This is an update of a post that I did back in 2018 [Original Post]. A reader had messaged me about the safety of soil based organisms probiotics. For hundreds of thousands of years, soil based organism was a part of our diet because of the absence of safe water, soil was often on the food consumed. I recall reading that the human gut bacteria has strong similarity to that seen around root vegetables. This is not surprising, pulling roots out of the ground (without washing!!!) was likely common for most of these thousands of years…

“But I read about someone getting sick from SBO!”

• There are two types of sick to consider: bacteremia or endocarditis (BAD), and herxheimer reaction (usually a good sign — I was really sick when I first started Mutaflor, it ebbed and I was much better afterwards)

This recent event caused me to revisit this item: “FDA investigating baby’s death linked to probiotic given by hospital” with FDA Letter pointing out that it was not legal to sell it with the claims it made.

Some Counts of Adverse Probiotic Infections

• 149 reports for Lactobacillus bacteremia probiotic
• 183 reports for Lactobacillus endocarditis
• 14 for Bifidobacteria bacteremia probiotic
• 17 for Enterococcus bacteremia probiotic 
• 13 for Bacillus bacteremia probiotic

The most dangerous probiotic (using report counts) are Lactobacillus.

There are similar risk from eating “safe” lactobacillus probiotics, cheese, yogurt, etc. Even deaths have been reported: “Lactobacillus-Cause of Death ” [2010]

” Lactobacillus has been used as a probiotic bacteria to treat diarrhea and is also present in dairy foods. It is hence commonly used. Lactobacillus endocarditis, an exceedingly unusual disorder, is accompanied by high mortality and poor response to treatment. ” – OUCH!

• “In recent years, infections caused by Lactobacillus and Bifidobacterium made up 0.05% to 0.4% of cases of endocarditis and bacteremia. In most cases, the infections were caused by endogenous microflora of the host or bacterial strains colonizing the host’s oral cavity. According to a review of cases of infections caused by bacteria of the genus Lactobacillus from 2005 (collected by J.P. Cannot’a), 1.7% of infections have been linked directly with intensive dairy probiotic consumption by patients. ” [Lactic acid bacteria and health: are probiotics safe for human?]. [2014]

Some more citations…’ bacteremia is a bad bacteria infection, endocarditis is a bacteria infection of the heart. It has been only in the last few years

• Lactobacillus gasseri endocarditis on the aortic valve bioprosthesis – a case report.[2017]
• Recurrent Lactobacillus Bacteremia in a Patient With Leukemia. [2017]
• Persistent bacteremia secondary to delayed identification of <i>Lactobacillus</i> in the setting of mitral valve endocarditis. [2017]
• Lactobacillus rhamnosus Endocarditis After Upper Endoscopy. [2017]
• Endocarditis due to Lactobacillus rhamnosus in a patient with bicuspid aortic valve: Potential role for the consumption of probiotics? [2017]
• Lactobacillus coryniformis Causing Pulmonary Infection in a Patient with Metastatic Small Cell Carcinoma: Case Report and Review of Literature on Lactobacillus Pleuro-Pulmonary Infections. [2017]
• Infective endocarditis due to Lactobacillus rhamnosus: Risks of probiotic consumption in a patient with structural heart disease. [2017]
• Lactobacillus rhamnosus endocarditis: An unusual culprit in a patient with Barlow’s disease. [2016]
• Lactobacillus paracasei endocarditis in a consumer of probiotics with advanced and severe bicuspid aortic valve stenosis complicated with diffuse left ventricular mid-layer fibrosis. [2016]
• Bacterial Endocarditis Caused by Lactobacillus acidophilus Leading to Rupture of Sinus of Valsalva Aneurysm. [2016]
• Importance of Molecular Methods to Determine Whether a Probiotic is the Source of LactobacillusBacteremia. [2016]
• Endocarditis of the native aortic valve caused by Lactobacillus jensenii. [2015]
• Isolated Lactobacillus chronic prosthetic knee infection. [2014]
• Lactobacillus paracasei endocarditis in a consumer of probiotics. [2013]
• Infectious endocarditis caused by Lactobacillus acidophilus in a patient with mistreated dental caries. [2012]

Bottom Line

Probiotics are generally safe. No probiotic is 100% safe. To me, soil based bacteria are likely more beneficial then lactobacillus because they went along with our ancestor’s diet long before we started domestication of milk producing animals. There may be considerable basis to the hygiene hypothesis which would result from our modern pathological obsession with sterilization of food in the belief that all bacteria are bad.

The general belief is that issues arise with a weak immune system, after surgeries, and with a “leaky gut”.

A reader messaged this to me:

People like (and expect) absolute certain answers. Statistician and Artificial Intelligence Engineers NEVER expect absolute answers… they expect fuzzy answers and just work with it.

There are two problems with determining levels from the microbiome:

• Correct identification of the bacteria from the test
• Determining if the bacteria produces the substance.

Accurate Bacteria Identification is HORRIBLE

For a basic understanding see these prior posts:

• The taxonomy nightmare before Christmas…
• The taxonomy nightmare — Episode II
• The taxonomy nightmare before Christmas… Episode III

So with the same data (FastQ) files, the number of bacteria producing each of the above will vary greatly.

Most Labs use INFERENCE data to identify producers

By inference, I mean looking at a sample with high butyrate etc and then (stupidly) looking at the bacteria that your specific lab identify there (see above!) and then publishing a paper that high X bacteria produces butyrate etc. Even having an alleged “sterile” environment with only one bacteria is questionable to assert (besides the behavior of a bacteria placed in “extended isolated confinement” is different – as it is with humans). Not many years ago, breast milk was deemed to be sterile. Improved testing resulted is this myth being disproved in Lactobacillus Bacteria in Breast Milk [2020], Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health.[2020], Characterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum.[2020]

These studies are used by many labs to determine amount being produced.

Microbiome Prescription Use Genetics

Is the bacteria capable of producing the chemical? Surprise, surprise, surprise… this list disagrees with the inference studies above. We still have the challenge of labs reports misidentifying the bacteria. Which is more reliable? Well, with genetics, we do not know if the production process is turned on or not. We do know which ones are incapable of producing.

The Wish List

I have tossed this request over to a person that has the academic skills (and creativity) to explore. Take the FASTQ files and the data from KEGG: Kyoto Encyclopedia of Genes and Genomes and see if you can determine the amount of genetic material producing each of these products. We totally side-step the key point of failure — identifying the bacteria!

That is, create software that takes in FASTQ files and provide estimates for all of the applicable Enzymes present! Remove bacteria naming from the process.

Possible software includes: Piphilin, Tax4Fun, PICRUSt2, PICRUSt

Human Analogy

You want to be rich. So you look at the rich and see expensive cars, big homes, trophy spouses etc. So you deduce that you just need to have those and you will become rich!! After all, there is a strong statistical association!! The alternative is to look at wealth production (the genes) and you see a different picture: high yield stocks, inherited money, professional licenses, etc. It is the same with looking at what bacteria produces.

Today I looked at a sample and when I looked at raising butyrate, there were ZERO bacteria selected. In other words, there were no butyrate bacteria reported by the lab. This could be defect with the reference library used by the lab or a hundred other reasons. I was also hit by requests for suggestions from OATS test.

