Backstory

• My son is 5.4 years old , he was diagnosed with autism at 22 months of age .
• We have been strict gluten free casein free sugar free no processed food since his diagnosis .
• For almost 2 years we followed the ne chek protocol with olive oil, fish oil and 1/32 spoon of inulin.
• My son was always verbal with alphabets , numbers colors , planets shapes , colors etc and the odd one / two word request sentences but never conversational.
• His receptive language was very poor until maybe the last year where he is able to follow simple one step instructions.
• He now repeats what is said to him and can answer to what is your name and other v simple questions .
• He is not potty trained and does not understand social norms . He interacts with family members and other adults ( other adults mostly for his needs ) 
• He eats mainly veg and chicken , fish or lamb . Occasionally rice but mostly carb free.
• He consumes a lot of bananas in a day (5-6).

Foreword – 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.

Reminder: the purpose of these posts is show the process. Every individual will get different suggestions, the suggestions should not be used viewed as suggestions for any symptom or condition.

For more posts on Autism and the Microbiome

Proforma Overview

The percentile overview shows a moderate bias toward rarer bacteria.

Percentile	Genus	Species
0 – 9	22	37
10 – 19	22	21
20 – 29	17	13
30 – 39	8	12
40 – 49	11	14
50 – 59	4	6
60 – 69	9	12
70 – 79	11	17
80 – 89	12	15
90 – 99	11	16

Potential Medical Conditions Detected has two very interesting items over 90%ile matches, namely:

• Brain Trauma (99%ile)
• Schizophrenia (98%ile)
• For Autism he is down at the 81%ile

Other items over 90% tend to be age related, i.e. Alopecia (Hair Loss), hypertension (High Blood Pressure)

Dr. Jason Hawrelak Recommendations came in at 95.6%ile healthy, so no issue there

Since the interpretation of the microbiome data was done thru biomesight, we see that the top matches include:

• Depression
• Autism
• Easily Irritated
• Brain Fog
• Neurocognitive: Attention, Memory, Focus

We have 8 significant pattern matches above and will use each to build a consensus of suggestions. A pattern match means that both of the following appear correct: microbiome pattern matches, the patients symptoms or issue are a reasonable match.

Speculation: The brain trauma and schizophrenia being a much stronger match than autism hints that this child issue may be more related to the microbiome than autism proper.

Consensus Overview

Probiotics

The top item using KEGG data was, Escherichia coli, the prescript assist/equilibrium bacteria and then Bacillus thuringiensis, Bacillus subtilis, Bacillus subtilis subsp. natto, Bacillus amyloliquefaciens, Bacillus licheniformis – further down the list, Akkermansia muciniphila.

We have agreement between two very different paths of picking them (i.e. one by using the genomics of the microbiome and looking at the genomics of the probiotics; the other was using clinical studies reporting desired shifts for the bacteria that was selected). To put some specific brands (when not named above) see this list.

Supplements and Food

Iron (Ferric citrate), Magnesium, l-citrulline, propionate, Reduce choline (Beef, Chicken Eggs) – i.e. more fish, cranberry bean flour or cranberries, blackcurrant, blueberry hydrogenated palm oil, Pulses (pea (fiber, protein), navy bean), Cottage Cheese, berberine, stevia, d-ribose, galactose (milk sugar), lactose.

Many of the above are clustered, i.e. d-ribose and e.coli probiotics (one feeds the other); high saturated milk fat diet and (cottage cheese, galactose, lactose).

Diet style

The Avoids

The avoidance list is rich in “you should be taking items” suggested on the social media on the internet. In fact, they are contrary to the pattern that I typically see with ME/CFS or Long COVID. Everyone is different and it is good to do an evidence based approach for suggestions.

Questions and Answers

Readers usually get a chance to provide more information and ask questions before postings.

Q: we have been on a strict diet for our son, mainly we have not been doing GF/CF diet. Do you recommend moving to a full diet, i.e giving him milk and Gluten.

A: Milk and milk products – yes. Chocolate milk made with real Cacao is supported by the suggestions. 
I checked gluten items:

• Gluten Free was a mild negative (-25) but checking for specific gluten foods, they were all more negative
• Wheat was also a negative – 103
• Oats was also a negative -32
• Barley was also a negative -146
  
  So, I would suggest keeping him gluten free

Q: (From Social Media): “I wonder what the effect is/was of 5 to 6 bananas a day”

A: In the suggestions, bananas was listed as a take in terms of the microbiome. Potassium is a factor for some autism (not all):

• Potassium channels and autism spectrum disorder: An overview [2021]
• Update on the implication of potassium channels in autism: K⁺ channel autism spectrum disorder [2015]
• One parent of a child with Autism experience is given in this post: Potassium may play an important role in Autistic Behaviors [2013]

The message from the parent was clear and with lots of documentation

 My 5 y.o. daughter is having major gut issues for which I am seeking your help. She is having these issues since her birth and we just stand helpless while she cries most of the night.  I have made an excel sheet explaining all her issues for your reference. I am also attaching  her Biomesight.csv file, HTMA Test, GI Map test and her other medical test and stool test results for your kind reference. 

Gut Issues	Sensory Issues	General Behaviour	Socialization	Speech	History, Curent Supplements & Diet
Excessive Gas mostly in evening and night.	Hitting Hard Objects/Plastic in the front teeth	No aggression , no self injurious behaviours	Doesn’t have age appropraite play behaviour	No true words. Only few nonsense syllables	Birth weight-3.45 kg. C-Section delivery.
Bloating	Crashing & Jumping on couch & bed.	Sweet frendly kid. Attention seeker.	More afectionate to adults than kids.	Started comprehending two word commands with gestures	She had several doses of Antibiotics due to flu, fever on more than 5 occasions. She had a teeth infection for which she was given antibiotics. She also had some gut bug for which she vomited more than 12 times in a single night, in the past (at the age of 20 months)
Fatulence/Burps	Looking from the corner of the eye.	Scratching others	Near Normal Eye Contact and Sitting behaviour.	Child expresses her needs through hand leading and dragging parents towards the desired object.	Child gained a lot of weight since childhood. She was 22kg at the age of 2.5 years. Now she is 40kg. Her height is 120 cm
Undigested food in stool mostly vegetables	Rocking back & forth while standing.	Biting other	Poor Focus & Attention		Celiac test is negative. Low in Vitamin D & Iron. Ultrasound test of abdomen is normal
Constipation. Bristol Stool Chart No.-3/4	Making sudden loud noises	Pinching & Hitting others	Shows no interest/high resistance  to any learning activity. Escape behaviour		Supplement– SunFiber, Liver Sauce, Chamomile Tea, Sodium BiCarbonate to relieve gas issues.
There is immediate relief as soon as she passes the gas through fart or burps.	Unusual laughter/ Teeth Grinding (Occassionally)	Restlessness, Crying and Yelling			Diet -GFCFSF diet. Vegetables- Okra, potato, carrots, beans, tomato,snow peas. Other food- boiled chicken, low GI- rice, millet, gluten free flour, gluten/diary free cookies. Fruits- Banana, kiwi, apples.
	Stifening of whole body and hitting with her finger tips	All the above problematic behaviour is noticed when the kid has gut issues
	Hitting her face on gym ball/mattress
	Hand Twirling infront of her face.

Initial Review

My expertise is statistics associated with the microbiome, not autism (although I am a high functioning ASD person).

First looking at distributions we see a predominance of rare bacteria. Usually that hints at herbs to reduce their numbers. Dr. Jason Hawrelak Recommendations placed her at the 95.6%ile, so a main stream solution is unlikely.

