile
52
82
84
Bacteria Under 10%ile
45
25
26
Bacteria Under 5%ile
15
10
4
Bacteria Under 1%ile
0
0
0
Lab: Thryve
Rarely Seen 1%
8
4
9
Rarely Seen 5%
27
29
51
Pathogens
29
33
28
Outside Range from JasonH
7
7
7
Outside Range from Medivere
15
15
14
Outside Range from Metagenomics
10
10
12
Outside Range from MyBioma
13
13
12
Outside Range from Nirvana/CosmosId
23
23
14
Outside Range from XenoGene
40
40
49
Outside Lab Range (+/- 1.96SD)
31
22
18
Outside Box-Plot-Whiskers
138
109
142
Outside Kaltoft-Moldrup
184
163
205
Condition Est. Over 99%ile
0
0
0
Condition Est. Over 95%ile
1
2
1
Condition Est. Over 90%ile
1
2
1
Enzymes Over 99%ile
3
9
0
Enzymes Over 95%ile
32
64
23
Enzymes Over 90%ile
65
194
71
Enzymes Under 10%ile
136
45
68
Enzymes Under 5%ile
42
21
37
Enzymes Under 1%ile
0
4
0
Compounds Over 99%ile
26
14
21
Compounds Over 95%ile
122
29
29
Compounds Over 90%ile
350
38
37
Compounds Under 10%ile
149
24
22
Compounds Under 5%ile
31
17
18
Compounds Under 1%ile
4
6
6
Looking at Special Studies:
2020 – 7%- 21% matched, 38%ile against PubMed Criteria
2021 – 5% – 18% matched, 32%ile against PubMed Criteria
2022 – 5% – 16% matched, 74%ile against PubMed Criteria
The top common ones across the years are:
Poor gut motility
ME/CFS without IBS
Easily irritated
Post-exertional malaise
Depression
We do not have sufficient samples yet to do a special study for Crohn’s disease.
There appears to be a weak indication of worsening — this may be due to not being able to get Mutaflor (E.Coli Nissle 1917) during COVID restrictions. This was remedied shortly after the last sample.
risperidone: was the top one, this is used to treat mood disorder (depression and irritability bacteria?)
hexestrol: a nonsteroidal estrogen which was previously used for estrogen replacement therapy (hot flashes)
ethopropazine hydrochloride: a drug uses for Parkinson’s disease. A blood family member had Parkinson’s and the person has seen the occasion “shake” in her hands that has raised concerns about that condition
The next items were antibiotics and significantly less confidence.
This is not totally surprising that prescription items appear to match conditions. The mechanism of action of these prescription drugs may be partially thru the microbiome.
Returning to the non-prescription world, in terms of priorities:
In one sense, the reader was very pleased with these suggestions being almost entirely supplements. The histamine issues greatly restricts her food choices (she is already gluten free!)
Food Suggestions
I did a walk thru of the food suggestions for this sample. See the video below.
Go to Microbiome Prescription, log in and go to [Changing Microbiome]. At the bottom of each section you will see a check box. Make your usual selection and then check this choice and click [Get Suggestions]
You may wish to do a regular suggestion first. It seems that the more bacteria being selected, the finer the suggestions are.
The suggestions are on a subdomain to distribute the load.
Clicking on a food shows the nutrients. Nutrient that are higher than typical have a * . These are the reason for the food being selected. One or more of these nutrients should help your microbiome.
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…
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