I did a series of detail posts on OATS in an Autism context which some may find informative:

• Organic Acids Tests (OATS) and Autism #1
• Organic Acids Tests (OATS) and Autism #2
• Organic Acids Tests (OATS) and Autism #3
• Organic Acids Tests (OATS) and Autism #4

I have created A Priori Reports for Pub Med reported conditions and it seems logical to create the same for compounds produced using KEGG: Kyoto Encyclopedia of Genes and Genomes data. Some examples are: Histamine (reduce), Butyrate (increase), and for SIBO(decrease): Hydrogen, Methane

This is experimental.

Logic Used

KEGG reports at the strain level using the full genome of each strain. From this information, we approximate the species genome (assuming the strains in the species are reasonably representative).

If the existing tests are 100% accurate at identifying all of these strains…. , we should have a smile. The reality is that tests do not report on many strains, and often disagree on species!! The problem is that they are not “safe” in their identification. For why, see these three posts:

• The taxonomy nightmare before Christmas…
• The taxonomy nightmare before Christmas… Episode II
• The taxonomy nightmare before Christmas… Episode III

To get around this defect, I used patterns from AI where dealing with imprecise data is normative. I assume that we could get reasonable suggestions by imagining that every species listed is present in equal amount and then generate suggestions from this synthetic microbiome.

Where is it available on the site?

Main Public Menu

The most commonly asks are under Information From Studies. They will produce a PDF download.

Using OATS Test Results

I have created a video of using both of these pages with explanation of what and how we are doing things.

I have also added a new feature beside Using OATS test to pick probiotics. The new page presents more choices

and produce a PDF report that aggregates the suggestions over everything marked out of range.

You will see a summary of what you entered:

A list of items to take or to avoid

Logged In – Advance Display

The “kitchen sink” is available after logging in and setting display level to advance. KEGG Derived Data appears on the menu

Under this menu are two items: one for compounds (like Organic Acids) and one for enzymes (like the one that creates histamine).

On these pages you can get the list of bacteria used for each calculation.

Cross Validation

I usually do some spot checks for reasonableness of suggestions. I picked the highest value item to reduce histamines: Thyme, and was lucky to find a study specifically for this.

Impact of Thyme Microcapsules on Histamine Production by Proteus bacillus in Xinjiang Smoked Horsemeat Sausage [2021] “Results showed that histamine accumulation was suppressed by thyme microcapsule inhibitory effect on the histamine-producing bacteria and the reduction in the transcription of hdcA and hdcP genes. “

So the suggestions appear to be reasonable.

Bottom Line

This is all an academic exercise for me. I do believe that this approach will likely produce superior results than random trial and error; or relying on influencers for approaches. As always, review with your medical professional before starting.

This has just been published: Efficacy of probiotics, prebiotics and synbiotics in irritable bowel syndrome: a systematic review and meta-analysis of randomized, double-blind, placebo-controlled trials [Sep 2023]

I have done a strikethru on items that are likely waste of money (based on P Value). 0.001 is better than .04.

	Number of trials	Number of patients	RR of persistence of global symptoms (95% CI)	P value for the difference	I2 (P value for χ2)
All patients
All combination probiotics	32	3369	0.78 (0.71–0.87)	<.001	71% (<.001)
VSL#3	4	155	0.78 (0.53–1.16)	.23	47% (.13)
Lactobacillus paracasei ssp paracasei F19, Lactobacillus acidophilus La5, and Bifidobacterium lactis Bb12	3	269	0.92 (0.76–1.11)	.38	14% (.31)
Enterococcus faecalis DSM16440 and Escherichia coli DSM17252	2	686	0.71 (0.33–1.51)	.37	97% (<.001)
LacClean Gold S	2	130	0.59 (0.37–0.93)	.02	0% (.56)
Duolac 7s	2	76	0.62 (0.43–0.89)	.009	0% (.62)
All Lactobacillus strains	16	1498	0.84 (0.72–0.98)	.03	69% (<.001)
Lactobacillus plantarum 299V	5	453	0.73 (0.59–0.92)	.007	59% (.04)
All Bifidobacterium strains	5	1161	0.82 (0.67–1.02)	.07	74% (.004)
Bifidobacterium bifidum MIMBb75	2	565	0.69 (0.46–1.04)	.07	83% (.01)
All Bacillus strains	3	216	0.44 (0.34–0.57)	<.001	0% (.48)
All Saccharomyces strains	2	469	0.94 (0.80–1.11)	.49	0% (.86)
All Escherichia strains	2	418	0.86 (0.79–0.93)	<.001	0% (.78)
All Blautia strains	1	366	0.93 (0.84–1.03)	.15	N/A
All Clostridium strains	1	200	0.80 (0.64–0.99)	.04	N/A
All Streptococcus strains	1	54	0.72 (0.53–0.99)	.04	N/A
Patients with IBS-D
All combination probiotics	13	1272	0.78 (0.67–0.92)	.002	69% (<.001)
VSL#3	2	49	0.42 (0.04–4.85)	.49	82% (.02)
Duolac 7s	2	76	0.62 (0.43–0.89)	.009	0% (.62)
All Lactobacillus strains	4	157	0.57 (0.36–0.89)	.01	27% (.25)
All Saccharomyces strains	2	169	0.99 (0.76–1.28)	.92	0% (.81)
All Clostridium strains	1	200	0.80 (0.64–0.99)	.04	N/A
All Blautia strains	1	202	0.94 (0.82–1.08)	.36	N/A
All Escherichia strains	1	54	1.00 (0.57–1.74)	1.00	N/A
All Bifidobacterium strains	1	44	0.64 (0.36–1.16)	.14	N/A
All Bacillus strains	1	40	0.57 (0.31–1.05)	.07	N/A
Patients with IBS-C
All combination probiotics	4	295	1.01 (0.89–1.14)	.87	8% (.35)
All Saccharomyces strains	1	180	0.82 (0.62–1.08)	.16	N/A
All Blautia strains	1	164	0.92 (0.78–1.07)	.26	N/A
All Escherichia strains	1	35	0.84 (0.41–1.73)	.64	N/A

The person in this prior post has done a retest. This analysis looks at what changed from selectively following suggestions from this prior post.

• ME/CFS Follow Up Microbiome Samples
• Follow up Microbiome Analysis from a prior post
• Rosacea, Circulation and mild CFS

His comments are below:

“Things that I have been taking since the last test in February 2023:

• Rosemary
• Grapefruit seed extract
• Turmeric
• Natto 
• Tetracycline 
• Clove
• Anise
• Acacia gum 
• Amoxicillin 
• Apple peel powder
• Thyme
• Symbioflor 2
• Neem 
• Jarlsberg cheese

My symptoms:

• Still get the red nose (some form of rosacea). But it is better than before.
• Still feel fatigued (both physically and mentally). But it is better than before.
• Feeling stressed. But it is better than before.
• Brain fog.
• Bloated.
• Lots of gas – I fart and burps a lot. “

This is his fifth sample. Multiple samples are not unusual because fixing the microbiome means a lot of course corrections.

Analysis

First, we will look at measures that were not available for the earlier posts. In the last period, we see a dramatic change of the histamine values!

Sample	Anti-Inflammation Value	Histamine Value	Butyrate Value
2021-08-31	97%ile	98%ile	25%ile
2021-12-03	96%ile	98%ile	57%ile
2022-03-25	18%ile	87%ile	62%ile
2022-08-11	30%ile	90%ile	73%ile
2023-02-22	65%ile	86%ile	82%ile
2023-09-12	87%ile	3.2%ile	80%ile

We also see a dramatic change in the Percentages of Percentiles charts that suggests improvement. In fact, there is no longer any statistically significant shifts (going from 0.99999… to .40!). Dropping below 0.95 is an objective target. The pattern went from the common ME/CFS and Long COVID pattern to an normal pattern.