Looking at the unhealthy bacteria, several stands out as items of concern:

• Escherichia coli – which are likely the unhealthy ones. This immediately causes me to suggest either Mutaflor (available where she lives) or Symbioflor-2, the good E.Coli probiotics. Given her age, I would start with Symbioflor-2 because it is given in drops and thus we can slowly ramp up (to avoid severe adverse effects). The other option would be to repackage one capsules of Mutaflor in eight capsules and start with lower dosages. Given the symptoms above — this would be my first course of action if it was my child.
• Bacteroides fragilis is high. In terms of non-prescription, pomegranate, lactobacillus reuteri (probiotics), N-Acetyl Cysteine (NAC), Cacao and Mangosteen are the most documented. REMEMBER: There is no literature on relative effects, the Confidence on suggestions is based on the number of studies showing desired effects on the number of bacteria we selected to alter.
• Serratia is also high. Usually associated with urinary tract infections. For this, we have less literature. I would suggest neem tea and perhaps  lactobacillus casei (probiotics)

At this point we have a little dilemma — Escherichia coli and Lactobacillus are hostile to each other, so it’s an either/or. I would usually resolve it by 2 weeks on one and then 2 weeks on the other, recording any changes seen.

Given the history of needing antibiotics in the past, I looked at the computed suggestions. If the needs arise again, see if your MD is willing to use any of the following:

1. macrolide ((antibiotic)s)   (0.444)
2. imipenem (antibiotic)s   (0.382)
3. fluoroquinolone (antibiotic)s   (0.337)
4. ciprofloxacin (antibiotic)s   (0.305)
5. clindamycin (antibiotic)s   (0.294)
6. erythromycin (antibiotic)   (0.274)

Please make sure that you check risk factors for the above, especially given her age. For example, fluoroquinolone has many! The above were calculated solely on the microbiome impact, not risk factors.

Other Medical Reports

After the first impressions above, I went to look at the other test results

• Hair shows slightly out of range for Arsenic (common for ASD)
• Celiac tests: negative
• Cortisol: in range
• Lipid Profile: normal
• Serum Free T3+Free T4+TSH: normal
• Ultrasound: normal
• Vitamin D + Iron: normal
• Gastrointestinal Pathogen PCR (Stool): Negative
• Liver Function: normal except for
  • Alkaline Phosphatase: high (2x upper limit)
  • Sodium and Potassium – slightly high (similar on hair above)
• GI Map
  • Bacteroides fragilis: High, as above
  • Enterococcus: High (versus 18%ile, low on Biomesight results)
  • Escherichia species: At top of reference range (97%ile on Biomesight results)
  • Akkermansia Munciniphila: none detected (none detected on Biomesight results)
  • Zonulin [literature] was very high indicating leaky gut.

Looking at Biomesight results

• Bacillus was not high
• None of the Enterococcus were reported and the family was a little low
• Morganella was not reported
• S. Aureus was not reported
• Streptococcus was low

I will make the assumption that at least one round of antibiotics were done between the GI Map (Mar 29,2022) results and the Biomesight results — although I have read studies questioning the reliability of some GI Map results.

Probable Symptoms

This was recently revised, and seems to match — especially the time since offset.

Symptom	Matches
less than 04 years since onset	77
Frequently loose train of thought	75
Lyme	74
Less Avoidance of Eye Contact or Poor Eye Contact	73

Where Do we go from here?

I picked the following to build the consensus report shown below:

• Special Studies: Autism (75)
• Special Studies: Inflammatory bowel disease ( 86 candidate bacteria) – given all of the bowel issues
• JasonH (15 Criteria) – just 7
• Standard Lab Ranges (+/- 2 Std Dev) – just 7
•  Box Plot Whisker – 45
•  Kaltoft-Moltrup Normal Ranges – 109
•  Percentile in top or bottom 10% – 134

It was interesting to note that the methods that selected the most bacteria, were the special studies, KM and the top/bottom 10%.

Consensus Suggestions

As always, the full consensus report is attached.

In reviewing the list, the ones that I would be most inclined to use are:

• Triphala
• Bofutsushosan (which will encourage Akkermansia!)
• Omega-3 fatty acids
• Lactobacillus rhamnosus (probiotics),
• berberine

I should note that symbioflor 2 e.coli probiotics is on the avoid list — this often happens when there is a need to increase lactobacillus which was sitting at 6%ile. When lactobacillus is low, I tend to ignore the avoid on E.Coli probiotics and point out the mutual hostility they have – so do one and then the other, noticing any changes (the one that gives the best positive change, do more of — but keep rotating). I usually suggest starting with the E.Coli probiotics because they are known to persist. This is rarely the case for Lactobacillus probiotics.

People who have uploaded their (or their children) samples have annotated some with easily irritated. On my main blog, I have been doing a series of deep statistical dives on my main microbiome blog site, and checked it the data available reaches the threshold for inclusion as defined in A new specialized selection of suggestions links (A summary table of various studies has been added there).

I am posting here to since it is a blog focused on Autism and easily irritated is a common symptom.

Study Populations:

Symptom	Reference	Study
Easily irritated	1108	55

• Bacteria Detected with z-score > 2.6: found 146 items, highest value was 9.9
• Enzymes Detected with z-score > 2.6: found 896 items, highest value was 5.9
• Compound Detected with z-score > 2.6: found ZERO items

For the number of samples, the z-score for bacteria are unusually high compared to other studies in the series. A high z-score means strong statistical significance. Enzymes has a huge numbers detected without any extreme values – this is interesting but unsure on how to interpret that.

Interesting Significant Bacteria

• All bacteria found significant had too low levels

The most significant ones are listed below. I should point out that these bacteria may not be the cause, rather they may be ‘the canaries in the coal mine’ of the microbiome. These studies’ methodology determines association and not causality.

Bacteria	Reference Mean	Study	Z-Score
Prevotella oulorum (species)	63	17	9.9
Prevotella copri (species)	65522	9089	8.8
Clostridium malenominatum (species)	57	22	6.3
Pediococcus (genus)	112	48	6.1
Phocaeicola coprocola (species)	7544	45	6.1
Actinobacillus pleuropneumoniae (species)	57	19	6
Opitutae (class)	169	43	5.8
Puniceicoccaceae (family)	163	40	5.8
Lactiplantibacillus pentosus (species)	122	17	5.8
Bifidobacterium cuniculi (species)	81	25	5.7
Cerasicoccus arenae (species)	552	87	5.5
Prevotella (genus)	73346	26681	5.5
Puniceicoccales (order)	114	35	5.4
Veillonella (genus)	4004	1945	5.4
Cerasicoccus (genus)	319	56	5.3
Tenericutes (phylum)	3138	1053	5.1

Interesting Enzymes

The first 100 enzymes (of 800+) found significant had too low levels.

Enzyme	Reference Mean	Study Mean	Z-Score
propanoyl-CoA:NADP+ oxidoreductase (1.3.1.84)	29	10	5.9
S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)	3653	1426	5.8
3-oxo-Delta1-steroid:acceptor 1-oxidoreductase (1.17.99.11)	28	10	5.7
cholest-4-en-3-one:acceptor oxidoreductase (25-hydroxylating) (1.17.99.10)	28	10	5.7
n/a (3.4.24.20)	40	16	5.2
malonyl-CoA:acetate malonyltransferase (tetracenomycin-F2-forming) (2.3.1.235)	41	11	5.2
malonyl-CoA:malonamoyl-[OxyC acyl-carrier protein] malonyltransferase (2.3.1.260)	41	11	5.2
NADPH:acceptor oxidoreductase (1.6.99.1)	5726	2382	4.8

I will leave it to the reader to go to Kyoto Encyclopedia of Genes and Genomes to learn about these enzymes (a steep learning curve).

