Opportunity to use Artificial Intelligence for Autism?

As a FYI, I have taught Artificial Intelligence for Chapman University, worked as a AI/Software developer for Amazon and Microsoft. Artificial Intelligence is composed of a large number of very different techniques, at one end you have “ponies” and at the other end “Space Shuttles”. One technique, expert system with fuzzy logic (ESFL), appears to be the best. Why? Most of the techniques require vast quantity of training data and usually produce black box suggestions/predictions which lacks explanations of why. ESFL provides a complete logic/evidence trail for each suggestions/predictions which can be walked. If one piece of evidence is disputed, it can be removed easily and a new set of suggestions/predictions produced.

Build our own AI Autism Model?

This post comes from the success of using AI on Microbiome Prescription. It would be nice to see if we can do the same with Autism. The goal is to use all available knowledge from studies.

I would suggest using SWI-PROLOG as the main engine. Prolog is a language that does not compute numbers but compute logic. The following is actual program code. It is almost english-like and prolog can resolved what you should take or not take.

  • increases(Modifier_A,Bacteria_31979).
  • decreases(Modifier_X,Bacteria_1236).
  • low(“person”,Bacteria_1239).
  • high(“person”,Bacteria_1234).
  • helps(Person,Modifier) :- high(Person,Taxon),decreases(Modifier,Taxon).
  • helps(Person,Modifier) :- low(Person,Taxon),increases(Modifier,Taxon).
  • hurts(Person,Modifier) :- low(Person,Taxon),decreases(Modifier,Taxon).
  • hurts(Person,Modifier) :- high(Person,Taxon),increases(Modifier,Taxon).
  • take(Person,Modifiler) :- remove(helps(Person,Modifier),is,hurts(Person,Modifier)).
  • contradict(Modifier,Taxon) :- decreases(Modifier,Taxon),increases(Modifier,Taxon).

“take” above says get the list of items that helps and then removes all items that hurts. I.e. only items without contradictions.

The number of lines (statements) to explicitly write Microbiome Prescription in SWI-PROLOG is about 15 million statements. That code code be licensed (for free or nominal cost) to a project of this type so building such a microbiome resource is not needed; rather just augment that data with autism specific data.

One key difference between ESFL is the ability to infer and not just parrot (typical Machine Learning). Bacteria A increases IL 10. A person with SNP ABC has decreased IL 10, thus we can desired to increase Bacteria A for people with SNP ABC.

Vision – Do it For Autism!

I have a web based data entry system (that is being used commercially) that can be made available to the project (with hosting of site and database). We have an almost ready to run system.

The Rub

This is a time consuming process to enter the data and then have the data reviewed (to insure correctness). Typically the people doing the entry and reviews are M.Sc., Ph.D. or M.D. Using students working on their degrees (summer work, part time) to do entry is often a way of keeping costs down. These students typically have access to the full text of articles through their educational institutes.

  • Typical time per study/article is 30 minutes to read and enter, 10 minutes to review
  • There are 72,000 studies citing Autism on the US National Library of Medicine.
    • A complete coverage would be 36,000 hours or 900 man-weeks or a team of 18 people working full time for a year.
  • The expected number of facts will likely be around 120,000.

Facts should be put in a Public Domain Type of License

This allows other groups to continue the work and prevents the need to duplicate the effort of encoding the same studies multiple times. The terms of license should require people that uses and extends it to also make their additional data available under the same terms.

Benefits

One of the key benefit is the identification of gaps in the knowledge base as well as identifying areas where there are contrary results. This allows better funding of research to fill gaps and not duplicate existing work.

A secondary benefit is that it could always be kept current and provide far more specific data for a patient based on all of the information available. The issue of MD’s knowledge being stale or bias is reduced.

What is needed — FUNDING AND MANAGEMENT

The Rub above takes money to happen — even if you are paying students the minimum wage, we quickly get a significant cost. Ideally one or more existing Autism Organizations can be persuaded to partially or fully fund this project.