Potential Medical Conditions Detected

We have the following candidates to consider that were not flagged in the prior sample (where nothing stood out):

• Allergic Rhinitis (Hay Fever): 100%ile
• Stress / posttraumatic stress disorder: 98%ile
• Irritable Bowel Syndrome: 97%ile

This may be just randomness or because the microbiome is calming down, patterns hidden by noise are showing up. Looking at Special Studies pattern matching, the top one was COVID19 (Long Hauler) at 28% match (prior was 41% match) — a definite improvement. Other items dropped about 8% match each, most were so low, that there may not be significance.

These appear to agree with his personal observations. We have Prevotella copri is at 76%ile, hinting that mycotoxin present (mold) may be in his environment (see this post for more exploration).

Going Forward

In terms of subjective and objective measurements, this person has improved. So time for the next course correction. I am going to just run with the “just give me suggestions” since nothing really stands out.

The non-prescription items from the PDF are by far the shortest that I have seen! So the safflower may be difficult because it does not mean safflower oil (an avoid), but the herb.lots of coffee and perhaps a little Aalborg Aquavit.

In terms of probiotics, he lucked out — Filmjölk is likely available to him

The avoid or reduce list is much longer!!

Going over to items computed from the Kyoto Encyclopedia of Genes and Genomes we have the top item being the typical one for ME/CFS: Escherichia coli (i.e. Mutaflor or Symbioflor-2). In terms of supplements, the two most significant one are: Glutamine, Threonine, Serine.

Since the person has a co-operative MD (i.e. two antibiotics were listed), I reviewed the prescription items. The top item was amoxicillin (antibiotic)s[CFS], which has already been used. We have gatifloxacin, ciprofloxacin (antibiotic)s[CFS], and clinafloxacin (antibiotic) which is a different family (a fluoroquinolones which has a lot of bad press). The next one worth considering is nadifloxacin (antibiotic): Nadifloxacin is a broad-spectrum quinolone antibiotic(in fluoroquinolones family) that has been approved for use in the treatment of acne vulgaris and skin infections. This may impact his rosacea. The next one down the list may be similar: fusidic acid sodium salt (antibiotic).

The following should be read before taking any fluoroquinolones by both the patient and the MD.

• Fluoroquinolone-Associated Tendinopathy: A Critical Review of the Literature [2003]
• Overview of Side-Effects of Antibacterial Fluoroquinolones: New Drugs versus Old Drugs, a Step Forward in the Safety Profile? [2023]

One factor to consider is that Cecil Jadin has been using fluoroquinolones for twenty years without seeing any adverse effects. The duration is only 10 days or less. Longer duration of use may be a significant factor. See this post and video for more information.

Questions

“All those antibiotics MUST be taken: after food ( not only water ) and without any dairy products. Patients must avoid sugar intake and some supplements(for example magnesium). Antibiotics should be taken in the morning and the evening. Patients must avoid sugar intake and supplements.”

Cecile Jadin, MD  Video Presentation of Dr. Jadin’s Current Protocol for ME/CFS, Q-Fever, Chronic Lyme and related conditions 

Q: I’m going to do another round with  amoxicillin.
— In Jadin’s presentation she says to only take it for 7 days, ain’t ok to take it for 14 days as we talked about before?
— Can’t I take other supplements like magnesium when I take antibiotics?

• A: The duration range of 7 – 14 days is, IMHO, fine. My main concern is long duration that can result in antibiotic resistance.
  • The other supplements while taking antibiotics is a good question. Jadin indicated that some items should not be taken. My IMHO (keeping to best odds thinking) would be to stop most of them with a few exceptions. We do not know that much about supplement-antibiotics interactions. The exceptions are antibiotic potentiators (items that allows the antibiotic to get deeper into “tissue”. See Antibiotic Potentiators Against Multidrug-Resistant Bacteria: Discovery, Development, and Clinical Relevance [2022] and my 2019 post Potentiators: Often the difference between success and failure. These include the following:
    • Bromelain
    • Serrapetase
    • Nattokinease
    • Lumbokinease
  • Word of warning: If there a herxing, it will get a lot worse!! so start on a Friday night (and consider a few vacation days after the weekend!)

Q: If I want to have a longer list for what to take / avoid, can I use the three that is blue below (as earlier)?

• A: What is shown above is from the PDF which I am preferring to use for posts because it keeps things simpler. You can do any combination you wish. You could also consider doing your last sample suggestions and this sample suggestions, an “uber consensus” which should produce suggestions of what has been out of range with both samples. Caution should be done because of how different the two samples are!

This does produce a massive list!!

I would then go thru the list and cross out items that are not shown with at least 7 of the possible 8 in the technical details.

Bottom Line

My own experience with recovery was that it took about a year for many symptoms to wear off. The body is not an electronic device with an on/off switch; think of a meadow that has been damaged by fire, flood, or chemical spill — it takes time for things to come back.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I can compute items to take, those computations do not provide solid information on rotations, dosages, etc.

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. Some suggestions may be counterindicated for other medications you are taking and medical conditions.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Backstory

Much longer and detailed than usual. Most of the data is “outside of my wheelhouse” of expertise, but readers may have additional insight.

• 22 Years ago, I had a UTI. It wouldn’t go. I had 5 antibiotics. None of them worked. By the sixth week I was beside myself. A new doctor gave me ciprofloxacin. Finally it went away. Unfortunately, being naïve and a bit dumb back in the day, I started drinking alcohol the following weekend and the UTI came back. I didn’t realize but the bladder lining was weakened and presumably still some residual bacteria there. They got to work again.
• I had ciprofloxacin again. 7 day course. My bladder sort of got back to normal but I had to drink more water than usual to stop it from feeling uncomfortable. This lasted four years. I could pee normally, everything was good but I was always conscious things weren’t quite the same as they had been. I stopped drinking alcohol completely.
• NB: I developed hay fever pretty immediately after finishing the second course of Cipro. I believe something got knocked out of my microbiome that I’ve never got back.
• After a period of huge stress at the age of 30, my bladder suddenly got very hot and tight and uncomfortable. Numerous tests showed no infection. I was offered a urethal stretch. This worked to some extent but I then landed in a pattern that lasted 18 years:
  • From days 5-14 of my cycle my bladder would feel like I had a UTI. But from days 15 – 28 and then days 1 – 4, I had pretty much no symptoms. My bladder during non-high estrogen days was good. My bladder was like normal. I could eat all foods and drink alcohol somewhat.