The top item S-adenosyl-L-methionine (SAMe), had significant literature associated with it, a few samples:

• “S-adenosyl methionine prevents ASD like behaviors triggered by…” [2019]
• “S-Adenosyl-Methionine alleviates sociability aversion and reduces changes in gene expression in a mouse model of social hierarchy” [2022]
• “Blood biomarker levels of methylation capacity in autism spectrum disorder: a systematic review and meta-analysis” [2020] – decrease SAMe in blood
  

Enzyme	Reference Mean	Study Mean	Z-Score
S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase (2.1.1.209)	151	70	7.6
GDP-alpha-D-rhamnose:NAD(P)+ 4-oxidoreductase (1.1.1.281)	481	120	6.4
ATP:D-galacturonate 1-phosphotransferase (2.7.1.44)	506	120	5.7
NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase (2.4.2.30)	505	120	5.6
beta-D-galactosyl-(1->4)-L-rhamnose:phosphate 1-alpha-D-galactosyltransferase (2.4.1.247)	505	120	5.6
delta/gamma-tocopherol lyase (ring-opening) (5.5.1.24)	703	213	5.6
all-trans-heptaprenyl-diphosphate diphosphate-lyase (cyclizing, tetraprenyl-beta-curcumene-forming) (4.2.3.130)	304	157	4.7
CDP-diacylglycerol:myo-inositol 3-phosphatidyltransferase (2.7.8.11)	133	88	4.6
Hg:NADP+ oxidoreductase (1.16.1.1)	774	195	4.6
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, molybdenum-dependent) (1.18.6.1)	2930	1478	4.4
myo-inositol-hexakisphosphate 4-phosphohydrolase (3.1.3.26)	2163	1074	4.2
phenol,NADPH:oxygen oxidoreductase (2-hydroxylating) (1.14.13.7)	326	51	4.1
1,2-beta-D-glucan:phosphate alpha-D-glucosyltransferase (2.4.1.333)	264	128	4
acetyl-CoA:2-oxoglutarate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (2.3.3.14)	936	341	4

Cross Validation To Literature

The term “irritability” on PubMed often links to  irritable bowel syndrome (IBS), making this difficult. The closest proxy appears to be stress (most people that are stressed tend to be irritable…) and there was some matches. We have agreement on the following being low.

• Atopobium
• Lactiplantibacillus plantarum
• Anaeroplasma
• Coriobacterium
• Tenericutes

Bottom Line

Lactiplantibacillus plantarum is the modern name for Lactobacillus Plantarum, a commonly available probiotic.

People who have uploaded their (or their children) samples have annotated some with Autism. On my main blog, I have been doing a series of deep statistical dives on my main microbiome blog site, and checked it the data available reaches the threshold for inclusion as defined in A new specialized selection of suggestions links (A summary table of various studies has been added there).

I am posting here to since it is a blog focused on Autism.

Study Populations:

Symptom	Reference	Study
Bloating	1082	67

• Bacteria Detected with z-score > 2.6: found 196 items, highest value was 8.2
• Enzymes Detected with z-score > 2.6: found 203 items, highest value was 7.6
• Compound Detected with z-score > 2.6: found ZERO items

For the number of samples, the z-score are unusually high compared to other studies in the series. A high z-score means strong statistical significance.

Interesting Significant Bacteria

All bacteria found significant had too low levels with the exception of the following that was too high:

• Prevotellaceae (family)
  • Prevotella copri (species)
  • Prevotella veroralis (species)
• Bifidobacterium gallicum (species)
• Peptococcaceae (family)

The most significant ones are listed below. I should point out that these bacteria may not be the cause, rather they may be ‘the canaries in the coal mine’ of the microbiome. These studies’ methodology determines association and not causality.

Bacteria	Reference Mean	Study	Z-Score
Acholeplasma (genus)	1421	215	8.2
Pseudoclostridium (genus)	146	70	7
Pseudoclostridium thermosuccinogenes (species)	145	70	7
Bacteroides rodentium (species)	3371	1481	6.9
Anaerovibrio lipolyticus (species)	1328	355	6.7
Anaerovibrio (genus)	1344	368	6.7
Anaerotruncus (genus)	1929	1150	6
Butyrivibrio (genus)	519	120	5.8
Xanthomonadaceae (family)	820	266	5.8
Blautia hydrogenotrophica (species)	252	73	5.7
Thiotrichaceae (family)	179	75	5.6
Thiothrix (genus)	179	75	5.6
Butyrivibrio proteoclasticus (species)	498	120	5.6
Thiotrichales (order)	179	78	5.5
Adlercreutzia equolifaciens (species)	232	90	5.5
Anaerotruncus colihominis (species)	1833	1140	5.4
Rubritalea (genus)	61	27	5.3

Interesting Enzymes

All enzymes found significant had too low levels.

I will leave it to the reader to go to Kyoto Encyclopedia of Genes and Genomes to learn about these enzymes (a steep learning curve).

The top item S-adenosyl-L-methionine (SAMe), had significant literature associated with it, a few samples:

• “S-adenosyl methionine prevents ASD like behaviors triggered by…” [2019]
• “S-Adenosyl-Methionine alleviates sociability aversion and reduces changes in gene expression in a mouse model of social hierarchy” [2022]
• “Blood biomarker levels of methylation capacity in autism spectrum disorder: a systematic review and meta-analysis” [2020] – decrease SAMe in blood
  

Enzyme	Reference Mean	Study Mean	Z-Score
S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase (2.1.1.209)	151	70	7.6
GDP-alpha-D-rhamnose:NAD(P)+ 4-oxidoreductase (1.1.1.281)	481	120	6.4
ATP:D-galacturonate 1-phosphotransferase (2.7.1.44)	506	120	5.7
NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase (2.4.2.30)	505	120	5.6
beta-D-galactosyl-(1->4)-L-rhamnose:phosphate 1-alpha-D-galactosyltransferase (2.4.1.247)	505	120	5.6
delta/gamma-tocopherol lyase (ring-opening) (5.5.1.24)	703	213	5.6
all-trans-heptaprenyl-diphosphate diphosphate-lyase (cyclizing, tetraprenyl-beta-curcumene-forming) (4.2.3.130)	304	157	4.7
CDP-diacylglycerol:myo-inositol 3-phosphatidyltransferase (2.7.8.11)	133	88	4.6
Hg:NADP+ oxidoreductase (1.16.1.1)	774	195	4.6
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, molybdenum-dependent) (1.18.6.1)	2930	1478	4.4
myo-inositol-hexakisphosphate 4-phosphohydrolase (3.1.3.26)	2163	1074	4.2
phenol,NADPH:oxygen oxidoreductase (2-hydroxylating) (1.14.13.7)	326	51	4.1
1,2-beta-D-glucan:phosphate alpha-D-glucosyltransferase (2.4.1.333)	264	128	4
acetyl-CoA:2-oxoglutarate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (2.3.3.14)	936	341	4

Cross Validation To Literature

Using microbiome studies from published studies is often difficult because the results often vary greatly due to the lab equipment used and the software used to interpret the data.

Checking against the literature we found:

• Items reported High
  • Prevotellaceae (NCBI:171552 ) is low in three studies, we found it high
  • Prevotella copri (NCBI:165179 ) is report low in one study and high in one study
  • Bifidobacterium (NCBI:1678 ) is reported low in some studies and high in other studies
  • Peptococcaceae is not reported in the literature
• Items Reported Low – none are reported in the literature

The purpose of these studies is to enable apple-to-apple-to-apple analysis and suggestions. The same lab is used for the raw read (Ombre and Biomesight uses the same lab) and all of the data is processed thru the same software (BiomeSight). Your sample (if you use the website) is processed thru the same process.

A final comment on most published studies, typically there are 25 Autism patients and 25 control patients. This actually results in much lower sensitivity in those studies than we have with over 1000 as the control.

Bottom Line

The SAMe “shouting out” in the enzymes being in agreement with published studies causes me to have considerable confidence in the analysis. Dr. Artificial Intelligence suggestions on Microbiome Prescription look like they are likely to have positive results.

P.S. If anyone does more drill down into the enzymes above in the literature, feel free to add your findings as comments.

Foreword – 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 purpose of this post is to educate on how to use the site.

