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Original From April

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?

Clearly we see:

• Too few bifidobacterium/Streptococcus
• Too low blautia
• 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 infantis probiotics (“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])

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles [2022],

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:

• Too low Bifidobacterium
• Too high Akkermansia (22% of the sample)

Looking at the Clostridium, we see that the species causing the high number was not identified.

For Akkermansia, the species identified was Akkermansia muciniphila.

I did a hand picked set of suggestions using only these two, the suggestions are below:

I then ran the sample thru the new experimental food suggestions to see what foods are suggested. The most interesting takes are:

• Grape pure juice
• For meats: none of the top recommended are available – the are all game meats (caribou, reindeer, elk, and seal lion)

I then did the usual 3 computed ranges (Standard Lab Ranges (+/- 2 Std Dev), Box Plot Whisker, Kaltoft-Moltrup Normal Ranges ).

The results from these are similar:

• ethanol (not appropriate for a child usually, but some cultures allow it)
• omega-3 fatty acids
• lactobacillus casei (probiotics)
• Cacao
• fat

The full set is attached below

Changing to the experimental food suggestions, we see the top items being:

• Date, dried
• Goose, domesticated, liver, raw — may be a challenge!
• Crackers, standard snack-type, regular — should be an easy!
• Snacks, potato chips, made from dried potatoes (preformed), multigrain
• Catsup (likely due to the Lycopene in it)
• Juice, tomato, canned
• Sauce, pasta, spaghetti or marinara, ready-to-serve
• Apricot, dried
• Pomegranate, peeled, raw
• Caramels, soft & hard (and a lot of sugary foods) – there is a prospect that for this child “Eating healthy may not be healthy!“

The full list is attached. For many of the foods, we see this pattern for why the food was directed

For items further down the list we see sugars are not there, and a variety of vitamins, etc

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:

• Administration of Saccharomyces boulardii mafic-1701 improves feed conversion ratio, promotes antioxidant capacity, alleviates intestinal inflammation and modulates gut microbiota in weaned piglets.
  Journal of animal science and biotechnology (J Anim Sci Biotechnol ) Vol: 11 Issue 1 Pages: 112
  Pub: 2020 Dec 4 Epub: 2020 Dec 4 Authors Zhang W , Bao C , Wang J , Zang J , Cao Y ,
• Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial.
  PloS one (PLoS One ) Vol: 12 Issue 4 Pages: e0173802 Pub: 2017 Epub: 2017 Apr 7 Authors Villar-García J , Güerri-Fernández R , Moya A , González A , Hernández JJ , Lerma E , Guelar A , Sorli L , Horcajada JP , Artacho A , D Auria G , Knobel H ,
  

This is not major evidence, because one of the Clostridium family, Clostridium difficile has been extensively studied. A Prevention of recurrent Clostridioides difficile infection: A systematic review of randomized controlled trials [2020] study cites that Saccharomyces boulardii and  oligofructose was efficacious for rCDI prevention, but not for treatment. The oligofructose is in agreement with the grape juice and other fruites cited above. This is echoed in “Saccharomyces boulardii has shown effect as a prophylactic agent. ” [12].

If we look at probiotics studied for 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