• However I did have to be careful. I couldn’t drink every night (not that I would anyway) and citrus, black tea, coffee, I had to wary. Too much and it would set things off. Same with stress. High stress periods would see my bladder get very hot and tight and it would take weeks for it to calm back down.
• During this 18 year period, I found this pattern that on estrogen-high phases my bladder would go off, feel like a UTI, reduced flow, more frequency, but once progesterone kicked in, everything was fine. During low hormone times, during my period, my bladder was best of all. Worked perfectly.
• Two years ago I found out I have osteoporosis. I trialed HRT, using estradiol gel. Within 24 hours, my bladder was very very unhappy. I felt like I needed to pee constantly. Tiny amounts. It was far worse than during my own cycle of estrogen.
• I stopped on day 20 because it was so uncomfortable. I really wanted to take the estrogen but I couldn’t. . But I don’t seem to be able to do this. I believe this messing with my hormones sent me straight into much stronger menopause symptoms. I suddenly gained weight around my middle (sign of leaky gut, low estrogen unable to keep the intestinal junctions tight) and my spine and sternum started to ache like they never had before. Brain fog, terrible sleep, frequency of peeing but this time for no reason, just bladder more sensitive overall.
• I trialed progesterone only this summer, in the hope that it helps my bladder usually – well my own progesterone seems to. However after a while the familiar burning and uncomfortable feeling came back. It seems like external hormones aren’t for me.
• I have rosacea on one cheek.
• I have got telogen effluvium [hair loss] which started 2.5 months ago.
• Prof XXXX from Imperial ran a DAO blood test on me and it came out at 8 U/mL. He said this shows I’m am histamine intolerant.
• I’m currently taking Hydroxyzine 25mg per day at night to calm my bladder down as it had another ‘episode’ this summer. Too much stress again.
• I think I have mast cell activation syndrome in my bladder. Prof says the same. I think estrogen kicks of the degranulation sequence and my immune pathways/signaling have got messed up. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537328/, https://www.mdpi.com/1422-0067/19/6/1554
• He trialed me on ketotifen but it made things worse. 5% of users can get cystitis type symptoms. Looks like I was one of them.
• He now wants me to trial Famotidine (stomach acid suppressant) and Loratadine to switch off H1 and H2 receptors. I’m reluctant to do that. He also thinks I may have a staph epidermis infection but I find this hard to believe because my bladder goes through very good periods for months at a time – it’s only with stress or estrogen that things get bad. It’s true to say though that with every period of stress, my bladder loses function and so now, it’s harder to get all the urine out. It is inflamed at the base, the ultrasound showed.
• He’s prescribed Nitrofurantoin twice per day for 2 weeks. I’m really reluctant to take yet more antibiotics.
• Additionally I’ve been diagnosed with stage 2 kidney disease just recently, sightly high creatinine and just on the cusp range of too high for calcium too in the blood.
• I am low in Vitamin D, just below normal. I am low in ferritin from a recent blood test in August. I am trying to correct these two with supplements the last few weeks but I know it takes time.
• I feel overall I’m inflamed. I feel like I don’t absorb things as well as I used to. I don’t sleep very well.
• Taking hydroxyzine helps with the aches in my spine and sternum. They have almost gone away. Nice side effect but I know antihistamines are not good long term. I see Fexofenadine seems to do the same thing too https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8421647/

I’d like to get to the stage where maybe I could take the hormones to protect my bones? At least have the choice.

Analysis

We have actually two samples taken a few weeks apart. Technically, there was a little improvement between the samples (one had 9 “9” and the other just 8 “9”).

Both samples had similar profile with Dr. Jason Hawrelak Recommendations. With the following significant items:

• Too high: Akkermansia,Bacteroides, Methanobrevibacter
• Too low: Bifidobacterium, Roseburia,Bilophila wadsworthia (was too high prior), Faecalibacterium prausnitzii
• Anti inflammatory Bacteria Score: 43%ile, Prior was 31%ile

Bacteria deemed Unhealthy had several items of interest:

• Bacteroides uniformis: 100%ile (100%ile prior) – 16% of the microbiome (was 18% prior)
• Bacteroides fragilis: 100% (99%ile prior) – 9% of the microbiome (was 7% prior)

Potential Medical Conditions Detected use pattern matching to published studies. We have the following items of note:

• hypertension (High Blood Pressure) risk
• Hyperlipidemia (High Blood Fats) risk
• Prior sample also had: Allergies risk and Colorectal Cancer risk.

Special Studies pattern matching (using other samples uploaded with their declared symptoms) had only one strong match: COVID19 (Long Hauler), with a weaker match for Allergies And Food Sensitivity. The person had COVID but appears to be full required (no symptoms for long hauler).

Going Forward

There are many things happening with this person. There are no really strong microbiome pattern matches for the main symptoms of concern, so I will just work from the standard “just give me suggestions” on each sample and then do an uber-consensus. Every microbiome report has some fuzz factors in measurements, combining two or more (close in time) reduces the noise from the fuzz.

The highest priority was 470 and the lowest was -543. Applying the 50% rule, we will focus on items over 235 or below -272.

Some interpretation notes:

• Avoid being a vegetarian does not mean avoid vegetables. It means have some fish or meat.
• Fruit is a take with some specific fruits being an avoid (cherry, grapes, lingonberries). Coconuts and Grapefruits
• Avoid fish oil is not inconsistent with taking omega-3 fatty acid. See this listing of what is in fish oil. So beware of supplements saying “high in omega-3” that is effectively fish oil. An example of a non fish oil source of Omega-3.

Review of Previous Consumptions

Items between -272 and 235 are unlikely to cause a significant contribution and likely complicates life without a clear benefit. All of the items cited fall in this indifference range.

• ciprofloxacin (antibiotic)s: 203
• hydroxyzine dihydrochloride,(prescription): 129
• ketotifen fumarate,(prescription): 129
• progesterone,(prescription): 129
• famotidine,(prescription): 132
• nitrofurantoin (antibiotic): 162
• vitamin d: -233
• Ferric citrate(iron): -157
• brown rice: 104
• oats: 34
• Coffee: 138, teas: -50 to 176 depending on type
• Cacao: 169
  • Cacoa flavonoids: -19

I also decided to look at the top prescription items as a discussion point with your MD. I have a hypothesis that many prescription items work via their impact on the microbiome. This leads down a speculation path that conditions associated to the top recommended prescription items may be in a pre-significant state — a potential developing risk.

I found what appear to be an association to be aware of. The earlier sample had a pattern matching to a form of cancer.

• daunorubicin hydrochloride,(prescription): 470, an anthracycline antibiotic mainly used to treat various types of cancers, especially leukemias. 
• cefoxitin (antibiotic)s: 421 – often used with cancer patients [1979]
• moxifloxacin (antibiotic): 417 – “Moxifloxacin is an orally administrated fourth‐generation quinolone with broad‐spectrum coverage against tumor‐associated bacteria” [2020]
• doxorubicin hydrochloride,(prescription): 327 – “Doxorubicin is an antibiotic derived from the Streptomyces peucetius bacterium. It has had wide use as a chemotherapeutic agent since the 1960s. ” [NIH]
• pentamidine isethionate,(prescription): 351 – Repurposing pentamidine for cancer immunotherapy by targeting the PD1/PD-L1 immune checkpoint [2023]

Questions

Q: Can I ask – would you consider taking any pre-biotics? Not probiotics but prebiotics? I’m looking at HMOs and PHGG? For increasing bifido? Not sure if this is a good idea…

• A: There are no prebiotics that makes it over the threshold for good odds to help. The two that you cite are both negative.
  • Human milk oligosaccharides (prebiotic, Holigos, Stachyose): -110
  • partially hydrolyzed guar gum: -125
• The suggestions are based on considering the impact on all abnormal bacteria. Trying to fix just one bacteria can often result in other bacteria being made worse. I looked at PHGG and found this 2021 study:
  • Increases Bacteroides fragilis – partially hydrolysed guar gum
  • Increases Bacteroides uniformis – partially hydrolysed guar gum
  • You are at 100%ile for both of these…. you do not want to feed them more!