Backstory

• This is a child with autism
• His major issue is his severe repetitive OCD behaviors, asking same questions 25 times a day, non-stop scripting of latest things that interests him. Watching and doing same things over and over again that he likes, very severe OCD with opening closing doors since age 3
• ADHD symptoms, can’t sit down still can’t focus on anything.
• Speech at 10 percentile, can understand well but cant express much, Recently started asking more what and when questions 
• Several type of tics. Started him on Mag citrate and Pure B complex his blinking tics vanished.
• Sensory seeking, likes to press chin and cheeks on me, jumping on me, rubbing his head and face on me
• General anxiety 
• Low muscle tone, mito issues
• NO aggression, NO head banging or self-injury, sweet friendly kid
• No socialization, does not know how to play or even talk to other kids, unappropriated behaviors 
• Smart kid can do advance math, was able to read since age 2 and a half, however comprehension and understanding of context is low 

Currently he takes following daily; Zinc picolinate 25mg, Klaire labs Benfotiamine 150mg, Pure B6 complex, Metagenics Ultra C, Designs for health Magcitrate powder, Vitamin D and high EPA fish oil, B12 injections twice a week.12 –

We did a 90 days gut-reset (killing and repopulate phases) with a functional doctor last year in November. And then we did 3 weeks of Sporonox. There was no improvement in his symptoms after finishing the protocol. Still have bloated belly.

Analysis

The usual health analysis raised nothing outstanding. Remember we are comparing a child against adult standards knowing that the microbiome change greatly during childhood. The sole medical condition raised in Acne, a very common condition. High counts of Bacteroides fragilis and Parabacteroides. Dr. Jason Hawrelak recommendations came in at the 56%ile, so a little concern.

KEGG (Genomes) based Suggestions

Nothing showed up — which cause me to look at the raw data. There are measurements on 1834 compounds. 415 of these compound were over 90%ile. One would expect 10% to be over 90%ile, i.e. just 183 compounds, not 415 compounds… hence the conclusion that it is not under production of compounds but over production. For Enzymes, his numbers are in line with expectations (203 out of 2045, i.e. the expected 10%). For end products (an old estimate from ad hoc data), he had nothing over 90% or under 10%.

Getting that information required me to go to the data directly and do some manipulations. To make life easier, I created a new section on the [Research Features] tab, shown below.

I then went to to check his bifidobacterium levels — because most kids with these types of conditions, especially autism, have sky-high levels here. This was NOT the case here, this sends up a red flag that this kid is atypical — and thus treatments that help others may have no effect or make him worst.

We happen to have an OATS test result also included. So on the Research Features, we went to see what would be suggested for actual levels (as reported by OATS) versus modelled levels (which found nothing).

We found that most of the items that were out of range were in a direction that probiotics could not help. Of the few that the shift was actionable on we got the following suggestions:

Pro Forma Consensus Building

This appears to be the best course here. I am going to do the usual, and then add some advance one that are specific for symptoms:

•  Use JasonH (15 Criteria) – 10 bacteria selected
•  Standard Lab Ranges (+/- 2 Std Dev) – 5 bacteria selected
•  Box Plot Whisker – 51 bacteria selected
•  Kaltoft-Moltrup Normal Ranges – 76 bacteria selected
•  Percentile in top or bottom 10 % – 70 bacteria selected

I then went to Research Features tab / Fine Tuning of suggestions. and picked OCD

I repeated for ADHD – no bacteria were selected.

Consensus Report

Going thru the list, filtering for what would likely be acceptable for a child:

• quercetin
• sucralose
• iron which is slightly contrary to low protein diet (usually low in iron)
• Indian Spices and Herbs: neem, Ajwain (trachyspermum ammi), ginko, Sumac(Rhus coriaria)

On the avoid:

• Grapes / resveratrol (grape seed/polyphenols/red wine), pomegranate
• lactulose (usually means less dairy), Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
• jerusalem artichoke (prebiotic), arabinoxylan oligosaccharides (prebiotic)

I would say do no probiotics (75% of them are on the avoid list). That would only increase lactobacillus which has a reported association to OCD. The one possible exception with a weak positive impact is saccharomyces cerevisiae (probiotics)

Looking at Vitamins…

I see Vitamin B12 injections — Cyanocobalamin (Vitamin B-12) came up as an AVOID for suggestions and OATS shows no issues. Was there documented evidence for these or was this a MD saying “lets try this”?

What came up in the suggestions were: vitamin b7 biotin (supplement) (vitamin B7) (which is in agreement with the OATS results of low biotin), pyridoxine hydrochloride (vitamin B6) and vitamin b3 (niacin). The following came up as avoid: vitamin d, vitamin b2(Riboflavin),fish oil with others being mild avoids: Vitamin C (ascorbic acid).

Again, the question to be resolved by you — are the some of the supplements being taken based on a clinical lab finding deficiency OR ad hoc suggestions received from people. Remember, we found an abnormal over production of many compounds above, pouring more compounds into his body without a clear lab verified need — may not be in his best interests.

Foreword – 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.

Back Story

I enclosed 3 labs: Her last GI MAP, an older OAT, and recent OMBRE. 

I have done work since the OAT, obviously. 

She was diagnosed with ASD around 20 months old. Since birth severe gastro problems. Re-occurring vomiting and severe GERD. Gastro preformed her first upper scope at age 2.5. He found some food in her stomach. Gave her a gasteopresis diagnosis. At age 5, her second scoop and biopsies and her gasteopresis  DX remained. Found nothing on biopsies. Her vomiting stopped once I changed diet by 3 years old. (It was a dairy allergy causing her to vomit once I figured it out, she never vomited again) I don’t believe the GP diagnose fits her and she can’t do the emptying study so he based this dx off food in gut per two scopes. 

• PANS/PANDAS dx at age 3.5.
• Has not had a fever since 12 months old. 

She is non speaking 6 years old and has cried on and off in pain her whole life. We’ve believed it was her gut from day one . She had a bad smell most of her life coming from her gut.(breathe) I believe this is clostridia as she has tested high with every stool test we’ve ever ran. It got better briefly with a course of abx but came back worse. The smell is the  worse when she wakes in the morning. Her stool has always been extremely foul smelling. She has taken some form of probiotics since she was 1 year of age. I have tried to use different strains but my knowledge is limited. 

• Severe ear infections since an infant so abx use is very high. 10 times or more. 

My next course of action after helping her gut is Lyme and coinfections testing. My research and her latest doctor have lead me there. So if you see anything hinting that way, be very helpful. It’s very expensive testing and I’m just unsure. 

Basic Analysis

The usual basics are below:

• Dr. Jason Hawrelak: 95.6%ile on both
• Same sets of bacteria deemed unhealthy, with all of these over 95%ile
  • [Ruminococcus] gnavus
  • Dorea
  • Eggerthella lenta
  • Erysipelatoclostridium ramosum
• Potential Medical Conditions Detected had some apparent hits:
  • ADHD at 96%
  • Functional constipation / chronic idiopathic constipation at 95%
  • Insomnia and Sleep Apnea likely matches

Clostridia was a specific area of concern, she is at 27.5%ile at the class level. Looking at lower levels we see some if its ‘kids’ are a problem. Three bacteria makes up 60% of the microbiome!

• 4% -> Dorea 97.7%ile
  • Dorea longicatena 99.3%ile
• 18.4% -> [Ruminococcus] gnavus 99.7%ile
• 21% -> Blautia 96.1%ile
• 21% -> Ruminococcus bromii 99.9%ile
• 17% -> Acidaminococcus 99%ile
• 26% -> Bifidobacterium 98.4%ile <- Typical with both children, especially with Autism and PANDA

My immediate thought is to look at the suggestions when we hand picked these four. They so dominate the microbiome that trying to adjust the other will likely be shouting in a hurricane (i.e. no one will hear).

Then do a second round including Bifidobacterium

The results we far less than ideal (i.e. very few items over 0.5)

It is interesting that the first prescription items is Risperidone, it is prescribed for irritability caused by autism [more information, including risks]. This hints that there is a match for the bacteria causing irritability in autism. My take away from this list is simple: remove any items on the Avoid list (which includes many vitamins and probiotics “deemed healthy”).  bacillus subtilis natto (probiotics) is available is the Japanese desert food Natto (I like it, a bit of an acquire taste) with nattokinase supplement being a potential alternative. The other top items(not prescription) to take are available as supplements etc. I attach the full list.

Adding in Bifidobacterium, we see many items that encourages bifidobacterium on the avoid list.