My own role would be at most, a process consultant. Working Pro Bono.

Some Video on Expert Systems

A model for aggressive response to some substances

Any ideas why olive oil would cause severe aggression tantrums?

From a reader

This is an interesting question.. When I see “severe aggression tantrums”, my mind goes to hypoxia (shortage of oxygen delivery to the brain).

The most significant impact of short-term memory loss for a person with hypoxia is that it impairs the ability to retain and recall new or unfamiliar information. Behavioural changes. The person may become more verbally and physically aggressive. They may also have issues with disinhibition

Hypoxia – – common causes, symptoms and treatment

I know that  olea europaea (olive leaf)   is an antimicrobial, that is, it kills off various bacteria and thus could result in Jarisch Herxheimer Reaction (Herx). Many of the symptoms associated with a herx could be explained from hypoxia. This is cited in the literature [Recurrent Jarisch-Herxheimer reaction: case report 2013].

Olive Oil does not have this reputation. When I checked the known impact of Olive Oil, I see that it increases Bilophila which is reported to increase cognitive impairment [2021], cognitive impairment is strongly associated with hypoxia. Olive Oil also decreases/inhibits/kills Prevotella bivia, Prevotella intermedia,Prevotella melaninogenica,Prevotella oris,Prevotella timonensis and Prevotella buccalis. A common by-product of a bacteria being inhibited is a dumping of toxins into the body, triggering inflammation (thus narrowing blood vessels and reducing oxygen delivery).

A continuous monitoring with a Saturated O2 monitor may reveal this shift (it may not, if the inflammation is in the brain — the monitor is unlikely to record it). For myself, I use a relatively cheap smart watch that records SO2 every 10-15 minutes as part of my normal proactive health monitoring, see Monitoring watch for CFS and other Conditions.

This is just a model, with some ability to check the mechanism.

From Social Media

5 yo Autistic Boy – Analysis

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.

PercentileGenusSpecies
0 – 92237
10 – 192221
20 – 291713
30 – 39812
40 – 491114
50 – 5946
60 – 69912
70 – 791117
80 – 891215
90 – 991116

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.

Consensus suggestions

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):

Daughter with ASD Level-III with Gut Issues

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 IssuesSensory IssuesGeneral BehaviourSocializationSpeechHistory, Curent Supplements & Diet
Excessive Gas mostly in evening and night.Hitting Hard Objects/Plastic in the front teethNo aggression , no self injurious behavioursDoesn’t have age appropraite play behaviourNo true words. Only few nonsense syllablesBirth weight-3.45 kg. C-Section delivery.
BloatingCrashing & 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/BurpsLooking from the corner of the eye.Scratching othersNear 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 otherPoor Focus & Attention Celiac test is negative. Low in Vitamin D & Iron. Ultrasound test of abdomen is normal
Constipation. Bristol Stool Chart No.-3/4Making sudden loud noisesPinching & Hitting othersShows 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 tipsAll 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.    
Slightly edited notes from parent

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.
From GI Map.

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.

SymptomMatches
less than 04 years since onset77
Frequently loose train of thought75
Lyme74
Less Avoidance of Eye Contact or Poor Eye Contact73

Where Do we go from here?

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

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:

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.

Special Studies: Easily irritated

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:

SymptomReferenceStudy
Easily irritated110855
  • 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.

BacteriaReference MeanStudyZ-Score
Prevotella oulorum (species)63179.9
Prevotella copri (species)6552290898.8
Clostridium malenominatum (species)57226.3
Pediococcus (genus)112486.1
Phocaeicola coprocola (species)7544456.1
Actinobacillus pleuropneumoniae (species)57196
Opitutae (class)169435.8
Puniceicoccaceae (family)163405.8
Lactiplantibacillus pentosus (species)122175.8
Bifidobacterium cuniculi (species)81255.7
Cerasicoccus arenae (species)552875.5
Prevotella (genus)73346266815.5
Puniceicoccales (order)114355.4
Veillonella (genus)400419455.4
Cerasicoccus (genus)319565.3
Tenericutes (phylum)313810535.1