Q: I wasn’t sure from what was written in the article if I should be seeking an antibiotic to reduce down the fragilis and uniformis?

• A:
•  IMHO, we should try non-antibiotic methods first. Often they may require minor diet changes that may become established and keep them away.
  If after 2 months and a retest show no improvement, then it is time to start negotiating with your MD.  This means reaching an agreement on an antibiotic that addresses them BUT does not make your gut worse… To get the first choice list of antibiotics, just click this button.
  NOTE: Not all are suitable. Some are for vet usage, others may be injected only, etc. Your MD has to evaluate them.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I can compute items to take, those computations do not provide solid information on rotations, dosages, etc.

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. Some suggestions may be counterindicated for other medications you are taking and medical conditions.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

This is a continuation with real numbers of my 2019 post The taxonomy nightmare before Christmas….

See also: The taxonomy nightmare — Episode II

I have just updated the site using a refinement of the Kaltoft-Moldrup algorithm that became available to the site this weekend. Before getting into the nerdy details, let us recap the purpose.

In general, studies find associations between higher or lower levels of some bacteria to symptoms or conditions. These are primitive calculations with many deficiencies. In general, they do not establish causality, only association.

The common hypothesis is that being too high increases the risk. A common assumption for many medical conditions (when there is insufficient studies) is that the “top or bottom 5 percentage of patients” may be at risk. This can also be expressed as those in the bottom 5 percentile and top 5 percentile.

In many branches of physical science, this can be computed from the mean and standard deviation. This requires the data to be a normal distribution. This is not the case with microbiome data. Our purpose is to identify the values where we suspect that the risk has become significant.

The tables in this post illustrates the nightmare in my earlier post!

Scope of Investigations

I am going to the bacteria cited in Dr. Jason Hawrelak Recommendations to illustrate the issues. His levels came from published studies, observations and the test results of his patients (which could have been done using labs not covered in this post).

Whether his ranges applies to your sample depends on the lab that did the sample. In some cases, many of the labs have reasonable agreement. In other cases, major differences.

Taxonomy	Rank	Low Percentage	High Percentage
Bacteroidia	class	0	35
Akkermansia	genus	1	3
Bacteroides	genus	0	20
Bifidobacterium	genus	2.5	5
Blautia	genus	5	10
Desulfovibrio	genus	0	0.25
Eubacterium	genus	0	15
Lactobacillus	genus	0.01	1
Methanobrevibacter	genus	0.0001	0.02
Roseburia	genus	5	10
Ruminococcus	genus	0	15
Proteobacteria	phylum	0	4
Bilophila wadsworthia	species	0	0.25
Escherichia coli	species	0	0.01
Faecalibacterium prausnitzii	species	10	15

What are the numbers?

Unless %ile is after the number, the numbers are percentages reported.

• Lab Ranges use a computational method that is common with medical labs
  • Lab Low means a value computed as Mean – 1.96 Standard Deviation. If the value is negative, it is set to zero because we cannot have a negative count.
  • Lab High means a value computed as Mean + 1.96 Standard Deviation.
• KM is the Kaltoft-Moltrup algorithm that detects data that is akin or not akin to other numbers in the data set.

Bacteroidia 0 -35%

My impression is that this measurement does not matter. All of the ranges are much greater than Jason’s guidance.

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	25.7360	26 %ile	89.6656	99 %ile	0	82.6916	40.9174	21.3133
BiomeSight	23.9060	21.4 %ile	81.0229	98.4 %ile	2.8476	74.5331	38.6903	18.2871
Ombre/Thryve	4.0813	11.8 %ile	100	100 %ile	0	90.2312	41.8556	24.6814
uBiome	37.0967	25.8 %ile	100	100 %ile	9.6504	88.5812	49.1158	20.1354

Akkermansia 1-3%

The consensus pattern seem to be 0-10%.

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0030	8.5 %ile	11.7689	97 %ile	0	10.4247	1.7598.9	44208
BiomeSight	0.0020	10.6 %ile	4.4380	92.6 %ile	0	9.6732	1.4131.3	42143.2
Ombre/Thryve	0.0061	16.6 %ile	10.8701	96.9 %ile	0	10.4304	1.7167.3	44457.7
uBiome	0	0 %ile	14.9127	95.9 %ile	0	13.3284	3.2611.9	51363.5

Bacteroides 0 – 20%

Jason’s high level is below the average of every lab! The consensus for high level is around 50%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab Hign	Mean	Standard Deviation
All	8.1100	20.5 %ile	58.9340	98.5 %ile	0	51.5806	22.9882	14.5879
BiomeSight	9.8480	19.8 %ile	58.5550	98.2 %ile	0	52.2943	23.7279	14.5746
Ombre/Thryve	2.0953	16.7 %ile	52.5618	96.8 %ile	0	51.6341	21.3098	15.4715
uBiome	18.0540	26.8 %ile	45.2831	95.4 %ile	16466	49.4790	25.5627	12.2021

Bifidobacterium 2.5 to 5%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0096	9 %ile	8.4552	95.2 %ile	0	13.0205	1.8287	5.7100
BiomeSight	0.0110	11 %ile	7.2080	97.4 %ile	0	7.2485	1.0863	3.1439
Ombre/Thryve	0.0053	7.5 %ile	10.1484	93.6 %ile	0	20.3438	3.0831	8.8064
uBiome	0	0 %ile	7.2945	93.9 %ile	0	12.8245	2.2096	5.4157

Blautia 5-10%

The consensus range appears to be 5-20%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	4.0480	19.4 %ile	21.4510	95.9 %ile	0	21.0998	8.8459	6.2519
BiomeSight	4.5750	18.7 %ile	28.5110	98.2 %ile	0	21.1671	9.1079	6.1526
Ombre/Thryve	2.9734	14.9 %ile	23.2938	96 %ile	0	22.2365	8.6022	6.9562
uBiome	6.6596	25.7 %ile	19.0282	94.9 %ile	0	20.1519	9.7336	5.3154

Desulfovibrio 0 – 0.25%

The consensus range appears to be 0- 1.5%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	.0020	9.3 %ile	1.9246	97.8 %ile	0	1.5114	0.3311	0.6021
BiomeSight	.0020	12.3 %ile	1.5980	97.6 %ile	0	1.1494	0.2244	0.4718
Ombre/Thryve	.0024	6.8 %ile	1.7445	96.9 %ile	0	1.5812	0.4033	0.6009
uBiome	0	0 %ile	2.1909	95.3 %ile	0	2.2996	0.5799	0.8773

Eubacterium 0 – 15%

The consensus range appears to be 0 – 7%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0060	9.9 %ile	7.1513	95.1 %ile	0	6.7982	1.4560	2.7256
BiomeSight	0.0040	10.5 %ile	1.4510	96 %ile	0	1.5494	.2440	0.6660
Ombre/Thryve	1.1858	16.1 %ile	11.7575	97.1 %ile	0	11.0002	3.9347	3.6048
uBiome	0	0 %ile	0.2976	94.1 %ile	0	7.053	0.0844	0.3167

Lactobacillus 0.1 – 1%

The numbers are all over the place.