I next did the usual consensus report (which I added to the above sets of suggestions)

•  Use JasonH (15 Criteria) – 6 bacteria selected
•  Standard Lab Ranges (+/- 2 Std Dev) – 26 bacteria selected
•  Box Plot Whisker – 38 bacteria selected
•  Kaltoft-Moltrup Normal Ranges – 110 bacteria selected
•  Percentile in top or bottom 10% – 136 bacteria selected

The full consensus report is below. Items to TAKE of note:

• melatonin supplement
• blackcurrant — Juice?
• rice
• vegetarians
• thiamine hydrochloride (vitamin B1) and Cyanocobalamin (Vitamin B-12)– seen above
• carboxymethyl cellulose (prebiotic) – this is available pure in bulk,

One item of caution: bacillus subtilis (probiotics) is a strong avoid, one specific species is a moderate take bacillus subtilis natto (probiotics). At the gene levels they are different.

Using KEGG data

Two probiotics showed up at the top that are not available on the shelves of any US Health store: symbiopharm / symbioflor 1 and bioflorin (deu) / bioflorin. In fact, the top items are rich in European probiotics. Symbioflor-1 is available from the German Apotheke and will ship world wide (we use them) as well as bioflorin (which is expensive per capsule, so try symbioflor-1 first for the sake of your wallet!).

In terms of supplements, the following should be reviewed with your MD

• Amylase (Enzyme) – Percentile: 1
• beta-alanine – Percentile: 2.6
• Glycine – Percentile: 2.8
• L-methionine – Percentile: 3.6
• Molybdenum – Percentile: 0.5
• NADH – Percentile: 3.4

Remember that the basis of the KEGG data is identifying compounds that a person is low in. This is based on the hypothesis that part of the microbiome disruption is caused by rationing and impeding the operation of various bacteria. Our data is incomplete — so it is a best estimate.

Dive into Antibiotics Taken

I started the easy way — just looking at the Special Reports for your MDs. Everyone given encouraged this child’s dysbiosis.

• Azithromycin for about two months straight at onset of PANS.  ( – 0.555 )
• Augmentin (amoxicillin) several times for ear infections and later in life with a functional medicine doctor to address her GI MAP.   ( – 0.487 )
• Sulfamethoxazole,  ( – 0.642 )
• Vancomycin – increases Acidaminococcus parent
• Cefdinir ( – 0.586 )

There are a small number of antibiotics that may help the microbiome — if antibiotics are required in the future. Discuss if any of these may be acceptable to the MD (i.e. negotiate!) for addressing his rational. Note that the general class macrolide contains both good and bad choices: bad choices (azithromycin), good choices (erythromycin).

Checking the Positive Benefit for Prescription items, it was very very short. the first suggestion was epinephrine (Adrenaline). This surprised me. A common pattern is too much epinephrine with autism. We need to tread carefully here because levels can be high or low in different parts of the body.

In a group of 22 autistic children aged 5 to 16 years and a group of normal controls matched for age and sex, catecholamines metabolism was investigated in plasma, platelets, and urine. This investigation was part of a research project in which several biological parameters (including serotonin) were explored simultaneously in the same children. In the autistic group, epinephrine and norepinephrine were significantly elevated in plasma, while epinephrine, norepinephrine, and dopamine were significantly lower in isolated platelets. No significant difference was found between the two groups for the urinary excretion of epinephrine, norepinephrine, dopamine, DOPAC, and MHPG. Other differences between the two groups in the statistical correlations of several biochemical parameters also suggest abnormalities of bioamine metabolism in the platelets of autistic children.

Catecholamines metabolism in infantile autism: A controlled study of 22 autistic children

Dive into the key bacteria

Above we have identified the bacteria that has taken over the gut

• [Ruminococcus] gnavus (literature)
  • “R. gnavus has been associated with numerous diseases, most prominently inflammatory bowel disease (IBD) ” [src]
• Ruminococcus bromii (literature)
  • It feeds especially on resistant starches [src] There are many lists on the web on what these foods are.
• Acidaminococcus (literature)

Questions and Answers

Q: How long do you recommend a follow up stool test after implementing some things? 

A: For most things I recommend rotation of suggestions. The purpose is to destabilize the stable dysfunctional microbiome. A typical rotation is 2 weeks. The soonest would be after 4 rotations (2 months), if things are improving then just keep going until things appear to stabilize — then do a new sample to get the next course correction.

Q: I saw high mycoplasma on the lab’s page – is that a concern? This could explain so much as it is a main trigger for many PANS kids. Did I see that correctly? 

A-1: The literature: “Anti-Mycoplasma pneumoniae antibodies and anti-Epstein-Barr virus Nuclear Antigen antibodies were found positive in 11 (42.3%) and 5 (19.2%) patients with PANS,” [2019] This can be tested for directly and that would be the best way to answer.

A-2: Labs (and Microbiome Prescription use different criteria to determine “high”. Your child reading for  Mycoplasma was 192 / 1,000,000 bacteria or 57.2%ile. Ombre reports 70% of all samples have some mycoplasma. The level is not abnormal. The chart of values, showing your sample is below

Q: Any evidence of Lyme Disease

A: Lyme is caused by Borrelia. It is reported on Ombre/Thryve tests 0.2% of the time. None was reported in report. Conclusion, unlikely. Given the degree of dysbiosis and the known high rate of false positive with many Lyme tests when there is dysbiosis (typically caused by EBV not being fully controlled due to the dysbiosis), I would say that without a red bull-eye rash on the child — do not bother testing. The antibiotics likely to be prescribe will make your child worst.

Foreword – 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 a knowledgeable medical professional before starting.

Patient Notes

My son has headache, lethargy and reduced sleep. He’s in the spectrum so there are a lot more symptoms associated with it. But these are things I am trying to figure out, help him at least have a life without pain.

Analysis

As a result on my involvement with Long Covid Study – VERY early data, I built some private tools (computational intense, with good statistical understanding requires) .

The number of bacteria flagged for the closest match to the symptoms (with good sample sizes) are shown below. Each set of suggests had a lot of similarity to each hour, especially with red wine near the top of most lists. Red wine to children was historically done (especially French and Italian kids), but . . .

Symptom Obs	No Symptom Obs	Symptom Name	Bacteria Flagged
83	901	General: Headaches	32
41	943	Post-exertional malaise: General	22
70	914	Neurological-Sleep: Chaotic diurnal sleep rhythms (Erratic Sleep)	72
77	907	Autism: Official Diagnosis	26

At this point, I decided not to grind thru the standard set of suggestions, instead look at the consensus data (which is attached as a download below). The list was less than usual, 180 items.

I also went over to the KEGG determined probiotics and saw some items had consensus between them for probiotics, the top agreements are below

• Prescript-Assist®/SBO Probiotic ( Equilibrium Probiotics are likely an alternatives)
• PIANETA FARMA/KefiBios

In terms of supplements:

• Biotin (Vitamin B-7), B-12, B-1
• Calcium

Check the diet for food that may be high in choline (aka choline deficiency) and reduce them. See NIH page for a list.

Pro Forma Analysis

I went on to do the usual analysis:

•  Use JasonH (15 Criteria) – 7 bacteria picked
•  Standard Lab Ranges (+/- 2 Std Dev) – 19 bacteria picked
•  Box Plot Whisker – 62 bacteria picked
•  Kaltoft-Moltrup Normal Ranges – 148 bacteria picked
•  Percentile in top or bottom 10% -324 bacteria picked (out of 696 available, 46%!!)

