Babe’s gut destroyed at mother’s breast..

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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.


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?

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

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 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:

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:

The full set is attached below

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

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

Baby cereal, containing milk, 12months, strawberry flavor, dry

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:

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.

2 thoughts on “Babe’s gut destroyed at mother’s breast..

  1. I have a 2.5 year old with ASD, and he has prevotella. hard to put this all together, but neat to compare with the healthy subjects. thank you for sharing

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