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0040	11.8 %ile	1.2353	91.1 %ile	0	7.0988	.5206	3.3562
BiomeSight	0.0020	7.2 %ile	0.1719	93.3 %ile	0	5.6439	.1551	2.8004
Ombre/Thryve	0.0129	14.9 %ile	5.2409	97.2 %ile	0	3.9082	.8646	1.5528
uBiome	0	0 %ile	0.3850	88.6 %ile	0	13.1376	1.0906	6.1463

Methanobrevibacter 0.0001 – 0.02%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0040	17.6 %ile	2.7228	96.7 %ile	0	4.2485	0.4806	1.9223
BiomeSight	0	0 %ile	0.4900	94.5 %ile	0	1.1064	0.1451	.4904
Ombre/Thryve	0.0021	16.5 %ile	1.6667	95.2 %ile	0	1.6743	0.3337	.6839
uBiome	0	0 %ile	100	100 %ile	0	4.1132	1.1688	1.5022

Roseburia 5-10%

Consensus range seems to be 0 – 10%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.1415	10.8 %ile	11.3278	95.5 %ile	0	10.9642	3.3780	3.8705
BiomeSight	0.0650	6.7 %ile	13.5910	97.5 %ile	0	10.6002	3.1089	3.8220
Ombre/Thryve	0.1083	14.5 %ile	11.1568	96.4 %ile	0	9.6754	2.6043	3.6076
uBiome	2.3416	22.9 %ile	13.2358	96.2 %ile	0	13.1313	5.5699	3.8578

Ruminococcus 0 – 15%

Note that there was not sufficient samples to compute KM for ubiome. In this case, the consensus is in close agreement with Jason’s target.

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	1.3430	18.9 %ile	14.0820	95.3 %ile	0	14.2090	5.0708	4.6623
BiomeSight	2.0310	13.4 %ile	13.1570	92.4 %ile	0	15.0357	5.9824	4.6190
Ombre/Thryve	0.1699	11.6 %ile	14.1344	97.2 %ile	0	12.2289	3.6302	4.3871
uBiome					15491	3.5828	2.5659	.5188

Proteobacteria 0 – 4%

Consensus range appears to be 1-15%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	1.1678	19.2 %ile	11.8997	93.6 %ile	0	18.5949	4.9788	6.9470
BiomeSight	1.3090	11.5 %ile	17.7560	97.4 %ile	0	15.6688	5.1765	5.3532
Ombre/Thryve	0.3683	12.9 %ile	9.1702	95.8 %ile	0	17.2016	3.5651	6.9573
uBiome	0.9504	11.4 %ile	15.9831	96.2 %ile	0	14.3449	5.1377	4.6975

Bilophila wadsworthia 0 – 0.25%

Ombre had no distinguishable difference in being akin. The consensus range appears to be 0- 1%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0080	10.3 %ile	0.9600	93.9 %ile	0	1.3219	.3356	.5032
BiomeSight	0.0040	7.5 %ile	0.8750	93.2 %ile	0	1.2979	.3219	.4979
Ombre/Thryve	0	0 %ile	100	100 %ile	0	.9597	.2778	.3478.7
uBiome	0	0 %ile	1.2214	94.6 %ile	0	1.5297	.4254	.5634

Escherichia coli 0 – 0.01%

This is badly measured by 16s tests. Xenogene full sequencing averages almost 4%. The consensus range appears to be 0 – 0.4%

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	0.0020	14.8 %ile	0.3190	90.8 %ile	0	0.16760	0.1377	0.7848
BiomeSight	0.0020	15.1 %ile	0.4690	96 %ile	0	0.5323	0.0703	0.2357
Ombre/Thryve	0	0 %ile	100	100 %ile	0	0.5519	0.0967	0.2322
uBiome							353

Faecalibacterium prausnitzii 10 – 15%

The consensus range appears to be 3 – 30%.

Lab	KM Low	KM Percentile Low	KM High	KM Percentile High	Lab Low	Lab High	Mean	Standard Deviation
All	2.6650	19.8 %ile	26.1824	95.7 %ile	0	26.5505	10.4139	8.2329
BiomeSight	4.0780	20.2 %ile	31.2240	98 %ile	0	27.9728	11.6385	8.3338
Ombre/Thryve	4.5133	25 %ile	33.3225	98.2 %ile	0	28.7057	11.5256	8.7653
uBiome	0.6753	17.5 %ile	16.7634	96.2 %ile	0	16.3190	6.0641	5.2320

Bottom Line

The purpose of this post is to demonstrate with actual sample numbers the issues raised in The taxonomy nightmare before Christmas….

To which we need to add:

You should ask for full disclosure from any source on how the ranges are calculated. Ignoring or dismissing the differences between different lab results suggests a low bandwidth understanding of the issues involved with the microbiome.

You can see the values when you look up bacteria as shown below

Back Story: 

Current Age: 25, male

Current Issues: chronic fatigue (not able to exercise or take walks longer than 10-15 min), strong brain fog & reduced cognitive abilities,

History: 

Covid-19 infection in June 2022 followed by intense fatigue, followed by 1.5M of recovery, followed by spontaneous, severe crash (Post-exercise malaise, fatigue, strong brain fog) and continuing since then
I tried a ketogenic diet for 6 months (and a carnivore 4:1 ketogenic diet for 1 month) to treat these issues but this actually seemed to make my symptoms worse. Tried a broad spectrum of high dose supplements, vitamins and minerals that did not help at all. Currently slow re-introduction of carbs into my diet again.

Analysis

I can only review the current state since I am microbiome data-bound in reviews. It was interesting that two popular approaches advocated by influencers made him worse. There is no universal solutions / cure. Solutions are specific to the individual.

My usual starting point for ME/CFS and post-COVID is the Percentages of Percentiles chart. It is not a match for the usual pattern seen for those conditions, but we see statistically significant abnormalities in the 10-19%ile range. I have not seen this pattern before.

Looking at Potential Medical Conditions Detected, only Mood Disorders stands out. This is consistent with his past history. For Dr. Jason Hawrelak Recommendations, he’s at the 75%ile with the main items of concern being high Bacteroides, Bilophila wadsworthia, and low Bifidobacterium, Roseburia, Akkermansia.

Looking at Special Studies, the top item is likely due to a hybrid ME/CFS with post-COVID:

Where Do We Go From Here?

I am going to build a consensus report from the 4 “Just Give Me Suggestions” to which we will add:

• Special Studies: COVID19 (Long Hauler)
• Potential Medical Conditions Detected: Mood Disorders

There are two ways of looking at suggestions (similar results but minor differences). Using the PDF Download or looking at the details.

In this case (these do not always appear), probiotics too.

Before moving onto the detail view, let us look at KEGG computed probiotics:

• #1 was Escherichia coli (which is symbioflor 2 above or Mutaflor). The items below are at 1/6th the estimated contribution.
• Latilactobacillus sakei subsp. sakei is also a positive in the list
• Lactococcus lactis and the other ones in Filmjolk (a Swedish drink) are positive. There are some retail variation availables else where, for example Siggi’s Filmjolk Drinkable Yogurt (other bacteria added) and some starters such as NW Ferments Filmjolk Yogurt Starter.
• Lacticaseibacillus casei, Lactobacillus gasseri are also positive

NOTE: Escherichia coli is a troublesome bacteria because it is poorly/not measured with the typical 16s technology.