Interesting Enzymes

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

EnzymeReference MeanStudy MeanZ-Score
propanoyl-CoA:NADP+ oxidoreductase (1.3.1.84)29105.9
S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase (2.4.2.28)365314265.8
3-oxo-Delta1-steroid:acceptor 1-oxidoreductase (1.17.99.11)28105.7
cholest-4-en-3-one:acceptor oxidoreductase (25-hydroxylating) (1.17.99.10)28105.7
n/a (3.4.24.20)40165.2
malonyl-CoA:acetate malonyltransferase (tetracenomycin-F2-forming) (2.3.1.235)41115.2
malonyl-CoA:malonamoyl-[OxyC acyl-carrier protein] malonyltransferase (2.3.1.260)41115.2
NADPH:acceptor oxidoreductase (1.6.99.1)572623824.8

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
EnzymeReference MeanStudy MeanZ-Score
S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase (2.1.1.209)151707.6
GDP-alpha-D-rhamnose:NAD(P)+ 4-oxidoreductase (1.1.1.281)4811206.4
ATP:D-galacturonate 1-phosphotransferase (2.7.1.44)5061205.7
NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase (2.4.2.30)5051205.6
beta-D-galactosyl-(1->4)-L-rhamnose:phosphate 1-alpha-D-galactosyltransferase (2.4.1.247)5051205.6
delta/gamma-tocopherol lyase (ring-opening) (5.5.1.24)7032135.6
all-trans-heptaprenyl-diphosphate diphosphate-lyase (cyclizing, tetraprenyl-beta-curcumene-forming) (4.2.3.130)3041574.7
CDP-diacylglycerol:myo-inositol 3-phosphatidyltransferase (2.7.8.11)133884.6
Hg:NADP+ oxidoreductase (1.16.1.1)7741954.6
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, molybdenum-dependent) (1.18.6.1)293014784.4
myo-inositol-hexakisphosphate 4-phosphohydrolase (3.1.3.26)216310744.2
phenol,NADPH:oxygen oxidoreductase (2-hydroxylating) (1.14.13.7)326514.1
1,2-beta-D-glucan:phosphate alpha-D-glucosyltransferase (2.4.1.333)2641284
acetyl-CoA:2-oxoglutarate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (2.3.3.14)9363414

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.

Special Studies: Autism

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.

On the [Changing Microbiome] tab

Study Populations:

SymptomReferenceStudy
Bloating108267
  • 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.

BacteriaReference MeanStudyZ-Score
Acholeplasma (genus)14212158.2
Pseudoclostridium (genus)146707
Pseudoclostridium thermosuccinogenes (species)145707
Bacteroides rodentium (species)337114816.9
Anaerovibrio lipolyticus (species)13283556.7
Anaerovibrio (genus)13443686.7
Anaerotruncus (genus)192911506
Butyrivibrio (genus)5191205.8
Xanthomonadaceae (family)8202665.8
Blautia hydrogenotrophica (species)252735.7
Thiotrichaceae (family)179755.6
Thiothrix (genus)179755.6
Butyrivibrio proteoclasticus (species)4981205.6
Thiotrichales (order)179785.5
Adlercreutzia equolifaciens (species)232905.5
Anaerotruncus colihominis (species)183311405.4
Rubritalea (genus)61275.3