The consensus report is attached, the suggestions appear similar but with shifting up and down on the list and a lot more items (567 vs 180 above). This video shows the process

Bottom Line

I did a VLookUp in Excel between the two lists to see the similarities and differences. There were a few difference. My usual advice is “if we don’t know the right answer, omit unless there is a strong reason to include”

Custom	Pro Forma	Modifier2
317.5	262.4	choline deficiency
309.3	382.7	rice bran
205.2	79.2	Prescript Assist (2018 Formula)
193.6	208.6	vitamin b7 biotin (supplement) (vitamin B7)
164.9	80.4	high red meat
153	-13.2	saccharomyces boulardii (probiotics)
152.3	63.6	low fodmap diet
152.3	159.4	low protein diet
138.8	-21.6	low-fat diets
130.8	62.8	calcium
124.2	-24.4	fructo-oligosaccharides (prebiotic)
118.5	-32.7	vsl#3 (probiotics)
108.5	72.3	saccharin
105.4	-15.6	red wine
105.4	2.4	schisandra chinensis(magnolia berry or five-flavor-fruit)
105.4	44.2	stevia
105.4	22.8	l-citrulline
98.4	74.7	Prescript Assist (Original Formula)

Questions and Answers

One of the fundamental challenges of the microbiome is a lack of information on many interactions because studies have not been done. The site attempts to use whatever fragments of information that is available as well as the genes of the bacteria (when the data is available).

• Question #1 PIANETA FARMA/KefiBios – I saw his Akkermansia is at a good level. Do you still recommend this probiotics?

The only known impact is on Akkermansia but that was not the basis of the suggestion. The suggestion came by looking at the amount of various compounds that he appears to be low in (using Kyoto Encyclopedia of Genes and Genomes on the bacteria he has, and the bacteria in various probiotics). Most of these compounds are not available as supplements.

Compound Name	OtherName	Formula
D-Alanine	D-2-Aminopropionic acid  D-Ala	C3H7NO2
L-Homocysteine	L-2-Amino-4-mercaptobutyric acid  Homocysteine	C4H9NO2S
Aromatic aldehyde		C7H6O
CDP-diacylglycerol	CDP-1,2-diacylglycerol  1,2-Diacyl-sn-glycero-3-cytidine-5′-diphosphate	C14H19N3O15P2R2
Thioredoxin	Reduced thioredoxin	C10H14N4O4S2R4
N-(L-Arginino)succinate	2-(Nomega-L-Arginino)succinate  L-Argininosuccinate  L-Argininosuccinic acid  L-Arginosuccinic acid	C10H18N4O6
2-Dehydro-3-deoxy-6-phospho-D-gluconate	6-Phospho-2-dehydro-3-deoxy-D-gluconate  2-Keto-3-deoxy-6-phosphogluconate  2-Dehydro-3-deoxy-D-gluconate 6-phosphate	C6H11O9P
4-O-[(2R)-1-Glycerophospho]-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol		C74H125N2O22P3

• Question #2: Prescript-Assist®/SBO Probiotic  –  I saw the list on your website. Sorry, I want to understand a little more detail about it. I know its soil based probiotics. I wanted to understand if it will help improve bifido .. I saw this has bacillus.
  • Answer: There is no known direct impact on bifido. If Bifidobacterium is your primary concern, excluding every other bacteria involved, then see this page. Suggestions are based on a holistic analysis, not a blinkered view.
• Question #3: Also do you have any recommendations to help reduce the histamine level?
  • Answer:  Diamine oxidase (DAO) is the supplement commonly used to reduce the impact of histamine [study]. “Histamine is a monoamine synthesized from the amino acid histidine through a reaction catalyzed by the enzyme histidine decarboxylase (HDC)”[2018] Trying to find the bacteria involved is a bit more speculative.

Searching for histidine involved enzymes, we see that he has very high levels of two:

The three greatest producers are: Erysipelatoclostridium ramosum,  [Clostridium] innocuum, Turicibacter sanguinis and Streptococcus iniae. For Erysipelatoclostridium ramosum, most items increases it ( dairy, resveratrol (grape seed/polyphenols/red wine)) but two items decreases it: xylooligosaccharide (prebiotic), bifidobacterium bifidum (probiotics). You could try hand assembling suggestions for these 4 bacteria.

The other way, using Diamine oxidase, is to go over to KEGG, it is Enzyme 1.4.3.22, none of the bacteria he has appear to produce it, nor do any of the bacteria reported from 16s samples.

• Question #4: Choline Deficiency – Does it mean we have to give him a PC?.  You had mentioned there might be Choline in his diet. So is it more or is it deficient?, I think choline and Ammonia might be impacted because of the Antifungal regimen he is in?.
  • Answer: Choline occurs naturally in food, Background: https://www.hsph.harvard.edu/nutritionsource/choline/ A study on choline deficiencies found that the bacteria we targeted were shifted in the desired direction. There is a lot of literature on choline ( https://pubmed.ncbi.nlm.nih.gov/?term=choline+deficient+diet ) and digesting that is a job for your medical professional. My usual takeaway is  check what is normally eaten for choline content and consider reducing it a bit by changing foods (after consulting with your medical professional). No need to go to extreme measures… it is just one possible factor.
• Question #5: Also the modifier 2 means he needs all those based on his microbiome, Is it right?
  • Answer: I do NOT know what he needs, the suggestions are strictly things that have been calculated from available data that has improved odds on shifting the microbiome towards the typical microbiome. Everything is probability and odds — nothing is definitive. In the absence of definitive knowledge, I believe that modelled data gives better suggestions than “let us try A,B,C”. For dealing with ME/CFS, the suggestions of what should help matches the literature on what helps – which increases my confidence in the model.

Some recent work has identified bacteria that are associated with Autism. For a summary of method, see this post. The following are the list of bacteria seen with Biomesight samples that are annotated with Autism. There are not sufficient samples yet for specific autism characteristics – so please check your uploaded samples and update the symptoms.

Note the list is BiomeSight.com specific and cannot be applied to other microbiome reports. There is a separate post for Ombre/Thryve samples.

These are bacteria that you want to reduce (with one caveat — the suggestions algorithm requires the percentile to be 50%ile or more). How to hand pick them? See below the list.

Note: you may only have a few of these. They are shown in the same sequence as seen on Microbiome Tree. The LAST item is what was found to be statistically significant.