In terms of detail view, the following are at the top:

• Cacao (540) see this 2012 post and 2017
• lactobacillus casei (probiotics)
• raffinose(sugar beet)
• lactobacillus gasseri (probiotics)

None of the antibiotics or prescription items are above 330; I am disinclined to consider them. During my own recovery, I found that I had a craving for peanut butter (some posts on peanuts: 2013, 2015). There is some evidence that it may improve the ability of the blood to delivery oxygen to the brain in some cases (which may help with cognitive issues). Peanuts do contain Resveratrol [2000] and the question arose below whether just resveratrol alone could be substituted?

Reviewing what he tried…

Ketogenic diet for 6 months… this actually seemed to make my symptoms worse.

I would expect that to make things worse — as shown above.

Tried a broad spectrum of high dose supplements, vitamins and minerals that did not help at all.

Remember that 50% of the highest value (540) is my usual demarcation line for suggestions (270). Interesting that not a single vitamin or mineral was even close! About half of them were negatives!

The response from what he tried pre microbiome-sample agrees with the predicted response.

What he should reduce or avoid

This leads us to the next item, items to avoid. They will definitely not sweeten up his life: minimum usage of sugar, saccharin, stevia – but raffinose is fine. Note that nuts are on this list — wait! How can this be? Peanuts is on the to take list. The answer is simple: misnaming. Peanuts are NOT nuts (they look like nuts) but a legume!

Questions and Answers

Q: the probiotics dosages stated on the page I was wondering: The page lists the CFUs as X*BCFUs (with the B meaning Billion I suppose?) tho the studies linked to the dosages used mostly dosages in the range of X*10^9 CFUs. Am I missing something? (Because e.g. for lactobacillus casei 48 x10^9 CFUs would seem a lot) 

• A: I do not know the number needed to insure effective change. The dosages are based on dosages used in Clinical studies and thus dosages that are inferred safe (and someone decided was needed — often the results of earlier studies where only a few responded). See 📏🍽️ Dosages for Supplements for links to the studies. There is a difference between maintenance dosages (keep the status quo) and therapeutic dosage (upset the microbiome’s apple cart).

Context for Next Questions

Cookbook Suggestions were created from a list of specific substances provided by a reader supporting Long COVID with some specific directions on how she wanted items evaluated. It is not the preferred list. The preferred methods are looking at the “Technical details” (in horrible complexities — with 1,774 entries for this sample) or using the PDF that filters to keep the number of items low but working off the same numbers.

Q: Cookbook suggestions:  Cookbook gave me a clear thumbs down for Bifidobacterium bifidum, and Lactobacillae Rhamnosus and plantarum, tho when I went into detail view or to the consensus suggestions they were ranked well along the other takes. Would you say therefore take or avoid is more recommendable (as I have two probiotics already at home that have these strains in them)

• A: As shown above, two are negative (thus avoid), the other one is low positive. (The values range from 539 down to -460). It is unlikely to have any significant impact.

Q: Peanut/ Resveratrol: In addition to eating peanuts, could I also use resveratrol extract to boost the process? 

• A: This raises the issue of humans wanting to simplify things, sometimes too far. Peanuts contains other things besides resveratrol. This could be it main mechanism of action — but other components may also be acting in isolation or combination. I checked the numbers, and would surmise that the other factors are significant contributors important here. Remember, we are working from very sparse data (despite having 1.9 million facts, we have 20,000 bacteria over 2000 modifiers. i.e. 1.9 million to 40 million combinations is only 5% (or less) hit rate).
  So, it may help — but not sufficiently to exclude peanuts (or that horrible American food: peanut butter!)

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I can compute items to take, those computations do not provide solid information on rotations, dosages, etc.

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. Some suggestions may be counterindicated for other medications you are taking and medical conditions.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Autism is a variety of conditions caused by DNA mutations, environmental influences and a host of other factors. A significant contributor can be the microbiome. This impact can be further amplified because many children with autism are picky eaters shifting the microbiome further. What is discussed in this post applies to this child and not autistic children in general.

Back Story

A son with autism. He had COVID in April 2021. With autism, it can be challenging to identify long COVID symptoms from autism symptoms. “We have seen marginal  improvements in his receptive language and command following. His social skills and emotional understanding is poor . His diet has largely remained the same , vegetables and chicken , lamb, beef or fish and spices. He is verbal but not conversational, does not sleep well at night, does stimming throughout the day, his understanding is minimal He has very good energy levels and is playing till he sleeps on most days. He has very good memory and learn preferred topics quickly but is unable to focus on any task , he is unable to write or hold pencil for long . He cannot always reply to questions and has ecolalia[unsolicited repetition of utterances made by others] . ” 

Analysis

Lookin at Percentages of Percentiles, I see a different pattern than seen with ME/CFS and Long COVID — my most frequent analysis types. He has statistically (between 2 and 5%) significant abnormalities, but far less than people with ME/CFS and Long COVID.

Looking at Potential Medical Conditions Detected we see that ADHD and Mood Disorders patterns are there. Everything is reasonably in range for Dr. Jason Hawrelak Recommendations with two significantly out of range (too low) is Akkermansia (which is available as a probiotic) and Faecalibacterium prausnitzii is too high (27%). This pattern is seen across all of his samples.

Going over to our Citizen Science Special studies, the top three pattern matches are for:

• COVID19 (Long Hauler)
• Autism
• Brain Fog

These also are seen with an earlier sample from 2020.

Plan for Suggestions

Since this is a persistent state with reasonable continuity across samples, I am going to go the Uber-Consensus route. By this I mean we will do for Each Sample:

• “Just Give Me Suggestions” which executes 4 algorithms
• Citizen Science using Autism

Then we combine the suggestions from each sample into one, an uber suggestion consensus. The advantage of this approach is to minimize minor fluctuations of the microbiome over time. This means that we have 20 sets of suggestions combined.

I was disappointed with the results — nothing was consistently suggested. I experimented and found that the last two samples gave more consistent results. This implies that there has been significant changes in the microbiome over the last two years.

The top suggestions from the PDF are below

As a FYI, in terms of how many times things were suggested:

• blackcurrant – all 10
• low-fat diets – all 10
• red alga Laurencia tristicha – all 10
• lard – all 10
• Methionine – all 10
• fat – all 10
• glycyrrhizic acid (licorice) was 9 for and 1 against

I should talk a bit about the apparent contradiction with low-fat diets vs lard and fat. These come from the terms that clinical studies used. Low fat diet tends towards fish and poultry, lard is a pork product – I speculate that the type of fat may be significant.

On the flip side, we have these avoids. One item seems to be to suggest gluten free (despite wheat being a to-take):

As an experiment/learning activity — I looked at some of the suggested prescription items and checked if any are used for autism. We are matching these items impact on the microbiome and the shifts that this person has (autism as a diagnosis was not considered).

• cycloserine – D‐cycloserine for autism spectrum disorder [2019]
• Bumetanide – Bumetanide for autism: Open‐label trial in six children [2021]
• cefixime – Beta-Lactam Antibiotics as A Possible Novel Therapy for Managing Epilepsy and Autism, A Case Report and Review of Literature [2015]
• chlorpromazine hydrochloride – The Pharmacological Treatment of Autistic Spectrum Disorders [2014]

Since the non-prescription items above should cause similar shifts (and likely with less risk of side effects), it appears that the algorithms are making reasonable suggestions.

The process of checking suggestions derived exclusively from the microbiome against clinical studies for a condition is called cross-validation. When there is a high percentage of agreement, it implies that the mechanism may be via the microbiome and generating candidate substance from the microbiome may produce good results.