• Cinnamon (Cinnamomum cassia): Dosage Information, Half life 6.7 hours
  • Cinnamaldehyde is the main mediator of cinnamon extract in mast cell inhibition [2015]
  • Cinnamon extract inhibits degranulation and de novo synthesis of inflammatory mediators in mast cells [2013]
  • Cinnamon extract reduces symptoms, inflammatory mediators and mast cell markers in murine IL-10(-/-) colitis [2016]
  • Cinnamon reduces inflammatory response in intestinal fibroblasts in vitro and in colitis in vivo leading to decreased fibrosis [2017]
• Resveratrol (Grape Seed Extract) Half Life 3 hours. Dosage: 2gm/day
  • Resveratrol Treatment Prevents Increase of Mast Cells in Both Murine OVA Enteritis and IL-10^-/- Colitis. [2017]
  • Resveratrol inhibits IL-33-mediated mast cell activation by targeting the MK2/3-PI3K/Akt axis. [2019]
  • Resveratrol Is a Natural Inhibitor of Human Intestinal Mast Cell Activation and Phosphorylation of Mitochondrial ERK1/2 and STAT3. [2021]
• Black Pepper (Piper Nigrum) Half life: 15 hours, 420mg/day
  • Piper nigrum extract ameliorated allergic inflammation through inhibiting Th2/Th17 responses and mast cells activation.
• Arginine and Glutamine: Arginine: 6gm/day, 2 hours. Glutamine: 1 hour, 30gm/day
  • Combined arginine and glutamine decrease release of de novo synthesized leukotrienes and expression of proinflammatory cytokines in activated human intestinal mast cells [2013]
  • Combined glutamine and arginine decrease proinflammatory cytokine production by biopsies from Crohn’s patients in association with changes in nuclear factor-kappaB and p38 mitogen-activated protein kinase pathways. [2008]
• Luteolin: 400 mg/day, 5 hours
  • Luteolin inhibits myelin basic protein-induced human mast cell activation and mast cell-dependent stimulation of Jurkat T cells. [2008]
  • Mast cells, T cells, and inhibition by luteolin: implications for the pathogenesis and treatment of multiple sclerosis. [2007]
  • Impact of polyphenols on mast cells with special emphasis on the effect of quercetin and luteolin. [2018]
• Quercetin: 2gm/day, 24 hours
  • Quercetin is more effective than cromolyn in blocking human mast cell cytokine release and inhibits contact dermatitis and photosensitivity in humans. [2012]Quercetin and Resveratrol Differentially Decrease Expression of the High-Affinity IgE Receptor (FcεRI) by Human and Mouse Mast Cells. [2022]
  • Inhibitory effect of quercetin on tryptase and interleukin-6 release, and histidine decarboxylase mRNA transcription by human mast cell-1 cell line. [2006]
  • Inhibitory effect of quercetin on tryptase and MCP-1 chemokine release, and histidine decarboxylase mRNA transcription by human mast cell-1 cell line. [2006]
• Taxifolin: 460 mg/day, 1.3 hours
  • Inhibitory effect of taxifolin on mast cell activation and mast cell-mediated allergic inflammatory response.
• Probiotics
  • See this list or probiotics for allergies

Reflection into the Microbiome

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.

Long COVID: This also applies here, “Tiny, Menacing Microclots May Explain Long COVID’s Symptoms“

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 (C_max) 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.

Supplement	Half Life	Max Dosage
Alpha Lipoic Acid	30 minutes [Full article: Alpha lipoic acid intoxication, treatment and outcome (tandfonline.com)	2400 mg/day (see Src)
Aspirin	3 hours at lower doses (300 to 600 mg), 5 to 6 hours (after 1 g), 10 hours with higher doses [source]	4000 mg/day [Aspirin Dosage – Drugsdb.com]
Grape Seed Extract / Resveratrol	2-5 hours [source]	2000   mg/day
Nattokinase	4-6 hours [source]	14,000   fibrinolytic units/day
Lumbrokinase	8.6 hours [source]	1470   mg/day
Serrapeptase	Could not find	30   mg/day
Boswellia Gum	6 hours	4800 mg/day [src]
Bromelain	6-9 hours	2000 mg/day
Piracetam	5 hours	24000   mg/day
Turmeric	6-7 hours	3000 mg/day
Licorice	3.5 hours	32   g/day
Ginseng	n/a	2000 mg/day
Coenzyme Q10	33 hours	1200   mg/d

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. 

Coenzyme Q10: absorption, tissue uptake, metabolism and pharmacokinetics – PubMed (nih.gov)

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.

Addendum: DAO – diamine oxidase

This is a troublesome one — with two answers!

• Toward Oral Supplementation of Diamine Oxidase for the … cites 18 hours
• Evaluation of porcine diamine oxidase for the conversion of histamine in food-relevant amounts [2020] cites 19 minutes

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.

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.

See also: A series of online meeting on using Microbiome Prescription [Sep 2023] update. Likely a better start point.

16s Samples

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

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.

Lab Name	Samples
Viome (No objective measures)	5
All Taxonomies from tests	67
Medivere: Gesundsheitscheck Darm (16s Limited)	15
GI360 Stool (UK)	29
Medivere: Darn Magen Diagnostik (16s Limited)	15
All Bacteria [Family] Reported	25
Smart Gut (ubiome 16s – Limited Taxonomy)	2
GI EcologiX (Invivo)	19
GanzImmun Diagnostics AG Befundbericht	14
DayTwo	8
GanzImmun Diagnostic A6 (cfu/gm)	80
Nordic Laboratories	2
InVitaLab (cfu/gm)	3
Biovis Microbiome Plus (cfu/g)	18
Diagnostic Solution GI-Map (cfu/gm)	498
Metagenomics Stool (De Meirleir) (16s Limited)	4
Genova Parasitology (cfu/g)	4
Verisana (cfu/ml) aka (kbe/ml)	2
Medivere: Darm Mikrobiom Stuhltest (16s limited)	12
Genova Gi Effects (cfu/g)	116
Kyber Kompakt (cfu/g)	2
All Bacteria [Genus] Reported	188
Bioscreen (cfu/gm)	13
NutriPATH	12
Gut Zoomer (vibrant-wellness)	6

New Food Features

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.