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
EnzymeReference MeanStudy MeanZ-Score
S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase (2.1.1.209)151707.6
GDP-alpha-D-rhamnose:NAD(P)+ 4-oxidoreductase (1.1.1.281)4811206.4
ATP:D-galacturonate 1-phosphotransferase (2.7.1.44)5061205.7
NAD+:poly(ADP-D-ribosyl)-acceptor ADP-D-ribosyl-transferase (2.4.2.30)5051205.6
beta-D-galactosyl-(1->4)-L-rhamnose:phosphate 1-alpha-D-galactosyltransferase (2.4.1.247)5051205.6
delta/gamma-tocopherol lyase (ring-opening) (5.5.1.24)7032135.6
all-trans-heptaprenyl-diphosphate diphosphate-lyase (cyclizing, tetraprenyl-beta-curcumene-forming) (4.2.3.130)3041574.7
CDP-diacylglycerol:myo-inositol 3-phosphatidyltransferase (2.7.8.11)133884.6
Hg:NADP+ oxidoreductase (1.16.1.1)7741954.6
ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing, molybdenum-dependent) (1.18.6.1)293014784.4
myo-inositol-hexakisphosphate 4-phosphohydrolase (3.1.3.26)216310744.2
phenol,NADPH:oxygen oxidoreductase (2-hydroxylating) (1.14.13.7)326514.1
1,2-beta-D-glucan:phosphate alpha-D-glucosyltransferase (2.4.1.333)2641284
acetyl-CoA:2-oxoglutarate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (2.3.3.14)9363414

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.

The taxonomy nightmare before Christmas…

Checking against the literature we found:

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.

Boy with ADHD and OCD

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.

The percentile chart came in reasonably balance with no major shifts

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).

On the [Changing Microbiome] tab

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:

Most of the suggestions had lactobacillus acidophilus in common — so if none of the above is available consider a probiotic that is L.acidophilus only

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:

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

9 Bacteria were selected that match the profile. One that was selected was Lactobacillus

I repeated for ADHD – no bacteria were selected.

Consensus Report

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

On the avoid:

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.

Child: ASD, PANDA, Severe Gastro Problems

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:

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!

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)

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

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.

The purpose is to give alternatives that may address medical needs while helping correct microbiome shifts.
  • 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).

These are computed from available literature.

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

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.

The Lyme Disease Rash

Autistic child with sleep, lethargy issues

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 ObsNo Symptom ObsSymptom
Name
Bacteria
Flagged
83901General: Headaches32
41943Post-exertional malaise: General22
70914Neurological-Sleep: Chaotic diurnal sleep rhythms (Erratic Sleep)72
77907Autism: Official Diagnosis26

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

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:

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”

CustomPro FormaModifier2
317.5262.4choline deficiency
309.3382.7rice bran
205.279.2Prescript Assist (2018 Formula)
193.6208.6vitamin b7 biotin (supplement) (vitamin B7)
164.980.4high red meat
153-13.2saccharomyces boulardii (probiotics)
152.363.6low fodmap diet
152.3159.4low protein diet
138.8-21.6low-fat diets
130.862.8calcium
124.2-24.4fructo-oligosaccharides (prebiotic)
118.5-32.7vsl#3 (probiotics)
108.572.3saccharin
105.4-15.6red wine
105.42.4schisandra chinensis(magnolia berry or five-flavor-fruit)
105.444.2stevia
105.422.8l-citrulline
98.474.7Prescript 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 NameOtherNameFormula
D-AlanineD-2-Aminopropionic acid  D-Ala C3H7NO2
L-HomocysteineL-2-Amino-4-mercaptobutyric acid  Homocysteine C4H9NO2S
Aromatic aldehydeC7H6O
CDP-diacylglycerolCDP-1,2-diacylglycerol  1,2-Diacyl-sn-glycero-3-cytidine-5′-diphosphate C14H19N3O15P2R2
ThioredoxinReduced thioredoxin C10H14N4O4S2R4
N-(L-Arginino)succinate2-(Nomega-L-Arginino)succinate  L-Argininosuccinate  L-Argininosuccinic acid  L-Arginosuccinic acid C10H18N4O6
2-Dehydro-3-deoxy-6-phospho-D-gluconate6-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-undecaprenolC74H125N2O22P3
The above were at the 5%ile or less
  • 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.
Clicking on Enzymes

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.

Bacteria to Hand-Pick for Autism with Biomesight samples

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.