KEGG Based Suggestions

These use data from Kyoto Encyclopedia of Genes and Genomes to try to identify substances that the microbiome and the body may be short of which can be obtain via supplements or probiotics.

• Probiotics (in decreasing priority)
  • Escherichia coli – which can be Mutaflor (recommended above) or Symbioflor-2 (which is easier for people in the US to get).
  • There were several items that are counter-indicated from the suggestions – when there is disagreement, don’t gamble — ignore
  • Akkermansia muciniphila – low positive score but also identify as low on Dr. Jason Hawrelak Recommendations
• Supplements (again double checking across suggestions and keeping only that both agree with)
  • Biotin, Vitamin B7
  • Arginine
  • Glutamine
  • N-Acetyl Cysteine (NAC),

Questions

Q:  His gut according to the test is in good condition. I have heard in the past from one of his doctors that his Gut results were one of the best that he has seen in Autistic children, but we have not been able to make a considerable shift in his symptoms in the last few years.

• A: My working hypothesis is simple: symptoms are associated to microbiome shifts. He has bacteria shifts that are matches to autism drugs (see above); so I believe further improvement of the gut and behaviors are possible and probable. He may be good; I believe he can be better.

Q: Faecalibacterium prausnitzii is high in my son , I have read it works as anti-inflammatory , but on the contrary I have heard that children with ASD have an inflamed Brian ,I would have thought this would have worked in his favor.

• A: Excellent question! Faecalibacterium prausnitzii is anti-inflammatory for Crohn’s disease[2008], colitis [2013]. I was unable to find any clear literature on its effect on the brain. I did found some information that cause me to suspect that it does not impact the brain significantly.
  • “A 15kDa protein with anti-inflammatory properties is produced by F. prausnitzii, a commensal bacterium involved in CD pathogenesis. This protein is able to inhibit the NF-κB pathway in intestinal epithelial cells and to prevent colitis in an animal model.” [2017] – the size of this is very important.
  • “Most proteins in the plasma are not able to cross the blood—brain barrier because of their size and hydrophilicity.” [Basic Neurochemistry]
  • “does not have a barrier against molecules less than 1 kDa.. may form a barrier against molecules larger than 4 kDa” [2020]
• Bottom Line — it appears the chemical produced by Faecalibacterium prausnitzii may be too big to reach the brain.
• We also find the following reported, suggesting we want to reduce it to a normal range, you should independently research this
  • “Faecalibacterium predicted social deficit scores in children with ASD” [2018]
  • “Faecalibacterium prausnitzii … were also found to be highly correlated with Autism Treatment Evaluation Checklist (a measure of Autism severity )” 
  • On the flip side, it reduces abdominal pain and improved bowel movement in ASD [2018].
  • “Gut microbiome data revealed Akkermansia sp. and Faecalibacterium prausnitzii to be statistically lower in abundance in autistic children than their neurotypical peers with a five and two-fold decrease” [2021] — which may account for the gut issues.
    • “Compared with healthy controls, Faecalibacterium,..were more abundant in ASD patients” [2021]
    • Your son’s range is thus very atypical being many, many times higher than expected.
• I have caution here, Faecalibacterium and cognitive issues have inconsistent reports [2021, 2023 ], Faecalibacterium is implicated in cognitive issues[2018]. IMHO, encouraging it to the normal ranges may be the wisest course.

Q: “His results are over all satisfactory ,same as last year about – Gut wellness score – 89.52.  I have noticed that Clostridia is about 79.7 % could this be the reason, would appreciate your help.”

• A: Clostridia has been high in most samples, I drilled down into it’s main components
  • 2023-08-21: 80% of the microbiome, 88%ile — Oscillospiraceae 89%ile,  Faecalibacterium prausnitzii 96%ile
  • 2022-07-11: 86% of the microbiome, 92%ile — Oscillospiraceae 94%ile,  Faecalibacterium prausnitzii 95%ile
  • 2021-11-29: 80% of the microbiome, 88%ile — Oscillospiraceae 79%ile,  Faecalibacterium prausnitzii 79%ile
  • 2020-10-14: 83% of the microbiome, 98%ile —  Oscillospiraceae 100%ile, Faecalibacterium prausnitzii 100%ile

Searching for Faecalibacterium + autism on PubMed resulted in 29+ studies. There was nothing found for Oscillospiraceae + autism. Looking at the latest sample, only 10% of the organisms in Oscillospiraceae could be identified in the sample — no smoking gun for which genus. Doing a Metagenomic Shotgun Sequencing test would like provide more information (for example, Thorne) — but it is unlikely that will produce more actionable item — just give names.

Looking at what reduces Oscillospiraceae, we see Bumetanide, cycloserine, cefixime and chlorpromazine in that list (as well as many of the above suggestions).

Some visuals: Clostridia is not that extreme, but two of it’s children are.

This post started from reading “Dietary quality and the gut microbiome in early-stage Parkinson’s disease patients [2023]”. I posted on some Facebook groups “People often are obsessives with getting high Lactobacillus and Bifidobacterium. The “dividend” of this desire appears to be increased risk of Parkinson’s disease.“

The question arises, what other conditions are associated with high levels of both of these? Fortunately, this can be obtained from the Microbiome Prescription databases.

• Amyotrophic lateral sclerosis (ALS) Motor Neuron
• Autism
• Crohn’s Disease
• Depression
• Graves’ disease
• Inflammatory Bowel Disease
• Irritable Bowel Syndrome
• Juvenile idiopathic arthritis
• Liver Cirrhosis
• Long COVID
• Metabolic Syndrome
• Mood Disorders
• Multiple Sclerosis
• Obesity
• Parkinson’s Disease
• Psoriasis
• rheumatoid arthritis (RA),Spondyloarthritis (SpA)
• Schizophrenia
• Stress / posttraumatic stress disorder
• Type 2 Diabetes
• Ulcerative colitis

I also pulled the studies where the study specifically cited both are high. The above list were occasionally from taking data from two different studies.

• A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis [2020]
• The Impact of Microbiota on the Pathogenesis of Amyotrophic Lateral Sclerosis and the Possible Benefits of Polyphenols. An Overview [2021]
• The Role of Gut Microbiota in Gastrointestinal Symptoms of Children with ASD [2019]
• Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease [2014]
• Gut Microbiota in Anxiety and Depression: Unveiling the Relationships and Management Options [2023]
• Gut microbiome in chronic rheumatic and inflammatory bowel diseases: Similarities and differences [2019]
• IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation [2012]
• Gut microbiota in pre-clinical rheumatoid arthritis: From pathogenesis to preventing progression [2023]
• A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome [2019]
• Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study [2021]
• Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls [2015]
• Changes of Colonic Bacterial Composition in Parkinson’s Disease and Other Neurodegenerative Diseases [2018]
• Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation [2021]
• Inflammatory microbes and genes as potential biomarkers of Parkinson’s disease [2022]
• Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms [2022]
• Altered fecal microbiota composition in all male aggressor-exposed rodent model simulating features of post-traumatic stress disorder [2018]
• Intestinal flora alterations in patients with ulcerative colitis and their association with inflammation [2021]
• The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies [2022]

Bottom Line

A responsible medical professional would test a patient’s Lactobacillus and Bifidobacterium levels before suggesting probiotics to a patient. If your MD makes that recommendation without testing and you have any of the above conditions — it may be time to file a complaint with their supervisors or governing body citing the studies.