1. Nevskiales Sinobacteraceae Hydrocarboniphaga
2. Gammaproteobacteria Enterobacterales Yersiniaceae
3. Enterobacterales Yersiniaceae Serratia
4. Yersiniaceae Serratia Serratia entomophila
5. Enterobacterales Enterobacteriaceae Lelliottia
6. Enterobacteriaceae Lelliottia Lelliottia amnigena
7. Enterobacterales Enterobacteriaceae Enterobacter
8. Enterobacteriaceae Enterobacter Enterobacter cloacae complex
9. Enterobacter Enterobacter cloacae complex Enterobacter hormaechei
10. Enterobacterales Enterobacteriaceae Escherichia
11. Enterobacteriaceae Escherichia Escherichia albertii
12. Enterobacteriaceae Escherichia Escherichia coli
13. Rhodocyclales Zoogloeaceae Azoarcus
14. Thiobacillaceae Thiobacillus Thiobacillus thiophilus
15. Betaproteobacteria Burkholderiales Burkholderiaceae
16. Burkholderiales Burkholderiaceae Limnobacter
17. Burkholderiaceae Limnobacter Limnobacter litoralis
18. Burkholderiales Genera incertae sedis Thiomonas Thiomonas thermosulfata
19. Betaproteobacteria Burkholderiales Oxalobacteraceae
20. Bacteroidia Bacteroidales Prevotellaceae
21. Bacteroidales Prevotellaceae Prevotella
22. Prevotellaceae Prevotella Prevotella copri
23. Prevotellaceae Prevotella Prevotella paludivivens
24. Prevotellaceae Prevotella Prevotella corporis
25. Prevotellaceae Prevotella Prevotella oulorum
26. Prevotellaceae Prevotella Prevotella veroralis
27. Bacteroidaceae Bacteroides Bacteroides denticanum
28. Bacteroidaceae Bacteroides Bacteroides gallinarum
29. Bacteroidaceae Bacteroides Bacteroides caccae
30. Bacteroidaceae Bacteroides Bacteroides graminisolvens
31. Bacteroidaceae Bacteroides Bacteroides fragilis
32. Peptostreptococcaceae Peptostreptococcaceae incertae sedis [Clostridium] paradoxum
33. Eubacteriales Clostridiaceae Sarcina
34. Clostridiaceae Sarcina Sarcina maxima
35. Clostridiaceae Clostridium Clostridium cellulovorans
36. Clostridiaceae Clostridium Clostridium frigoris
37. Clostridiaceae Clostridium Clostridium chartatabidum
38. Clostridiaceae Clostridium Clostridium nitrophenolicum
39. Terrabacteria group Firmicutes Negativicutes
40. Acidaminococcaceae Acidaminococcus Acidaminococcus fermentans
41. Firmicutes Negativicutes Veillonellales
42. Negativicutes Veillonellales Veillonellaceae
43. Veillonellales Veillonellaceae Veillonella
44. Veillonellaceae Veillonella Veillonella criceti
45. Veillonellaceae Veillonella Veillonella dispar
46. Veillonellales Veillonellaceae Megasphaera
47. Veillonellaceae Megasphaera Megasphaera hominis
48. Veillonellales Veillonellaceae Negativicoccus
49. Veillonellaceae Negativicoccus Negativicoccus succinicivorans
50. Selenomonadaceae Megamonas Megamonas funiformis
51. Selenomonadales Selenomonadaceae Pectinatus
52. Selenomonadaceae Pectinatus Pectinatus cerevisiiphilus
53. Bacillales Planococcaceae Viridibacillus
54. Bacilli Bacillales Sporolactobacillaceae
55. Bacillales Sporolactobacillaceae Sporolactobacillus
56. Sporolactobacillaceae Sporolactobacillus Sporolactobacillus putidus
57. Staphylococcaceae Staphylococcus Staphylococcus pseudolugdunensis
58. Bacillales Staphylococcaceae Salinicoccus
59. Streptococcaceae Streptococcus Streptococcus thermophilus
60. Streptococcaceae Streptococcus Streptococcus mutans
61. Streptococcaceae Streptococcus Streptococcus vestibularis
62. Cyanobacteria/Melainabacteria group Cyanobacteria Oscillatoriophycideae
63. Cyanobacteria Oscillatoriophycideae Chroococcales
64. Bifidobacteriaceae Bifidobacterium Bifidobacterium scardovii
65. Bifidobacteriaceae Bifidobacterium Bifidobacterium adolescentis
66. Bifidobacteriaceae Bifidobacterium Bifidobacterium angulatum
67. Bifidobacteriaceae Bifidobacterium Bifidobacterium breve
68. Bifidobacteriaceae Bifidobacterium Bifidobacterium catenulatum
69. Bifidobacterium Bifidobacterium catenulatum Bifidobacterium catenulatum subsp. kashiwanohense
70. Bifidobacterium catenulatum Bifidobacterium catenulatum subsp. kashiwanohense Bifidobacterium kashiwanohense PV20-2
71. Bifidobacteriaceae Bifidobacterium Bifidobacterium cuniculi
72. Bifidobacteriaceae Bifidobacterium Bifidobacterium indicum
73. Bifidobacteriaceae Bifidobacterium Bifidobacterium longum
74. Bifidobacteriaceae Bifidobacterium Bifidobacterium thermacidophilum
75. Bifidobacteriaceae Bifidobacterium Bifidobacterium pseudocatenulatum
76. Bifidobacteriaceae Bifidobacterium Bifidobacterium choerinum
77. Bifidobacteriaceae Bifidobacterium Bifidobacterium gallicum
78. Bifidobacteriales Bifidobacteriaceae Parascardovia
79. Corynebacteriaceae Corynebacterium Corynebacterium durum

To make a selection, just check the appropriate checkboxes.

Backstory

My son is born in 2009 and diagnosed with autism in 2011. When he was 3 months old he has lot of reflux and unable to digest milk always used to throw up and we ended up using antibiotics because of mucus forming issues and at 10 months he had few words.

• And at 18 months he got diagnosis’s of autism and was completely Non-Verbal.
• After removing gluten and dairy from his diet at age 3.5 he started saying words
• he also got diagnosed with Lyme and coinfections like bartonella and Babesia .
• Now he is 11 years still having lot of issues like his weight is just 55 Lbs  he has focus issues and lot/severe OCDs and tantrums and lot of rigidity and not conversational yet ,cognitive issues cannot understand abstract concepts and has lot of echolilia and  no social skills and gets head pain all of a sudden which might be PANS will last for few minutes and will be fine again.
• And he has lot of Gut issues like  failure to thrive even though his diet his healthy he does not gain weight at all and he has leaky gut and always have constipation issues  and poor digestion issues and picky eating and he complaints some times that his stomach hurts and some times his stomach gets very tight like gas forming. And he has brain and Gut inflammation.
• Very recently from couple of months  he started having Acid Reflux issues after eating he will be spitting for an hour as if something is coming back from his stomach. 
  • We also noticed that when ever he eats chicken and eggs he is more constipated. We did the GI work up and everything came up normal except one thing that he does not have enzymes to digest lactose and also we make sure he is not constipated and his bowls are moving everyday with some laxative.

We have two samples for this person, while we will use the last one for suggestions, a comparison may be spark insights.

Basic Analysis

Looking at the two samples, we see that things are very different than with the ME/CFS person in this post. Instead of over representation in rare bacteria, there is over representation in common bacteria (i.e. the bacteria that most people have).

	Earlier	Sample	Latest	Sample
Percentile	Genus	Species	Genus	Species
0 – 9	10	1	7	7
10 – 19	10	9	9	12
20 – 29	6	9	8	13
30 – 39	10	18	7	10
40 – 49	12	9	6	12
50 – 59	12	15	9	18
60 – 69	10	7	8	12
70 – 79	10	16	10	16
80 – 89	25	39	22	38
90 – 99	103	149	40	64
Std Dev	29.31	44.00	10.65	17.61

• Looking at “Potential Medical Conditions Detected” for both samples we see a very long list of candidate conditions for both samples
• For “Bacteria deemed Unhealthy”, again we have some long lists
• For “Dr. Jason Hawrelak Recommendations”, we have the earlier sample at 75%ile and the latest sample at 98.8%ile, i.e. “no issues”
• AI Computer Probiotics.
  • Earlier sample: L. Bulgaricus Probiotic Powder, miyarisan (jp) / miyarisan, PIANETA FARMA/KefiBios were top suggestions by with a low weight (1.0)
  • Later sample: Prescript-Assist®/SBO Probiotic as only suggest and with almost no weight (0.07)
• AI Computed supplements at 10% level: Neither sample had any.

There is the appearance of improvement between the sample. This may be solely due to the changes due to age (18 months between samples), or moving further away from microbiome disruptive events of the past.

Going Forward

We need to go with some caution because the child microbiome is different than an adult’s and most of the data we are using are from adults.

I am going to build the consensus in a slightly different way than usual:

•  Use JasonH (15 Criteria) – 6 bacteria picked
•  Standard Lab Ranges (+/- 2 Std Dev) – 17 bacteria picked
•  Box Plot Whisker – 59 bacteria picked
•  Kaltoft-Moltrup Normal Ranges – 92 bacteria picked
•  Percentile in top or bottom  10 % – 160 bacteria picked
• Canned Autism using U.S. Nation Library of Medicine Data – 8 bacteria picked
• Using Experimental Page using Official Diagnosis Autism only – 9 bacteria picked

Looking at Consensus Items

I scanned the top items and picked items that I suspect will be acceptable, easy to obtain and reasonable cost:

Take / Add to regime

• Herbs (may be added to food, tea or as capsules)
  • neem
  • syzygium aromaticum (clove)
  • thyme (thymol, thyme oil)
  • Ajwain (trachyspermum ammi)
  • ashwagandha (withania somnifera)
  • olea europaea (olive leaf)
• Probiotics (better choices are hard to obtain in the US at reasonable costs)
  • Lactobacillus salivarius
• Diet Style
  • Vegetarians
  • tea
  • rice
  • mastic gum (prebiotic)
  • saccharin
  • stevia
• Vitamins
  • vitamin b3 (niacin)
  • Cyanocobalamin (Vitamin B-12)
  • pyridoxine hydrochloride (vitamin B6)
  • retinoic acid,(Vitamin A derivative)
  • thiamine hydrochloride (vitamin B1)

There were some interesting AVOIDS (very different than ME/CFS people)

Avoid / Remove or Reduce use of

• magnesium (and foods rich in it, like walnuts)
• selenium
• zinc
• Conjugated Linoleic Acid (CLA)
• quercetin
• resveratrol (grape seed/polyphenols/red wine)
• oregano (origanum vulgare, oil) |
• noni
• Ginseng
• ginko
• inulin (prebiotic), jerusalem artichoke (prebiotic), chicory (prebiotic)
• Most probiotics!
• raffinose(sugar beet), lactulose

Seeing lactulose as a very strong to be avoid agrees so much with no tolerance for milk. I checked the antibiotics positive/negative benefit and was actually surprise to see on the positive impact many of the antibiotics used for ME/CFS and Lyme: fluoroquinolone (antibiotic)s, tetracycline (antibiotic)s, minocycline (antibiotic)s with the best one being vancomycin (antibiotic). This was interesting because “Vancomycin is used to treat colitis (inflammation of the intestine caused by certain bacteria) that may occur after antibiotic treatment.”[MedlinePlus]

Questions And Answers

1. Do you mean your current recommendations is not to use any probiotics or use only Lactobacillus salivarius strain of probiotics ?
   1. Only a very small number of probiotics appear to have a positive impact, less than 18. The other 39 came out with a negative effect. You need to read the labels carefully.
2. I also for the earlier sample you mentioned the PDF use of prescript assist soil based probiotic and also lactobacillus bulgaricus (probiotics) and lactobacillus kefiri . I have not used these so now do you think using them might be helpful based on the analysis 
   1. Those are on the recommended list, so YES
3. And based on your analysis what is most pathogenic bacteria that I need to address from the sample which is problematic such that I research and see how to reduce it?
   1. Unlike most people, this child has a huge amount of Lactobacillus bacteria, he has 98% more than anyone else in the database. Clicking on the link above (and those below) are the worst offenders where his levels are higher than 95% of peoples
   2. [Ruminococcus] gnavus, Actinomyces, Bacillus, Dorea, Erysipelatoclostridium ramosum, Shigella (especially Shigella dysenteriae),Streptococcus pyogenes, Streptococcus sanguinis
   3. In the video, I will show how you can find suggestions EXPLICIT for these.
4. What key strains of good bacteria do you think is missing for weight gain or in general ?
   1. Every good strain becomes bad if there are too many of them, for example Lactobacillus above. The microbiome should be viewed as “Yin/Yang” and not good and bad. I really do not have a clean answer for that question.
5. Which Lactobacillus strains does he have has 95% which I need to avoid further is it Lactobacillus Reutri and Lactobacillus Johnson and Lactobacillus planetarium are those the ones which I need to avoid completely to give or any other list?
   1. ALL Lactobacillus are similar with only small changes between them. They are a family. As with human families, they cross support each other. You want to lower all of the Lactobacillus, ideally have no lactobacillus probiotics.
6. Currently I started using sauerkraut , thinking he needs more Lactobacillus strains and I read sauerkraut has lot of different good strains. Would it be still okay to use it?
   1. He DOES NOT need more Lactobacillus strains — he needs a lot less!
   2. In my humble opinion NO. Two main reasons:
      1. You have no idea of which bacteria are in. Commercial versions usually do not list the
         species. On the few that do, it is very questionable if the label is correct.
         ” the species of lactic acid bacteria present in sauerkraut fermentations are more diverse than previously reported and include Leuconostoc citreum, Leuconostoc argentinum, Lactobacillus paraplantarum, Lactobacillus coryniformis, and Weissella sp.” [2007]
         For Weissella, he is at 90%ile — too high. He does not need more
7. Do I need to do anything to reduce Lactobacillus strains that are high?
   1. There is no studies that target explicit strains.
   2. melatonin supplement, B-vitamins reduce it too.
   3. A word of caution here. Are you going to target just one item of concern in several dozens by focusing on this item (with the potential cost of many other things becoming worst); or work from suggestions that are targeted to improve the microbiome as a whole?

In response to question #3, I did a hand picked of all of those over 95%ile on the Health Summary with the results shown below

A short list of Suggestions

To be discussed with family MD before starting

• Antibiotics
  • A course of vancomycin (antibiotic) to start
  • 3 weeks after this course is finished one of (piperacillin-tazobactam or gentamicin)
• Supplements (add one a week for 3 weeks than take 2 weeks off)
  • A baby aspirin once a day — watch especially for any improvement in brain activity
    • He may have a sub-clinical (mild) form of Antiphospholipid syndrome (thick blood) triggered by the microbiome shifts – I am reflecting my own experience here.
  • Vitamins B-3, B-6, B-12
  • N-Acetyl Cysteine (NAC),
• Diet
  • low carbohydrate diet with either (high-saturated fat diet/high beef diet or vegetarians)
    • Avoid magnesium rich foods
    • Use sunflower oil
    • rice
    • cruciferous vegetables (broccoli cabbage)
  • Ample use of the following herbs in cooking, as tea (or as capsules)
    • neem
    • syzygium aromaticum (clove)
    • Sumac(Rhus coriaria)
    • thyme (thymol, thyme oil)
    • Ajwain (trachyspermum ammi)
    • ashwagandha (withania somnifera)
• Probiotics
  • bacillus laterosporus (probiotic) would be the best choice — but finding that may be a challenge
  • REMEMBER he is very high in Lactobacillus and Bifidobacterium — what is in most probiotics…
• Fruit/ Juices
  • cherry
  • lemon
  • blackcurrant
  • strawberry
  • papaya
• Misc
  • melatonin supplement

Items to AVOID (You may wish to read the full list

• sesame cake/meal
• almonds/ almond skins, walnuts
• barley,oat whole grain,bran, wheat, quinoa
• pea (fiber, protein), bean
• fish oil
• apple
• pomegranate
• Kiwifruit
• Goji (berry,juice)
• dates
• corn
• plantain bananas
• Cacao

One of the easiest modern ways to do it, is to download this data as a CSV and save on your smart phone when shopping.

REMINDER: The items indicate odds/confidence in shifting the microbiome is the intended direction. It is NOT how effective it is. Each item in the take likely improves your odds of improving when taken; keep taking items the avoid list — continuing likely increase the odds of not changing.

Example_ConsensusDownload

As a result of some work with BiomeSight, I ended up rethinking how to handle the symptoms to bacteria process. I had been thinking linearly in terms of building regression. I got some traction with that, but was definitely unhappy because once multiple symptoms are added the regression faded out.

• This is done using the free site: Microbiome Prescription
• Upload data from a suitable lab with this page Detail Microbiome Uploads:

A novel approach is simple, take all of the people with the same set of symptoms and create a composite of their microbiomes. In this composite identify outliers and then see where those outliers match the sample that you are looking at. Take those that match and create a Hand Picked Bacteria set and then generate suggestions from those.

So simple, just pick the symptoms and then see the bacteria identified. But you must first enter the symptoms for the person!

You will see the list of all of the symptoms you entered for the sample, they are listed in descending order of the number of samples sharing the same symptoms.

Experimental: Picking Bacteria via Symptoms – YouTube

Pick the first one and click add to list

Adding another example, reduces the choices.

You can keep adding as many as you wish (you do not need to add)

When you are ready (or just interested in seeing the bacteria picked), click the green button

You will get a short or long list of bacteria. If a long list, you may wish to go for stronger relationships.

Increasing to Expected, caused a major drop in the numbers

Having more is not always better. I reduced it to just Autism, and the list was much fewer than when I had multiple symptoms. Note that the list will be different for different people and different samples

Examples for some autistic children

Bottom Line

The key thing to remember is that the symptom is NOT caused by a specific set of bacteria but by different combinations of bacteria acting in similar ways. This approach attempt to capture the probable combinations for a symptom set.

Second Example for Long COVID

This was mainly done to show that we can get strong relationships.

For Very Strong — nothing was listed.